---
_id: '11479'
abstract:
- lang: eng
text: Understanding population divergence that eventually leads to speciation is
essential for evolutionary biology. High species diversity in the sea was regarded
as a paradox when strict allopatry was considered necessary for most speciation
events because geographical barriers seemed largely absent in the sea, and many
marine species have high dispersal capacities. Combining genome-wide data with
demographic modelling to infer the demographic history of divergence has introduced
new ways to address this classical issue. These models assume an ancestral population
that splits into two subpopulations diverging according to different scenarios
that allow tests for periods of gene flow. Models can also test for heterogeneities
in population sizes and migration rates along the genome to account, respectively,
for background selection and selection against introgressed ancestry. To investigate
how barriers to gene flow arise in the sea, we compiled studies modelling the
demographic history of divergence in marine organisms and extracted preferred
demographic scenarios together with estimates of demographic parameters. These
studies show that geographical barriers to gene flow do exist in the sea but that
divergence can also occur without strict isolation. Heterogeneity of gene flow
was detected in most population pairs suggesting the predominance of semipermeable
barriers during divergence. We found a weak positive relationship between the
fraction of the genome experiencing reduced gene flow and levels of genome-wide
differentiation. Furthermore, we found that the upper bound of the ‘grey zone
of speciation’ for our dataset extended beyond that found before, implying that
gene flow between diverging taxa is possible at higher levels of divergence than
previously thought. Finally, we list recommendations for further strengthening
the use of demographic modelling in speciation research. These include a more
balanced representation of taxa, more consistent and comprehensive modelling,
clear reporting of results and simulation studies to rule out nonbiological explanations
for general results.
acknowledgement: 'We greatly thank all the corresponding authors of the studies that
were included in our synthesis for the sharing of additional data: Thomas Broquet,
Dmitry Filatov, Quentin Rougemont, Paolo Momigliano, Pierre-Alexandre Gagnaire,
Carlos Prada, Ahmed Souissi, Michael Møller Hansen, Sylvie Lapègue, Joseph Di Battista,
Michael Hellberg and Carlos Prada. RKB and ADJ were supported by the European Research
Council. MR was supported by the Swedish Research Council Vetenskapsrådet (grant
number 2021-05243; to MR) and Formas (grant number 2019-00882; to KJ and MR), and
by additional grants from the European Research Council (to RKB) and Vetenskapsrådet
(to KJ) through the Centre for Marine Evolutionary Biology (https://www.gu.se/en/cemeb-marine-evolutionary-biology).'
article_processing_charge: No
article_type: original
author:
- first_name: Aurélien
full_name: De Jode, Aurélien
last_name: De Jode
- first_name: Alan
full_name: Le Moan, Alan
last_name: Le Moan
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
- first_name: Marina
full_name: Rafajlović, Marina
last_name: Rafajlović
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
citation:
ama: De Jode A, Le Moan A, Johannesson K, et al. Ten years of demographic modelling
of divergence and speciation in the sea. Evolutionary Applications. 2023;16(2):542-559.
doi:10.1111/eva.13428
apa: De Jode, A., Le Moan, A., Johannesson, K., Faria, R., Stankowski, S., Westram,
A. M., … Fraisse, C. (2023). Ten years of demographic modelling of divergence
and speciation in the sea. Evolutionary Applications. Wiley. https://doi.org/10.1111/eva.13428
chicago: De Jode, Aurélien, Alan Le Moan, Kerstin Johannesson, Rui Faria, Sean Stankowski,
Anja M Westram, Roger K. Butlin, Marina Rafajlović, and Christelle Fraisse. “Ten
Years of Demographic Modelling of Divergence and Speciation in the Sea.” Evolutionary
Applications. Wiley, 2023. https://doi.org/10.1111/eva.13428.
ieee: A. De Jode et al., “Ten years of demographic modelling of divergence
and speciation in the sea,” Evolutionary Applications, vol. 16, no. 2.
Wiley, pp. 542–559, 2023.
ista: De Jode A, Le Moan A, Johannesson K, Faria R, Stankowski S, Westram AM, Butlin
RK, Rafajlović M, Fraisse C. 2023. Ten years of demographic modelling of divergence
and speciation in the sea. Evolutionary Applications. 16(2), 542–559.
mla: De Jode, Aurélien, et al. “Ten Years of Demographic Modelling of Divergence
and Speciation in the Sea.” Evolutionary Applications, vol. 16, no. 2,
Wiley, 2023, pp. 542–59, doi:10.1111/eva.13428.
short: A. De Jode, A. Le Moan, K. Johannesson, R. Faria, S. Stankowski, A.M. Westram,
R.K. Butlin, M. Rafajlović, C. Fraisse, Evolutionary Applications 16 (2023) 542–559.
date_created: 2022-07-03T22:01:33Z
date_published: 2023-02-01T00:00:00Z
date_updated: 2023-08-01T12:25:44Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
- _id: BeVi
doi: 10.1111/eva.13428
external_id:
isi:
- '000815663700001'
file:
- access_level: open_access
checksum: d4d6fa9ddf36643af994a6a757919afb
content_type: application/pdf
creator: dernst
date_created: 2023-02-27T07:10:17Z
date_updated: 2023-02-27T07:10:17Z
file_id: '12685'
file_name: 2023_EvolutionaryApplications_DeJode.pdf
file_size: 2269822
relation: main_file
success: 1
file_date_updated: 2023-02-27T07:10:17Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '2'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '02'
oa: 1
oa_version: Published Version
page: 542-559
publication: Evolutionary Applications
publication_identifier:
eissn:
- 1752-4571
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ten years of demographic modelling of divergence and speciation in the sea
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 16
year: '2023'
...
---
_id: '12514'
abstract:
- lang: eng
text: The concept of a “speciation continuum” has gained popularity in recent decades.
It emphasizes speciation as a continuous process that may be studied by comparing
contemporary population pairs that show differing levels of divergence. In their
recent perspective article in Evolution, Stankowski and Ravinet provided a valuable
service by formally defining the speciation continuum as a continuum of reproductive
isolation, based on opinions gathered from a survey of speciation researchers.
While we agree that the speciation continuum has been a useful concept to advance
the understanding of the speciation process, some intrinsic limitations exist.
Here, we advocate for a multivariate extension, the speciation hypercube, first
proposed by Dieckmann et al. in 2004, but rarely used since. We extend the idea
of the speciation cube and suggest it has strong conceptual and practical advantages
over a one-dimensional model. We illustrate how the speciation hypercube can be
used to visualize and compare different speciation trajectories, providing new
insights into the processes and mechanisms of speciation. A key strength of the
speciation hypercube is that it provides a unifying framework for speciation research,
as it allows questions from apparently disparate subfields to be addressed in
a single conceptual model.
acknowledgement: "The authors of this article were supported by LMU Munich (J.B.W.W.),
a James S. McDonnell Foundation postdoctoral fellowship (A.K.H.). P.N. received
funding from the European Research Council (ERC) under the European Union’s Horizon
2020 research and innovation program (Grant agreement No. 770826 EE-Dynamics).\r\nWe
thank participants in the 2019 Gordon Conference on Speciation for the extensive
conversation on this topic. Thanks to Dan Funk for providing permission to use data
from Funk et al. 2006, and for comments on the manuscript."
article_processing_charge: No
article_type: original
author:
- first_name: Daniel I.
full_name: Bolnick, Daniel I.
last_name: Bolnick
- first_name: Amanda K.
full_name: Hund, Amanda K.
last_name: Hund
- first_name: Patrik
full_name: Nosil, Patrik
last_name: Nosil
- first_name: Foen
full_name: Peng, Foen
last_name: Peng
- first_name: Mark
full_name: Ravinet, Mark
last_name: Ravinet
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Swapna
full_name: Subramanian, Swapna
last_name: Subramanian
- first_name: Jochen B.W.
full_name: Wolf, Jochen B.W.
last_name: Wolf
- first_name: Roman
full_name: Yukilevich, Roman
last_name: Yukilevich
citation:
ama: 'Bolnick DI, Hund AK, Nosil P, et al. A multivariate view of the speciation
continuum. Evolution: International journal of organic evolution. 2023;77(1):318-328.
doi:10.1093/evolut/qpac004'
apa: 'Bolnick, D. I., Hund, A. K., Nosil, P., Peng, F., Ravinet, M., Stankowski,
S., … Yukilevich, R. (2023). A multivariate view of the speciation continuum.
Evolution: International Journal of Organic Evolution. Oxford University
Press. https://doi.org/10.1093/evolut/qpac004'
chicago: 'Bolnick, Daniel I., Amanda K. Hund, Patrik Nosil, Foen Peng, Mark Ravinet,
Sean Stankowski, Swapna Subramanian, Jochen B.W. Wolf, and Roman Yukilevich. “A
Multivariate View of the Speciation Continuum.” Evolution: International Journal
of Organic Evolution. Oxford University Press, 2023. https://doi.org/10.1093/evolut/qpac004.'
ieee: 'D. I. Bolnick et al., “A multivariate view of the speciation continuum,”
Evolution: International journal of organic evolution, vol. 77, no. 1.
Oxford University Press, pp. 318–328, 2023.'
ista: 'Bolnick DI, Hund AK, Nosil P, Peng F, Ravinet M, Stankowski S, Subramanian
S, Wolf JBW, Yukilevich R. 2023. A multivariate view of the speciation continuum.
Evolution: International journal of organic evolution. 77(1), 318–328.'
mla: 'Bolnick, Daniel I., et al. “A Multivariate View of the Speciation Continuum.”
Evolution: International Journal of Organic Evolution, vol. 77, no. 1,
Oxford University Press, 2023, pp. 318–28, doi:10.1093/evolut/qpac004.'
short: 'D.I. Bolnick, A.K. Hund, P. Nosil, F. Peng, M. Ravinet, S. Stankowski, S.
Subramanian, J.B.W. Wolf, R. Yukilevich, Evolution: International Journal of Organic
Evolution 77 (2023) 318–328.'
date_created: 2023-02-05T23:00:59Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2023-08-01T12:58:30Z
day: '01'
department:
- _id: NiBa
doi: 10.1093/evolut/qpac004
external_id:
isi:
- '001021686300024'
pmid:
- '36622661'
intvolume: ' 77'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/evolut/qpac004
month: '01'
oa: 1
oa_version: Published Version
page: 318-328
pmid: 1
publication: 'Evolution: International journal of organic evolution'
publication_identifier:
eissn:
- 1558-5646
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: A multivariate view of the speciation continuum
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 77
year: '2023'
...
---
_id: '12159'
abstract:
- lang: eng
text: The term “haplotype block” is commonly used in the developing field of haplotype-based
inference methods. We argue that the term should be defined based on the structure
of the Ancestral Recombination Graph (ARG), which contains complete information
on the ancestry of a sample. We use simulated examples to demonstrate key features
of the relationship between haplotype blocks and ancestral structure, emphasizing
the stochasticity of the processes that generate them. Even the simplest cases
of neutrality or of a “hard” selective sweep produce a rich structure, often missed
by commonly used statistics. We highlight a number of novel methods for inferring
haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate
how they can be used to define haplotype blocks using an empirical data set. While
the advent of new, computationally efficient methods makes it possible to apply
these concepts broadly, they (and additional new methods) could benefit from adding
features to explore haplotype blocks, as we define them. Understanding and applying
the concept of the haplotype block will be essential to fully exploit long and
linked-read sequencing technologies.
acknowledgement: 'We thank the Barton group for useful discussion and feedback during
the writing of this article. Comments from Roger Butlin, Molly Schumer''s Group,
the tskit development team, editors and three reviewers greatly improved the manuscript.
Funding was provided by SCAS (Natural Sciences Programme, Knut and Alice Wallenberg
Foundation), an FWF Wittgenstein grant (PT1001Z211), an FWF standalone grant (grant
P 32166), and an ERC Advanced Grant. YFC was supported by the Max Planck Society
and an ERC Proof of Concept Grant #101069216 (HAPLOTAGGING).'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Daria
full_name: Shipilina, Daria
id: 428A94B0-F248-11E8-B48F-1D18A9856A87
last_name: Shipilina
orcid: 0000-0002-1145-9226
- first_name: Arka
full_name: Pal, Arka
id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425
last_name: Pal
orcid: 0000-0002-4530-8469
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Yingguang Frank
full_name: Chan, Yingguang Frank
last_name: Chan
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure
of haplotype blocks. Molecular Ecology. 2023;32(6):1441-1457. doi:10.1111/mec.16793
apa: Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., & Barton, N. H. (2023).
On the origin and structure of haplotype blocks. Molecular Ecology. Wiley.
https://doi.org/10.1111/mec.16793
chicago: Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and
Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” Molecular
Ecology. Wiley, 2023. https://doi.org/10.1111/mec.16793.
ieee: D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the
origin and structure of haplotype blocks,” Molecular Ecology, vol. 32,
no. 6. Wiley, pp. 1441–1457, 2023.
ista: Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. 2023. On the origin
and structure of haplotype blocks. Molecular Ecology. 32(6), 1441–1457.
mla: Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.”
Molecular Ecology, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:10.1111/mec.16793.
short: D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology
32 (2023) 1441–1457.
date_created: 2023-01-12T12:09:17Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-16T08:18:47Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/mec.16793
external_id:
isi:
- '000900762000001'
pmid:
- '36433653'
file:
- access_level: open_access
checksum: b10e0f8fa3dc4d72aaf77a557200978a
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T08:15:41Z
date_updated: 2023-08-16T08:15:41Z
file_id: '14062'
file_name: 2023_MolecularEcology_Shipilina.pdf
file_size: 7144607
relation: main_file
success: 1
file_date_updated: 2023-08-16T08:15:41Z
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
issue: '6'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 1441-1457
pmid: 1
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: The maintenance of alternative adaptive peaks in snapdragons
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the origin and structure of haplotype blocks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2023'
...
---
_id: '14452'
abstract:
- lang: eng
text: The classical infinitesimal model is a simple and robust model for the inheritance
of quantitative traits. In this model, a quantitative trait is expressed as the
sum of a genetic and an environmental component, and the genetic component of
offspring traits within a family follows a normal distribution around the average
of the parents’ trait values, and has a variance that is independent of the parental
traits. In previous work, we showed that when trait values are determined by the
sum of a large number of additive Mendelian factors, each of small effect, one
can justify the infinitesimal model as a limit of Mendelian inheritance. In this
paper, we show that this result extends to include dominance. We define the model
in terms of classical quantities of quantitative genetics, before justifying it
as a limit of Mendelian inheritance as the number, M, of underlying loci tends
to infinity. As in the additive case, the multivariate normal distribution of
trait values across the pedigree can be expressed in terms of variance components
in an ancestral population and probabilities of identity by descent determined
by the pedigree. Now, with just first-order dominance effects, we require two-,
three-, and four-way identities. We also show that, even if we condition on parental
trait values, the “shared” and “residual” components of trait values within each
family will be asymptotically normally distributed as the number of loci tends
to infinity, with an error of order 1/M−−√. We illustrate our results with some
numerical examples.
acknowledgement: NHB was supported in part by ERC Grants 250152 and 101055327. AV
was partly supported by the chaire Modélisation Mathématique et Biodiversité of
Veolia Environment—Ecole Polytechnique—Museum National d’Histoire Naturelle—Fondation
X.
article_number: iyad133
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison M.
full_name: Etheridge, Alison M.
last_name: Etheridge
- first_name: Amandine
full_name: Véber, Amandine
last_name: Véber
citation:
ama: Barton NH, Etheridge AM, Véber A. The infinitesimal model with dominance. Genetics.
2023;225(2). doi:10.1093/genetics/iyad133
apa: Barton, N. H., Etheridge, A. M., & Véber, A. (2023). The infinitesimal
model with dominance. Genetics. Oxford Academic. https://doi.org/10.1093/genetics/iyad133
chicago: Barton, Nicholas H, Alison M. Etheridge, and Amandine Véber. “The Infinitesimal
Model with Dominance.” Genetics. Oxford Academic, 2023. https://doi.org/10.1093/genetics/iyad133.
ieee: N. H. Barton, A. M. Etheridge, and A. Véber, “The infinitesimal model with
dominance,” Genetics, vol. 225, no. 2. Oxford Academic, 2023.
ista: Barton NH, Etheridge AM, Véber A. 2023. The infinitesimal model with dominance.
Genetics. 225(2), iyad133.
mla: Barton, Nicholas H., et al. “The Infinitesimal Model with Dominance.” Genetics,
vol. 225, no. 2, iyad133, Oxford Academic, 2023, doi:10.1093/genetics/iyad133.
short: N.H. Barton, A.M. Etheridge, A. Véber, Genetics 225 (2023).
date_created: 2023-10-29T23:01:15Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2023-10-30T13:04:11Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/genetics/iyad133
ec_funded: 1
external_id:
arxiv:
- '2211.03515'
file:
- access_level: open_access
checksum: 3f65b1fbe813e2f4dbb5d2b5e891844a
content_type: application/pdf
creator: dernst
date_created: 2023-10-30T12:57:53Z
date_updated: 2023-10-30T12:57:53Z
file_id: '14469'
file_name: 2023_Genetics_Barton.pdf
file_size: 1439032
relation: main_file
success: 1
file_date_updated: 2023-10-30T12:57:53Z
has_accepted_license: '1'
intvolume: ' 225'
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication: Genetics
publication_identifier:
eissn:
- 1943-2631
issn:
- 0016-6731
publication_status: published
publisher: Oxford Academic
quality_controlled: '1'
related_material:
record:
- id: '12949'
relation: research_data
status: public
scopus_import: '1'
status: public
title: The infinitesimal model with dominance
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 225
year: '2023'
...
---
_id: '12949'
abstract:
- lang: eng
text: The classical infinitesimal model is a simple and robust model for the inheritance
of quantitative traits. In this model, a quantitative trait is expressed as the
sum of a genetic and a non-genetic (environmental) component and the genetic component
of offspring traits within a family follows a normal distribution around the average
of the parents’ trait values, and has a variance that is independent of the trait
values of the parents. Although the trait distribution across the whole population
can be far from normal, the trait distributions within families are normally distributed
with a variance-covariance matrix that is determined entirely by that in the
ancestral population and the probabilities of identity determined by the pedigree.
Moreover, conditioning on some of the trait values within the pedigree has predictable
effects on the mean and variance within and between families. In previous work,
Barton et al. (2017), we showed that when trait values are determined by the sum
of a large number of Mendelian factors, each of small effect, one can justify
the infinitesimal model as limit of Mendelian inheritance. It was also shown that
under some forms of epistasis, trait values within a family are still normally
distributed.
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. The infinitesimal model with dominance. 2023. doi:10.15479/AT:ISTA:12949
apa: Barton, N. H. (2023). The infinitesimal model with dominance. Institute of
Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12949
chicago: Barton, Nicholas H. “The Infinitesimal Model with Dominance.” Institute
of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12949.
ieee: N. H. Barton, “The infinitesimal model with dominance.” Institute of Science
and Technology Austria, 2023.
ista: Barton NH. 2023. The infinitesimal model with dominance, Institute of Science
and Technology Austria, 10.15479/AT:ISTA:12949.
mla: Barton, Nicholas H. The Infinitesimal Model with Dominance. Institute
of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12949.
short: N.H. Barton, (2023).
contributor:
- contributor_type: researcher
first_name: Amandine
last_name: Veber
- contributor_type: researcher
first_name: Alison
last_name: Etheridge
date_created: 2023-05-13T09:49:09Z
date_published: 2023-05-13T00:00:00Z
date_updated: 2023-10-30T13:04:11Z
day: '13'
ddc:
- '576'
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keyword:
- Quantitative genetics
- infinitesimal model
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '14452'
relation: used_in_publication
status: public
status: public
title: The infinitesimal model with dominance
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14556'
abstract:
- lang: eng
text: Inversions are structural mutations that reverse the sequence of a chromosome
segment and reduce the effective rate of recombination in the heterozygous state.
They play a major role in adaptation, as well as in other evolutionary processes
such as speciation. Although inversions have been studied since the 1920s, they
remain difficult to investigate because the reduced recombination conferred by
them strengthens the effects of drift and hitchhiking, which in turn can obscure
signatures of selection. Nonetheless, numerous inversions have been found to be
under selection. Given recent advances in population genetic theory and empirical
study, here we review how different mechanisms of selection affect the evolution
of inversions. A key difference between inversions and other mutations, such as
single nucleotide variants, is that the fitness of an inversion may be affected
by a larger number of frequently interacting processes. This considerably complicates
the analysis of the causes underlying the evolution of inversions. We discuss
the extent to which these mechanisms can be disentangled, and by which approach.
acknowledgement: 'We are grateful to two referees and Luke Holman for valuable comments
on a previous version of our manuscript. This paper was conceived at the ESEB Progress
Meeting ‘Disentangling neutral versus adaptive evolution in chromosomal inversions’,
organized by ELB, KJ and TF and held at Tjärnö Marine Laboratory (Sweden) between
28 February and 3 March 2022. We are indebted to ESEB for sponsoring our workshop
and to the following funding bodies for supporting our research: ERC AdG 101055327
to NHB; Swedish Research Council (VR) 2018-03695 and Leverhulme Trust RPG-2021-141
to RKB; Fundação para a Ciência e a Tecnologia (FCT) contract 2020.00275.CEECIND
and research project PTDC/BIA-1232 EVL/1614/2021 to RF; Fundação para a Ciência
e a Tecnologia (FCT) junior researcher contract CEECIND/02616/2018 to IF; Swiss
National Science Foundation (SNSF) Ambizione #PZ00P3_185952 to KJG; National Science
Foundation NSF-OCE 2043905 and NSF-DEB 1655701 to KEL; Swiss National Science Foundation
(SNSF) 310030_204681 to CLP; Swedish Research Council (VR) 2021-05243 to MR; Norwegian
Research Council grant 315287 to AMW; Swiss National Science Foundation (SNSF) 31003A-182262
and FZEB-0-214654 to TF. We also thank Luca Ferretti for the discussion and Eliane
Zinn (Flatt lab) for help with reference formatting.'
article_number: '14242'
article_processing_charge: No
article_type: review
author:
- first_name: Emma L.
full_name: Berdan, Emma L.
last_name: Berdan
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
- first_name: Brian
full_name: Charlesworth, Brian
last_name: Charlesworth
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Inês
full_name: Fragata, Inês
last_name: Fragata
- first_name: Kimberly J.
full_name: Gilbert, Kimberly J.
last_name: Gilbert
- first_name: Paul
full_name: Jay, Paul
last_name: Jay
- first_name: Martin
full_name: Kapun, Martin
last_name: Kapun
- first_name: Katie E.
full_name: Lotterhos, Katie E.
last_name: Lotterhos
- first_name: Claire
full_name: Mérot, Claire
last_name: Mérot
- first_name: Esra
full_name: Durmaz Mitchell, Esra
last_name: Durmaz Mitchell
- first_name: Marta
full_name: Pascual, Marta
last_name: Pascual
- first_name: Catherine L.
full_name: Peichel, Catherine L.
last_name: Peichel
- first_name: Marina
full_name: Rafajlović, Marina
last_name: Rafajlović
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Stephen W.
full_name: Schaeffer, Stephen W.
last_name: Schaeffer
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Thomas
full_name: Flatt, Thomas
last_name: Flatt
citation:
ama: Berdan EL, Barton NH, Butlin R, et al. How chromosomal inversions reorient
the evolutionary process. Journal of Evolutionary Biology. 2023. doi:10.1111/jeb.14242
apa: Berdan, E. L., Barton, N. H., Butlin, R., Charlesworth, B., Faria, R., Fragata,
I., … Flatt, T. (2023). How chromosomal inversions reorient the evolutionary process.
Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.14242
chicago: Berdan, Emma L., Nicholas H Barton, Roger Butlin, Brian Charlesworth, Rui
Faria, Inês Fragata, Kimberly J. Gilbert, et al. “How Chromosomal Inversions Reorient
the Evolutionary Process.” Journal of Evolutionary Biology. Wiley, 2023.
https://doi.org/10.1111/jeb.14242.
ieee: E. L. Berdan et al., “How chromosomal inversions reorient the evolutionary
process,” Journal of Evolutionary Biology. Wiley, 2023.
ista: Berdan EL, Barton NH, Butlin R, Charlesworth B, Faria R, Fragata I, Gilbert
KJ, Jay P, Kapun M, Lotterhos KE, Mérot C, Durmaz Mitchell E, Pascual M, Peichel
CL, Rafajlović M, Westram AM, Schaeffer SW, Johannesson K, Flatt T. 2023. How
chromosomal inversions reorient the evolutionary process. Journal of Evolutionary
Biology., 14242.
mla: Berdan, Emma L., et al. “How Chromosomal Inversions Reorient the Evolutionary
Process.” Journal of Evolutionary Biology, 14242, Wiley, 2023, doi:10.1111/jeb.14242.
short: E.L. Berdan, N.H. Barton, R. Butlin, B. Charlesworth, R. Faria, I. Fragata,
K.J. Gilbert, P. Jay, M. Kapun, K.E. Lotterhos, C. Mérot, E. Durmaz Mitchell,
M. Pascual, C.L. Peichel, M. Rafajlović, A.M. Westram, S.W. Schaeffer, K. Johannesson,
T. Flatt, Journal of Evolutionary Biology (2023).
date_created: 2023-11-19T23:00:55Z
date_published: 2023-11-08T00:00:00Z
date_updated: 2023-11-20T08:51:09Z
day: '08'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/jeb.14242
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/jeb.14242
month: '11'
oa: 1
oa_version: Published Version
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: epub_ahead
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: How chromosomal inversions reorient the evolutionary process
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14552'
abstract:
- lang: eng
text: Interactions between plants and herbivores are central in most ecosystems,
but their strength is highly variable. The amount of variability within a system
is thought to influence most aspects of plant-herbivore biology, from ecological
stability to plant defense evolution. Our understanding of what influences variability,
however, is limited by sparse data. We collected standardized surveys of herbivory
for 503 plant species at 790 sites across 116° of latitude. With these data, we
show that within-population variability in herbivory increases with latitude,
decreases with plant size, and is phylogenetically structured. Differences in
the magnitude of variability are thus central to how plant-herbivore biology varies
across macroscale gradients. We argue that increased focus on interaction variability
will advance understanding of patterns of life on Earth.
acknowledgement: The authors acknowledge funding for central project coordination
from NSF Research Coordination Network grant DEB-2203582; the Ecology, Evolution,
and Behavior Program at Michigan State University; and AgBioResearch at Michigan
State University. Site-specific funding is listed in the supplementary materials.
article_processing_charge: No
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- first_name: M. L.
full_name: Robinson, M. L.
last_name: Robinson
- first_name: P. G.
full_name: Hahn, P. G.
last_name: Hahn
- first_name: B. D.
full_name: Inouye, B. D.
last_name: Inouye
- first_name: N.
full_name: Underwood, N.
last_name: Underwood
- first_name: S. R.
full_name: Whitehead, S. R.
last_name: Whitehead
- first_name: K. C.
full_name: Abbott, K. C.
last_name: Abbott
- first_name: E. M.
full_name: Bruna, E. M.
last_name: Bruna
- first_name: N. I.
full_name: Cacho, N. I.
last_name: Cacho
- first_name: L. A.
full_name: Dyer, L. A.
last_name: Dyer
- first_name: L.
full_name: Abdala-Roberts, L.
last_name: Abdala-Roberts
- first_name: W. J.
full_name: Allen, W. J.
last_name: Allen
- first_name: J. F.
full_name: Andrade, J. F.
last_name: Andrade
- first_name: D. F.
full_name: Angulo, D. F.
last_name: Angulo
- first_name: D.
full_name: Anjos, D.
last_name: Anjos
- first_name: D. N.
full_name: Anstett, D. N.
last_name: Anstett
- first_name: R.
full_name: Bagchi, R.
last_name: Bagchi
- first_name: S.
full_name: Bagchi, S.
last_name: Bagchi
- first_name: M.
full_name: Barbosa, M.
last_name: Barbosa
- first_name: S.
full_name: Barrett, S.
last_name: Barrett
- first_name: Carina
full_name: Baskett, Carina
id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87
last_name: Baskett
orcid: 0000-0002-7354-8574
- first_name: E.
full_name: Ben-Simchon, E.
last_name: Ben-Simchon
- first_name: K. J.
full_name: Bloodworth, K. J.
last_name: Bloodworth
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full_name: Bronstein, J. L.
last_name: Bronstein
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full_name: Buckley, Y. M.
last_name: Buckley
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full_name: Burghardt, K. T.
last_name: Burghardt
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full_name: Bustos-Segura, C.
last_name: Bustos-Segura
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full_name: Calixto, E. S.
last_name: Calixto
- first_name: R. L.
