---
_id: '6858'
article_processing_charge: No
article_type: review
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. Is speciation driven by cycles of mixing and isolation? National
Science Review. 2019;6(2):291-292. doi:10.1093/nsr/nwy113
apa: Barton, N. H. (2019). Is speciation driven by cycles of mixing and isolation?
National Science Review. Oxford University Press. https://doi.org/10.1093/nsr/nwy113
chicago: Barton, Nicholas H. “Is Speciation Driven by Cycles of Mixing and Isolation?”
National Science Review. Oxford University Press, 2019. https://doi.org/10.1093/nsr/nwy113.
ieee: N. H. Barton, “Is speciation driven by cycles of mixing and isolation?,” National
Science Review, vol. 6, no. 2. Oxford University Press, pp. 291–292, 2019.
ista: Barton NH. 2019. Is speciation driven by cycles of mixing and isolation? National
Science Review. 6(2), 291–292.
mla: Barton, Nicholas H. “Is Speciation Driven by Cycles of Mixing and Isolation?”
National Science Review, vol. 6, no. 2, Oxford University Press, 2019,
pp. 291–92, doi:10.1093/nsr/nwy113.
short: N.H. Barton, National Science Review 6 (2019) 291–292.
date_created: 2019-09-07T14:43:02Z
date_published: 2019-03-01T00:00:00Z
date_updated: 2023-08-29T07:51:09Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/nsr/nwy113
external_id:
isi:
- '000467957400025'
file:
- access_level: open_access
checksum: 571d60fa21a568607d1fd04e119da88c
content_type: application/pdf
creator: dernst
date_created: 2020-10-02T09:16:44Z
date_updated: 2020-10-02T09:16:44Z
file_id: '8595'
file_name: 2019_NSR_Barton.pdf
file_size: 106463
relation: main_file
success: 1
file_date_updated: 2020-10-02T09:16:44Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
issue: '2'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '03'
oa: 1
oa_version: Published Version
page: 291-292
publication: National Science Review
publication_identifier:
eissn:
- 2053-714X
issn:
- 2095-5138
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Is speciation driven by cycles of mixing and 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: 6
year: '2019'
...
---
_id: '6857'
abstract:
- lang: eng
text: "Gene Drives are regarded as future tools with a high potential for population
control. Due to their inherent ability to overcome the rules of Mendelian inheritance,
gene drives (GD) may spread genes rapidly through populations of sexually reproducing
organisms. A release of organisms carrying a GD would constitute a paradigm shift
in the handling of genetically modified organisms because gene drive organisms
(GDO) are designed to drive their transgenes into wild populations and thereby
increase the number of GDOs. The rapid development in this field and its focus
on wild populations demand a prospective risk assessment with a focus on exposure
related aspects. Presently, it is unclear how adequate risk management could be
guaranteed to limit the spread of GDs in time and space, in order to avoid potential
adverse effects in socio‐ecological systems.\r\n\r\nThe recent workshop on the
“Evaluation of Spatial and Temporal Control of Gene Drives” hosted by the Institute
of Safety/Security and Risk Sciences (ISR) in Vienna aimed at gaining some insight
into the potential population dynamic behavior of GDs and appropriate measures
of control. Scientists from France, Germany, England, and the USA discussed both
topics in this meeting on April 4–5, 2019. This article summarizes results of
the workshop."
article_number: '1900151'
article_processing_charge: No
article_type: original
author:
- first_name: B
full_name: Giese, B
last_name: Giese
- first_name: J L
full_name: Friess, J L
last_name: Friess
- first_name: 'M F '
full_name: 'Schetelig, M F '
last_name: Schetelig
- 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: Philip
full_name: Messer, Philip
last_name: Messer
- first_name: Florence
full_name: Debarre, Florence
last_name: Debarre
- first_name: H
full_name: Meimberg, H
last_name: Meimberg
- first_name: N
full_name: Windbichler, N
last_name: Windbichler
- first_name: C
full_name: Boete, C
last_name: Boete
citation:
ama: 'Giese B, Friess JL, Schetelig MF, et al. Gene Drives: Dynamics and regulatory
matters – A report from the workshop “Evaluation of spatial and temporal control
of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 2019;41(11). doi:10.1002/bies.201900151'
apa: 'Giese, B., Friess, J. L., Schetelig, M. F., Barton, N. H., Messer, P., Debarre,
F., … Boete, C. (2019). Gene Drives: Dynamics and regulatory matters – A report
from the workshop “Evaluation of spatial and temporal control of Gene Drives”,
4 – 5 April 2019, Vienna. BioEssays. Wiley. https://doi.org/10.1002/bies.201900151'
chicago: 'Giese, B, J L Friess, M F Schetelig, Nicholas H Barton, Philip Messer,
Florence Debarre, H Meimberg, N Windbichler, and C Boete. “Gene Drives: Dynamics
and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and
Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” BioEssays.
