---
_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
day: '15'
ddc:
- '570'
department:
- _id: GradSch
- _id: NiBa
- _id: BeVi
doi: 10.15479/AT:ISTA:12933
file:
- access_level: open_access
checksum: 0ba0bcd0bb8b18d84792136a4370df90
content_type: text/csv
creator: gpuixeus
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date_updated: 2023-05-10T09:41:43Z
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file_size: 8029982
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creator: gpuixeus
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content_type: text/csv
creator: gpuixeus
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date_updated: 2023-05-11T12:50:18Z
file_id: '12944'
file_name: readme.txt
file_size: 4566
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file_date_updated: 2023-05-11T12:50:18Z
has_accepted_license: '1'
license: https://creativecommons.org/licenses/by/4.0/
month: '05'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '14058'
relation: used_in_publication
status: public
- id: '14077'
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:
- access_level: open_access
checksum: 520bdb61e95e66070e02824947d2c5fa
content_type: application/pdf
creator: larathoo
date_created: 2023-12-13T15:37:55Z
date_updated: 2023-12-13T15:37:55Z
file_id: '14684'
file_name: Phd_Thesis_LA.pdf
file_size: 34101468
relation: main_file
success: 1
- access_level: closed
checksum: d8e59afd0817c98fba2564a264508e5c
content_type: application/zip
creator: larathoo
date_created: 2023-12-13T15:42:23Z
date_updated: 2023-12-14T08:58:18Z
file_id: '14685'
file_name: Phd_Thesis_LA.zip
file_size: 31052872
relation: source_file
- access_level: closed
checksum: 9a778c949932286f4519e1f1fca2820d
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:
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checksum: ba6f9102d3a9fe6631c4fa398c5e4313
content_type: application/pdf
creator: dernst
date_created: 2024-01-23T08:10:00Z
date_updated: 2024-01-23T08:10:00Z
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file_size: 3408944
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success: 1
file_date_updated: 2024-01-23T08:10:00Z
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month: '08'
oa: 1
oa_version: Published Version
publication: Evolutionary Journal of the Linnean Society
publication_identifier:
eissn:
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publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
status: public
title: Whole-genome phylogeography of the intertidal snail Littorina saxatilis
tmp:
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type: journal_article
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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:
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relation: dissertation_contains
status: public
status: public
title: Genetic load, eco-evolutionary feedback and extinction in a metapopulation
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legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
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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:
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url: https://doi.org/10.5281/zenodo.8318995
month: '09'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
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relation: used_in_publication
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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
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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
- _id: NiBa
doi: 10.15479/at:ista:12800
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file_size: 1741364
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has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
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:
- '570'
department:
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doi: 10.1073/pnas.2122147119
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