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last_name: Carvalho
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full_name: Castagneyrol, B.
last_name: Castagneyrol
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full_name: Chiuffo, M. C.
last_name: Chiuffo
- first_name: D.
full_name: Cinoğlu, D.
last_name: Cinoğlu
- first_name: E.
full_name: Cinto Mejía, E.
last_name: Cinto Mejía
- first_name: M. C.
full_name: Cock, M. C.
last_name: Cock
- first_name: R.
full_name: Cogni, R.
last_name: Cogni
- first_name: O. L.
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last_name: Cope
- first_name: T.
full_name: Cornelissen, T.
last_name: Cornelissen
- first_name: D. R.
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last_name: Cortez
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full_name: Crowder, D. W.
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full_name: Eisenring, M.
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- first_name: A.
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last_name: Ejomah
- first_name: B. D.
full_name: Elderd, B. D.
last_name: Elderd
- first_name: M. J.
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last_name: Endara
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full_name: Eubanks, M. D.
last_name: Eubanks
- first_name: S. E.
full_name: Everingham, S. E.
last_name: Everingham
- first_name: K. N.
full_name: Farah, K. N.
last_name: Farah
- first_name: R. P.
full_name: Farias, R. P.
last_name: Farias
- first_name: A. P.
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- first_name: G. W.
full_name: Fernandes, G. W.
last_name: Fernandes
- first_name: M.
full_name: Ferrante, M.
last_name: Ferrante
- first_name: A.
full_name: Finn, A.
last_name: Finn
- first_name: G. A.
full_name: Florjancic, G. A.
last_name: Florjancic
- first_name: M. L.
full_name: Forister, M. L.
last_name: Forister
- first_name: Q. N.
full_name: Fox, Q. N.
last_name: Fox
- first_name: E.
full_name: Frago, E.
last_name: Frago
- first_name: F. M.
full_name: França, F. M.
last_name: França
- first_name: A. S.
full_name: Getman-Pickering, A. S.
last_name: Getman-Pickering
- first_name: Z.
full_name: Getman-Pickering, Z.
last_name: Getman-Pickering
- first_name: E.
full_name: Gianoli, E.
last_name: Gianoli
- first_name: B.
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- first_name: M. M.
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- first_name: H. M.
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- first_name: T. N.
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- first_name: D. M.
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last_name: Massad
- first_name: A. C.
full_name: Mccall, A. C.
last_name: Mccall
- first_name: K.
full_name: Mcgurrin, K.
last_name: Mcgurrin
- first_name: A. C.
full_name: Merwin, A. C.
last_name: Merwin
- first_name: Z.
full_name: Mijango-Ramos, Z.
last_name: Mijango-Ramos
- first_name: C. H.
full_name: Mills, C. H.
last_name: Mills
- first_name: A. T.
full_name: Moles, A. T.
last_name: Moles
- first_name: C. M.
full_name: Moore, C. M.
last_name: Moore
- first_name: X.
full_name: Moreira, X.
last_name: Moreira
- first_name: C. R.
full_name: Morrison, C. R.
last_name: Morrison
- first_name: M. C.
full_name: Moshobane, M. C.
last_name: Moshobane
- first_name: A.
full_name: Muola, A.
last_name: Muola
- first_name: R.
full_name: Nakadai, R.
last_name: Nakadai
- first_name: K.
full_name: Nakajima, K.
last_name: Nakajima
- first_name: S.
full_name: Novais, S.
last_name: Novais
- first_name: C. O.
full_name: Ogbebor, C. O.
last_name: Ogbebor
- first_name: H.
full_name: Ohsaki, H.
last_name: Ohsaki
- first_name: V. S.
full_name: Pan, V. S.
last_name: Pan
- first_name: N. A.
full_name: Pardikes, N. A.
last_name: Pardikes
- first_name: M.
full_name: Pareja, M.
last_name: Pareja
- first_name: N.
full_name: Parthasarathy, N.
last_name: Parthasarathy
- first_name: R. R.
full_name: Pawar, R. R.
last_name: Pawar
- first_name: Q.
full_name: Paynter, Q.
last_name: Paynter
- first_name: I. S.
full_name: Pearse, I. S.
last_name: Pearse
- first_name: R. M.
full_name: Penczykowski, R. M.
last_name: Penczykowski
- first_name: A. A.
full_name: Pepi, A. A.
last_name: Pepi
- first_name: C. C.
full_name: Pereira, C. C.
last_name: Pereira
- first_name: S. S.
full_name: Phartyal, S. S.
last_name: Phartyal
- first_name: F. I.
full_name: Piper, F. I.
last_name: Piper
- first_name: K.
full_name: Poveda, K.
last_name: Poveda
- first_name: E. G.
full_name: Pringle, E. G.
last_name: Pringle
- first_name: J.
full_name: Puy, J.
last_name: Puy
- first_name: T.
full_name: Quijano, T.
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- first_name: C.
full_name: Quintero, C.
last_name: Quintero
- first_name: S.
full_name: Rasmann, S.
last_name: Rasmann
- first_name: C.
full_name: Rosche, C.
last_name: Rosche
- first_name: L. Y.
full_name: Rosenheim, L. Y.
last_name: Rosenheim
- first_name: J. A.
full_name: Rosenheim, J. A.
last_name: Rosenheim
- first_name: J. B.
full_name: Runyon, J. B.
last_name: Runyon
- first_name: A.
full_name: Sadeh, A.
last_name: Sadeh
- first_name: Y.
full_name: Sakata, Y.
last_name: Sakata
- first_name: D. M.
full_name: Salcido, D. M.
last_name: Salcido
- first_name: C.
full_name: Salgado-Luarte, C.
last_name: Salgado-Luarte
- first_name: B. A.
full_name: Santos, B. A.
last_name: Santos
- first_name: Y.
full_name: Sapir, Y.
last_name: Sapir
- first_name: Y.
full_name: Sasal, Y.
last_name: Sasal
- first_name: Y.
full_name: Sato, Y.
last_name: Sato
- first_name: M.
full_name: Sawant, M.
last_name: Sawant
- first_name: H.
full_name: Schroeder, H.
last_name: Schroeder
- first_name: I.
full_name: Schumann, I.
last_name: Schumann
- first_name: M.
full_name: Segoli, M.
last_name: Segoli
- first_name: H.
full_name: Segre, H.
last_name: Segre
- first_name: O.
full_name: Shelef, O.
last_name: Shelef
- first_name: N.
full_name: Shinohara, N.
last_name: Shinohara
- first_name: R. P.
full_name: Singh, R. P.
last_name: Singh
- first_name: D. S.
full_name: Smith, D. S.
last_name: Smith
- first_name: M.
full_name: Sobral, M.
last_name: Sobral
- first_name: G. C.
full_name: Stotz, G. C.
last_name: Stotz
- first_name: A. J.M.
full_name: Tack, A. J.M.
last_name: Tack
- first_name: M.
full_name: Tayal, M.
last_name: Tayal
- first_name: J. F.
full_name: Tooker, J. F.
last_name: Tooker
- first_name: D.
full_name: Torrico-Bazoberry, D.
last_name: Torrico-Bazoberry
- first_name: K.
full_name: Tougeron, K.
last_name: Tougeron
- first_name: A. M.
full_name: Trowbridge, A. M.
last_name: Trowbridge
- first_name: S.
full_name: Utsumi, S.
last_name: Utsumi
- first_name: O.
full_name: Uyi, O.
last_name: Uyi
- first_name: J. L.
full_name: Vaca-Uribe, J. L.
last_name: Vaca-Uribe
- first_name: A.
full_name: Valtonen, A.
last_name: Valtonen
- first_name: L. J.A.
full_name: Van Dijk, L. J.A.
last_name: Van Dijk
- first_name: V.
full_name: Vandvik, V.
last_name: Vandvik
- first_name: J.
full_name: Villellas, J.
last_name: Villellas
- first_name: L. P.
full_name: Waller, L. P.
last_name: Waller
- first_name: M. G.
full_name: Weber, M. G.
last_name: Weber
- first_name: A.
full_name: Yamawo, A.
last_name: Yamawo
- first_name: S.
full_name: Yim, S.
last_name: Yim
- first_name: P. L.
full_name: Zarnetske, P. L.
last_name: Zarnetske
- first_name: L. N.
full_name: Zehr, L. N.
last_name: Zehr
- first_name: Z.
full_name: Zhong, Z.
last_name: Zhong
- first_name: W. C.
full_name: Wetzel, W. C.
last_name: Wetzel
citation:
ama: Robinson ML, Hahn PG, Inouye BD, et al. Plant size, latitude, and phylogeny
explain within-population variability in herbivory. Science. 2023;382(6671):679-683.
doi:10.1126/science.adh8830
apa: Robinson, M. L., Hahn, P. G., Inouye, B. D., Underwood, N., Whitehead, S. R.,
Abbott, K. C., … Wetzel, W. C. (2023). Plant size, latitude, and phylogeny explain
within-population variability in herbivory. Science. AAAS. https://doi.org/10.1126/science.adh8830
chicago: Robinson, M. L., P. G. Hahn, B. D. Inouye, N. Underwood, S. R. Whitehead,
K. C. Abbott, E. M. Bruna, et al. “Plant Size, Latitude, and Phylogeny Explain
within-Population Variability in Herbivory.” Science. AAAS, 2023. https://doi.org/10.1126/science.adh8830.
ieee: M. L. Robinson et al., “Plant size, latitude, and phylogeny explain
within-population variability in herbivory,” Science, vol. 382, no. 6671.
AAAS, pp. 679–683, 2023.
ista: Robinson ML et al. 2023. Plant size, latitude, and phylogeny explain within-population
variability in herbivory. Science. 382(6671), 679–683.
mla: Robinson, M. L., et al. “Plant Size, Latitude, and Phylogeny Explain within-Population
Variability in Herbivory.” Science, vol. 382, no. 6671, AAAS, 2023, pp.
679–83, doi:10.1126/science.adh8830.
short: M.L. Robinson, P.G. Hahn, B.D. Inouye, N. Underwood, S.R. Whitehead, K.C.
Abbott, E.M. Bruna, N.I. Cacho, L.A. Dyer, L. Abdala-Roberts, W.J. Allen, J.F.
Andrade, D.F. Angulo, D. Anjos, D.N. Anstett, R. Bagchi, S. Bagchi, M. Barbosa,
S. Barrett, C. Baskett, E. Ben-Simchon, K.J. Bloodworth, J.L. Bronstein, Y.M.
Buckley, K.T. Burghardt, C. Bustos-Segura, E.S. Calixto, R.L. Carvalho, B. Castagneyrol,
M.C. Chiuffo, D. Cinoğlu, E. Cinto Mejía, M.C. Cock, R. Cogni, O.L. Cope, T. Cornelissen,
D.R. Cortez, D.W. Crowder, C. Dallstream, W. Dáttilo, J.K. Davis, R.D. Dimarco,
H.E. Dole, I.N. Egbon, M. Eisenring, A. Ejomah, B.D. Elderd, M.J. Endara, M.D.
Eubanks, S.E. Everingham, K.N. Farah, R.P. Farias, A.P. Fernandes, G.W. Fernandes,
M. Ferrante, A. Finn, G.A. Florjancic, M.L. Forister, Q.N. Fox, E. Frago, F.M.
França, A.S. Getman-Pickering, Z. Getman-Pickering, E. Gianoli, B. Gooden, M.M.
Gossner, K.A. Greig, S. Gripenberg, R. Groenteman, P. Grof-Tisza, N. Haack, L.
Hahn, S.M. Haq, A.M. Helms, J. Hennecke, S.L. Hermann, L.M. Holeski, S. Holm,
M.C. Hutchinson, E.E. Jackson, S. Kagiya, A. Kalske, M. Kalwajtys, R. Karban,
R. Kariyat, T. Keasar, M.F. Kersch-Becker, H.M. Kharouba, T.N. Kim, D.M. Kimuyu,
J. Kluse, S.E. Koerner, K.J. Komatsu, S. Krishnan, M. Laihonen, L. Lamelas-López,
M.C. Lascaleia, N. Lecomte, C.R. Lehn, X. Li, R.L. Lindroth, E.F. Lopresti, M.
Losada, A.M. Louthan, V.J. Luizzi, S.C. Lynch, J.S. Lynn, N.J. Lyon, L.F. Maia,
R.A. Maia, T.L. Mannall, B.S. Martin, T.J. Massad, A.C. Mccall, K. Mcgurrin, A.C.
Merwin, Z. Mijango-Ramos, C.H. Mills, A.T. Moles, C.M. Moore, X. Moreira, C.R.
Morrison, M.C. Moshobane, A. Muola, R. Nakadai, K. Nakajima, S. Novais, C.O. Ogbebor,
H. Ohsaki, V.S. Pan, N.A. Pardikes, M. Pareja, N. Parthasarathy, R.R. Pawar, Q.
Paynter, I.S. Pearse, R.M. Penczykowski, A.A. Pepi, C.C. Pereira, S.S. Phartyal,
F.I. Piper, K. Poveda, E.G. Pringle, J. Puy, T. Quijano, C. Quintero, S. Rasmann,
C. Rosche, L.Y. Rosenheim, J.A. Rosenheim, J.B. Runyon, A. Sadeh, Y. Sakata, D.M.
Salcido, C. Salgado-Luarte, B.A. Santos, Y. Sapir, Y. Sasal, Y. Sato, M. Sawant,
H. Schroeder, I. Schumann, M. Segoli, H. Segre, O. Shelef, N. Shinohara, R.P.
Singh, D.S. Smith, M. Sobral, G.C. Stotz, A.J.M. Tack, M. Tayal, J.F. Tooker,
D. Torrico-Bazoberry, K. Tougeron, A.M. Trowbridge, S. Utsumi, O. Uyi, J.L. Vaca-Uribe,
A. Valtonen, L.J.A. Van Dijk, V. Vandvik, J. Villellas, L.P. Waller, M.G. Weber,
A. Yamawo, S. Yim, P.L. Zarnetske, L.N. Zehr, Z. Zhong, W.C. Wetzel, Science 382
(2023) 679–683.
date_created: 2023-11-19T23:00:54Z
date_published: 2023-11-09T00:00:00Z
date_updated: 2023-11-20T11:17:34Z
day: '09'
department:
- _id: NiBa
doi: 10.1126/science.adh8830
external_id:
pmid:
- '37943897'
intvolume: ' 382'
issue: '6671'
language:
- iso: eng
month: '11'
oa_version: None
page: 679-683
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
publication_status: published
publisher: AAAS
quality_controlled: '1'
related_material:
record:
- id: '14579'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Plant size, latitude, and phylogeny explain within-population variability in
herbivory
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 382
year: '2023'
...
---
_id: '14579'
abstract:
- lang: eng
text: "This is associated with our paper \"Plant size, latitude, and phylogeny explain
within-population variability in herbivory\" published in Science.\r\n"
article_processing_charge: No
author:
- first_name: William
full_name: Wetzel, William
last_name: Wetzel
citation:
ama: 'Wetzel W. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. 2023. doi:10.5281/ZENODO.8133117'
apa: 'Wetzel, W. (2023). HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. Zenodo.
https://doi.org/10.5281/ZENODO.8133117'
chicago: 'Wetzel, William. “HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0.”
Zenodo, 2023. https://doi.org/10.5281/ZENODO.8133117.'
ieee: 'W. Wetzel, “HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0.” Zenodo,
2023.'
ista: 'Wetzel W. 2023. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0, Zenodo,
10.5281/ZENODO.8133117.'
mla: 'Wetzel, William. HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0.
Zenodo, 2023, doi:10.5281/ZENODO.8133117.'
short: W. Wetzel, (2023).
date_created: 2023-11-20T11:07:45Z
date_published: 2023-07-11T00:00:00Z
date_updated: 2023-11-20T11:17:33Z
day: '11'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5281/ZENODO.8133117
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.8133118
month: '07'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '14552'
relation: used_in_publication
status: public
status: public
title: 'HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0'
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14058'
abstract:
- lang: eng
text: "Females and males across species are subject to divergent selective pressures
arising\r\nfrom di↵erent reproductive interests and ecological niches. This often
translates into a\r\nintricate array of sex-specific natural and sexual selection
on traits that have a shared\r\ngenetic basis between both sexes, causing a genetic
sexual conflict. The resolution of\r\nthis conflict mostly relies on the evolution
of sex-specific expression of the shared genes,\r\nleading to phenotypic sexual
dimorphism. Such sex-specific gene expression is thought\r\nto evolve via modifications
of the genetic networks ultimately linked to sex-determining\r\ntranscription
factors. Although much empirical and theoretical evidence supports this\r\nstandard
picture of the molecular basis of sexual conflict resolution, there still are
a\r\nfew open questions regarding the complex array of selective forces driving
phenotypic\r\ndi↵erentiation between the sexes, as well as the molecular mechanisms
underlying sexspecific adaptation. I address some of these open questions in my
PhD thesis.\r\nFirst, how do patterns of phenotypic sexual dimorphism vary within
populations,\r\nas a response to the temporal and spatial changes in sex-specific
selective forces? To\r\ntackle this question, I analyze the patterns of sex-specific
phenotypic variation along\r\nthree life stages and across populations spanning
the whole geographical range of Rumex\r\nhastatulus, a wind-pollinated angiosperm,
in the first Chapter of the thesis.\r\nSecond, how do gene expression patterns
lead to phenotypic dimorphism, and what\r\nare the molecular mechanisms underlying
the observed transcriptomic variation? I\r\naddress this question by examining
the sex- and tissue-specific expression variation in\r\nnewly-generated datasets
of sex-specific expression in heads and gonads of Drosophila\r\nmelanogaster.
I additionally used two complementary approaches for the study of the\r\ngenetic
basis of sex di↵erences in gene expression in the second and third Chapters of\r\nthe
thesis.\r\nThird, how does intersex correlation, thought to be one of the main
aspects constraining the ability for the two sexes to decouple, interact with
the evolution of sexual\r\ndimorphism? I develop models of sex-specific stabilizing
selection, mutation and drift\r\nto formalize common intuition regarding the patterns
of covariation between intersex\r\ncorrelation and sexual dimorphism in the fourth
Chapter of the thesis.\r\nAlltogether, the work described in this PhD thesis provides
useful insights into the\r\nlinks between genetic, transcriptomic and phenotypic
layers of sex-specific variation,\r\nand contributes to our general understanding
of the dynamics of sexual dimorphism\r\nevolution."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Gemma
full_name: Puixeu Sala, Gemma
id: 33AB266C-F248-11E8-B48F-1D18A9856A87
last_name: Puixeu Sala
orcid: 0000-0001-8330-1754
citation:
ama: 'Puixeu Sala G. The molecular basis of sexual dimorphism: Experimental and
theoretical characterization of phenotypic, transcriptomic and genetic patterns
of sex-specific adaptation. 2023. doi:10.15479/at:ista:14058'
apa: 'Puixeu Sala, G. (2023). The molecular basis of sexual dimorphism: Experimental
and theoretical characterization of phenotypic, transcriptomic and genetic patterns
of sex-specific adaptation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14058'
chicago: 'Puixeu Sala, Gemma. “The Molecular Basis of Sexual Dimorphism: Experimental
and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns
of Sex-Specific Adaptation.” Institute of Science and Technology Austria, 2023.
https://doi.org/10.15479/at:ista:14058.'
ieee: 'G. Puixeu Sala, “The molecular basis of sexual dimorphism: Experimental and
theoretical characterization of phenotypic, transcriptomic and genetic patterns
of sex-specific adaptation,” Institute of Science and Technology Austria, 2023.'
ista: 'Puixeu Sala G. 2023. The molecular basis of sexual dimorphism: Experimental
and theoretical characterization of phenotypic, transcriptomic and genetic patterns
of sex-specific adaptation. Institute of Science and Technology Austria.'
mla: 'Puixeu Sala, Gemma. The Molecular Basis of Sexual Dimorphism: Experimental
and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns
of Sex-Specific Adaptation. Institute of Science and Technology Austria, 2023,
doi:10.15479/at:ista:14058.'
short: 'G. Puixeu Sala, The Molecular Basis of Sexual Dimorphism: Experimental and
Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns
of Sex-Specific Adaptation, Institute of Science and Technology Austria, 2023.'
date_created: 2023-08-15T10:20:40Z
date_published: 2023-08-15T00:00:00Z
date_updated: 2023-12-13T12:15:36Z
day: '15'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: GradSch
- _id: NiBa
- _id: BeVi
doi: 10.15479/at:ista:14058
ec_funded: 1
file:
- access_level: closed
checksum: 4e44e169f2724ee8c9324cd60bcc2b71
content_type: application/zip
creator: gpuixeus
date_created: 2023-08-16T18:15:17Z
date_updated: 2023-08-17T06:55:24Z
file_id: '14075'
file_name: Thesis_latex_forpdfa.zip
file_size: 10891454
relation: source_file
- access_level: open_access
checksum: e10b04cd8f3fecc0d9ef6e6868b6e1e8
content_type: application/pdf
creator: gpuixeus
date_created: 2023-08-18T10:47:55Z
date_updated: 2023-08-18T10:47:55Z
file_id: '14079'
file_name: PhDThesis_PuixeuG.pdf
file_size: 19856686
relation: main_file
success: 1
file_date_updated: 2023-08-18T10:47:55Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '230'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 9B9DFC9E-BA93-11EA-9121-9846C619BF3A
grant_number: '25817'
name: 'Sexual conflict: resolution, constraints and biomedical implications'
publication_identifier:
isbn:
- 978-3-99078-035-0
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9803'
relation: research_data
status: public
- id: '12933'
relation: research_data
status: public
- id: '6831'
relation: part_of_dissertation
status: public
- id: '14077'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: 'The molecular basis of sexual dimorphism: Experimental and theoretical characterization
of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14077'
abstract:
- lang: eng
text: "The regulatory architecture of gene expression is known to differ substantially
between sexes in Drosophila, but most studies performed\r\nso far used whole-body
data and only single crosses, which may have limited their scope to detect patterns
that are robust across tissues\r\nand biological replicates. Here, we use allele-specific
gene expression of parental and reciprocal hybrid crosses between 6 Drosophila\r\nmelanogaster
inbred lines to quantify cis- and trans-regulatory variation in heads and gonads
of both sexes separately across 3 replicate\r\ncrosses. Our results suggest that
female and male heads, as well as ovaries, have a similar regulatory architecture.
On the other hand,\r\ntestes display more and substantially different cis-regulatory
effects, suggesting that sex differences in the regulatory architecture that\r\nhave
been previously observed may largely derive from testis-specific effects. We also
examine the difference in cis-regulatory variation\r\nof genes across different
levels of sex bias in gonads and heads. Consistent with the idea that intersex
correlations constrain expression\r\nand can lead to sexual antagonism, we find
more cis variation in unbiased and moderately biased genes in heads. In ovaries,
reduced cis\r\nvariation is observed for male-biased genes, suggesting that cis
variants acting on these genes in males do not lead to changes in ovary\r\nexpression.
Finally, we examine the dominance patterns of gene expression and find that sex-
and tissue-specific patterns of inheritance\r\nas well as trans-regulatory variation
are highly variable across biological crosses, although these were performed in
highly controlled\r\nexperimental conditions. This highlights the importance of
using various genetic backgrounds to infer generalizable patterns."
acknowledged_ssus:
- _id: ScienComp
acknowledgement: We thank members of the Vicoso Group for comments on the manuscript,
the Scientific Computing Unit at ISTA for technical support, and 2 anonymous reviewers
for useful feedback. GP is the recipient of a DOC Fellowship of the Austrian Academy
of Sciences at the Institute of Science and Technology Austria (DOC 25817) and received
funding from the European Union’s Horizon 2020 research and innovation program under
the Marie Skłodowska-Curie Grant (agreement no. 665385).
article_processing_charge: Yes
article_type: original
author:
- first_name: Gemma
full_name: Puixeu Sala, Gemma
id: 33AB266C-F248-11E8-B48F-1D18A9856A87
last_name: Puixeu Sala
orcid: 0000-0001-8330-1754
- first_name: Ariana
full_name: Macon, Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: 'Puixeu Sala G, Macon A, Vicoso B. Sex-specific estimation of cis and trans
regulation of gene expression in heads and gonads of Drosophila melanogaster.
G3: Genes, Genomes, Genetics. 2023;13(8). doi:10.1093/g3journal/jkad121'
apa: 'Puixeu Sala, G., Macon, A., & Vicoso, B. (2023). Sex-specific estimation
of cis and trans regulation of gene expression in heads and gonads of Drosophila
melanogaster. G3: Genes, Genomes, Genetics. Oxford University Press. https://doi.org/10.1093/g3journal/jkad121'
chicago: 'Puixeu Sala, Gemma, Ariana Macon, and Beatriz Vicoso. “Sex-Specific Estimation
of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila
Melanogaster.” G3: Genes, Genomes, Genetics. Oxford University Press, 2023.
https://doi.org/10.1093/g3journal/jkad121.'
ieee: 'G. Puixeu Sala, A. Macon, and B. Vicoso, “Sex-specific estimation of cis
and trans regulation of gene expression in heads and gonads of Drosophila melanogaster,”
G3: Genes, Genomes, Genetics, vol. 13, no. 8. Oxford University Press,
2023.'
ista: 'Puixeu Sala G, Macon A, Vicoso B. 2023. Sex-specific estimation of cis and
trans regulation of gene expression in heads and gonads of Drosophila melanogaster.