Wiley, 2019. https://doi.org/10.1002/bies.201900151.'
ieee: 'B. Giese et al., “Gene Drives: Dynamics and regulatory matters – A
report from the workshop ‘Evaluation of spatial and temporal control of Gene Drives’,
4 – 5 April 2019, Vienna,” BioEssays, vol. 41, no. 11. Wiley, 2019.'
ista: 'Giese B, Friess JL, Schetelig MF, Barton NH, Messer P, Debarre F, Meimberg
H, Windbichler N, Boete C. 2019. Gene Drives: Dynamics and regulatory matters
– A report from the workshop “Evaluation of spatial and temporal control of Gene
Drives”, 4 – 5 April 2019, Vienna. BioEssays. 41(11), 1900151.'
mla: 'Giese, B., et al. “Gene Drives: Dynamics and Regulatory Matters – A Report
from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’,
4 – 5 April 2019, Vienna.” BioEssays, vol. 41, no. 11, 1900151, Wiley,
2019, doi:10.1002/bies.201900151.'
short: B. Giese, J.L. Friess, M.F. Schetelig, N.H. Barton, P. Messer, F. Debarre,
H. Meimberg, N. Windbichler, C. Boete, BioEssays 41 (2019).
date_created: 2019-09-07T14:40:03Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-08-30T06:56:26Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1002/bies.201900151
external_id:
isi:
- '000489502000001'
file:
- access_level: open_access
checksum: 8cc7551bff70b2658f8d5630f228ee12
content_type: application/pdf
creator: dernst
date_created: 2019-10-11T06:59:26Z
date_updated: 2020-07-14T12:47:42Z
file_id: '6939'
file_name: 2019_BioEssays_Giese.pdf
file_size: 193248
relation: main_file
file_date_updated: 2020-07-14T12:47:42Z
has_accepted_license: '1'
intvolume: ' 41'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: BioEssays
publication_identifier:
eissn:
- 1521-1878
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Gene Drives: Dynamics and regulatory matters – A report from the workshop
“Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna'
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: 41
year: '2019'
...
---
_id: '13067'
abstract:
- lang: eng
text: Genetic incompatibilities contribute to reproductive isolation between many
diverging populations, but it is still unclear to what extent they play a role
if divergence happens with gene flow. In contact zones between the "Crab" and
"Wave" ecotypes of the snail Littorina saxatilis divergent selection forms strong
barriers to gene flow, while the role of postzygotic barriers due to selection
against hybrids remains unclear. High embryo abortion rates in this species could
indicate the presence of such barriers. Postzygotic barriers might include genetic
incompatibilities (e.g. Dobzhansky-Muller incompatibilities) but also maladaptation,
both expected to be most pronounced in contact zones. In addition, embryo abortion
might reflect physiological stress on females and embryos independent of any genetic
stress. We examined all embryos of >500 females sampled outside and inside
contact zones of three populations in Sweden. Females' clutch size ranged from
0 to 1011 embryos (mean 130±123) and abortion rates varied between 0 and100% (mean
12%). We described female genotypes by using a hybrid index based on hundreds
of SNPs differentiated between ecotypes with which we characterised female genotypes.
We also calculated female SNP heterozygosity and inversion karyotype. Clutch size
did not vary with female hybrid index and abortion rates were only weakly related
to hybrid index in two sites but not at all in a third site. No additional variation
in abortion rate was explained by female SNP heterozygosity, but increased female
inversion heterozygosity added slightly to increased abortion. Our results show
only weak and probably biologically insignificant postzygotic barriers contributing
to ecotype divergence and the high and variable abortion rates were marginally,
if at all, explained by hybrid index of females.
article_processing_charge: No
author:
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Zuzanna
full_name: Zagrodzka, Zuzanna
last_name: Zagrodzka
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- 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: 'Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. Data from: Is embryo
abortion a postzygotic barrier to gene flow between Littorina ecotypes? 2019.
doi:10.5061/DRYAD.TB2RBNZWK'
apa: 'Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R.