G3: Genes, Genomes, Genetics. 13(8).'
mla: 'Puixeu Sala, Gemma, et al. “Sex-Specific Estimation of Cis and Trans Regulation
of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” G3: Genes,
Genomes, Genetics, vol. 13, no. 8, Oxford University Press, 2023, doi:10.1093/g3journal/jkad121.'
short: 'G. Puixeu Sala, A. Macon, B. Vicoso, G3: Genes, Genomes, Genetics 13 (2023).'
date_created: 2023-08-18T06:52:14Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2023-12-13T12:15:37Z
day: '01'
ddc:
- '570'
department:
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- _id: NiBa
- _id: GradSch
doi: 10.1093/g3journal/jkad121
ec_funded: 1
external_id:
isi:
- '001002997200001'
file:
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file_size: 845642
relation: main_file
success: 1
file_date_updated: 2023-11-07T09:00:19Z
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intvolume: ' 13'
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keyword:
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- Genetics
- Molecular Biology
language:
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month: '08'
oa: 1
oa_version: Published Version
project:
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call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 9B9DFC9E-BA93-11EA-9121-9846C619BF3A
grant_number: '25817'
name: 'Sexual conflict: resolution, constraints and biomedical implications'
publication: 'G3: Genes, Genomes, Genetics'
publication_identifier:
issn:
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publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
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relation: research_data
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relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Sex-specific estimation of cis and trans regulation of gene expression in heads
and gonads of Drosophila melanogaster
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2023'
...
---
_id: '12933'
abstract:
- lang: eng
text: Datasets of the publication "Sex-specific estimation of cis and trans regulation
of gene expression in heads and gonads of Drosophila melanogaster".
article_processing_charge: No
author:
- first_name: Gemma
full_name: Puixeu Sala, Gemma
id: 33AB266C-F248-11E8-B48F-1D18A9856A87
last_name: Puixeu Sala
orcid: 0000-0001-8330-1754
citation:
ama: 'Puixeu Sala G. Data from: Sex-specific estimation of cis and trans regulation
of gene expression in heads and gonads of Drosophila melanogaster. 2023. doi:10.15479/AT:ISTA:12933'
apa: 'Puixeu Sala, G. (2023). Data from: Sex-specific estimation of cis and trans
regulation of gene expression in heads and gonads of Drosophila melanogaster.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12933'
chicago: 'Puixeu Sala, Gemma. “Data from: Sex-Specific Estimation of Cis and Trans
Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12933.'
ieee: 'G. Puixeu Sala, “Data from: Sex-specific estimation of cis and trans regulation
of gene expression in heads and gonads of Drosophila melanogaster.” Institute
of Science and Technology Austria, 2023.'
ista: 'Puixeu Sala G. 2023. Data from: Sex-specific estimation of cis and trans
regulation of gene expression in heads and gonads of Drosophila melanogaster,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:12933.'
mla: 'Puixeu Sala, Gemma. Data from: Sex-Specific Estimation of Cis and Trans
Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.
Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12933.'
short: G. Puixeu Sala, (2023).
contributor:
- first_name: Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
date_created: 2023-05-10T10:00:49Z
date_published: 2023-05-15T00:00:00Z
date_updated: 2023-12-13T12:15:36Z
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ddc:
- '570'
department:
- _id: GradSch
- _id: NiBa
- _id: BeVi
doi: 10.15479/AT:ISTA:12933
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oa: 1
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publisher: Institute of Science and Technology Austria
related_material:
record:
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status: public
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relation: used_in_publication
status: public
status: public
title: 'Data from: Sex-specific estimation of cis and trans regulation of gene expression
in heads and gonads of Drosophila melanogaster'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14463'
abstract:
- lang: eng
text: Inversions are thought to play a key role in adaptation and speciation, suppressing
recombination between diverging populations. Genes influencing adaptive traits
cluster in inversions, and changes in inversion frequencies are associated with
environmental differences. However, in many organisms, it is unclear if inversions
are geographically and taxonomically widespread. The intertidal snail, Littorina
saxatilis, is one such example. Strong associations between putative polymorphic
inversions and phenotypic differences have been demonstrated between two ecotypes
of L. saxatilis in Sweden and inferred elsewhere, but no direct evidence for inversion
polymorphism currently exists across the species range. Using whole genome data
from 107 snails, most inversion polymorphisms were found to be widespread across
the species range. The frequencies of some inversion arrangements were significantly
different among ecotypes, suggesting a parallel adaptive role. Many inversions
were also polymorphic in the sister species, L. arcana, hinting at an ancient
origin.
acknowledgement: We would like to thank members of the Littorina team for their advice
and feedback during this project. In particular, we thank Alan Le Moan, who inspired
us to look at heterozygosity differences to identify inversions, and Katherine Hearn
for helping with the PCA scripts. We thank Edinburgh Genomics for library preparation
and sequencing. Sample collections, sequencing and data preparation were supported
by the European Research Council (ERC-2015-AdG-693030- BARRIERS) and the Natural
Environment Research Council (NE/P001610/1). The analysis was supported by the Swedish
Research Council (vetenskaprådet; 2018-03695_VR) and the Portuguese Foundation for
Science and Technology (Fundación para a Ciência e Tecnologia) through a research
project (PTDC/BIA-EVL/1614/2021) and CEEC contract (2020.00275.CEECIND).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: James
full_name: Reeve, James
last_name: Reeve
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
- first_name: Eva L.
full_name: Koch, Eva L.
last_name: Koch
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
citation:
ama: Reeve J, Butlin RK, Koch EL, Stankowski S, Faria R. Chromosomal inversion polymorphisms
are widespread across the species ranges of rough periwinkles (Littorina saxatilis
and L. arcana). Molecular Ecology. 2023. doi:10.1111/mec.17160
apa: Reeve, J., Butlin, R. K., Koch, E. L., Stankowski, S., & Faria, R. (2023).
Chromosomal inversion polymorphisms are widespread across the species ranges of
rough periwinkles (Littorina saxatilis and L. arcana). Molecular Ecology.
Wiley. https://doi.org/10.1111/mec.17160
chicago: Reeve, James, Roger K. Butlin, Eva L. Koch, Sean Stankowski, and Rui Faria.
“Chromosomal Inversion Polymorphisms Are Widespread across the Species Ranges
of Rough Periwinkles (Littorina Saxatilis and L. Arcana).” Molecular Ecology.
Wiley, 2023. https://doi.org/10.1111/mec.17160.
ieee: J. Reeve, R. K. Butlin, E. L. Koch, S. Stankowski, and R. Faria, “Chromosomal
inversion polymorphisms are widespread across the species ranges of rough periwinkles
(Littorina saxatilis and L. arcana),” Molecular Ecology. Wiley, 2023.
ista: Reeve J, Butlin RK, Koch EL, Stankowski S, Faria R. 2023. Chromosomal inversion
polymorphisms are widespread across the species ranges of rough periwinkles (Littorina
saxatilis and L. arcana). Molecular Ecology.
mla: Reeve, James, et al. “Chromosomal Inversion Polymorphisms Are Widespread across
the Species Ranges of Rough Periwinkles (Littorina Saxatilis and L. Arcana).”
Molecular Ecology, Wiley, 2023, doi:10.1111/mec.17160.
short: J. Reeve, R.K. Butlin, E.L. Koch, S. Stankowski, R. Faria, Molecular Ecology
(2023).
date_created: 2023-10-29T23:01:17Z
date_published: 2023-10-16T00:00:00Z
date_updated: 2023-12-13T13:05:27Z
day: '16'
department:
- _id: NiBa
doi: 10.1111/mec.17160
external_id:
isi:
- '001085119000001'
pmid:
- '37843465'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/mec.17160
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: epub_ahead
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chromosomal inversion polymorphisms are widespread across the species ranges
of rough periwinkles (Littorina saxatilis and L. arcana)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14651'
abstract:
- lang: eng
text: 'For self-incompatibility (SI) to be stable in a population, theory predicts
that sufficient inbreeding depression (ID) is required: the fitness of offspring
from self-mated individuals must be low enough to prevent the spread of self-compatibility
(SC). Reviews of natural plant populations have supported this theory, with SI
species generally showing high levels of ID. However, there is thought to be an
under-sampling of self-incompatible taxa in the current literature. In this thesis,
I study inbreeding depression in the SI plant species Antirrhinum majus using
both greenhouse crosses and a large collected field dataset. Additionally, the
gametophytic S-locus of A. majus is highly heterozygous and polymorphic, thus
making assembly and discovery of S-alleles very difficult. Here, 206 new alleles
of the male component SLFs are presented, along with a phylogeny showing the high
conservation with alleles from another Antirrhinum species. Lastly, selected sites
within the protein structure of SLFs are investigated, with one site in particular
highlighted as potentially being involved in the SI recognition mechanism.'
acknowledged_ssus:
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Louise S
full_name: Arathoon, Louise S
id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87
last_name: Arathoon
orcid: 0000-0003-1771-714X
citation:
ama: Arathoon LS. Investigating inbreeding depression and the self-incompatibility
locus of Antirrhinum majus. 2023. doi:10.15479/at:ista:14651
apa: Arathoon, L. S. (2023). Investigating inbreeding depression and the self-incompatibility
locus of Antirrhinum majus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14651
chicago: Arathoon, Louise S. “Investigating Inbreeding Depression and the Self-Incompatibility
Locus of Antirrhinum Majus.” Institute of Science and Technology Austria, 2023.
https://doi.org/10.15479/at:ista:14651.
ieee: L. S. Arathoon, “Investigating inbreeding depression and the self-incompatibility
locus of Antirrhinum majus,” Institute of Science and Technology Austria, 2023.
ista: Arathoon LS. 2023. Investigating inbreeding depression and the self-incompatibility
locus of Antirrhinum majus. Institute of Science and Technology Austria.
mla: Arathoon, Louise S. Investigating Inbreeding Depression and the Self-Incompatibility
Locus of Antirrhinum Majus. Institute of Science and Technology Austria, 2023,
doi:10.15479/at:ista:14651.
short: L.S. Arathoon, Investigating Inbreeding Depression and the Self-Incompatibility
Locus of Antirrhinum Majus, Institute of Science and Technology Austria, 2023.
date_created: 2023-12-11T19:30:37Z
date_published: 2023-12-12T00:00:00Z
date_updated: 2023-12-22T11:04:45Z
day: '12'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/at:ista:14651
ec_funded: 1
file:
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creator: larathoo
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creator: larathoo
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file_size: 31052872
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content_type: application/zip
creator: larathoo
date_created: 2023-12-11T19:24:59Z
date_updated: 2023-12-14T08:58:18Z
file_id: '14681'
file_name: Supplementary_Materials.zip
file_size: 10713896
relation: supplementary_material
file_date_updated: 2023-12-14T08:58:18Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '96'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11411'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum
majus
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14742'
abstract:
- lang: eng
text: "Chromosomal rearrangements (CRs) have been known since almost the beginning
of genetics.\r\nWhile an important role for CRs in speciation has been suggested,
evidence primarily stems\r\nfrom theoretical and empirical studies focusing on
the microevolutionary level (i.e., on taxon\r\npairs where speciation is often
incomplete). Although the role of CRs in eukaryotic speciation at\r\na macroevolutionary
level has been supported by associations between species diversity and\r\nrates
of evolution of CRs across phylogenies, these findings are limited to a restricted
range of\r\nCRs and taxa. Now that more broadly applicable and precise CR detection
approaches have\r\nbecome available, we address the challenges in filling some
of the conceptual and empirical\r\ngaps between micro- and macroevolutionary studies
on the role of CRs in speciation. We\r\nsynthesize what is known about the macroevolutionary
impact of CRs and suggest new research avenues to overcome the pitfalls of previous
studies to gain a more comprehensive understanding of the evolutionary significance
of CRs in speciation across the tree of life."
acknowledgement: "K.L. was funded by a Swiss National Science Foundation Eccellenza
project: The evolution of strong reproductive barriers towards the completion of
speciation (PCEFP3_202869). R.F.\r\nwas funded by an FCT CEEC (Fundação para a Ciênca
e a Tecnologia, Concurso Estímulo ao\r\nEmprego Científico) contract (2020.00275.
CEECIND) and by an FCT research project\r\n(PTDC/BIA-EVL/1614/2021). M.R. was funded
by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243). A.M.W.
was partly funded by the Norwegian Research Council RCN. We thank Luis Silva for
his help preparing Figure 1. We are grateful to Maren Wellenreuther, Daniel Bolnick,
and two anonymous reviewers for their constructive feedback on an earlier version
of this paper."
article_number: a041447
article_processing_charge: No
article_type: original
author:
- first_name: Kay
full_name: Lucek, Kay
last_name: Lucek
- first_name: Mabel D.
full_name: Giménez, Mabel D.
last_name: Giménez
- first_name: Mathieu
full_name: Joron, Mathieu
last_name: Joron
- first_name: Marina
full_name: Rafajlović, Marina
last_name: Rafajlović
- first_name: Jeremy B.
full_name: Searle, Jeremy B.
last_name: Searle
- first_name: Nora
full_name: Walden, Nora
last_name: Walden
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
citation:
ama: 'Lucek K, Giménez MD, Joron M, et al. The impact of chromosomal rearrangements
in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives
in Biology. 2023;15(11). doi:10.1101/cshperspect.a041447'
apa: 'Lucek, K., Giménez, M. D., Joron, M., Rafajlović, M., Searle, J. B., Walden,
N., … Faria, R. (2023). The impact of chromosomal rearrangements in speciation:
From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology.
Cold Spring Harbor Laboratory. https://doi.org/10.1101/cshperspect.a041447'
chicago: 'Lucek, Kay, Mabel D. Giménez, Mathieu Joron, Marina Rafajlović, Jeremy
B. Searle, Nora Walden, Anja M Westram, and Rui Faria. “The Impact of Chromosomal
Rearrangements in Speciation: From Micro- to Macroevolution.” Cold Spring Harbor
Perspectives in Biology. Cold Spring Harbor Laboratory, 2023. https://doi.org/10.1101/cshperspect.a041447.'
ieee: 'K. Lucek et al., “The impact of chromosomal rearrangements in speciation:
From micro- to macroevolution,” Cold Spring Harbor Perspectives in Biology,
vol. 15, no. 11. Cold Spring Harbor Laboratory, 2023.'
ista: 'Lucek K, Giménez MD, Joron M, Rafajlović M, Searle JB, Walden N, Westram
AM, Faria R. 2023. The impact of chromosomal rearrangements in speciation: From
micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. 15(11),
a041447.'
mla: 'Lucek, Kay, et al. “The Impact of Chromosomal Rearrangements in Speciation:
From Micro- to Macroevolution.” Cold Spring Harbor Perspectives in Biology,
vol. 15, no. 11, a041447, Cold Spring Harbor Laboratory, 2023, doi:10.1101/cshperspect.a041447.'
short: K. Lucek, M.D. Giménez, M. Joron, M. Rafajlović, J.B. Searle, N. Walden,
A.M. Westram, R. Faria, Cold Spring Harbor Perspectives in Biology 15 (2023).
date_created: 2024-01-08T12:43:48Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2024-01-08T12:52:29Z
day: '01'
department:
- _id: NiBa
- _id: BeVi
doi: 10.1101/cshperspect.a041447
external_id:
pmid:
- '37604585'
intvolume: ' 15'
issue: '11'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/cshperspect.a041447
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Cold Spring Harbor Perspectives in Biology
publication_identifier:
issn:
- 1943-0264
publication_status: published
publisher: Cold Spring Harbor Laboratory
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The impact of chromosomal rearrangements in speciation: From micro- to macroevolution'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2023'
...
---
_id: '14787'
abstract:
- lang: eng
text: Understanding the phenotypic and genetic architecture of reproductive isolation
is a long‐standing goal of speciation research. In several systems, large‐effect
loci contributing to barrier phenotypes have been characterized, but such causal
connections are rarely known for more complex genetic architectures. In this study,
we combine “top‐down” and “bottom‐up” approaches with demographic modelling toward
an integrated understanding of speciation across a monkeyflower hybrid zone. Previous
work suggests that pollinator visitation acts as a primary barrier to gene flow
between two divergent red‐ and yellow‐flowered ecotypes ofMimulus
aurantiacus. Several candidate isolating traits and anonymous single
nucleotide polymorphism loci under divergent selection have been identified, but
their genomic positions remain unknown. Here, we report findings from demographic
analyses that indicate this hybrid zone formed by secondary contact, but that
subsequent gene flow was restricted by widespread barrier loci across the genome.
Using a novel, geographic cline‐based genome scan, we demonstrate that candidate
barrier loci are broadly distributed across the genome, rather than mapping to
one or a few “islands of speciation.” Quantitative trait locus (QTL) mapping reveals
that most floral traits are highly polygenic, with little evidence that QTL colocalize,
indicating that most traits are genetically independent. Finally, we find little
evidence that QTL and candidate barrier loci overlap, suggesting that some loci
contribute to other forms of reproductive isolation. Our findings highlight the
challenges of understanding the genetic architecture of reproductive isolation
and reveal that barriers to gene flow other than pollinator isolation may play
an important role in this system.
acknowledgement: We thank Julian Catchen for making modifications to Stacks to aid
this project. Peter L. Ralph, Thomas Nelson, Roger K. Butlin, Anja M. Westram and
Nicholas H. Barton provided advice, stimulating discussion and critical feedback.
The project was supported by National Science Foundation grant DEB-1258199.
article_processing_charge: No
article_type: original
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Madeline A.
full_name: Chase, Madeline A.
last_name: Chase
- first_name: Hanna
full_name: McIntosh, Hanna
last_name: McIntosh
- first_name: Matthew A.
full_name: Streisfeld, Matthew A.
last_name: Streisfeld
citation:
ama: Stankowski S, Chase MA, McIntosh H, Streisfeld MA. Integrating top‐down and
bottom‐up approaches to understand the genetic architecture of speciation across
a monkeyflower hybrid zone. Molecular Ecology. 2023;32(8):2041-2054. doi:10.1111/mec.16849
apa: Stankowski, S., Chase, M. A., McIntosh, H., & Streisfeld, M. A. (2023).
Integrating top‐down and bottom‐up approaches to understand the genetic architecture
of speciation across a monkeyflower hybrid zone. Molecular Ecology. Wiley.
https://doi.org/10.1111/mec.16849
chicago: Stankowski, Sean, Madeline A. Chase, Hanna McIntosh, and Matthew A. Streisfeld.
“Integrating Top‐down and Bottom‐up Approaches to Understand the Genetic Architecture
of Speciation across a Monkeyflower Hybrid Zone.” Molecular Ecology. Wiley,
2023. https://doi.org/10.1111/mec.16849.
ieee: S. Stankowski, M. A. Chase, H. McIntosh, and M. A. Streisfeld, “Integrating
top‐down and bottom‐up approaches to understand the genetic architecture of speciation
across a monkeyflower hybrid zone,” Molecular Ecology, vol. 32, no. 8.
Wiley, pp. 2041–2054, 2023.
ista: Stankowski S, Chase MA, McIntosh H, Streisfeld MA. 2023. Integrating top‐down
and bottom‐up approaches to understand the genetic architecture of speciation
across a monkeyflower hybrid zone. Molecular Ecology. 32(8), 2041–2054.
mla: Stankowski, Sean, et al. “Integrating Top‐down and Bottom‐up Approaches to
Understand the Genetic Architecture of Speciation across a Monkeyflower Hybrid
Zone.” Molecular Ecology, vol. 32, no. 8, Wiley, 2023, pp. 2041–54, doi:10.1111/mec.16849.
short: S. Stankowski, M.A. Chase, H. McIntosh, M.A. Streisfeld, Molecular Ecology
32 (2023) 2041–2054.
date_created: 2024-01-10T10:44:45Z
date_published: 2023-04-01T00:00:00Z
date_updated: 2024-01-16T10:10:00Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/mec.16849
external_id:
isi:
- '000919244600001'
pmid:
- '36651268'
intvolume: ' 32'
isi: 1
issue: '8'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2022.01.28.478139
month: '04'
oa: 1
oa_version: Preprint
page: 2041-2054
pmid: 1
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Integrating top‐down and bottom‐up approaches to understand the genetic architecture
of speciation across a monkeyflower hybrid zone
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2023'
...
---
_id: '14833'
abstract:
- lang: eng
text: Understanding the factors that have shaped the current distributions and diversity
of species is a central and longstanding aim of evolutionary biology. The recent
inclusion of genomic data into phylogeographic studies has dramatically improved
our understanding in organisms where evolutionary relationships have been challenging
to infer. We used whole-genome sequences to study the phylogeography of the intertidal
snail Littorina saxatilis, which has successfully colonized and diversified across
a broad range of coastal environments in the Northern Hemisphere amid repeated
cycles of glaciation. Building on past studies based on short DNA sequences, we
used genome-wide data to provide a clearer picture of the relationships among
samples spanning most of the species natural range. Our results confirm the trans-Atlantic
colonization of North America from Europe, and have allowed us to identify rough
locations of glacial refugia and to infer likely routes of colonization within
Europe. We also investigated the signals in different datasets to account for
the effects of genomic architecture and non-neutral evolution, which provides
new insights about diversification of four ecotypes of L. saxatilis (the crab,
wave, barnacle, and brackish ecotypes) at different spatial scales. Overall, we
provide a much clearer picture of the biogeography of L. saxatilis, providing
a foundation for more detailed phylogenomic and demographic studies.
acknowledgement: Isobel Eyres, Richard Turney, Graciela Sotelo, Jenny Larson, and
Stéphane Loisel helped with the collection and processing of samples. Petri Kemppainen
kindly provided samples from Trondheim Fjord. Mark Dunning helped with the development
of bioinformatic pipelines. The analysis of genomic data was conducted on the University
of Sheffield high-performance computing cluster, ShARC. Funding was provided by
the Natural Environment Research Council (NERC) and the European Research Council
(ERC). J.G. was funded by a Juntas Industriales y Navales (JIN) project (Ministerio
de Ciencia, Innovación y Universidades, code RTI2018-101274-J-I00).
article_number: kzad002
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Zuzanna B
full_name: Zagrodzka, Zuzanna B
last_name: Zagrodzka
- first_name: Juan
full_name: Galindo, Juan
last_name: Galindo
- first_name: Mauricio
full_name: Montaño-Rendón, Mauricio
last_name: Montaño-Rendón
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Natalia
full_name: Mikhailova, Natalia
last_name: Mikhailova
- first_name: April M H
full_name: Blakeslee, April M H
last_name: Blakeslee
- first_name: Einar
full_name: Arnason, Einar
last_name: Arnason
- first_name: Thomas
full_name: Broquet, Thomas
last_name: Broquet
- first_name: Hernán E
full_name: Morales, Hernán E
last_name: Morales
- first_name: John W
full_name: Grahame, John W
last_name: Grahame
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger K
full_name: Butlin, Roger K
last_name: Butlin
citation:
ama: Stankowski S, Zagrodzka ZB, Galindo J, et al. Whole-genome phylogeography of
the intertidal snail Littorina saxatilis. Evolutionary Journal of the Linnean
Society. 2023;2(1). doi:10.1093/evolinnean/kzad002
apa: Stankowski, S., Zagrodzka, Z. B., Galindo, J., Montaño-Rendón, M., Faria, R.,
Mikhailova, N., … Butlin, R. K. (2023). Whole-genome phylogeography of the intertidal
snail Littorina saxatilis. Evolutionary Journal of the Linnean Society.
Oxford University Press. https://doi.org/10.1093/evolinnean/kzad002
chicago: Stankowski, Sean, Zuzanna B Zagrodzka, Juan Galindo, Mauricio Montaño-Rendón,
Rui Faria, Natalia Mikhailova, April M H Blakeslee, et al. “Whole-Genome Phylogeography
of the Intertidal Snail Littorina Saxatilis.” Evolutionary Journal of the Linnean
Society. Oxford University Press, 2023. https://doi.org/10.1093/evolinnean/kzad002.
ieee: S. Stankowski et al., “Whole-genome phylogeography of the intertidal
snail Littorina saxatilis,” Evolutionary Journal of the Linnean Society,
vol. 2, no. 1. Oxford University Press, 2023.
ista: Stankowski S, Zagrodzka ZB, Galindo J, Montaño-Rendón M, Faria R, Mikhailova
N, Blakeslee AMH, Arnason E, Broquet T, Morales HE, Grahame JW, Westram AM, Johannesson
K, Butlin RK. 2023. Whole-genome phylogeography of the intertidal snail Littorina
saxatilis. Evolutionary Journal of the Linnean Society. 2(1), kzad002.
mla: Stankowski, Sean, et al. “Whole-Genome Phylogeography of the Intertidal Snail
Littorina Saxatilis.” Evolutionary Journal of the Linnean Society, vol.
2, no. 1, kzad002, Oxford University Press, 2023, doi:10.1093/evolinnean/kzad002.
short: S. Stankowski, Z.B. Zagrodzka, J. Galindo, M. Montaño-Rendón, R. Faria, N.
Mikhailova, A.M.H. Blakeslee, E. Arnason, T. Broquet, H.E. Morales, J.W. Grahame,
A.M. Westram, K. Johannesson, R.K. Butlin, Evolutionary Journal of the Linnean
Society 2 (2023).
date_created: 2024-01-18T07:54:10Z
date_published: 2023-08-17T00:00:00Z
date_updated: 2024-01-23T08:13:43Z
day: '17'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/evolinnean/kzad002
file:
- access_level: open_access
checksum: ba6f9102d3a9fe6631c4fa398c5e4313
content_type: application/pdf
creator: dernst
date_created: 2024-01-23T08:10:00Z
date_updated: 2024-01-23T08:10:00Z
file_id: '14875'
file_name: 2023_EvolJourLinneanSociety_Stankowski.pdf
file_size: 3408944
relation: main_file
success: 1
file_date_updated: 2024-01-23T08:10:00Z
has_accepted_license: '1'
intvolume: ' 2'
issue: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: Evolutionary Journal of the Linnean Society
publication_identifier:
eissn:
- 2752-938X
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
status: public
title: Whole-genome phylogeography of the intertidal snail Littorina saxatilis
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2023'
...
---
_id: '14732'
abstract:
- lang: eng
text: 'Fragmented landscapes pose a significant threat to the persistence of species
as they are highly susceptible to heightened risk of extinction due to the combined
effects of genetic and demographic factors such as genetic drift and demographic
stochasticity. This paper explores the intricate interplay between genetic load
and extinction risk within metapopulations with a focus on understanding the impact
of eco-evolutionary feedback mechanisms. We distinguish between two models of
selection: soft selection, characterised by subpopulations maintaining carrying
capacity despite load, and hard selection, where load can significantly affect
population size. Within the soft selection framework, we investigate the impact
of gene flow on genetic load at a single locus, while also considering the effect
of selection strength and dominance coefficient. We subsequently build on this
to examine how gene flow influences both population size and load under hard selection
as well as identify critical thresholds for metapopulation persistence. Our analysis
employs the diffusion, semi-deterministic and effective migration approximations.
Our findings reveal that under soft selection, even modest levels of migration
can significantly alleviate the burden of load. In sharp contrast, with hard selection,
a much higher degree of gene flow is required to mitigate load and prevent the
collapse of the metapopulation. Overall, this study sheds light into the crucial
role migration plays in shaping the dynamics of genetic load and extinction risk
in fragmented landscapes, offering valuable insights for conservation strategies
and the preservation of diversity in a changing world.'
article_processing_charge: No
author:
- first_name: Oluwafunmilola O
full_name: Olusanya, Oluwafunmilola O
id: 41AD96DC-F248-11E8-B48F-1D18A9856A87
last_name: Olusanya
orcid: 0000-0003-1971-8314
- first_name: Kseniia
full_name: Khudiakova, Kseniia
id: 4E6DC800-AE37-11E9-AC72-31CAE5697425
last_name: Khudiakova
orcid: 0000-0002-6246-1465
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
citation:
ama: Olusanya OO, Khudiakova K, Sachdeva H. Genetic load, eco-evolutionary feedback
and extinction in a metapopulation. bioRxiv. doi:10.1101/2023.12.02.569702
apa: Olusanya, O. O., Khudiakova, K., & Sachdeva, H. (n.d.). Genetic load, eco-evolutionary
feedback and extinction in a metapopulation. bioRxiv. https://doi.org/10.1101/2023.12.02.569702
chicago: Olusanya, Oluwafunmilola O, Kseniia Khudiakova, and Himani Sachdeva. “Genetic
Load, Eco-Evolutionary Feedback and Extinction in a Metapopulation.” BioRxiv,
n.d. https://doi.org/10.1101/2023.12.02.569702.
ieee: O. O. Olusanya, K. Khudiakova, and H. Sachdeva, “Genetic load, eco-evolutionary
feedback and extinction in a metapopulation,” bioRxiv. .
ista: Olusanya OO, Khudiakova K, Sachdeva H. Genetic load, eco-evolutionary feedback
and extinction in a metapopulation. bioRxiv, 10.1101/2023.12.02.569702.
mla: Olusanya, Oluwafunmilola O., et al. “Genetic Load, Eco-Evolutionary Feedback
and Extinction in a Metapopulation.” BioRxiv, doi:10.1101/2023.12.02.569702.
short: O.O. Olusanya, K. Khudiakova, H. Sachdeva, BioRxiv (n.d.).
date_created: 2024-01-04T09:35:54Z
date_published: 2023-12-04T00:00:00Z
date_updated: 2024-01-26T12:00:53Z
day: '04'
department:
- _id: NiBa
- _id: JaMa
doi: 10.1101/2023.12.02.569702
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2023.12.02.569702v1
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: c08d3278-5a5b-11eb-8a69-fdb09b55f4b8
grant_number: P32896
name: Causes and consequences of population fragmentation
- _id: 34d33d68-11ca-11ed-8bc3-ec13763c0ca8
grant_number: '26293'
name: The impact of deleterious mutations on small populations
- _id: 34c872fe-11ca-11ed-8bc3-8534b82131e6
grant_number: '26380'
name: Polygenic Adaptation in a Metapopulation
publication: bioRxiv
publication_status: submitted
related_material:
record:
- id: '14711'
relation: dissertation_contains
status: public
status: public
title: Genetic load, eco-evolutionary feedback and extinction in a metapopulation
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14812'
abstract:
- lang: eng
text: This repository contains the code and VCF files needed to conduct the analyses
in our MS. Each folder contains a readMe document explaining the nature of each
file and dataset and the results and analyses that they relate to. The same anlaysis
code (but not VCF files) is also available at https://github.com/seanstankowski/Littorina_reproductive_mode
article_processing_charge: No
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
citation:
ama: 'Stankowski S. Data and code for: The genetic architecture of a recent transition
to live-bearing in marine snails. 2023. doi:10.5281/ZENODO.8318995'
apa: 'Stankowski, S. (2023). Data and code for: The genetic architecture of a recent
transition to live-bearing in marine snails. Zenodo. https://doi.org/10.5281/ZENODO.8318995'
chicago: 'Stankowski, Sean. “Data and Code for: The Genetic Architecture of a Recent
Transition to Live-Bearing in Marine Snails.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8318995.'
ieee: 'S. Stankowski, “Data and code for: The genetic architecture of a recent transition
to live-bearing in marine snails.” Zenodo, 2023.'
ista: 'Stankowski S. 2023. Data and code for: The genetic architecture of a recent
transition to live-bearing in marine snails, Zenodo, 10.5281/ZENODO.8318995.'
mla: 'Stankowski, Sean. Data and Code for: The Genetic Architecture of a Recent
Transition to Live-Bearing in Marine Snails. Zenodo, 2023, doi:10.5281/ZENODO.8318995.'
short: S. Stankowski, (2023).
contributor:
- first_name: Zusanna
last_name: Zagrodzka
- first_name: Martin
last_name: Garlovsky
- first_name: Arka
id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425
last_name: Pal
orcid: 0000-0002-4530-8469
- first_name: Daria
id: 428A94B0-F248-11E8-B48F-1D18A9856A87
last_name: Shipilina
orcid: 0000-0002-1145-9226
- first_name: Diego Fernando
id: ae681a14-dc74-11ea-a0a7-c6ef18161701
last_name: Garcia Castillo
- first_name: Hila
id: d6ab5470-2fb3-11ed-8633-986a9b84edac
last_name: Lifchitz
- first_name: Alan
last_name: Le Moan
- first_name: Erica
last_name: Leder
- first_name: James
last_name: Reeve
- first_name: Kerstin
last_name: Johannesson
- first_name: Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Roger
last_name: Butlin
date_created: 2024-01-16T10:23:01Z
date_published: 2023-09-05T00:00:00Z
date_updated: 2024-03-05T09:35:25Z
day: '05'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5281/ZENODO.8318995
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.8318995
month: '09'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '14796'
relation: used_in_publication
status: public
status: public
title: 'Data and code for: The genetic architecture of a recent transition to live-bearing
in marine snails'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12800'
abstract:
- lang: eng
text: 'The evolutionary processes that brought about today’s plethora of living
species and the many billions more ancient ones all underlie biology. Evolutionary
pathways are neither directed nor deterministic, but rather an interplay between
selection, migration, mutation, genetic drift and other environmental factors.
Hybrid zones, as natural crossing experiments, offer a great opportunity to use
cline analysis to deduce different evolutionary processes - for example, selection
strength. Theoretical cline models, largely assuming uniform distribution of individuals,
often lack the capability of incorporating population structure. Since in reality
organisms mostly live in patchy distributions and their dispersal is hardly ever
Gaussian, it is necessary to unravel the effect of these different elements of
population structure on cline parameters and shape. In this thesis, I develop
a simulation inspired by the A. majus hybrid zone of a single selected locus under
frequency dependent selection. This simulation enables us to untangle the effects
of different elements of population structure as for example a low-density center
and long-range dispersal. This thesis is therefore a first step towards theoretically
untangling the effects of different elements of population structure on cline
parameters and shape. '
alternative_title:
- ISTA Master's Thesis
article_processing_charge: No
author:
- first_name: Mara
full_name: Julseth, Mara
id: 1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1
last_name: Julseth
citation:
ama: Julseth M. The effect of local population structure on genetic variation at
selected loci in the A. majus hybrid zone. 2023. doi:10.15479/at:ista:12800
apa: Julseth, M. (2023). The effect of local population structure on genetic
variation at selected loci in the A. majus hybrid zone. Institute of Science
and Technology Austria. https://doi.org/10.15479/at:ista:12800
chicago: Julseth, Mara. “The Effect of Local Population Structure on Genetic Variation
at Selected Loci in the A. Majus Hybrid Zone.” Institute of Science and Technology
Austria, 2023. https://doi.org/10.15479/at:ista:12800.
ieee: M. Julseth, “The effect of local population structure on genetic variation
at selected loci in the A. majus hybrid zone,” Institute of Science and Technology
Austria, 2023.
ista: Julseth M. 2023. The effect of local population structure on genetic variation
at selected loci in the A. majus hybrid zone. Institute of Science and Technology
Austria.
mla: Julseth, Mara. The Effect of Local Population Structure on Genetic Variation
at Selected Loci in the A. Majus Hybrid Zone. Institute of Science and Technology
Austria, 2023, doi:10.15479/at:ista:12800.
short: M. Julseth, The Effect of Local Population Structure on Genetic Variation
at Selected Loci in the A. Majus Hybrid Zone, Institute of Science and Technology
Austria, 2023.
date_created: 2023-04-04T18:57:11Z
date_published: 2023-04-05T00:00:00Z
date_updated: 2023-06-02T22:30:05Z
day: '05'
ddc:
- '576'
degree_awarded: MS
department:
- _id: GradSch
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page: '21'
publication_identifier:
issn:
- 2791-4585
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: The effect of local population structure on genetic variation at selected loci
in the A. majus hybrid zone
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '11702'
abstract:
- lang: eng
text: When Mendel’s work was rediscovered in 1900, and extended to establish classical
genetics, it was initially seen in opposition to Darwin’s theory of evolution
by natural selection on continuous variation, as represented by the biometric
research program that was the foundation of quantitative genetics. As Fisher,
Haldane, and Wright established a century ago, Mendelian inheritance is exactly
what is needed for natural selection to work efficiently. Yet, the synthesis remains
unfinished. We do not understand why sexual reproduction and a fair meiosis predominate
in eukaryotes, or how far these are responsible for their diversity and complexity.
Moreover, although quantitative geneticists have long known that adaptive variation
is highly polygenic, and that this is essential for efficient selection, this
is only now becoming appreciated by molecular biologists—and we still do not have
a good framework for understanding polygenic variation or diffuse function.
acknowledgement: I thank Laura Hayward, Jitka Polechova, and Anja Westram for discussions
and comments.
article_number: e2122147119
article_processing_charge: No
article_type: original
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. The “New Synthesis.” Proceedings of the National Academy of Sciences
of the United States of America. 2022;119(30). doi:10.1073/pnas.2122147119
apa: Barton, N. H. (2022). The “New Synthesis.” Proceedings of the National Academy
of Sciences of the United States of America. Proceedings of the National Academy
of Sciences. https://doi.org/10.1073/pnas.2122147119
chicago: Barton, Nicholas H. “The ‘New Synthesis.’” Proceedings of the National
Academy of Sciences of the United States of America. Proceedings of the National
Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2122147119.
ieee: N. H. Barton, “The ‘New Synthesis,’” Proceedings of the National Academy
of Sciences of the United States of America, vol. 119, no. 30. Proceedings
of the National Academy of Sciences, 2022.
ista: Barton NH. 2022. The ‘New Synthesis’. Proceedings of the National Academy
of Sciences of the United States of America. 119(30), e2122147119.
mla: Barton, Nicholas H. “The ‘New Synthesis.’” Proceedings of the National Academy
of Sciences of the United States of America, vol. 119, no. 30, e2122147119,
Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2122147119.
short: N.H. Barton, Proceedings of the National Academy of Sciences of the United
States of America 119 (2022).
date_created: 2022-07-31T22:01:47Z
date_published: 2022-07-18T00:00:00Z
date_updated: 2022-08-01T11:00:25Z
day: '18'
ddc:
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department:
- _id: NiBa
doi: 10.1073/pnas.2122147119
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month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
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issn:
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publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: The "New Synthesis"
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short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 119
year: '2022'
...
---
_id: '11128'
abstract:
- lang: eng
text: "Although we often see studies focusing on simple or even discrete traits
in studies of colouration,\r\nthe variation of “appearance” phenotypes found in
nature is often more complex, continuous\r\nand high-dimensional. Therefore, we
developed automated methods suitable for large datasets\r\nof genomes and images,
striving to account for their complex nature, while minimising human\r\nbias.
We used these methods on a dataset of more than 20, 000 plant SNP genomes and\r\ncorresponding
fower images from a hybrid zone of two subspecies of Antirrhinum majus with\r\ndistinctly
coloured fowers to improve our understanding of the genetic nature of the fower\r\ncolour
in our study system.\r\nFirstly, we use the advantage of large numbers of genotyped
plants to estimate the haplotypes in\r\nthe main fower colour regulating region.
We study colour- and geography-related characteristics\r\nof the estimated haplotypes
and how they connect to their relatedness. We show discrepancies\r\nfrom the expected
fower colour distributions given the genotype and identify particular\r\nhaplotypes
leading to unexpected phenotypes. We also confrm a signifcant defcit of the\r\ndouble
recessive recombinant and quite surprisingly, we show that haplotypes of the most\r\nfrequent
parental type are much less variable than others.\r\nSecondly, we introduce our
pipeline capable of processing tens of thousands of full fower\r\nimages without
human interaction and summarising each image into a set of informative scores.\r\nWe
show the compatibility of these machine-measured fower colour scores with the
previously\r\nused manual scores and study impact of external efect on the resulting
scores. Finally, we use\r\nthe machine-measured fower colour scores to ft and
examine a phenotype cline across the\r\nhybrid zone in Planoles using full fower
images as opposed to discrete, manual scores and\r\ncompare it with the genotypic
cline."
acknowledged_ssus:
- _id: ScienComp
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Lenka
full_name: Matejovicova, Lenka
id: 2DFDEC72-F248-11E8-B48F-1D18A9856A87
last_name: Matejovicova
citation:
ama: Matejovicova L. Genetic basis of flower colour as a model for adaptive evolution.
2022. doi:10.15479/at:ista:11128
apa: Matejovicova, L. (2022). Genetic basis of flower colour as a model for adaptive
evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11128
chicago: Matejovicova, Lenka. “Genetic Basis of Flower Colour as a Model for Adaptive
Evolution.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11128.
ieee: L. Matejovicova, “Genetic basis of flower colour as a model for adaptive evolution,”
Institute of Science and Technology Austria, 2022.
ista: Matejovicova L. 2022. Genetic basis of flower colour as a model for adaptive
evolution. Institute of Science and Technology Austria.
mla: Matejovicova, Lenka. Genetic Basis of Flower Colour as a Model for Adaptive
Evolution. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11128.
short: L. Matejovicova, Genetic Basis of Flower Colour as a Model for Adaptive Evolution,
Institute of Science and Technology Austria, 2022.
date_created: 2022-04-07T08:19:54Z
date_published: 2022-04-06T00:00:00Z
date_updated: 2023-06-23T06:26:41Z
day: '06'
ddc:
- '576'
- '582'
degree_awarded: PhD
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/at:ista:11128
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creator: cchlebak
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file_name: LenkaPhD Official_source.zip
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language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '112'
publication_identifier:
isbn:
- 978-3-99078-016-9
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: Genetic basis of flower colour as a model for adaptive evolution
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_id: '10604'
abstract:
- lang: eng
text: Maternally inherited Wolbachia transinfections are being introduced into natural
mosquito populations to reduce the transmission of dengue, Zika, and other arboviruses.
Wolbachia-induced cytoplasmic incompatibility provides a frequency-dependent reproductive
advantage to infected females that can spread transinfections within and among
populations. However, because transinfections generally reduce host fitness, they
tend to spread within populations only after their frequency exceeds a critical
threshold. This produces bistability with stable equilibrium frequencies at both
0 and 1, analogous to the bistability produced by underdominance between alleles
or karyotypes and by population dynamics under Allee effects. Here, we analyze
how stochastic frequency variation produced by finite population size can facilitate
the local spread of variants with bistable dynamics into areas where invasion
is unexpected from deterministic models. Our exemplar is the establishment of
wMel Wolbachia in the Aedes aegypti population of Pyramid Estates (PE), a small
community in far north Queensland, Australia. In 2011, wMel was stably introduced
into Gordonvale, separated from PE by barriers to A. aegypti dispersal. After
nearly 6 years during which wMel was observed only at low frequencies in PE, corresponding
to an apparent equilibrium between immigration and selection, wMel rose to fixation
by 2018. Using analytic approximations and statistical analyses, we demonstrate
that the observed fixation of wMel at PE is consistent with both stochastic transition
past an unstable threshold frequency and deterministic transformation produced
by steady immigration at a rate just above the threshold required for deterministic
invasion. The indeterminacy results from a delicate balance of parameters needed
to produce the delayed transition observed. Our analyses suggest that once Wolbachia
transinfections are established locally through systematic introductions, stochastic
“threshold crossing” is likely to only minimally enhance spatial spread, providing
a local ratchet that slightly—but systematically—aids area-wide transformation
of disease-vector populations in heterogeneous landscapes.
acknowledgement: We thank S. O'Neill, C. Simmons, and the World Mosquito Project for
providing access to unpublished data. S. Ritchie provided valuable insights into
Aedes aegypti biology and the literature describing A. aegypti populations near
Cairns. We thank B. Cooper for help with the figures and D. Shropshire, S. O'Neill,
S. Ritchie, A. Hoffmann, B. Cooper, and members of the Cooper lab for comments on
an earlier draft. Comments from three reviewers greatly improved our presentation.
article_processing_charge: No
article_type: original
author:
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Turelli M, Barton NH. Why did the Wolbachia transinfection cross the road?
Drift, deterministic dynamics, and disease control. Evolution Letters.
2022;6(1):92-105. doi:10.1002/evl3.270
apa: Turelli, M., & Barton, N. H. (2022). Why did the Wolbachia transinfection
cross the road? Drift, deterministic dynamics, and disease control. Evolution
Letters. Wiley. https://doi.org/10.1002/evl3.270
chicago: Turelli, Michael, and Nicholas H Barton. “Why Did the Wolbachia Transinfection
Cross the Road? Drift, Deterministic Dynamics, and Disease Control.” Evolution
Letters. Wiley, 2022. https://doi.org/10.1002/evl3.270.
ieee: M. Turelli and N. H. Barton, “Why did the Wolbachia transinfection cross the
road? Drift, deterministic dynamics, and disease control,” Evolution Letters,
vol. 6, no. 1. Wiley, pp. 92–105, 2022.
ista: Turelli M, Barton NH. 2022. Why did the Wolbachia transinfection cross the
road? Drift, deterministic dynamics, and disease control. Evolution Letters. 6(1),
92–105.
mla: Turelli, Michael, and Nicholas H. Barton. “Why Did the Wolbachia Transinfection
Cross the Road? Drift, Deterministic Dynamics, and Disease Control.” Evolution
Letters, vol. 6, no. 1, Wiley, 2022, pp. 92–105, doi:10.1002/evl3.270.
short: M. Turelli, N.H. Barton, Evolution Letters 6 (2022) 92–105.
date_created: 2022-01-09T09:45:17Z
date_published: 2022-02-01T00:00:00Z
date_updated: 2023-08-02T13:50:09Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1002/evl3.270
external_id:
isi:
- '000754412600008'
file:
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checksum: 7e9a37e3b65b480cd7014a6a4a7e460a
content_type: application/pdf
creator: dernst
date_created: 2022-07-29T06:59:10Z
date_updated: 2022-07-29T06:59:10Z
file_id: '11689'
file_name: 2022_EvolutionLetters_Turelli.pdf
file_size: 2435185
relation: main_file
success: 1
file_date_updated: 2022-07-29T06:59:10Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
issue: '1'
keyword:
- genetics
- ecology
- evolution
- behavior and systematics
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 92-105
publication: Evolution Letters
publication_identifier:
eissn:
- 2056-3744
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '11686'
relation: research_data
status: public
status: public
title: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics,
and disease control
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 6
year: '2022'
...
---
_id: '11686'
abstract:
- lang: eng
text: Maternally inherited Wolbachia transinfections are being introduced into natural
mosquito populations to reduce the transmission of dengue, Zika and other arboviruses.
Wolbachia-induced cytoplasmic incompatibility provides a frequency-dependent reproductive
advantage to infected females that can spread transinfections within and among
populations. However, because transinfections generally reduce host fitness, they
tend to spread within populations only after their frequency exceeds a critical
threshold. This produces bistability with stable equilibrium frequencies at both
0 and 1, analogous to the bistability produced by underdominance between alleles
or karyotypes and by population dynamics under Allee effects. Here, we analyze
how stochastic frequency variation produced by finite population size can facilitate
the local spread of variants with bistable dynamics into areas where invasion
is unexpected from deterministic models. Our exemplar is the establishment of
wMel Wolbachia in the Aedes aegypti population of Pyramid Estates (PE), a small
community in far north Queensland, Australia. In 2011, wMel was stably introduced
into Gordonvale, separated from PE by barriers to Ae. aegypti dispersal. After
nearly six years during which wMel was observed only at low frequencies in PE,
corresponding to an apparent equilibrium between immigration and selection, wMel
rose to fixation by 2018. Using analytic approximations and statistical analyses,
we demonstrate that the observed fixation of wMel at PE is consistent with both
stochastic transition past an unstable threshold frequency and deterministic transformation
produced by steady immigration at a rate just above the threshold required for
deterministic invasion. The indeterminacy results from a delicate balance of parameters
needed to produce the delayed transition observed. Our analyses suggest that once
Wolbachia transinfections are established locally through systematic introductions,
stochastic “threshold crossing” is likely to only minimally enhance spatial spread,
providing a local ratchet that slightly – but systematically – aids area-wide
transformation of disease-vector populations in heterogeneous landscapes.
acknowledgement: 'Bill and Melinda Gates Foundation, Award: OPP1180815'
article_processing_charge: No
author:
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Turelli M, Barton NH. Wolbachia frequency data from: Why did the Wolbachia
transinfection cross the road? Drift, deterministic dynamics and disease control.
2022. doi:10.25338/B81931'
apa: 'Turelli, M., & Barton, N. H. (2022). Wolbachia frequency data from: Why
did the Wolbachia transinfection cross the road? Drift, deterministic dynamics
and disease control. Dryad. https://doi.org/10.25338/B81931'
chicago: 'Turelli, Michael, and Nicholas H Barton. “Wolbachia Frequency Data from:
Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics
and Disease Control.” Dryad, 2022. https://doi.org/10.25338/B81931.'
ieee: 'M. Turelli and N. H. Barton, “Wolbachia frequency data from: Why did the
Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease
control.” Dryad, 2022.'
ista: 'Turelli M, Barton NH. 2022. Wolbachia frequency data from: Why did the Wolbachia
transinfection cross the road? Drift, deterministic dynamics and disease control,
Dryad, 10.25338/B81931.'
mla: 'Turelli, Michael, and Nicholas H. Barton. Wolbachia Frequency Data from:
Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics
and Disease Control. Dryad, 2022, doi:10.25338/B81931.'
short: M. Turelli, N.H. Barton, (2022).
date_created: 2022-07-29T06:45:41Z
date_published: 2022-01-06T00:00:00Z
date_updated: 2023-08-02T13:50:08Z
day: '06'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.25338/B81931
keyword:
- Biological sciences
license: https://creativecommons.org/publicdomain/zero/1.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.25338/B81931
month: '01'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '10604'
relation: used_in_publication
status: public
status: public
title: 'Wolbachia frequency data from: Why did the Wolbachia transinfection cross
the road? Drift, deterministic dynamics and disease control'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2022'
...
---
_id: '10736'
abstract:
- lang: eng
text: Predicting function from sequence is a central problem of biology. Currently,
this is possible only locally in a narrow mutational neighborhood around a wildtype
sequence rather than globally from any sequence. Using random mutant libraries,
we developed a biophysical model that accounts for multiple features of σ70 binding
bacterial promoters to predict constitutive gene expression levels from any sequence.
We experimentally and theoretically estimated that 10–20% of random sequences
lead to expression and ~80% of non-expressing sequences are one mutation away
from a functional promoter. The potential for generating expression from random
sequences is so pervasive that selection acts against σ70-RNA polymerase binding
sites even within inter-genic, promoter-containing regions. This pervasiveness
of σ70-binding sites implies that emergence of promoters is not the limiting step
in gene regulatory evolution. Ultimately, the inclusion of novel features of promoter
function into a mechanistic model enabled not only more accurate predictions of
gene expression levels, but also identified that promoters evolve more rapidly
than previously thought.
acknowledgement: 'We thank Hande Acar, Nicholas H Barton, Rok Grah, Tiago Paixao,
Maros Pleska, Anna Staron, and Murat Tugrul for insightful comments and input on
the manuscript. This work was supported by: Sir Henry Dale Fellowship jointly funded
by the Wellcome Trust and the Royal Society (grant number 216779/Z/19/Z) to ML;
IPC Grant from IST Austria to ML and SS; European Research Council Funding Programme
7 (2007–2013, grant agreement number 648440) to JPB.'
article_number: e64543
article_processing_charge: No
article_type: original
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Srdjan
full_name: Sarikas, Srdjan
id: 35F0286E-F248-11E8-B48F-1D18A9856A87
last_name: Sarikas
- first_name: Magdalena
full_name: Steinrueck, Magdalena
last_name: Steinrueck
- first_name: David
full_name: Toledo-Aparicio, David
last_name: Toledo-Aparicio
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Lagator M, Sarikas S, Steinrueck M, et al. Predicting bacterial promoter function
and evolution from random sequences. eLife. 2022;11. doi:10.7554/eLife.64543
apa: Lagator, M., Sarikas, S., Steinrueck, M., Toledo-Aparicio, D., Bollback, J.
P., Guet, C. C., & Tkačik, G. (2022). Predicting bacterial promoter function
and evolution from random sequences. ELife. eLife Sciences Publications.
https://doi.org/10.7554/eLife.64543
chicago: Lagator, Mato, Srdjan Sarikas, Magdalena Steinrueck, David Toledo-Aparicio,
Jonathan P Bollback, Calin C Guet, and Gašper Tkačik. “Predicting Bacterial Promoter
Function and Evolution from Random Sequences.” ELife. eLife Sciences Publications,
2022. https://doi.org/10.7554/eLife.64543.
ieee: M. Lagator et al., “Predicting bacterial promoter function and evolution
from random sequences,” eLife, vol. 11. eLife Sciences Publications, 2022.
ista: Lagator M, Sarikas S, Steinrueck M, Toledo-Aparicio D, Bollback JP, Guet CC,
Tkačik G. 2022. Predicting bacterial promoter function and evolution from random
sequences. eLife. 11, e64543.
mla: Lagator, Mato, et al. “Predicting Bacterial Promoter Function and Evolution
from Random Sequences.” ELife, vol. 11, e64543, eLife Sciences Publications,
2022, doi:10.7554/eLife.64543.
short: M. Lagator, S. Sarikas, M. Steinrueck, D. Toledo-Aparicio, J.P. Bollback,
C.C. Guet, G. Tkačik, ELife 11 (2022).
date_created: 2022-02-06T23:01:32Z
date_published: 2022-01-26T00:00:00Z
date_updated: 2023-08-02T14:09:02Z
day: '26'
ddc:
- '576'
department:
- _id: CaGu
- _id: GaTk
- _id: NiBa
doi: 10.7554/eLife.64543
ec_funded: 1
external_id:
isi:
- '000751104400001'
pmid:
- '35080492'
file:
- access_level: open_access
checksum: decdcdf600ff51e9a9703b49ca114170
content_type: application/pdf
creator: cchlebak
date_created: 2022-02-07T07:14:09Z
date_updated: 2022-02-07T07:14:09Z
file_id: '10739'
file_name: 2022_ELife_Lagator.pdf
file_size: 5604343
relation: main_file
success: 1
file_date_updated: 2022-02-07T07:14:09Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Predicting bacterial promoter function and evolution from random sequences
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2022'
...
---
_id: '11334'
abstract:
- lang: eng
text: Hybridization is a common evolutionary process with multiple possible outcomes.