(2019). Data from: Is embryo abortion a postzygotic barrier to gene flow between
Littorina ecotypes? Dryad. https://doi.org/10.5061/DRYAD.TB2RBNZWK'
chicago: 'Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and
Roger Butlin. “Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow
between Littorina Ecotypes?” Dryad, 2019. https://doi.org/10.5061/DRYAD.TB2RBNZWK.'
ieee: 'K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. Butlin, “Data
from: Is embryo abortion a postzygotic barrier to gene flow between Littorina
ecotypes?” Dryad, 2019.'
ista: 'Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. 2019. Data from:
Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?,
Dryad, 10.5061/DRYAD.TB2RBNZWK.'
mla: 'Johannesson, Kerstin, et al. Data from: Is Embryo Abortion a Postzygotic
Barrier to Gene Flow between Littorina Ecotypes? Dryad, 2019, doi:10.5061/DRYAD.TB2RBNZWK.'
short: K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R. Butlin, (2019).
date_created: 2023-05-23T16:36:27Z
date_published: 2019-12-02T00:00:00Z
date_updated: 2023-09-06T14:48:57Z
day: '02'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5061/DRYAD.TB2RBNZWK
license: https://creativecommons.org/publicdomain/zero/1.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.tb2rbnzwk
month: '12'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '7205'
relation: used_in_publication
status: public
status: public
title: 'Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina
ecotypes?'
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: '2019'
...
---
_id: '7393'
abstract:
- lang: eng
text: The study of parallel ecological divergence provides important clues to the
operation of natural selection. Parallel divergence often occurs in heterogeneous
environments with different kinds of environmental gradients in different locations,
but the genomic basis underlying this process is unknown. We investigated the
genomics of rapid parallel adaptation in the marine snail Littorina saxatilis
in response to two independent environmental axes (crab-predation versus wave-action
and low-shore versus high-shore). Using pooled whole-genome resequencing, we show
that sharing of genomic regions of high differentiation between environments is
generally low but increases at smaller spatial scales. We identify different shared
genomic regions of divergence for each environmental axis and show that most of
these regions overlap with candidate chromosomal inversions. Several inversion
regions are divergent and polymorphic across many localities. We argue that chromosomal
inversions could store shared variation that fuels rapid parallel adaptation to
heterogeneous environments, possibly as balanced polymorphism shared by adaptive
gene flow.
article_number: eaav9963
article_processing_charge: No
article_type: original
author:
- first_name: Hernán E.
full_name: Morales, Hernán E.
last_name: Morales
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Tomas
full_name: Larsson, Tomas
last_name: Larsson
- first_name: Marina
full_name: Panova, Marina
last_name: Panova
- 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
citation:
ama: 'Morales HE, Faria R, Johannesson K, et al. Genomic architecture of parallel
ecological divergence: Beyond a single environmental contrast. Science Advances.
2019;5(12). doi:10.1126/sciadv.aav9963'
apa: 'Morales, H. E., Faria, R., Johannesson, K., Larsson, T., Panova, M., Westram,
A. M., & Butlin, R. K. (2019). Genomic architecture of parallel ecological
divergence: Beyond a single environmental contrast. Science Advances. AAAS.
https://doi.org/10.1126/sciadv.aav9963'
chicago: 'Morales, Hernán E., Rui Faria, Kerstin Johannesson, Tomas Larsson, Marina
Panova, Anja M Westram, and Roger K. Butlin. “Genomic Architecture of Parallel
Ecological Divergence: Beyond a Single Environmental Contrast.” Science Advances.
AAAS, 2019. https://doi.org/10.1126/sciadv.aav9963.'
ieee: 'H. E. Morales et al., “Genomic architecture of parallel ecological
divergence: Beyond a single environmental contrast,” Science Advances,
vol. 5, no. 12. AAAS, 2019.'
ista: 'Morales HE, Faria R, Johannesson K, Larsson T, Panova M, Westram AM, Butlin
RK. 2019. Genomic architecture of parallel ecological divergence: Beyond a single
environmental contrast. Science Advances. 5(12), eaav9963.'
mla: 'Morales, Hernán E., et al. “Genomic Architecture of Parallel Ecological Divergence:
Beyond a Single Environmental Contrast.” Science Advances, vol. 5, no.