In vertebrates, interspecific hybridization has repeatedly generated parthenogenetic
hybrid species. However, it is unknown whether the generation of parthenogenetic
hybrids is a rare outcome of frequent hybridization between sexual species within
a genus or the typical outcome of rare hybridization events. Darevskia is a genus
of rock lizards with both hybrid parthenogenetic and sexual species. Using capture
sequencing, we estimate phylogenetic relationships and gene flow among the sexual
species, to determine how introgressive hybridization relates to the origins of
parthenogenetic hybrids. We find evidence for widespread hybridization with gene
flow, both between recently diverged species and deep branches. Surprisingly,
we find no signal of gene flow between parental species of the parthenogenetic
hybrids, suggesting that the parental pairs were either reproductively or geographically
isolated early in their divergence. The generation of parthenogenetic hybrids
in Darevskia is, then, a rare outcome of the total occurrence of hybridization
within the genus, but the typical outcome when specific species pairs hybridize.
Our results question the conventional view that parthenogenetic lineages are generated
by hybridization in a window of divergence. Instead, they suggest that some lineages
possess specific properties that underpin successful parthenogenetic reproduction.
acknowledgement: "The authors thank A. van der Meijden and F. Ahmadzadeh for providing
specimens and tissue samples, and A. Vardanyan, C. Corti, F. Jorge, and S. Drovetski
for support during field work. The authors also thank S. Qiu for assistance with
python scripting, S. Rocha for her support in BEAST analysis, and B. Wielstra for
his comments on\r\na previous version of the manuscript. SF was funded by FCT grant
SFRH/BD/81483/2011 (a PhD individual grant). AMW was funded by the European Union’s
Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant
agreement no. 797747. TS acknowledges funding from the Swiss National Science Foundation
(grants\r\nPP00P3_170627 and 31003A_182495). The work was carried out under financial
support of the projects “Preserving Armenian biodiversity: Joint Portuguese – Armenian
program for training in modern conservation biology” of Gulbenkian Foundation (Portugal)
and PTDC/BIABEC/101256/2008 of Fundação para a Ciência e a Tecnologia (FCT, Portugal)."
article_processing_charge: No
article_type: original
author:
- first_name: Susana
full_name: Freitas, Susana
last_name: Freitas
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Tanja
full_name: Schwander, Tanja
last_name: Schwander
- first_name: Marine
full_name: Arakelyan, Marine
last_name: Arakelyan
- first_name: Çetin
full_name: Ilgaz, Çetin
last_name: Ilgaz
- first_name: Yusuf
full_name: Kumlutas, Yusuf
last_name: Kumlutas
- first_name: David James
full_name: Harris, David James
last_name: Harris
- first_name: Miguel A.
full_name: Carretero, Miguel A.
last_name: Carretero
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: 'Freitas S, Westram AM, Schwander T, et al. Parthenogenesis in Darevskia lizards:
A rare outcome of common hybridization, not a common outcome of rare hybridization.
Evolution. 2022;76(5):899-914. doi:10.1111/evo.14462'
apa: 'Freitas, S., Westram, A. M., Schwander, T., Arakelyan, M., Ilgaz, Ç., Kumlutas,
Y., … Butlin, R. K. (2022). Parthenogenesis in Darevskia lizards: A rare outcome
of common hybridization, not a common outcome of rare hybridization. Evolution.
Wiley. https://doi.org/10.1111/evo.14462'
chicago: 'Freitas, Susana, Anja M Westram, Tanja Schwander, Marine Arakelyan, Çetin
Ilgaz, Yusuf Kumlutas, David James Harris, Miguel A. Carretero, and Roger K. Butlin.
“Parthenogenesis in Darevskia Lizards: A Rare Outcome of Common Hybridization,
Not a Common Outcome of Rare Hybridization.” Evolution. Wiley, 2022. https://doi.org/10.1111/evo.14462.'
ieee: 'S. Freitas et al., “Parthenogenesis in Darevskia lizards: A rare outcome
of common hybridization, not a common outcome of rare hybridization,” Evolution,
vol. 76, no. 5. Wiley, pp. 899–914, 2022.'
ista: 'Freitas S, Westram AM, Schwander T, Arakelyan M, Ilgaz Ç, Kumlutas Y, Harris
DJ, Carretero MA, Butlin RK. 2022. Parthenogenesis in Darevskia lizards: A rare
outcome of common hybridization, not a common outcome of rare hybridization. Evolution.
76(5), 899–914.'
mla: 'Freitas, Susana, et al. “Parthenogenesis in Darevskia Lizards: A Rare Outcome
of Common Hybridization, Not a Common Outcome of Rare Hybridization.” Evolution,
vol. 76, no. 5, Wiley, 2022, pp. 899–914, doi:10.1111/evo.14462.'
short: S. Freitas, A.M. Westram, T. Schwander, M. Arakelyan, Ç. Ilgaz, Y. Kumlutas,
D.J. Harris, M.A. Carretero, R.K. Butlin, Evolution 76 (2022) 899–914.
date_created: 2022-04-24T22:01:44Z
date_published: 2022-05-01T00:00:00Z
date_updated: 2023-08-03T07:00:28Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
- _id: BeVi
doi: 10.1111/evo.14462
ec_funded: 1
external_id:
isi:
- '000781632500001'
pmid:
- '35323995'
file:
- access_level: open_access
checksum: c27c025ae9afcf6c804d46a909775ee5
content_type: application/pdf
creator: dernst
date_created: 2022-08-05T06:19:28Z
date_updated: 2022-08-05T06:19:28Z
file_id: '11729'
file_name: 2022_Evolution_Freitas.pdf
file_size: 2855214
relation: main_file
success: 1
file_date_updated: 2022-08-05T06:19:28Z
has_accepted_license: '1'
intvolume: ' 76'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 899-914
pmid: 1
project:
- _id: 265B41B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '797747'
name: Theoretical and empirical approaches to understanding Parallel Adaptation
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization,
not a common outcome of rare hybridization'
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 76
year: '2022'
...
---
_id: '11447'
abstract:
- lang: eng
text: Empirical essays of fitness landscapes suggest that they may be rugged, that
is having multiple fitness peaks. Such fitness landscapes, those that have multiple
peaks, necessarily have special local structures, called reciprocal sign epistasis
(Poelwijk et al. in J Theor Biol 272:141–144, 2011). Here, we investigate the
quantitative relationship between the number of fitness peaks and the number of
reciprocal sign epistatic interactions. Previously, it has been shown (Poelwijk
et al. in J Theor Biol 272:141–144, 2011) that pairwise reciprocal sign epistasis
is a necessary but not sufficient condition for the existence of multiple peaks.
Applying discrete Morse theory, which to our knowledge has never been used in
this context, we extend this result by giving the minimal number of reciprocal
sign epistatic interactions required to create a given number of peaks.
acknowledgement: We are grateful to Herbert Edelsbrunner and Jeferson Zapata for helpful
discussions. Open access funding provided by Austrian Science Fund (FWF). Partially
supported by the ERC Consolidator (771209–CharFL) and the FWF Austrian Science Fund
(I5127-B) grants to FAK.
article_number: '74'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Raimundo J
full_name: Saona Urmeneta, Raimundo J
id: BD1DF4C4-D767-11E9-B658-BC13E6697425
last_name: Saona Urmeneta
orcid: 0000-0001-5103-038X
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Kseniia
full_name: Khudiakova, Kseniia
id: 4E6DC800-AE37-11E9-AC72-31CAE5697425
last_name: Khudiakova
orcid: 0000-0002-6246-1465
citation:
ama: Saona Urmeneta RJ, Kondrashov F, Khudiakova K. Relation between the number
of peaks and the number of reciprocal sign epistatic interactions. Bulletin
of Mathematical Biology. 2022;84(8). doi:10.1007/s11538-022-01029-z
apa: Saona Urmeneta, R. J., Kondrashov, F., & Khudiakova, K. (2022). Relation
between the number of peaks and the number of reciprocal sign epistatic interactions.
Bulletin of Mathematical Biology. Springer Nature. https://doi.org/10.1007/s11538-022-01029-z
chicago: Saona Urmeneta, Raimundo J, Fyodor Kondrashov, and Kseniia Khudiakova.
“Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic
Interactions.” Bulletin of Mathematical Biology. Springer Nature, 2022.
https://doi.org/10.1007/s11538-022-01029-z.
ieee: R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between
the number of peaks and the number of reciprocal sign epistatic interactions,”
Bulletin of Mathematical Biology, vol. 84, no. 8. Springer Nature, 2022.
ista: Saona Urmeneta RJ, Kondrashov F, Khudiakova K. 2022. Relation between the
number of peaks and the number of reciprocal sign epistatic interactions. Bulletin
of Mathematical Biology. 84(8), 74.
mla: Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and
the Number of Reciprocal Sign Epistatic Interactions.” Bulletin of Mathematical
Biology, vol. 84, no. 8, 74, Springer Nature, 2022, doi:10.1007/s11538-022-01029-z.
short: R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical
Biology 84 (2022).
date_created: 2022-06-17T16:16:15Z
date_published: 2022-06-17T00:00:00Z
date_updated: 2023-08-03T07:20:53Z
day: '17'
ddc:
- '510'
- '570'
department:
- _id: GradSch
- _id: NiBa
- _id: JaMa
doi: 10.1007/s11538-022-01029-z
ec_funded: 1
external_id:
isi:
- '000812509800001'
file:
- access_level: open_access
checksum: 05a1fe7d10914a00c2bca9b447993a65
content_type: application/pdf
creator: dernst
date_created: 2022-06-20T07:51:32Z
date_updated: 2022-06-20T07:51:32Z
file_id: '11455'
file_name: 2022_BulletinMathBiology_Saona.pdf
file_size: 463025
relation: main_file
success: 1
file_date_updated: 2022-06-20T07:51:32Z
has_accepted_license: '1'
intvolume: ' 84'
isi: 1
issue: '8'
keyword:
- Computational Theory and Mathematics
- General Agricultural and Biological Sciences
- Pharmacology
- General Environmental Science
- General Biochemistry
- Genetics and Molecular Biology
- General Mathematics
- Immunology
- General Neuroscience
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
- _id: c098eddd-5a5b-11eb-8a69-abe27170a68f
grant_number: I05127
name: Evolutionary analysis of gene regulation
publication: Bulletin of Mathematical Biology
publication_identifier:
eissn:
- 1522-9602
issn:
- 0092-8240
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1007/s11538-022-01118-z
scopus_import: '1'
status: public
title: Relation between the number of peaks and the number of reciprocal sign epistatic
interactions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 84
year: '2022'
...
---
_id: '11546'
abstract:
- lang: eng
text: Local adaptation leads to differences between populations within a species.
In many systems, similar environmental contrasts occur repeatedly, sometimes driving
parallel phenotypic evolution. Understanding the genomic basis of local adaptation
and parallel evolution is a major goal of evolutionary genomics. It is now known
that by preventing the break-up of favourable combinations of alleles across multiple
loci, genetic architectures that reduce recombination, like chromosomal inversions,
can make an important contribution to local adaptation. However, little is known
about whether inversions also contribute disproportionately to parallel evolution.
Our aim here is to highlight this knowledge gap, to showcase existing studies,
and to illustrate the differences between genomic architectures with and without
inversions using simple models. We predict that by generating stronger effective
selection, inversions can sometimes speed up the parallel adaptive process or
enable parallel adaptation where it would be impossible otherwise, but this is
highly dependent on the spatial setting. We highlight that further empirical work
is needed, in particular to cover a broader taxonomic range and to understand
the relative importance of inversions compared to genomic regions without inversions.
acknowledgement: We thank the editor and two anonymous reviewers for their helpful
and interesting comments on this manuscript.
article_number: '20210203'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. Inversions and parallel
evolution. Philosophical Transactions of the Royal Society B: Biological Sciences.
2022;377(1856). doi:10.1098/rstb.2021.0203'
apa: 'Westram, A. M., Faria, R., Johannesson, K., Butlin, R., & Barton, N. H.
(2022). Inversions and parallel evolution. Philosophical Transactions of the
Royal Society B: Biological Sciences. Royal Society of London. https://doi.org/10.1098/rstb.2021.0203'
chicago: 'Westram, Anja M, Rui Faria, Kerstin Johannesson, Roger Butlin, and Nicholas
H Barton. “Inversions and Parallel Evolution.” Philosophical Transactions of
the Royal Society B: Biological Sciences. Royal Society of London, 2022. https://doi.org/10.1098/rstb.2021.0203.'
ieee: 'A. M. Westram, R. Faria, K. Johannesson, R. Butlin, and N. H. Barton, “Inversions
and parallel evolution,” Philosophical Transactions of the Royal Society B:
Biological Sciences, vol. 377, no. 1856. Royal Society of London, 2022.'
ista: 'Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. 2022. Inversions
and parallel evolution. Philosophical Transactions of the Royal Society B: Biological
Sciences. 377(1856), 20210203.'
mla: 'Westram, Anja M., et al. “Inversions and Parallel Evolution.” Philosophical
Transactions of the Royal Society B: Biological Sciences, vol. 377, no. 1856,
20210203, Royal Society of London, 2022, doi:10.1098/rstb.2021.0203.'
short: 'A.M. Westram, R. Faria, K. Johannesson, R. Butlin, N.H. Barton, Philosophical
Transactions of the Royal Society B: Biological Sciences 377 (2022).'
date_created: 2022-07-08T11:41:56Z
date_published: 2022-08-01T00:00:00Z
date_updated: 2023-08-03T11:55:42Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1098/rstb.2021.0203
external_id:
isi:
- '000812317300005'
file:
- access_level: open_access
checksum: 49f69428f3dcf5ce3ff281f7d199e9df
content_type: application/pdf
creator: dernst
date_created: 2023-02-02T08:20:29Z
date_updated: 2023-02-02T08:20:29Z
file_id: '12479'
file_name: 2022_PhilosophicalTransactionsB_Westram.pdf
file_size: 920304
relation: main_file
success: 1
file_date_updated: 2023-02-02T08:20:29Z
has_accepted_license: '1'
intvolume: ' 377'
isi: 1
issue: '1856'
keyword:
- General Agricultural and Biological Sciences
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: The maintenance of alternative adaptive peaks in snapdragons
publication: 'Philosophical Transactions of the Royal Society B: Biological Sciences'
publication_identifier:
eissn:
- 1471-2970
issn:
- 0962-8436
publication_status: published
publisher: Royal Society of London
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inversions and parallel evolution
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 377
year: '2022'
...
---
_id: '11640'
abstract:
- lang: eng
text: Spatially explicit population genetic models have long been developed, yet
have rarely been used to test hypotheses about the spatial distribution of genetic
diversity or the genetic divergence between populations. Here, we use spatially
explicit coalescence simulations to explore the properties of the island and the
two-dimensional stepping stone models under a wide range of scenarios with spatio-temporal
variation in deme size. We avoid the simulation of genetic data, using the fact
that under the studied models, summary statistics of genetic diversity and divergence
can be approximated from coalescence times. We perform the simulations using gridCoal,
a flexible spatial wrapper for the software msprime (Kelleher et al., 2016, Theoretical
Population Biology, 95, 13) developed herein. In gridCoal, deme sizes can change
arbitrarily across space and time, as well as migration rates between individual
demes. We identify different factors that can cause a deviation from theoretical
expectations, such as the simulation time in comparison to the effective deme
size and the spatio-temporal autocorrelation across the grid. Our results highlight
that FST, a measure of the strength of population structure, principally depends
on recent demography, which makes it robust to temporal variation in deme size.
In contrast, the amount of genetic diversity is dependent on the distant past
when Ne is large, therefore longer run times are needed to estimate Ne than FST.
Finally, we illustrate the use of gridCoal on a real-world example, the range
expansion of silver fir (Abies alba Mill.) since the last glacial maximum, using
different degrees of spatio-temporal variation in deme size.
acknowledgement: ES was supported by an IST studentship provided by IST Austria. BT
was funded by the European Union's Horizon 2020 research and innovation programme
under the Marie Sklodowska-Curie Independent Fellowship (704172, RACE). This project
received further funding awarded to KC from the Swiss National Science Foundation
(SNSF CRSK-3_190288) and the Swiss Federal Research Institute WSL. We thank Nick
Barton for many invaluable discussions and his comments on the thesis chapter and
this manuscript. We thank Peter Ralph and Jerome Kelleher for useful discussions
and Bisschop Gertjan for comments on this manuscript. We thank Fortunat Joos for
providing us with the raw data from the LPX-Bern model for silver fir, and Willy
Tinner for helpful insights about the demographic history of silver fir. We also
thank the editor Alana Alexander for useful comments and advice on the manuscript.
Open access funding provided by Eidgenossische Technische Hochschule Zurich.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Eniko
full_name: Szep, Eniko
id: 485BB5A4-F248-11E8-B48F-1D18A9856A87
last_name: Szep
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
- first_name: Katalin
full_name: Csilléry, Katalin
last_name: Csilléry
citation:
ama: Szep E, Trubenova B, Csilléry K. Using gridCoal to assess whether standard
population genetic theory holds in the presence of spatio-temporal heterogeneity
in population size. Molecular Ecology Resources. 2022;22(8):2941-2955.
doi:10.1111/1755-0998.13676
apa: Szep, E., Trubenova, B., & Csilléry, K. (2022). Using gridCoal to assess
whether standard population genetic theory holds in the presence of spatio-temporal
heterogeneity in population size. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.13676
chicago: Szep, Eniko, Barbora Trubenova, and Katalin Csilléry. “Using GridCoal to
Assess Whether Standard Population Genetic Theory Holds in the Presence of Spatio-Temporal
Heterogeneity in Population Size.” Molecular Ecology Resources. Wiley,
2022. https://doi.org/10.1111/1755-0998.13676.
ieee: E. Szep, B. Trubenova, and K. Csilléry, “Using gridCoal to assess whether
standard population genetic theory holds in the presence of spatio-temporal heterogeneity
in population size,” Molecular Ecology Resources, vol. 22, no. 8. Wiley,
pp. 2941–2955, 2022.
ista: Szep E, Trubenova B, Csilléry K. 2022. Using gridCoal to assess whether standard
population genetic theory holds in the presence of spatio-temporal heterogeneity
in population size. Molecular Ecology Resources. 22(8), 2941–2955.
mla: Szep, Eniko, et al. “Using GridCoal to Assess Whether Standard Population Genetic
Theory Holds in the Presence of Spatio-Temporal Heterogeneity in Population Size.”
Molecular Ecology Resources, vol. 22, no. 8, Wiley, 2022, pp. 2941–55,
doi:10.1111/1755-0998.13676.
short: E. Szep, B. Trubenova, K. Csilléry, Molecular Ecology Resources 22 (2022)
2941–2955.
date_created: 2022-07-24T22:01:43Z
date_published: 2022-11-01T00:00:00Z
date_updated: 2023-08-03T12:11:01Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/1755-0998.13676
ec_funded: 1
external_id:
isi:
- '000825873600001'
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checksum: 3102e203e77b884bffffdbe8e548da88
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date_created: 2023-02-02T08:11:23Z
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language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 2941-2955
project:
- _id: 25AEDD42-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '704172'
name: Rate of Adaptation in Changing Environment
publication: Molecular Ecology Resources
publication_identifier:
eissn:
- 1755-0998
issn:
- 1755-098X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Using gridCoal to assess whether standard population genetic theory holds in
the presence of spatio-temporal heterogeneity in population size
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
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type: journal_article
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volume: 22
year: '2022'
...
---
_id: '12001'
abstract:
- lang: eng
text: 'Sexual antagonism is a common hypothesis for driving the evolution of sex
chromosomes, whereby recombination suppression is favored between sexually antagonistic
loci and the sex-determining locus to maintain beneficial combinations of alleles.
This results in the formation of a sex-determining region. Chromosomal inversions
may contribute to recombination suppression but their precise role in sex chromosome
evolution remains unclear. Because local adaptation is frequently facilitated
through the suppression of recombination between adaptive loci by chromosomal
inversions, there is potential for inversions that cover sex-determining regions
to be involved in local adaptation as well, particularly if habitat variation
creates environment-dependent sexual antagonism. With these processes in mind,
we investigated sex determination in a well-studied example of local adaptation
within a species: the intertidal snail, Littorina saxatilis. Using SNP data from
a Swedish hybrid zone, we find novel evidence for a female-heterogametic sex determination
system that is restricted to one ecotype. Our results suggest that four putative
chromosomal inversions, two previously described and two newly discovered, span
the putative sex chromosome pair. We determine their differing associations with
sex, which suggest distinct strata of differing ages. The same inversions are
found in the second ecotype but do not show any sex association. The striking
disparity in inversion-sex associations between ecotypes that are connected by
gene flow across a habitat transition that is just a few meters wide indicates
a difference in selective regime that has produced a distinct barrier to the spread
of the newly discovered sex-determining region between ecotypes. Such sex chromosome-environment
interactions have not previously been uncovered in L. saxatilis and are known
in few other organisms. A combination of both sex-specific selection and divergent
natural selection is required to explain these highly unusual patterns.'
acknowledgement: We thank A. Wright and four anonymous reviewers for valuable comments
on an earlier draft of this manuscript and all members of the Littorina group for
helpful discussions. This work was supported by a European Research Council grant
to RKB and by a Natural Environment Research Council studentship to KEH through
the ACCE doctoral training program. KJ acknowledges support from the Swedish Science
Research Council VR (Vetenskaprådet) (2017-03798). RF was supported by an FCT CEEC
(Fundação para a Ciênca e a Tecnologia, Concurso Estímulo ao Emprego Científico)
contract (2020.00275.CEECIND).
article_processing_charge: Yes
article_type: original
author:
- first_name: Katherine E.
full_name: Hearn, Katherine E.
last_name: Hearn
- first_name: Eva L.
full_name: Koch, Eva L.
last_name: Koch
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
citation:
ama: Hearn KE, Koch EL, Stankowski S, et al. Differing associations between sex
determination and sex-linked inversions in two ecotypes of Littorina saxatilis.
Evolution Letters. 2022;6(5):358-374. doi:10.1002/evl3.295
apa: Hearn, K. E., Koch, E. L., Stankowski, S., Butlin, R. K., Faria, R., Johannesson,
K., & Westram, A. M. (2022). Differing associations between sex determination
and sex-linked inversions in two ecotypes of Littorina saxatilis. Evolution
Letters. Oxford Academic. https://doi.org/10.1002/evl3.295
chicago: Hearn, Katherine E., Eva L. Koch, Sean Stankowski, Roger K. Butlin, Rui
Faria, Kerstin Johannesson, and Anja M Westram. “Differing Associations between
Sex Determination and Sex-Linked Inversions in Two Ecotypes of Littorina Saxatilis.”
Evolution Letters. Oxford Academic, 2022. https://doi.org/10.1002/evl3.295.
ieee: K. E. Hearn et al., “Differing associations between sex determination
and sex-linked inversions in two ecotypes of Littorina saxatilis,” Evolution
Letters, vol. 6, no. 5. Oxford Academic, pp. 358–374, 2022.
ista: Hearn KE, Koch EL, Stankowski S, Butlin RK, Faria R, Johannesson K, Westram
AM. 2022. Differing associations between sex determination and sex-linked inversions
in two ecotypes of Littorina saxatilis. Evolution Letters. 6(5), 358–374.
mla: Hearn, Katherine E., et al. “Differing Associations between Sex Determination
and Sex-Linked Inversions in Two Ecotypes of Littorina Saxatilis.” Evolution
Letters, vol. 6, no. 5, Oxford Academic, 2022, pp. 358–74, doi:10.1002/evl3.295.
short: K.E. Hearn, E.L. Koch, S. Stankowski, R.K. Butlin, R. Faria, K. Johannesson,
A.M. Westram, Evolution Letters 6 (2022) 358–374.
date_created: 2022-08-28T22:02:02Z
date_published: 2022-10-01T00:00:00Z
date_updated: 2023-08-03T13:18:17Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1002/evl3.295
external_id:
isi:
- '000839621100001'
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checksum: 2dcd06186a11b7d1be4cddc6b189f8fb
content_type: application/pdf
creator: dernst
date_created: 2023-02-27T07:17:42Z
date_updated: 2023-02-27T07:17:42Z
file_id: '12686'
file_name: 2022_EvolutionLetters_Hearn.pdf
file_size: 2368965
relation: main_file
success: 1
file_date_updated: 2023-02-27T07:17:42Z
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intvolume: ' 6'
isi: 1
issue: '5'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 358-374
publication: Evolution Letters
publication_identifier:
eissn:
- 2056-3744
publication_status: published
publisher: Oxford Academic
quality_controlled: '1'
scopus_import: '1'
status: public
title: Differing associations between sex determination and sex-linked inversions
in two ecotypes of Littorina saxatilis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 6
year: '2022'
...
---
_id: '12157'
abstract:
- lang: eng
text: 'Polygenic adaptation is thought to be ubiquitous, yet remains poorly understood.
Here, we model this process analytically, in the plausible setting of a highly
polygenic, quantitative trait that experiences a sudden shift in the fitness optimum.
We show how the mean phenotype changes over time, depending on the effect sizes
of loci that contribute to variance in the trait, and characterize the allele
dynamics at these loci. Notably, we describe the two phases of the allele dynamics:
The first is a rapid phase, in which directional selection introduces small frequency
differences between alleles whose effects are aligned with or opposed to the shift,
ultimately leading to small differences in their probability of fixation during
a second, longer phase, governed by stabilizing selection. As we discuss, key
results should hold in more general settings and have important implications for
efforts to identify the genetic basis of adaptation in humans and other species.'
acknowledgement: "We thank Guy Amster, Jeremy Berg, Nick Barton, Yuval Simons and
Molly Przeworski for many helpful discussions, and Jeremy Berg, Graham Coop, Joachim
Hermisson, Guillaume Martin, Will Milligan, Peter Ralph, Yuval Simons, Leo Speidel
and Molly Przeworski for comments on the manuscript.\r\nNational Institutes of Health
GM115889 Laura Katharine Hayward Guy Sella \r\nNational Institutes of Health GM121372
Laura Katharine Hayward"
article_number: '66697'
article_processing_charge: No
article_type: original
author:
- first_name: Laura
full_name: Hayward, Laura
id: fc885ee5-24bf-11eb-ad7b-bcc5104c0c1b
last_name: Hayward
- first_name: Guy
full_name: Sella, Guy
last_name: Sella
citation:
ama: Hayward L, Sella G. Polygenic adaptation after a sudden change in environment.
eLife. 2022;11. doi:10.7554/elife.66697
apa: Hayward, L., & Sella, G. (2022). Polygenic adaptation after a sudden change
in environment. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.66697
chicago: Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change
in Environment.” ELife. eLife Sciences Publications, 2022. https://doi.org/10.7554/elife.66697.
ieee: L. Hayward and G. Sella, “Polygenic adaptation after a sudden change in environment,”
eLife, vol. 11. eLife Sciences Publications, 2022.
ista: Hayward L, Sella G. 2022. Polygenic adaptation after a sudden change in environment.
eLife. 11, 66697.
mla: Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change
in Environment.” ELife, vol. 11, 66697, eLife Sciences Publications, 2022,
doi:10.7554/elife.66697.
short: L. Hayward, G. Sella, ELife 11 (2022).
date_created: 2023-01-12T12:09:00Z
date_published: 2022-09-26T00:00:00Z
date_updated: 2023-08-04T09:04:58Z
day: '26'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.7554/elife.66697
external_id:
isi:
- '000890735600001'
file:
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checksum: 28de155b231ac1c8d4501c98b2fb359a
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creator: dernst
date_created: 2023-01-24T12:21:32Z
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file_id: '12363'
file_name: 2022_eLife_Hayward.pdf
file_size: 18935612
relation: main_file
success: 1
file_date_updated: 2023-01-24T12:21:32Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
eissn:
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publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Polygenic adaptation after a sudden change in environment
tmp:
image: /images/cc_by.png
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short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2022'
...
---
_id: '12166'
abstract:
- lang: eng
text: Kerstin Johannesson is a marine ecologist and evolutionary biologist based
at the Tjärnö Marine Laboratory of the University of Gothenburg, which is situated
in the beautiful Kosterhavet National Park on the Swedish west coast. Her work,
using marine periwinkles (especially Littorina saxatilis and L. fabalis) as main
model systems, has made a remarkable contribution to marine evolutionary biology
and our understanding of local adaptation and its genetic underpinnings.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
citation:
ama: Westram AM, Butlin R. Professor Kerstin Johannesson–winner of the 2022 Molecular
Ecology Prize. Molecular Ecology. 2022;32(1):26-29. doi:10.1111/mec.16779
apa: Westram, A. M., & Butlin, R. (2022). Professor Kerstin Johannesson–winner
of the 2022 Molecular Ecology Prize. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.16779
chicago: Westram, Anja M, and Roger Butlin. “Professor Kerstin Johannesson–Winner
of the 2022 Molecular Ecology Prize.” Molecular Ecology. Wiley, 2022. https://doi.org/10.1111/mec.16779.
ieee: A. M. Westram and R. Butlin, “Professor Kerstin Johannesson–winner of the
2022 Molecular Ecology Prize,” Molecular Ecology, vol. 32, no. 1. Wiley,
pp. 26–29, 2022.
ista: Westram AM, Butlin R. 2022. Professor Kerstin Johannesson–winner of the 2022
Molecular Ecology Prize. Molecular Ecology. 32(1), 26–29.
mla: Westram, Anja M., and Roger Butlin. “Professor Kerstin Johannesson–Winner of
the 2022 Molecular Ecology Prize.” Molecular Ecology, vol. 32, no. 1, Wiley,
2022, pp. 26–29, doi:10.1111/mec.16779.
short: A.M. Westram, R. Butlin, Molecular Ecology 32 (2022) 26–29.
date_created: 2023-01-12T12:10:28Z
date_published: 2022-11-28T00:00:00Z
date_updated: 2023-08-04T09:09:15Z
day: '28'
department:
- _id: NiBa
doi: 10.1111/mec.16779
external_id:
isi:
- '000892168800001'
intvolume: ' 32'
isi: 1
issue: '1'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
main_file_link:
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url: https://doi.org/10.1111/mec.16779
month: '11'
oa: 1
oa_version: Published Version
page: 26-29
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 32
year: '2022'
...
---
_id: '12234'
abstract:
- lang: eng
text: Hybrid speciation—the origin of new species resulting from the hybridization
of genetically divergent lineages—was once considered rare, but genomic data suggest
that it may occur more often than once thought. In this study, Noguerales and
Ortego found genomic evidence supporting the hybrid origin of a grasshopper that
is able to exploit a broader range of host plants than either of its putative
parents.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
citation:
ama: 'Stankowski S. Digest: On the origin of a possible hybrid species. Evolution.
2022;76(11):2784-2785. doi:10.1111/evo.14632'
apa: 'Stankowski, S. (2022). Digest: On the origin of a possible hybrid species.
Evolution. Wiley. https://doi.org/10.1111/evo.14632'
chicago: 'Stankowski, Sean. “Digest: On the Origin of a Possible Hybrid Species.”
Evolution. Wiley, 2022. https://doi.org/10.1111/evo.14632.'
ieee: 'S. Stankowski, “Digest: On the origin of a possible hybrid species,” Evolution,
vol. 76, no. 11. Wiley, pp. 2784–2785, 2022.'
ista: 'Stankowski S. 2022. Digest: On the origin of a possible hybrid species. Evolution.
76(11), 2784–2785.'
mla: 'Stankowski, Sean. “Digest: On the Origin of a Possible Hybrid Species.” Evolution,
vol. 76, no. 11, Wiley, 2022, pp. 2784–85, doi:10.1111/evo.14632.'
short: S. Stankowski, Evolution 76 (2022) 2784–2785.
date_created: 2023-01-16T09:50:48Z
date_published: 2022-11-01T00:00:00Z
date_updated: 2023-08-04T09:35:48Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/evo.14632
external_id:
isi:
- '000855751600001'
file:
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checksum: 4c0f05083b414ac0323a1b9ee1abc275
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creator: dernst
date_created: 2023-01-27T11:28:38Z
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file_size: 287282
relation: main_file
success: 1
file_date_updated: 2023-01-27T11:28:38Z
has_accepted_license: '1'
intvolume: ' 76'
isi: 1
issue: '11'
keyword:
- General Agricultural and Biological Sciences
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 2784-2785
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Digest: On the origin of a possible hybrid species'
tmp:
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volume: 76
year: '2022'
...
---
_id: '12247'
abstract:
- lang: eng
text: Chromosomal inversions have been shown to play a major role in a local adaptation
by suppressing recombination between alternative arrangements and maintaining
beneficial allele combinations. However, so far, their importance relative to
the remaining genome remains largely unknown. Understanding the genetic architecture
of adaptation requires better estimates of how loci of different effect sizes
contribute to phenotypic variation. Here, we used three Swedish islands where
the marine snail Littorina saxatilis has repeatedly evolved into two distinct
ecotypes along a habitat transition. We estimated the contribution of inversion
polymorphisms to phenotypic divergence while controlling for polygenic effects
in the remaining genome using a quantitative genetics framework. We confirmed
the importance of inversions but showed that contributions of loci outside inversions
are of similar magnitude, with variable proportions dependent on the trait and
the population. Some inversions showed consistent effects across all sites, whereas
others exhibited site-specific effects, indicating that the genomic basis for
replicated phenotypic divergence is only partly shared. The contributions of sexual
dimorphism as well as environmental factors to phenotypic variation were significant
but minor compared to inversions and polygenic background. Overall, this integrated
approach provides insight into the multiple mechanisms contributing to parallel
phenotypic divergence.
acknowledgement: We thank everyone who helped with fieldwork, snail processing, and
DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo, Anne-Lise
Liabot, Irena Senčić, and Zuzanna Zagrodzka. We also thank Rui Faria and Jenny Larsson
for their contributions, with inversions and shell shape respectively. KJ was funded
by the Swedish research council Vetenskapsrådet, grant number 2017-03798. R.K.B.
and E.K. were funded by the European Research Council (ERC-2015-AdG-693030-BARRIERS).
R.K.B. was also funded by the Natural Environment Research Council and the Swedish
Research Council Vetenskapsrådet.
article_processing_charge: No
article_type: original
author:
- first_name: Eva L.
full_name: Koch, Eva L.
last_name: Koch
- first_name: Mark
full_name: Ravinet, Mark
last_name: Ravinet
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: Koch EL, Ravinet M, Westram AM, Johannesson K, Butlin RK. Genetic architecture
of repeated phenotypic divergence in Littorina saxatilis evolution. Evolution.
2022;76(10):2332-2346. doi:10.1111/evo.14602
apa: Koch, E. L., Ravinet, M., Westram, A. M., Johannesson, K., & Butlin, R.
K. (2022). Genetic architecture of repeated phenotypic divergence in Littorina
saxatilis evolution. Evolution. Wiley. https://doi.org/10.1111/evo.14602
chicago: Koch, Eva L., Mark Ravinet, Anja M Westram, Kerstin Johannesson, and Roger
K. Butlin. “Genetic Architecture of Repeated Phenotypic Divergence in Littorina
Saxatilis Evolution.” Evolution. Wiley, 2022. https://doi.org/10.1111/evo.14602.
ieee: E. L. Koch, M. Ravinet, A. M. Westram, K. Johannesson, and R. K. Butlin, “Genetic
architecture of repeated phenotypic divergence in Littorina saxatilis evolution,”
Evolution, vol. 76, no. 10. Wiley, pp. 2332–2346, 2022.
ista: Koch EL, Ravinet M, Westram AM, Johannesson K, Butlin RK. 2022. Genetic architecture
of repeated phenotypic divergence in Littorina saxatilis evolution. Evolution.
76(10), 2332–2346.
mla: Koch, Eva L., et al. “Genetic Architecture of Repeated Phenotypic Divergence
in Littorina Saxatilis Evolution.” Evolution, vol. 76, no. 10, Wiley, 2022,
pp. 2332–46, doi:10.1111/evo.14602.
short: E.L. Koch, M. Ravinet, A.M. Westram, K. Johannesson, R.K. Butlin, Evolution
76 (2022) 2332–2346.
date_created: 2023-01-16T09:54:15Z
date_published: 2022-10-01T00:00:00Z
date_updated: 2023-08-04T09:42:11Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/evo.14602
external_id:
isi:
- '000848449100001'
pmid:
- '35994296'
file:
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checksum: defd8a4bea61cf00a3c88d4a30e2728c
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creator: dernst
date_created: 2023-01-30T08:45:35Z
date_updated: 2023-01-30T08:45:35Z
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file_size: 2990581
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success: 1
file_date_updated: 2023-01-30T08:45:35Z
has_accepted_license: '1'
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keyword:
- General Agricultural and Biological Sciences
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
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- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 2332-2346
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issn:
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title: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis
evolution
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 76
year: '2022'
...
---
_id: '13066'
abstract:
- lang: eng
text: Chromosomal inversions have been shown to play a major role in local adaptation
by suppressing recombination between alternative arrangements and maintaining
beneficial allele combinations. However, so far, their importance relative to
the remaining genome remains largely unknown. Understanding the genetic architecture
of adaptation requires better estimates of how loci of different effect sizes
contribute to phenotypic variation. Here, we used three Swedish islands where
the marine snail Littorina saxatilis has repeatedly evolved into two distinct
ecotypes along a habitat transition. We estimated the contribution of inversion
polymorphisms to phenotypic divergence while controlling for polygenic effects
in the remaining genome using a quantitative genetics framework. We confirmed
the importance of inversions but showed that contributions of loci outside inversions
are of similar magnitude, with variable proportions dependent on the trait and
the population. Some inversions showed consistent effects across all sites, whereas
others exhibited site-specific effects, indicating that the genomic basis for
replicated phenotypic divergence is only partly shared. The contributions of sexual
dimorphism as well as environmental factors to phenotypic variation were significant
but minor compared to inversions and polygenic background. Overall, this integrated
approach provides insight into the multiple mechanisms contributing to parallel
phenotypic divergence.
article_processing_charge: No
author:
- first_name: Eva
full_name: Koch, Eva
last_name: Koch
- first_name: Mark
full_name: Ravinet, Mark
last_name: Ravinet
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Kerstin
full_name: Jonannesson, Kerstin
last_name: Jonannesson
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
citation:
ama: 'Koch E, Ravinet M, Westram AM, Jonannesson K, Butlin R. Data from: Genetic
architecture of repeated phenotypic divergence in Littorina saxatilis ecotype
evolution. 2022. doi:10.5061/DRYAD.M905QFV4B'
apa: 'Koch, E., Ravinet, M., Westram, A. M., Jonannesson, K., & Butlin, R. (2022).
Data from: Genetic architecture of repeated phenotypic divergence in Littorina
saxatilis ecotype evolution. Dryad. https://doi.org/10.5061/DRYAD.M905QFV4B'
chicago: 'Koch, Eva, Mark Ravinet, Anja M Westram, Kerstin Jonannesson, and Roger
Butlin. “Data from: Genetic Architecture of Repeated Phenotypic Divergence in
Littorina Saxatilis Ecotype Evolution.” Dryad, 2022. https://doi.org/10.5061/DRYAD.M905QFV4B.'
ieee: 'E. Koch, M. Ravinet, A. M. Westram, K. Jonannesson, and R. Butlin, “Data
from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis
ecotype evolution.” Dryad, 2022.'
ista: 'Koch E, Ravinet M, Westram AM, Jonannesson K, Butlin R. 2022. Data from:
Genetic architecture of repeated phenotypic divergence in Littorina saxatilis
ecotype evolution, Dryad, 10.5061/DRYAD.M905QFV4B.'
mla: 'Koch, Eva, et al. Data from: Genetic Architecture of Repeated Phenotypic
Divergence in Littorina Saxatilis Ecotype Evolution. Dryad, 2022, doi:10.5061/DRYAD.M905QFV4B.'
short: E. Koch, M. Ravinet, A.M. Westram, K. Jonannesson, R. Butlin, (2022).
date_created: 2023-05-23T16:33:12Z
date_published: 2022-07-28T00:00:00Z
date_updated: 2023-08-04T09:42:10Z
day: '28'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5061/DRYAD.M905QFV4B
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.m905qfv4b
month: '07'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '12247'
relation: used_in_publication
status: public
status: public
title: 'Data from: Genetic architecture of repeated phenotypic divergence in Littorina
saxatilis ecotype evolution'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '12264'
abstract:
- lang: eng
text: Reproductive isolation (RI) is a core concept in evolutionary biology. It
has been the central focus of speciation research since the modern synthesis and
is the basis by which biological species are defined. Despite this, the term is
used in seemingly different ways, and attempts to quantify RI have used very different
approaches. After showing that the field lacks a clear definition of the term,
we attempt to clarify key issues, including what RI is, how it can be quantified
in principle, and how it can be measured in practice. Following other definitions
with a genetic focus, we propose that RI is a quantitative measure of the effect
that genetic differences between populations have on gene flow. Specifically,
RI compares the flow of neutral alleles in the presence of these genetic differences
to the flow without any such differences. RI is thus greater than zero when genetic
differences between populations reduce the flow of neutral alleles between populations.
We show how RI can be quantified in a range of scenarios. A key conclusion is
that RI depends strongly on circumstances—including the spatial, temporal and
genomic context—making it difficult to compare across systems. After reviewing
methods for estimating RI from data, we conclude that it is difficult to measure
in practice. We discuss our findings in light of the goals of speciation research
and encourage the use of methods for estimating RI that integrate organismal and
genetic approaches.
acknowledgement: 'We are grateful to the participants of the ESEB satellite symposium
‘Understanding reproductive isolation: bridging conceptual barriers in speciation research’ in 2021 for the interesting discussions that helped us clarify the thoughts presented in this article. We thank Roger
Butlin, Michael Turelli and two anonymous reviewers for their thoughtful comments
on this manuscript. We are also very grateful to Roger Butlin and the Barton Group
for the continued conversa-tions about RI. In addition, we thank all participants
of the speciation survey. Part of this work was funded by the Austrian Science Fund
FWF (grant P 32166)'
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Parvathy
full_name: Surendranadh, Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Westram AM, Stankowski S, Surendranadh P, Barton NH. What is reproductive isolation?
Journal of Evolutionary Biology. 2022;35(9):1143-1164. doi:10.1111/jeb.14005
apa: Westram, A. M., Stankowski, S., Surendranadh, P., & Barton, N. H. (2022).
What is reproductive isolation? Journal of Evolutionary Biology. Wiley.
https://doi.org/10.1111/jeb.14005
chicago: Westram, Anja M, Sean Stankowski, Parvathy Surendranadh, and Nicholas H
Barton. “What Is Reproductive Isolation?” Journal of Evolutionary Biology.
Wiley, 2022. https://doi.org/10.1111/jeb.14005.
ieee: A. M. Westram, S. Stankowski, P. Surendranadh, and N. H. Barton, “What is
reproductive isolation?,” Journal of Evolutionary Biology, vol. 35, no.
9. Wiley, pp. 1143–1164, 2022.
ista: Westram AM, Stankowski S, Surendranadh P, Barton NH. 2022. What is reproductive
isolation? Journal of Evolutionary Biology. 35(9), 1143–1164.
mla: Westram, Anja M., et al. “What Is Reproductive Isolation?” Journal of Evolutionary
Biology, vol. 35, no. 9, Wiley, 2022, pp. 1143–64, doi:10.1111/jeb.14005.
short: A.M. Westram, S. Stankowski, P. Surendranadh, N.H. Barton, Journal of Evolutionary
Biology 35 (2022) 1143–1164.
date_created: 2023-01-16T09:59:24Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2023-08-04T09:53:40Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/jeb.14005
external_id:
isi:
- '000849851100002'
pmid:
- '36063156'
file:
- access_level: open_access
checksum: f08de57112330a7ee88d2e1b20576a1e
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T10:05:31Z
date_updated: 2023-01-30T10:05:31Z
file_id: '12448'
file_name: 2022_JourEvoBiology_Westram.pdf
file_size: 3146793
relation: main_file
success: 1
file_date_updated: 2023-01-30T10:05:31Z
has_accepted_license: '1'
intvolume: ' 35'
isi: 1
issue: '9'
keyword:
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1143-1164
pmid: 1
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: The maintenance of alternative adaptive peaks in snapdragons
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '12265'
relation: other
status: public
scopus_import: '1'
status: public
title: What is reproductive isolation?
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 35
year: '2022'
...
---
_id: '12265'
acknowledgement: We are very grateful to the authors of the commentaries for the interesting
discussion and to Luke Holman for handling this set of manuscripts. Part of this
work was funded by the Austrian Science Fund FWF (grant P 32166).
article_processing_charge: Yes (via OA deal)
article_type: letter_note
author:
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Parvathy
full_name: Surendranadh, Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Westram AM, Stankowski S, Surendranadh P, Barton NH. Reproductive isolation,
speciation, and the value of disagreement: A reply to the commentaries on ‘What
is reproductive isolation?’ Journal of Evolutionary Biology. 2022;35(9):1200-1205.
doi:10.1111/jeb.14082'
apa: 'Westram, A. M., Stankowski, S., Surendranadh, P., & Barton, N. H. (2022).
Reproductive isolation, speciation, and the value of disagreement: A reply to
the commentaries on ‘What is reproductive isolation?’ Journal of Evolutionary
Biology. Wiley. https://doi.org/10.1111/jeb.14082'
chicago: 'Westram, Anja M, Sean Stankowski, Parvathy Surendranadh, and Nicholas
H Barton. “Reproductive Isolation, Speciation, and the Value of Disagreement:
A Reply to the Commentaries on ‘What Is Reproductive Isolation?’” Journal of
Evolutionary Biology. Wiley, 2022. https://doi.org/10.1111/jeb.14082.'
ieee: 'A. M. Westram, S. Stankowski, P. Surendranadh, and N. H. Barton, “Reproductive
isolation, speciation, and the value of disagreement: A reply to the commentaries
on ‘What is reproductive isolation?,’” Journal of Evolutionary Biology,
vol. 35, no. 9. Wiley, pp. 1200–1205, 2022.'
ista: 'Westram AM, Stankowski S, Surendranadh P, Barton NH. 2022. Reproductive isolation,
speciation, and the value of disagreement: A reply to the commentaries on ‘What
is reproductive isolation?’ Journal of Evolutionary Biology. 35(9), 1200–1205.'
mla: 'Westram, Anja M., et al. “Reproductive Isolation, Speciation, and the Value
of Disagreement: A Reply to the Commentaries on ‘What Is Reproductive Isolation?’”
Journal of Evolutionary Biology, vol. 35, no. 9, Wiley, 2022, pp. 1200–05,
doi:10.1111/jeb.14082.'
short: A.M. Westram, S. Stankowski, P. Surendranadh, N.H. Barton, Journal of Evolutionary
Biology 35 (2022) 1200–1205.
date_created: 2023-01-16T09:59:37Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2023-08-04T09:53:41Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/jeb.14082
external_id:
isi:
- '000849851100009'
file:
- access_level: open_access
checksum: 27268009e5eec030bc10667a4ac5ed4c
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T10:14:09Z
date_updated: 2023-01-30T10:14:09Z
file_id: '12449'
file_name: 2022_JourEvoBiology_Westram_Response.pdf
file_size: 349603
relation: main_file
success: 1
file_date_updated: 2023-01-30T10:14:09Z
has_accepted_license: '1'
intvolume: ' 35'
isi: 1
issue: '9'
keyword:
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1200-1205
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: The maintenance of alternative adaptive peaks in snapdragons
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '12264'
relation: other
status: public
scopus_import: '1'
status: public
title: 'Reproductive isolation, speciation, and the value of disagreement: A reply
to the commentaries on ‘What is reproductive isolation?’'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 35
year: '2022'
...
---
_id: '10787'
abstract:
- lang: eng
text: "A species distributed across diverse environments may adapt to local conditions.
We ask how quickly such a species changes its range in response to changed conditions.
Szép et al. (Szép E, Sachdeva H, Barton NH. 2021 Polygenic local adaptation in
metapopulations: a stochastic eco-evolutionary model. Evolution75, 1030–1045 (doi:10.1111/evo.14210))
used the infinite island model to find the stationary distribution of allele frequencies
and deme sizes. We extend this to find how a metapopulation responds to changes
in carrying capacity, selection strength, or migration rate when deme sizes are
fixed. We further develop a ‘fixed-state’ approximation. Under this approximation,
polymorphism is only possible for a narrow range of habitat proportions when selection
is weak compared to drift, but for a much wider range otherwise. When rates of
selection or migration relative to drift change in a single deme of the metapopulation,
the population takes a time of order m−1 to reach the new equilibrium. However,
even with many loci, there can be substantial fluctuations in net adaptation,
because at each locus, alleles randomly get lost or fixed. Thus, in a finite metapopulation,
variation may gradually be lost by chance, even if it would persist in an infinite
metapopulation. When conditions change across the whole metapopulation, there
can be rapid change, which is predicted well by the fixed-state approximation.
This work helps towards an understanding of how metapopulations extend their range
across diverse environments.\r\nThis article is part of the theme issue ‘Species’
ranges in the face of changing environments (Part II)’."
acknowledgement: This research was partly funded by the Austrian Science Fund (FWF)
[FWF P-32896B].
article_processing_charge: No
article_type: original
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Oluwafunmilola O
full_name: Olusanya, Oluwafunmilola O
id: 41AD96DC-F248-11E8-B48F-1D18A9856A87
last_name: Olusanya
orcid: 0000-0003-1971-8314
citation:
ama: 'Barton NH, Olusanya OO. The response of a metapopulation to a changing environment.
Philosophical Transactions of the Royal Society B: Biological Sciences.
2022;377(1848). doi:10.1098/rstb.2021.0009'
apa: 'Barton, N. H., & Olusanya, O. O. (2022). The response of a metapopulation
to a changing environment. Philosophical Transactions of the Royal Society
B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2021.0009'
chicago: 'Barton, Nicholas H, and Oluwafunmilola O Olusanya. “The Response of a
Metapopulation to a Changing Environment.” Philosophical Transactions of the
Royal Society B: Biological Sciences. The Royal Society, 2022. https://doi.org/10.1098/rstb.2021.0009.'
ieee: 'N. H. Barton and O. O. Olusanya, “The response of a metapopulation to a changing
environment,” Philosophical Transactions of the Royal Society B: Biological
Sciences, vol. 377, no. 1848. The Royal Society, 2022.'
ista: 'Barton NH, Olusanya OO. 2022. The response of a metapopulation to a changing
environment. Philosophical Transactions of the Royal Society B: Biological Sciences.
377(1848).'
mla: 'Barton, Nicholas H., and Oluwafunmilola O. Olusanya. “The Response of a Metapopulation
to a Changing Environment.” Philosophical Transactions of the Royal Society
B: Biological Sciences, vol. 377, no. 1848, The Royal Society, 2022, doi:10.1098/rstb.2021.0009.'
short: 'N.H. Barton, O.O. Olusanya, Philosophical Transactions of the Royal Society
B: Biological Sciences 377 (2022).'
date_created: 2022-02-21T16:08:10Z
date_published: 2022-04-11T00:00:00Z
date_updated: 2024-01-26T12:00:53Z
day: '11'
ddc:
- '570'
department:
- _id: GradSch
- _id: NiBa
doi: 10.1098/rstb.2021.0009
external_id:
isi:
- '000758140300001'
pmid:
- '35184588'
file:
- access_level: open_access
checksum: 3b0243738f01bf3c07e0d7e8dc64f71d
content_type: application/pdf
creator: dernst
date_created: 2022-08-02T06:14:32Z
date_updated: 2022-08-02T06:14:32Z
file_id: '11719'
file_name: 2022_PhilosophicalTransactionsRSB_Barton.pdf
file_size: 1349672
relation: main_file
success: 1
file_date_updated: 2022-08-02T06:14:32Z
has_accepted_license: '1'
intvolume: ' 377'
isi: 1
issue: '1848'
keyword:
- General Agricultural and Biological Sciences
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: c08d3278-5a5b-11eb-8a69-fdb09b55f4b8
grant_number: P32896
name: Causes and consequences of population fragmentation
publication: 'Philosophical Transactions of the Royal Society B: Biological Sciences'
publication_identifier:
eissn:
- 1471-2970
issn:
- 0962-8436
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
related_material:
record:
- id: '14711'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: The response of a metapopulation to a changing environment
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 377
year: '2022'
...
---
_id: '10658'
abstract:
- lang: eng
text: We analyse how migration from a large mainland influences genetic load and
population numbers on an island, in a scenario where fitness-affecting variants
are unconditionally deleterious, and where numbers decline with increasing load.
Our analysis shows that migration can have qualitatively different effects, depending
on the total mutation target and fitness effects of deleterious variants. In particular,
we find that populations exhibit a genetic Allee effect across a wide range of
parameter combinations, when variants are partially recessive, cycling between
low-load (large-population) and high-load (sink) states. Increased migration reduces
load in the sink state (by increasing heterozygosity) but further inflates load
in the large-population state (by hindering purging). We identify various critical
parameter thresholds at which one or other stable state collapses, and discuss
how these thresholds are influenced by the genetic versus demographic effects
of migration. Our analysis is based on a ‘semi-deterministic’ analysis, which
accounts for genetic drift but neglects demographic stochasticity. We also compare
against simulations which account for both demographic stochasticity and drift.
Our results clarify the importance of gene flow as a key determinant of extinction
risk in peripheral populations, even in the absence of ecological gradients. This
article is part of the theme issue ‘Species’ ranges in the face of changing environments
(part I)’.
acknowledgement: This research was partly funded by the Austrian Science Fund (FWF)
(grant no. P-32896B).
article_number: '20210010'
article_processing_charge: No
article_type: original
author:
- first_name: Himani
full_name: Sachdeva, Himani
last_name: Sachdeva
- first_name: Oluwafunmilola O
full_name: Olusanya, Oluwafunmilola O
id: 41AD96DC-F248-11E8-B48F-1D18A9856A87
last_name: Olusanya
orcid: 0000-0003-1971-8314
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Sachdeva H, Olusanya OO, Barton NH. Genetic load and extinction in peripheral
populations: The roles of migration, drift and demographic stochasticity. Philosophical
Transactions of the Royal Society B. 2022;377(1846). doi:10.1098/rstb.2021.0010'
apa: 'Sachdeva, H., Olusanya, O. O., & Barton, N. H. (2022). Genetic load and
extinction in peripheral populations: The roles of migration, drift and demographic
stochasticity. Philosophical Transactions of the Royal Society B. The Royal
Society. https://doi.org/10.1098/rstb.2021.0010'
chicago: 'Sachdeva, Himani, Oluwafunmilola O Olusanya, and Nicholas H Barton. “Genetic
Load and Extinction in Peripheral Populations: The Roles of Migration, Drift and
Demographic Stochasticity.” Philosophical Transactions of the Royal Society
B. The Royal Society, 2022. https://doi.org/10.1098/rstb.2021.0010.'
ieee: 'H. Sachdeva, O. O. Olusanya, and N. H. Barton, “Genetic load and extinction
in peripheral populations: The roles of migration, drift and demographic stochasticity,”
Philosophical Transactions of the Royal Society B, vol. 377, no. 1846.
The Royal Society, 2022.'
ista: 'Sachdeva H, Olusanya OO, Barton NH. 2022. Genetic load and extinction in
peripheral populations: The roles of migration, drift and demographic stochasticity.
Philosophical Transactions of the Royal Society B. 377(1846), 20210010.'
mla: 'Sachdeva, Himani, et al. “Genetic Load and Extinction in Peripheral Populations:
The Roles of Migration, Drift and Demographic Stochasticity.” Philosophical
Transactions of the Royal Society B, vol. 377, no. 1846, 20210010, The Royal
Society, 2022, doi:10.1098/rstb.2021.0010.'
short: H. Sachdeva, O.O. Olusanya, N.H. Barton, Philosophical Transactions of the
Royal Society B 377 (2022).
date_created: 2022-01-24T10:34:53Z
date_published: 2022-01-24T00:00:00Z
date_updated: 2024-01-26T12:00:53Z
day: '24'
ddc:
- '576'
department:
- _id: GradSch
- _id: NiBa
doi: 10.1098/rstb.2021.0010
external_id:
isi:
- '000745854300008'
pmid:
- '35067097'
file:
- access_level: open_access
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project:
- _id: c08d3278-5a5b-11eb-8a69-fdb09b55f4b8
grant_number: P32896
name: Causes and consequences of population fragmentation
publication: Philosophical Transactions of the Royal Society B
publication_identifier:
eissn:
- 1471-2970
issn:
- 0962-8436
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
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url: https://doi.org/10.1101/2021.08.05.455207
record:
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relation: dissertation_contains
status: public
status: public
title: 'Genetic load and extinction in peripheral populations: The roles of migration,
drift and demographic stochasticity'
tmp:
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name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
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type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 377
year: '2022'
...
---
_id: '11411'
abstract:
- lang: eng
text: Many studies have quantified the distribution of heterozygosity and relatedness
in natural populations, but few have examined the demographic processes driving
these patterns. In this study, we take a novel approach by studying how population
structure affects both pairwise identity and the distribution of heterozygosity
in a natural population of the self-incompatible plant Antirrhinum majus. Excess
variance in heterozygosity between individuals is due to identity disequilibrium,
which reflects the variance in inbreeding between individuals; it is measured
by the statistic g2. We calculated g2 together with FST and pairwise relatedness
(Fij) using 91 SNPs in 22,353 individuals collected over 11 years. We find that
pairwise Fij declines rapidly over short spatial scales, and the excess variance
in heterozygosity between individuals reflects significant variation in inbreeding.
Additionally, we detect an excess of individuals with around half the average
heterozygosity, indicating either selfing or matings between close relatives.
We use 2 types of simulation to ask whether variation in heterozygosity is consistent
with fine-scale spatial population structure. First, by simulating offspring using
parents drawn from a range of spatial scales, we show that the known pollen dispersal
kernel explains g2. Second, we simulate a 1,000-generation pedigree using the
known dispersal and spatial distribution and find that the resulting g2 is consistent
with that observed from the field data. In contrast, a simulated population with
uniform density underestimates g2, indicating that heterogeneous density promotes
identity disequilibrium. Our study shows that heterogeneous density and leptokurtic
dispersal can together explain the distribution of heterozygosity.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "Part of this work was funded by Marie Curie COFUND Doctoral Fellowship
and Austrian Science Fund FWF (grant P32166).\r\nWe thank the many volunteers and
friends who have contributed to data collection in the field site over the years,
in particular those who have managed field seasons: Barbora Trubenova, Maria Clara
Melo, Tom Ellis, Eva Cereghetti, Lenka Matejovicova, Beatriz Pablo Carmona. Frederic
Ferrer and Eva Salmerón Mateu have been immensely helpful with logistics at our
informal field station, El Serrat de Planoles. We thank Sean Stankowski for technical
help in\r\nproducing figure 1. This research was also supported by the Scientific
Service Units (SSU) of IST Austria through resources provided by Scientific Computing
(SciComp)."
article_number: iyac083
article_processing_charge: No
article_type: original
author:
- first_name: Parvathy
full_name: Surendranadh, Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
- first_name: Louise S
full_name: Arathoon, Louise S
id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87
last_name: Arathoon
orcid: 0000-0003-1771-714X
- first_name: Carina
full_name: Baskett, Carina
id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87
last_name: Baskett
orcid: 0000-0002-7354-8574
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects
of fine-scale population structure on the distribution of heterozygosity in a
long-term study of Antirrhinum majus. Genetics. 2022;221(3). doi:10.1093/genetics/iyac083
apa: Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., &
Barton, N. H. (2022). Effects of fine-scale population structure on the distribution
of heterozygosity in a long-term study of Antirrhinum majus. Genetics.
Oxford University Press. https://doi.org/10.1093/genetics/iyac083
chicago: Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field,
Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure
on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.”
Genetics. Oxford University Press, 2022. https://doi.org/10.1093/genetics/iyac083.
ieee: P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H.
Barton, “Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus,” Genetics, vol. 221, no. 3.
Oxford University Press, 2022.
ista: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022.
Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus. Genetics. 221(3), iyac083.
mla: Surendranadh, Parvathy, et al. “Effects of Fine-Scale Population Structure
on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.”
Genetics, vol. 221, no. 3, iyac083, Oxford University Press, 2022, doi:10.1093/genetics/iyac083.
short: P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton,
Genetics 221 (2022).
date_created: 2022-05-26T13:44:50Z
date_published: 2022-07-01T00:00:00Z
date_updated: 2024-02-21T12:38:33Z
day: '01'
ddc:
- '576'
department:
- _id: GradSch
- _id: NiBa
doi: 10.1093/genetics/iyac083
external_id:
isi:
- '000803735800001'
pmid:
- '35639938'
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grant_number: P32166
name: The maintenance of alternative adaptive peaks in snapdragons
publication: Genetics
publication_identifier:
eissn:
- 1943-2631
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
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relation: research_data
status: public
scopus_import: '1'
status: public
title: Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 221
year: '2022'
...
---
_id: '11321'
abstract:
- lang: eng
text: 'Here are the research data underlying the publication "Effects of fine-scale
population structure on the distribution of heterozygosity in a long-term study
of Antirrhinum majus" Further information are summed up in the README document. '
article_processing_charge: No
author:
- first_name: Parvathy
full_name: Surendranadh, Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
- first_name: Louise S
full_name: Arathoon, Louise S
id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87
last_name: Arathoon
orcid: 0000-0003-1771-714X
- first_name: Carina
full_name: Baskett, Carina
id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87
last_name: Baskett
orcid: 0000-0002-7354-8574
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects
of fine-scale population structure on the distribution of heterozygosity in a
long-term study of Antirrhinum majus. 2022. doi:10.15479/at:ista:11321
apa: Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., &
Barton, N. H. (2022). Effects of fine-scale population structure on the distribution
of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science
and Technology Austria. https://doi.org/10.15479/at:ista:11321
chicago: Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field,
Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure
on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.”
Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11321.
ieee: P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H.
Barton, “Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus.” Institute of Science and Technology
Austria, 2022.
ista: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022.
Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus, Institute of Science and Technology
Austria, 10.15479/at:ista:11321.
mla: Surendranadh, Parvathy, et al. Effects of Fine-Scale Population Structure
on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.
Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11321.
short: P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton,
(2022).
contributor:
- contributor_type: project_member
first_name: Louise S
id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87
last_name: Arathoon
- contributor_type: project_member
first_name: Carina
id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87
last_name: Baskett
orcid: 0000-0002-7354-8574
- contributor_type: project_member
first_name: David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- contributor_type: project_member
first_name: Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- contributor_type: project_member
first_name: Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
date_created: 2022-04-22T09:42:24Z
date_published: 2022-04-28T00:00:00Z
date_updated: 2024-02-21T12:41:09Z
day: '28'
ddc:
- '570'
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/at:ista:11321
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month: '04'
oa: 1
oa_version: Published Version
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related_material:
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relation: used_in_publication
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status: public
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relation: earlier_version
status: public
status: public
title: Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '12081'
abstract:
- lang: eng
text: 'Selection accumulates information in the genome—it guides stochastically
evolving populations toward states (genotype frequencies) that would be unlikely
under neutrality. This can be quantified as the Kullback–Leibler (KL) divergence
between the actual distribution of genotype frequencies and the corresponding
neutral distribution. First, we show that this population-level information sets
an upper bound on the information at the level of genotype and phenotype, limiting
how precisely they can be specified by selection. Next, we study how the accumulation
and maintenance of information is limited by the cost of selection, measured as
the genetic load or the relative fitness variance, both of which we connect to
the control-theoretic KL cost of control. The information accumulation rate is
upper bounded by the population size times the cost of selection. This bound is
very general, and applies across models (Wright–Fisher, Moran, diffusion) and
to arbitrary forms of selection, mutation, and recombination. Finally, the cost
of maintaining information depends on how it is encoded: Specifying a single allele
out of two is expensive, but one bit encoded among many weakly specified loci
(as in a polygenic trait) is cheap.'
acknowledgement: We thank Ksenia Khudiakova, Wiktor Młynarski, Sean Stankowski, and
two anonymous reviewers for discussions and comments on the manuscript. G.T. and
M.H. acknowledge funding from the Human Frontier Science Program Grant RGP0032/2018.
N.B. acknowledges funding from ERC Grant 250152 “Information and Evolution.”
article_number: e2123152119
article_processing_charge: No
article_type: original
author:
- first_name: Michal
full_name: Hledik, Michal
id: 4171253A-F248-11E8-B48F-1D18A9856A87
last_name: Hledik
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: '1'
citation:
ama: Hledik M, Barton NH, Tkačik G. Accumulation and maintenance of information
in evolution. Proceedings of the National Academy of Sciences. 2022;119(36).
doi:10.1073/pnas.2123152119
apa: Hledik, M., Barton, N. H., & Tkačik, G. (2022). Accumulation and maintenance
of information in evolution. Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2123152119
chicago: Hledik, Michal, Nicholas H Barton, and Gašper Tkačik. “Accumulation and
Maintenance of Information in Evolution.” Proceedings of the National Academy
of Sciences. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2123152119.
ieee: M. Hledik, N. H. Barton, and G. Tkačik, “Accumulation and maintenance of information
in evolution,” Proceedings of the National Academy of Sciences, vol. 119,
no. 36. Proceedings of the National Academy of Sciences, 2022.
ista: Hledik M, Barton NH, Tkačik G. 2022. Accumulation and maintenance of information
in evolution. Proceedings of the National Academy of Sciences. 119(36), e2123152119.
mla: Hledik, Michal, et al. “Accumulation and Maintenance of Information in Evolution.”
Proceedings of the National Academy of Sciences, vol. 119, no. 36, e2123152119,
Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2123152119.
short: M. Hledik, N.H. Barton, G. Tkačik, Proceedings of the National Academy of
Sciences 119 (2022).
date_created: 2022-09-11T22:01:55Z
date_published: 2022-08-29T00:00:00Z
date_updated: 2024-03-06T14:22:51Z
day: '29'
ddc:
- '570'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1073/pnas.2123152119
ec_funded: 1
external_id:
isi:
- '000889278400014'
pmid:
- '36037343'
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date_created: 2022-09-12T08:08:12Z
date_updated: 2022-09-12T08:08:12Z
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oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 2665AAFE-B435-11E9-9278-68D0E5697425
grant_number: RGP0034/2018
name: Can evolution minimize spurious signaling crosstalk to reach optimal performance?
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
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issn:
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publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
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scopus_import: '1'
status: public
title: Accumulation and maintenance of information in evolution
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legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 119
year: '2022'
...
---
_id: '11388'
abstract:
- lang: eng
text: "In evolve and resequence experiments, a population is sequenced, subjected
to selection and\r\nthen sequenced again, so that genetic changes before and after
selection can be observed at\r\nthe genetic level. Here, I use these studies to
better understand the genetic basis of complex\r\ntraits - traits which depend
on more than a few genes.\r\nIn the first chapter, I discuss the first evolve
and resequence experiment, in which a population\r\nof mice, the so-called \"Longshanks\"
mice, were selected for tibia length while their body mass\r\nwas kept constant.
The full pedigree is known. We observed a selection response on all\r\nchromosomes
and used the infinitesimal model with linkage, a model which assumes an infinite\r\nnumber
of genes with infinitesimally small effect sizes, as a null model. Results implied
a very\r\npolygenic basis with a few loci of major effect standing out and changing
in parallel. There\r\nwas large variability between the different chromosomes
in this study, probably due to LD.\r\nIn chapter two, I go on to discuss the impact
of LD, on the variability in an allele-frequency\r\nbased summary statistic, giving
an equation based on the initial allele frequencies, average\r\npairwise LD, and
the first four moments of the haplotype block copy number distribution. I\r\ndescribe
this distribution by referring back to the founder generation. I then demonstrate\r\nhow
to infer selection via a maximum likelihood scheme on the example of a single
locus and\r\ndiscuss how to extend this to more realistic scenarios.\r\nIn chapter
three, I discuss the second evolve and resequence experiment, in which a small\r\npopulation
of Drosophila melanogaster was selected for increased pupal case size over 6\r\ngenerations.
The experiment was highly replicated with 27 lines selected within family and
a\r\nknown pedigree. We observed a phenotypic selection response of over one standard
deviation.\r\nI describe the patterns in allele frequency data, including allele
frequency changes and patterns\r\nof heterozygosity, and give ideas for future
work."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Stefanie
full_name: Belohlavy, Stefanie
id: 43FE426A-F248-11E8-B48F-1D18A9856A87
last_name: Belohlavy
orcid: 0000-0002-9849-498X
citation:
ama: Belohlavy S. The genetic basis of complex traits studied via analysis of evolve
and resequence experiments. 2022. doi:10.15479/at:ista:11388
apa: Belohlavy, S. (2022). The genetic basis of complex traits studied via analysis
of evolve and resequence experiments. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:11388
chicago: Belohlavy, Stefanie. “The Genetic Basis of Complex Traits Studied via Analysis
of Evolve and Resequence Experiments.” Institute of Science and Technology Austria,
2022. https://doi.org/10.15479/at:ista:11388.
ieee: S. Belohlavy, “The genetic basis of complex traits studied via analysis of
evolve and resequence experiments,” Institute of Science and Technology Austria,
2022.
ista: Belohlavy S. 2022. The genetic basis of complex traits studied via analysis
of evolve and resequence experiments. Institute of Science and Technology Austria.
mla: Belohlavy, Stefanie. The Genetic Basis of Complex Traits Studied via Analysis
of Evolve and Resequence Experiments. Institute of Science and Technology
Austria, 2022, doi:10.15479/at:ista:11388.
short: S. Belohlavy, The Genetic Basis of Complex Traits Studied via Analysis of
Evolve and Resequence Experiments, Institute of Science and Technology Austria,
2022.
date_created: 2022-05-16T16:49:18Z
date_published: 2022-05-18T00:00:00Z
date_updated: 2023-08-29T06:41:51Z
day: '18'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/at:ista:11388
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date_created: 2022-05-19T13:03:13Z
date_updated: 2023-05-20T22:30:03Z
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language:
- iso: eng
month: '05'
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oa_version: Published Version
page: '98'
publication_identifier:
isbn:
- 978-3-99078-018-3
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6713'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: The genetic basis of complex traits studied via analysis of evolve and resequence
experiments
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_id: '10535'
abstract:
- lang: eng
text: Realistic models of biological processes typically involve interacting components
on multiple scales, driven by changing environment and inherent stochasticity.
Such models are often analytically and numerically intractable. We revisit a dynamic
maximum entropy method that combines a static maximum entropy with a quasi-stationary
approximation. This allows us to reduce stochastic non-equilibrium dynamics expressed
by the Fokker-Planck equation to a simpler low-dimensional deterministic dynamics,
without the need to track microscopic details. Although the method has been previously
applied to a few (rather complicated) applications in population genetics, our
main goal here is to explain and to better understand how the method works. We
demonstrate the usefulness of the method for two widely studied stochastic problems,
highlighting its accuracy in capturing important macroscopic quantities even in
rapidly changing non-stationary conditions. For the Ornstein-Uhlenbeck process,
the method recovers the exact dynamics whilst for a stochastic island model with
migration from other habitats, the approximation retains high macroscopic accuracy
under a wide range of scenarios in a dynamic environment.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "Computational resources for the study were provided by the Institute
of Science and Technology, Austria.\r\nKB received funding from the Scientific Grant
Agency of the Slovak Republic under the Grants Nos. 1/0755/19 and 1/0521/20."
article_number: e1009661
article_processing_charge: No
article_type: original
author:
- first_name: Katarína
full_name: Bod'ová, Katarína
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bod'ová
orcid: 0000-0002-7214-0171
- first_name: Eniko
full_name: Szep, Eniko
id: 485BB5A4-F248-11E8-B48F-1D18A9856A87
last_name: Szep
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Bodova K, Szep E, Barton NH. Dynamic maximum entropy provides accurate approximation
of structured population dynamics. PLoS Computational Biology. 2021;17(12).
doi:10.1371/journal.pcbi.1009661
apa: Bodova, K., Szep, E., & Barton, N. H. (2021). Dynamic maximum entropy provides
accurate approximation of structured population dynamics. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1009661
chicago: Bodova, Katarina, Eniko Szep, and Nicholas H Barton. “Dynamic Maximum Entropy
Provides Accurate Approximation of Structured Population Dynamics.” PLoS Computational
Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1009661.
ieee: K. Bodova, E. Szep, and N. H. Barton, “Dynamic maximum entropy provides accurate
approximation of structured population dynamics,” PLoS Computational Biology,
vol. 17, no. 12. Public Library of Science, 2021.
ista: Bodova K, Szep E, Barton NH. 2021. Dynamic maximum entropy provides accurate
approximation of structured population dynamics. PLoS Computational Biology. 17(12),
e1009661.
mla: Bodova, Katarina, et al. “Dynamic Maximum Entropy Provides Accurate Approximation
of Structured Population Dynamics.” PLoS Computational Biology, vol. 17,
no. 12, e1009661, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1009661.
short: K. Bodova, E. Szep, N.H. Barton, PLoS Computational Biology 17 (2021).
date_created: 2021-12-12T23:01:27Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2022-08-01T10:48:04Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1371/journal.pcbi.1009661
external_id:
arxiv:
- '2102.03669'
pmid:
- '34851948'
file:
- access_level: open_access
checksum: dcd185d4f7e0acee25edf1d6537f447e
content_type: application/pdf
creator: dernst
date_created: 2022-05-16T08:53:11Z
date_updated: 2022-05-16T08:53:11Z
file_id: '11383'
file_name: 2021_PLOsComBio_Bodova.pdf
file_size: 2299486
relation: main_file
success: 1
file_date_updated: 2022-05-16T08:53:11Z
has_accepted_license: '1'
intvolume: ' 17'
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Computational Biology
publication_identifier:
eissn:
- 1553-7358
issn:
- 1553-734X
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic maximum entropy provides accurate approximation of structured population
dynamics
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2021'
...
---
_id: '8708'
abstract:
- lang: eng
text: The Mytilus complex of marine mussel species forms a mosaic of hybrid zones,
found across temperate regions of the globe. This allows us to study ‘replicated’
instances of secondary contact between closely related species. Previous work
on this complex has shown that local introgression is both widespread and highly
heterogeneous, and has identified SNPs that are outliers of differentiation between
lineages. Here, we developed an ancestry‐informative panel of such SNPs. We then
compared their frequencies in newly sampled populations, including samples from
within the hybrid zones, and parental populations at different distances from
the contact. Results show that close to the hybrid zones, some outlier loci are
near to fixation for the heterospecific allele, suggesting enhanced local introgression,
or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses,
treating local parental populations as the reference, reveal a globally high concordance
among loci, albeit with a few signals of asymmetric introgression. Enhanced local
introgression at specific loci is consistent with the early transfer of adaptive
variants after contact, possibly including asymmetric bi‐stable variants (Dobzhansky‐Muller
incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having
escaped one barrier, however, these variants can be trapped or delayed at the
next barrier, confining the introgression locally. These results shed light on
the decay of species barriers during phases of contact.
acknowledgement: Data used in this work were partly produced through the genotyping
and sequencing facilities of ISEM and LabEx CeMEB, an ANR ‘Investissements d'avenir’
program (ANR‐10‐LABX‐04‐01) This project benefited from the Montpellier Bioinformatics
Biodiversity platform supported by the LabEx CeMEB. We thank Norah Saarman, Grant
Pogson, Célia Gosset and Pierre‐Alexandre Gagnaire for providing samples. This work
was funded by a Languedoc‐Roussillon ‘Chercheur(se)s d'Avenir’ grant (Connect7 project).
P. Strelkov was supported by the Russian Science Foundation project 19‐74‐20024.
This is article 2020‐240 of Institut des Sciences de l'Evolution de Montpellier.
article_processing_charge: No
article_type: original
author:
- first_name: Alexis
full_name: Simon, Alexis
last_name: Simon
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Tahani
full_name: El Ayari, Tahani
last_name: El Ayari
- first_name: Cathy
full_name: Liautard‐Haag, Cathy
last_name: Liautard‐Haag
- first_name: Petr
full_name: Strelkov, Petr
last_name: Strelkov
- first_name: John J
full_name: Welch, John J
last_name: Welch
- first_name: Nicolas
full_name: Bierne, Nicolas
last_name: Bierne
citation:
ama: Simon A, Fraisse C, El Ayari T, et al. How do species barriers decay? Concordance
and local introgression in mosaic hybrid zones of mussels. Journal of Evolutionary
Biology. 2021;34(1):208-223. doi:10.1111/jeb.13709
apa: Simon, A., Fraisse, C., El Ayari, T., Liautard‐Haag, C., Strelkov, P., Welch,
J. J., & Bierne, N. (2021). How do species barriers decay? Concordance and
local introgression in mosaic hybrid zones of mussels. Journal of Evolutionary
Biology. Wiley. https://doi.org/10.1111/jeb.13709
chicago: Simon, Alexis, Christelle Fraisse, Tahani El Ayari, Cathy Liautard‐Haag,
Petr Strelkov, John J Welch, and Nicolas Bierne. “How Do Species Barriers Decay?
Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” Journal
of Evolutionary Biology. Wiley, 2021. https://doi.org/10.1111/jeb.13709.
ieee: A. Simon et al., “How do species barriers decay? Concordance and local
introgression in mosaic hybrid zones of mussels,” Journal of Evolutionary Biology,
vol. 34, no. 1. Wiley, pp. 208–223, 2021.
ista: Simon A, Fraisse C, El Ayari T, Liautard‐Haag C, Strelkov P, Welch JJ, Bierne
N. 2021. How do species barriers decay? Concordance and local introgression in
mosaic hybrid zones of mussels. Journal of Evolutionary Biology. 34(1), 208–223.
mla: Simon, Alexis, et al. “How Do Species Barriers Decay? Concordance and Local
Introgression in Mosaic Hybrid Zones of Mussels.” Journal of Evolutionary Biology,
vol. 34, no. 1, Wiley, 2021, pp. 208–23, doi:10.1111/jeb.13709.
short: A. Simon, C. Fraisse, T. El Ayari, C. Liautard‐Haag, P. Strelkov, J.J. Welch,
N. Bierne, Journal of Evolutionary Biology 34 (2021) 208–223.
date_created: 2020-10-25T23:01:20Z
date_published: 2021-01-01T00:00:00Z
date_updated: 2023-08-04T11:04:11Z
day: '01'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1111/jeb.13709
external_id:
isi:
- '000579599700001'
pmid:
- '33045123'
intvolume: ' 34'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/818559
month: '01'
oa: 1
oa_version: Preprint
page: 208-223
pmid: 1
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- '14209101'
issn:
- 1010061X
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '13073'
relation: research_data
status: public
scopus_import: '1'
status: public
title: How do species barriers decay? Concordance and local introgression in mosaic
hybrid zones of mussels
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 34
year: '2021'
...
---
_id: '8743'
abstract:
- lang: eng
text: 'Montane cloud forests are areas of high endemism, and are one of the more
vulnerable terrestrial ecosystems to climate change. Thus, understanding how they
both contribute to the generation of biodiversity, and will respond to ongoing
climate change, are important and related challenges. The widely accepted model
for montane cloud forest dynamics involves upslope forcing of their range limits
with global climate warming. However, limited climate data provides some support
for an alternative model, where range limits are forced downslope with climate
warming. Testing between these two models is challenging, due to the inherent
limitations of climate and pollen records. We overcome this with an alternative
source of historical information, testing between competing model predictions
using genomic data and demographic analyses for a species of beetle tightly associated
to an oceanic island cloud forest. Results unequivocally support the alternative
model: populations that were isolated at higher elevation peaks during the Last
Glacial Maximum are now in contact and hybridizing at lower elevations. Our results
suggest that genomic data are a rich source of information to further understand
how montane cloud forest biodiversity originates, and how it is likely to be impacted
by ongoing climate change.'
acknowledgement: 'This work was financed by the Spanish Agencia Estatal de Investigación
(CGL2017‐85718‐P), awarded to BCE, and co‐financed by FEDER. It was also supported
by the Spanish Ministerio de Ciencia, Innovación y Universidades (EQC2018‐004418‐P),
awarded to BCE. AS‐C was funded by the Spanish Ministerio de Ciencia, Innovación
y Universidades through an FPU PhD fellowship (FPU014/02948). The authors thank
Instituto Tecnológico y de Energías Renovables (ITER), S.A for providing access
to the Teide High‐Performance Computing facility (Teide‐HPC). Fieldwork was supported
by collecting permit AFF 107/17 (sigma number 2017‐00572) kindly provided by the
Cabildo of Tenerife. The authors wish to thank the following for field work and
sample sorting and identification: A. J. Pérez‐Delgado, H. López, and C. Andújar.
We also thank V. García‐Olivares for assistance with laboratory and bioinformatic
work.'
article_processing_charge: No
article_type: original
author:
- first_name: Antonia
full_name: Salces-Castellano, Antonia
last_name: Salces-Castellano
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Paula
full_name: Arribas, Paula
last_name: Arribas
- first_name: Jairo
full_name: Patino, Jairo
last_name: Patino
- first_name: 'Dirk N. '
full_name: 'Karger, Dirk N. '
last_name: Karger
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
- first_name: Brent C.
full_name: Emerson, Brent C.
last_name: Emerson
citation:
ama: Salces-Castellano A, Stankowski S, Arribas P, et al. Long-term cloud forest
response to climate warming revealed by insect speciation history. Evolution.
2021;75(2):231-244. doi:10.1111/evo.14111
apa: Salces-Castellano, A., Stankowski, S., Arribas, P., Patino, J., Karger, D.
N., Butlin, R., & Emerson, B. C. (2021). Long-term cloud forest response to
climate warming revealed by insect speciation history. Evolution. Wiley.
https://doi.org/10.1111/evo.14111
chicago: Salces-Castellano, Antonia, Sean Stankowski, Paula Arribas, Jairo Patino,
Dirk N. Karger, Roger Butlin, and Brent C. Emerson. “Long-Term Cloud Forest Response
to Climate Warming Revealed by Insect Speciation History.” Evolution. Wiley,
2021. https://doi.org/10.1111/evo.14111.
ieee: A. Salces-Castellano et al., “Long-term cloud forest response to climate
warming revealed by insect speciation history,” Evolution, vol. 75, no.
2. Wiley, pp. 231–244, 2021.
ista: Salces-Castellano A, Stankowski S, Arribas P, Patino J, Karger DN, Butlin
R, Emerson BC. 2021. Long-term cloud forest response to climate warming revealed
by insect speciation history. Evolution. 75(2), 231–244.
mla: Salces-Castellano, Antonia, et al. “Long-Term Cloud Forest Response to Climate
Warming Revealed by Insect Speciation History.” Evolution, vol. 75, no.
2, Wiley, 2021, pp. 231–44, doi:10.1111/evo.14111.
short: A. Salces-Castellano, S. Stankowski, P. Arribas, J. Patino, D.N. Karger,
R. Butlin, B.C. Emerson, Evolution 75 (2021) 231–244.
date_created: 2020-11-08T23:01:26Z
date_published: 2021-02-01T00:00:00Z
date_updated: 2023-08-04T11:09:49Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/evo.14111
external_id:
isi:
- '000583190600001'
pmid:
- '33078844'
intvolume: ' 75'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://hdl.handle.net/10261/223937
month: '02'
oa: 1
oa_version: Submitted Version
page: 231-244
pmid: 1
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1111/evo.14225
scopus_import: '1'
status: public
title: Long-term cloud forest response to climate warming revealed by insect speciation
history
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 75
year: '2021'
...
---
_id: '8928'
abstract:
- lang: eng
text: Domestication is a human‐induced selection process that imprints the genomes
of domesticated populations over a short evolutionary time scale and that occurs
in a given demographic context. Reconstructing historical gene flow, effective
population size changes and their timing is therefore of fundamental interest
to understand how plant demography and human selection jointly shape genomic divergence
during domestication. Yet, the comparison under a single statistical framework
of independent domestication histories across different crop species has been
little evaluated so far. Thus, it is unclear whether domestication leads to convergent
demographic changes that similarly affect crop genomes. To address this question,
we used existing and new transcriptome data on three crop species of Solanaceae
(eggplant, pepper and tomato), together with their close wild relatives. We fitted
twelve demographic models of increasing complexity on the unfolded joint allele
frequency spectrum for each wild/crop pair, and we found evidence for both shared
and species‐specific demographic processes between species. A convergent history
of domestication with gene flow was inferred for all three species, along with
evidence of strong reduction in the effective population size during the cultivation
stage of tomato and pepper. The absence of any reduction in size of the crop in
eggplant stands out from the classical view of the domestication process; as does
the existence of a “protracted period” of management before cultivation. Our results
also suggest divergent management strategies of modern cultivars among species
as their current demography substantially differs. Finally, the timing of domestication
is species‐specific and supported by the few historical records available.
acknowledgement: This work was supported by the EU Marie Curie Career Integration
grant (FP7‐PEOPLE‐2011‐CIG grant agreement PCIG10‐GA‐2011‐304164) attributed to
CS. SA was supported by a PhD fellowship from the French Région PACA and the Plant
Breeding division of INRA, in partnership with Gautier Semences. CF was supported
by an Austrian Science Foundation FWF grant (Project M 2463‐B29). Authors thank
Mathilde Causse and Beatriz Vicoso for their team leading. Thanks to the Italian
Eggplant Genome Consortium, which includes the DISAFA, Plant Genetics and Breeding
(University of Torino), the Biotechnology Department (University of Verona), the
CREA‐ORL in Montanaso Lombardo (LO) and the ENEA in Rome for providing access to
the eggplant genome reference. Thanks to CRB‐lég ( https://www6.paca.inra.fr/gafl_eng/Vegetables-GRC
) for managing and providing the genetic resources, to Marie‐Christine Daunay and
Alain Palloix (INRA UR1052) for assistance in choosing the biological material used,
to Muriel Latreille and Sylvain Santoni from the UMR AGAP (INRA Montpellier, France)
for their help with RNAseq library preparation, to Jean‐Paul Bouchet and Jacques
Lagnel (INRA UR1052) for their Bioinformatics assistance.
article_processing_charge: No
article_type: original
author:
- first_name: Stéphanie
full_name: Arnoux, Stéphanie
last_name: Arnoux
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Christopher
full_name: Sauvage, Christopher
last_name: Sauvage
citation:
ama: Arnoux S, Fraisse C, Sauvage C. Genomic inference of complex domestication
histories in three Solanaceae species. Journal of Evolutionary Biology.
2021;34(2):270-283. doi:10.1111/jeb.13723
apa: Arnoux, S., Fraisse, C., & Sauvage, C. (2021). Genomic inference of complex
domestication histories in three Solanaceae species. Journal of Evolutionary
Biology. Wiley. https://doi.org/10.1111/jeb.13723
chicago: Arnoux, Stéphanie, Christelle Fraisse, and Christopher Sauvage. “Genomic
Inference of Complex Domestication Histories in Three Solanaceae Species.” Journal
of Evolutionary Biology. Wiley, 2021. https://doi.org/10.1111/jeb.13723.
ieee: S. Arnoux, C. Fraisse, and C. Sauvage, “Genomic inference of complex domestication
histories in three Solanaceae species,” Journal of Evolutionary Biology,
vol. 34, no. 2. Wiley, pp. 270–283, 2021.
ista: Arnoux S, Fraisse C, Sauvage C. 2021. Genomic inference of complex domestication
histories in three Solanaceae species. Journal of Evolutionary Biology. 34(2),
270–283.
mla: Arnoux, Stéphanie, et al. “Genomic Inference of Complex Domestication Histories
in Three Solanaceae Species.” Journal of Evolutionary Biology, vol. 34,
no. 2, Wiley, 2021, pp. 270–83, doi:10.1111/jeb.13723.
short: S. Arnoux, C. Fraisse, C. Sauvage, Journal of Evolutionary Biology 34 (2021)
270–283.
date_created: 2020-12-06T23:01:16Z
date_published: 2021-02-01T00:00:00Z
date_updated: 2023-08-04T11:19:26Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/jeb.13723
external_id:
isi:
- '000587769700001'
pmid:
- '33107098'
intvolume: ' 34'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/jeb.13723
month: '02'
oa: 1
oa_version: Published Version
page: 270-283
pmid: 1
project:
- _id: 2662AADE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02463
name: Sex chromosomes and species barriers
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- '14209101'
issn:
- 1010061X
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '13065'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Genomic inference of complex domestication histories in three Solanaceae species
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 34
year: '2021'
...
---
_id: '9100'
abstract:
- lang: eng
text: 'Marine environments are inhabited by a broad representation of the tree of
life, yet our understanding of speciation in marine ecosystems is extremely limited
compared with terrestrial and freshwater environments. Developing a more comprehensive
picture of speciation in marine environments requires that we ''dive under the
surface'' by studying a wider range of taxa and ecosystems is necessary for a
more comprehensive picture of speciation. Although studying marine evolutionary
processes is often challenging, recent technological advances in different fields,
from maritime engineering to genomics, are making it increasingly possible to
study speciation of marine life forms across diverse ecosystems and taxa. Motivated
by recent research in the field, including the 14 contributions in this issue,
we highlight and discuss six axes of research that we think will deepen our understanding
of speciation in the marine realm: (a) study a broader range of marine environments
and organisms; (b) identify the reproductive barriers driving speciation between
marine taxa; (c) understand the role of different genomic architectures underlying
reproductive isolation; (d) infer the evolutionary history of divergence using
model‐based approaches; (e) study patterns of hybridization and introgression
between marine taxa; and (f) implement highly interdisciplinary, collaborative
research programmes. In outlining these goals, we hope to inspire researchers
to continue filling this critical knowledge gap surrounding the origins of marine
biodiversity.'
acknowledgement: "We would like to thank all the participants in the speciation symposium
of the Marine Evolution Conference in Sweden for the interesting discussions and
to all the contributors to this special\r\nissue. We thank Nicolas Bierne and Wolf
Blanckenhorn (reviewer and editor, respectively) for valuable suggestions during
the revision of the manuscript, and Roger K. Butlin and Anja M. Westram for very
helpful comments on a previous draft. We would also like to thank Wolf Blanckenhorn
and Nicola Cook, the Editor in Chief and the Managing Editor of the Journal of Evolutionary
Biology, respectively, for the encouragement and support in putting together this
special issue, and to all reviewers involved. RF was financed by the European Union's
Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie
Grant Agreement Number 706376 and is currently financed by the FEDER Funds through
the Operational Competitiveness Factors Program COMPETE and by National Funds through
the Foundation for Science and Technology (FCT) within the scope of the project
‘Hybrabbid' (PTDC/BIA-EVL/30628/2017-POCI-01-0145-FEDER-030628). KJ was funded by
the Swedish\r\nResearch Council, VR. SS was supported by NERC and ERC funding awarded
to Roger K. Butlin."
article_processing_charge: No
article_type: original
author:
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
citation:
ama: 'Faria R, Johannesson K, Stankowski S. Speciation in marine environments: Diving
under the surface. Journal of Evolutionary Biology. 2021;34(1):4-15. doi:10.1111/jeb.13756'
apa: 'Faria, R., Johannesson, K., & Stankowski, S. (2021). Speciation in marine
environments: Diving under the surface. Journal of Evolutionary Biology.
Wiley. https://doi.org/10.1111/jeb.13756'
chicago: 'Faria, Rui, Kerstin Johannesson, and Sean Stankowski. “Speciation in Marine
Environments: Diving under the Surface.” Journal of Evolutionary Biology.
Wiley, 2021. https://doi.org/10.1111/jeb.13756.'
ieee: 'R. Faria, K. Johannesson, and S. Stankowski, “Speciation in marine environments:
Diving under the surface,” Journal of Evolutionary Biology, vol. 34, no.
1. Wiley, pp. 4–15, 2021.'
ista: 'Faria R, Johannesson K, Stankowski S. 2021. Speciation in marine environments:
Diving under the surface. Journal of Evolutionary Biology. 34(1), 4–15.'
mla: 'Faria, Rui, et al. “Speciation in Marine Environments: Diving under the Surface.”
Journal of Evolutionary Biology, vol. 34, no. 1, Wiley, 2021, pp. 4–15,
doi:10.1111/jeb.13756.'
short: R. Faria, K. Johannesson, S. Stankowski, Journal of Evolutionary Biology
34 (2021) 4–15.
date_created: 2021-02-07T23:01:13Z
date_published: 2021-01-18T00:00:00Z
date_updated: 2023-08-07T13:42:08Z
day: '18'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/jeb.13756
external_id:
isi:
- '000608367500001'
file:
- access_level: open_access
checksum: 5755856a5368d4b4cdd6fad5ab27f4d1
content_type: application/pdf
creator: dernst
date_created: 2021-02-09T09:04:02Z
date_updated: 2021-02-09T09:04:02Z
file_id: '9108'
file_name: 2021_JourEvolBiology_Faria.pdf
file_size: 561340
relation: main_file
success: 1
file_date_updated: 2021-02-09T09:04:02Z
has_accepted_license: '1'
intvolume: ' 34'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 4-15
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- '14209101'
issn:
- 1010061X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Speciation in marine environments: Diving under the surface'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 34
year: '2021'
...
---
_id: '9168'
abstract:
- lang: eng
text: Interspecific crossing experiments have shown that sex chromosomes play a
major role in reproductive isolation between many pairs of species. However, their
ability to act as reproductive barriers, which hamper interspecific genetic exchange,
has rarely been evaluated quantitatively compared to Autosomes. This genome-wide
limitation of gene flow is essential for understanding the complete separation
of species, and thus speciation. Here, we develop a mainland-island model of secondary
contact between hybridizing species of an XY (or ZW) sexual system. We obtain
theoretical predictions for the frequency of introgressed alleles, and the strength
of the barrier to neutral gene flow for the two types of chromosomes carrying
multiple interspecific barrier loci. Theoretical predictions are obtained for
scenarios where introgressed alleles are rare. We show that the same analytical
expressions apply for sex chromosomes and autosomes, but with different sex-averaged
effective parameters. The specific features of sex chromosomes (hemizygosity and
absence of recombination in the heterogametic sex) lead to reduced levels of introgression
on the X (or Z) compared to autosomes. This effect can be enhanced by certain
types of sex-biased forces, but it remains overall small (except when alleles
causing incompatibilities are recessive). We discuss these predictions in the
light of empirical data comprising model-based tests of introgression and cline
surveys in various biological systems.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "The computations were performed with the IST Austria High-Performance
Computing (HPC) Cluster and the Institut Français de Bioinformatique (IFB) Core
Cluster. We are grateful to Nick Barton and Beatriz Vicoso for critical comments
on the model and the manuscript. We also thank Brian Charlesworth, Stuart Baird,
and an anonymous reviewer for insightful comments.\r\nC.F. was supported by an Austrian
Science Foundation FWF grant (Project M 2463-B29)."
article_number: iyaa025
article_processing_charge: No
article_type: original
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
citation:
ama: 'Fraisse C, Sachdeva H. The rates of introgression and barriers to genetic
exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics.
2021;217(2). doi:10.1093/genetics/iyaa025'
apa: 'Fraisse, C., & Sachdeva, H. (2021). The rates of introgression and barriers
to genetic exchange between hybridizing species: Sex chromosomes vs autosomes.
Genetics. Genetics Society of America. https://doi.org/10.1093/genetics/iyaa025'
chicago: 'Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression
and Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes
vs Autosomes.” Genetics. Genetics Society of America, 2021. https://doi.org/10.1093/genetics/iyaa025.'
ieee: 'C. Fraisse and H. Sachdeva, “The rates of introgression and barriers to genetic
exchange between hybridizing species: Sex chromosomes vs autosomes,” Genetics,
vol. 217, no. 2. Genetics Society of America, 2021.'
ista: 'Fraisse C, Sachdeva H. 2021. The rates of introgression and barriers to genetic
exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics.
217(2), iyaa025.'
mla: 'Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression and
Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes vs Autosomes.”
Genetics, vol. 217, no. 2, iyaa025, Genetics Society of America, 2021,
doi:10.1093/genetics/iyaa025.'
short: C. Fraisse, H. Sachdeva, Genetics 217 (2021).
date_created: 2021-02-18T14:41:30Z
date_published: 2021-02-01T00:00:00Z
date_updated: 2023-08-07T13:47:01Z
day: '01'
department:
- _id: NiBa
doi: 10.1093/genetics/iyaa025
external_id:
isi:
- '000637218100005'
intvolume: ' 217'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/genetics/iyaa025
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 2662AADE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02463
name: Sex chromosomes and species barriers
publication: Genetics
publication_identifier:
issn:
- 1943-2631
publication_status: published
publisher: Genetics Society of America
quality_controlled: '1'
status: public
title: 'The rates of introgression and barriers to genetic exchange between hybridizing
species: Sex chromosomes vs autosomes'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 217
year: '2021'
...
---
_id: '9119'
abstract:
- lang: eng
text: 'We present DILS, a deployable statistical analysis platform for conducting
demographic inferences with linked selection from population genomic data using
an Approximate Bayesian Computation framework. DILS takes as input single‐population
or two‐population data sets (multilocus fasta sequences) and performs three types
of analyses in a hierarchical manner, identifying: (a) the best demographic model
to study the importance of gene flow and population size change on the genetic
patterns of polymorphism and divergence, (b) the best genomic model to determine
whether the effective size Ne and migration rate N, m are heterogeneously distributed
along the genome (implying linked selection) and (c) loci in genomic regions most
associated with barriers to gene flow. Also available via a Web interface, an
objective of DILS is to facilitate collaborative research in speciation genomics.
Here, we show the performance and limitations of DILS by using simulations and
finally apply the method to published data on a divergence continuum composed
by 28 pairs of Mytilus mussel populations/species.'
article_processing_charge: No
article_type: original
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Iva
full_name: Popovic, Iva
last_name: Popovic
- first_name: Clément
full_name: Mazoyer, Clément
last_name: Mazoyer
- first_name: Bruno
full_name: Spataro, Bruno
last_name: Spataro
- first_name: Stéphane
full_name: Delmotte, Stéphane
last_name: Delmotte
- first_name: Jonathan
full_name: Romiguier, Jonathan
last_name: Romiguier
- first_name: Étienne
full_name: Loire, Étienne
last_name: Loire
- first_name: Alexis
full_name: Simon, Alexis
last_name: Simon
- first_name: Nicolas
full_name: Galtier, Nicolas
last_name: Galtier
- first_name: Laurent
full_name: Duret, Laurent
last_name: Duret
- first_name: Nicolas
full_name: Bierne, Nicolas
last_name: Bierne
- first_name: Xavier
full_name: Vekemans, Xavier
last_name: Vekemans
- first_name: Camille
full_name: Roux, Camille
last_name: Roux
citation:
ama: 'Fraisse C, Popovic I, Mazoyer C, et al. DILS: Demographic inferences with
linked selection by using ABC. Molecular Ecology Resources. 2021;21:2629-2644.
doi:10.1111/1755-0998.13323'
apa: 'Fraisse, C., Popovic, I., Mazoyer, C., Spataro, B., Delmotte, S., Romiguier,
J., … Roux, C. (2021). DILS: Demographic inferences with linked selection by using
ABC. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.13323'
chicago: 'Fraisse, Christelle, Iva Popovic, Clément Mazoyer, Bruno Spataro, Stéphane
Delmotte, Jonathan Romiguier, Étienne Loire, et al. “DILS: Demographic Inferences
with Linked Selection by Using ABC.” Molecular Ecology Resources. Wiley,
2021. https://doi.org/10.1111/1755-0998.13323.'
ieee: 'C. Fraisse et al., “DILS: Demographic inferences with linked selection
by using ABC,” Molecular Ecology Resources, vol. 21. Wiley, pp. 2629–2644,
2021.'
ista: 'Fraisse C, Popovic I, Mazoyer C, Spataro B, Delmotte S, Romiguier J, Loire
É, Simon A, Galtier N, Duret L, Bierne N, Vekemans X, Roux C. 2021. DILS: Demographic
inferences with linked selection by using ABC. Molecular Ecology Resources. 21,
2629–2644.'
mla: 'Fraisse, Christelle, et al. “DILS: Demographic Inferences with Linked Selection
by Using ABC.” Molecular Ecology Resources, vol. 21, Wiley, 2021, pp. 2629–44,
doi:10.1111/1755-0998.13323.'
short: C. Fraisse, I. Popovic, C. Mazoyer, B. Spataro, S. Delmotte, J. Romiguier,
É. Loire, A. Simon, N. Galtier, L. Duret, N. Bierne, X. Vekemans, C. Roux, Molecular
Ecology Resources 21 (2021) 2629–2644.
date_created: 2021-02-14T23:01:14Z
date_published: 2021-01-15T00:00:00Z
date_updated: 2023-08-07T13:45:18Z
day: '15'
department:
- _id: NiBa
doi: 10.1111/1755-0998.13323
external_id:
isi:
- '000614183100001'
intvolume: ' 21'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2020.06.15.151597v2
month: '01'
oa: 1
oa_version: Preprint
page: 2629-2644
publication: Molecular Ecology Resources
publication_identifier:
eissn:
- '17550998'
issn:
- 1755098X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'DILS: Demographic inferences with linked selection by using ABC'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 21
year: '2021'
...
---
_id: '9375'
abstract:
- lang: eng
text: Genetic variation segregates as linked sets of variants, or haplotypes. Haplotypes
and linkage are central to genetics and underpin virtually all genetic and selection
analysis. And yet, genomic data often lack haplotype information, due to constraints
in sequencing technologies. Here we present “haplotagging”, a simple, low-cost
linked-read sequencing technique that allows sequencing of hundreds of individuals
while retaining linkage information. We apply haplotagging to construct megabase-size
haplotypes for over 600 individual butterflies (Heliconius erato and H. melpomene),
which form overlapping hybrid zones across an elevational gradient in Ecuador.
Haplotagging identifies loci controlling distinctive high- and lowland wing color
patterns. Divergent haplotypes are found at the same major loci in both species,
while chromosome rearrangements show no parallelism. Remarkably, in both species
the geographic clines for the major wing pattern loci are displaced by 18 km,
leading to the rise of a novel hybrid morph in the centre of the hybrid zone.
We propose that shared warning signalling (Müllerian mimicry) may couple the cline
shifts seen in both species, and facilitate the parallel co-emergence of a novel
hybrid morph in both co-mimetic species. Our results show the power of efficient
haplotyping methods when combined with large-scale sequencing data from natural
populations.
acknowledgement: 'We thank Felicity Jones for input into experimental design, helpful
discussion and improving the manuscript. We thank the Rolian, Jiggins, Chan and
Jones Labs members for support, insightful scientific discussion and improving the
manuscript. We thank the Rolian lab members, the Animal Resource Centre staff at
the University of Calgary, and Caroline Schmid and Ann-Katrin Geysel at the Friedrich
Miescher Laboratory for animal husbandry. We thank Christa Lanz, Rebecca Schwab
and Ilja Bezrukov for assistance with high-throughput sequencing and associated
data processing; Andre Noll and the MPI Tübingen IT team for computational support.
We thank Ben Haller and Richard Durbin for helpful discussions. We thank David M.
Kingsley for thoughtful input that has greatly improved our manuscript. J.I.M. is
supported by a Research Fellowship from St. John’s College, Cambridge. A.D. was
supported by a European Research Council Consolidator Grant (No. 617279 “EvolRecombAdapt”,
P/I Felicity Jones). C.R. is supported by Discovery Grant #4181932 from the Natural
Sciences and Engineering Research Council of Canada and by the Faculty of Veterinary
Medicine at the University of Calgary. C.D.J. is supported by a BBSRC grant BB/R007500
and a European Research Council Advanced Grant (No. 339873 “SpeciationGenetics”).
M.K. and Y.F.C. are supported by the Max Planck Society and a European Research
Council Starting Grant (No. 639096 “HybridMiX”).'
article_number: e2015005118
article_processing_charge: No
article_type: original
author:
- first_name: Joana I.
full_name: Meier, Joana I.
last_name: Meier
- first_name: Patricio A.
full_name: Salazar, Patricio A.
last_name: Salazar
- first_name: Marek
full_name: Kučka, Marek
last_name: Kučka
- first_name: Robert William
full_name: Davies, Robert William
last_name: Davies
- first_name: Andreea
full_name: Dréau, Andreea
last_name: Dréau
- first_name: Ismael
full_name: Aldás, Ismael
last_name: Aldás
- first_name: Olivia Box
full_name: Power, Olivia Box
last_name: Power
- first_name: Nicola J.
full_name: Nadeau, Nicola J.
last_name: Nadeau
- first_name: Jon R.
full_name: Bridle, Jon R.
last_name: Bridle
- first_name: Campbell
full_name: Rolian, Campbell
last_name: Rolian
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: W. Owen
full_name: McMillan, W. Owen
last_name: McMillan
- first_name: Chris D.
full_name: Jiggins, Chris D.
last_name: Jiggins
- first_name: Yingguang Frank
full_name: Chan, Yingguang Frank
last_name: Chan
citation:
ama: Meier JI, Salazar PA, Kučka M, et al. Haplotype tagging reveals parallel formation
of hybrid races in two butterfly species. PNAS. 2021;118(25). doi:10.1073/pnas.2015005118
apa: Meier, J. I., Salazar, P. A., Kučka, M., Davies, R. W., Dréau, A., Aldás, I.,
… Chan, Y. F. (2021). Haplotype tagging reveals parallel formation of hybrid races
in two butterfly species. PNAS. Proceedings of the National Academy of
Sciences. https://doi.org/10.1073/pnas.2015005118
chicago: Meier, Joana I., Patricio A. Salazar, Marek Kučka, Robert William Davies,
Andreea Dréau, Ismael Aldás, Olivia Box Power, et al. “Haplotype Tagging Reveals
Parallel Formation of Hybrid Races in Two Butterfly Species.” PNAS. Proceedings
of the National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2015005118.
ieee: J. I. Meier et al., “Haplotype tagging reveals parallel formation of
hybrid races in two butterfly species,” PNAS, vol. 118, no. 25. Proceedings
of the National Academy of Sciences, 2021.
ista: Meier JI, Salazar PA, Kučka M, Davies RW, Dréau A, Aldás I, Power OB, Nadeau
NJ, Bridle JR, Rolian C, Barton NH, McMillan WO, Jiggins CD, Chan YF. 2021. Haplotype
tagging reveals parallel formation of hybrid races in two butterfly species. PNAS.
118(25), e2015005118.
mla: Meier, Joana I., et al. “Haplotype Tagging Reveals Parallel Formation of Hybrid
Races in Two Butterfly Species.” PNAS, vol. 118, no. 25, e2015005118, Proceedings
of the National Academy of Sciences, 2021, doi:10.1073/pnas.2015005118.
short: J.I. Meier, P.A. Salazar, M. Kučka, R.W. Davies, A. Dréau, I. Aldás, O.B.
Power, N.J. Nadeau, J.R. Bridle, C. Rolian, N.H. Barton, W.O. McMillan, C.D. Jiggins,
Y.F. Chan, PNAS 118 (2021).
date_created: 2021-05-07T17:10:21Z
date_published: 2021-06-21T00:00:00Z
date_updated: 2023-08-08T13:33:09Z
day: '21'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1073/pnas.2015005118
external_id:
isi:
- '000671755600001'
pmid:
- '34155138'
file:
- access_level: open_access
checksum: cb30c6166b2132ee60d616b31a1a7c29
content_type: application/pdf
creator: dernst
date_created: 2022-03-08T08:18:16Z
date_updated: 2022-03-08T08:18:16Z
file_id: '10835'
file_name: 2021_PNAS_Meier.pdf
file_size: 20592929
relation: main_file
success: 1
file_date_updated: 2022-03-08T08:18:16Z
has_accepted_license: '1'
intvolume: ' 118'
isi: 1
issue: '25'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: PNAS
publication_identifier:
eissn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Haplotype tagging reveals parallel formation of hybrid races in two butterfly
species
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 118
year: '2021'
...