12, eaav9963, AAAS, 2019, doi:10.1126/sciadv.aav9963.'
short: H.E. Morales, R. Faria, K. Johannesson, T. Larsson, M. Panova, A.M. Westram,
R.K. Butlin, Science Advances 5 (2019).
date_created: 2020-01-29T15:58:27Z
date_published: 2019-12-04T00:00:00Z
date_updated: 2023-09-06T15:35:56Z
day: '04'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1126/sciadv.aav9963
ec_funded: 1
external_id:
isi:
- '000505069600008'
pmid:
- '31840052'
file:
- access_level: open_access
checksum: af99a5dcdc66c6d6102051faf3be48d8
content_type: application/pdf
creator: dernst
date_created: 2020-02-03T13:33:25Z
date_updated: 2020-07-14T12:47:57Z
file_id: '7442'
file_name: 2019_ScienceAdvances_Morales.pdf
file_size: 1869449
relation: main_file
file_date_updated: 2020-07-14T12:47:57Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '12'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 265B41B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '797747'
name: Theoretical and empirical approaches to understanding Parallel Adaptation
publication: Science Advances
publication_identifier:
issn:
- 2375-2548
publication_status: published
publisher: AAAS
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Genomic architecture of parallel ecological divergence: Beyond a single environmental
contrast'
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 5
year: '2019'
...
---
_id: '8281'
abstract:
- lang: eng
text: We review the history of population genetics, starting with its origins a
century ago from the synthesis between Mendel and Darwin's ideas, through to the
recent development of sophisticated schemes of inference from sequence data, based
on the coalescent. We explain the close relation between the coalescent and a
diffusion process, which we illustrate by their application to understand spatial
structure. We summarise the powerful methods available for analysis of multiple
loci, when linkage equilibrium can be assumed, and then discuss approaches to
the more challenging case, where associations between alleles require that we
follow genotype, rather than allele, frequencies. Though we can hardly cover the
whole of population genetics, we give an overview of the current state of the
subject, and future challenges to it.
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
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
citation:
ama: 'Barton NH, Etheridge A. Mathematical models in population genetics. In: Balding
D, Moltke I, Marioni J, eds. Handbook of Statistical Genomics. 4th ed.
Wiley; 2019:115-144. doi:10.1002/9781119487845.ch4'
apa: Barton, N. H., & Etheridge, A. (2019). Mathematical models in population
genetics. In D. Balding, I. Moltke, & J. Marioni (Eds.), Handbook of statistical
genomics (4th ed., pp. 115–144). Wiley. https://doi.org/10.1002/9781119487845.ch4
chicago: Barton, Nicholas H, and Alison Etheridge. “Mathematical Models in Population
Genetics.” In Handbook of Statistical Genomics, edited by David Balding,
Ida Moltke, and John Marioni, 4th ed., 115–44. Wiley, 2019. https://doi.org/10.1002/9781119487845.ch4.
ieee: N. H. Barton and A. Etheridge, “Mathematical models in population genetics,”
in Handbook of statistical genomics, 4th ed., D. Balding, I. Moltke, and
J. Marioni, Eds. Wiley, 2019, pp. 115–144.
ista: 'Barton NH, Etheridge A. 2019.Mathematical models in population genetics.
In: Handbook of statistical genomics. , 115–144.'
mla: Barton, Nicholas H., and Alison Etheridge. “Mathematical Models in Population
Genetics.” Handbook of Statistical Genomics, edited by David Balding et
al., 4th ed., Wiley, 2019, pp. 115–44, doi:10.1002/9781119487845.ch4.
short: N.H. Barton, A. Etheridge, in:, D. Balding, I. Moltke, J. Marioni (Eds.),
Handbook of Statistical Genomics, 4th ed., Wiley, 2019, pp. 115–144.
date_created: 2020-08-21T04:25:39Z
date_published: 2019-07-29T00:00:00Z
date_updated: 2023-09-08T11:24:15Z
day: '29'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1002/9781119487845.ch4
edition: '4'
editor:
- first_name: David
full_name: Balding, David
last_name: Balding
- first_name: Ida
full_name: Moltke, Ida
last_name: Moltke
- first_name: John
full_name: Marioni, John
last_name: Marioni
external_id:
isi:
- '000261343000003'
isi: 1
language:
- iso: eng
month: '07'
oa_version: None
page: 115-144
publication: Handbook of statistical genomics
publication_identifier:
isbn:
- '9781119429142'
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Mathematical models in population genetics
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '9805'
abstract:
- lang: eng
text: The spread of adaptive alleles is fundamental to evolution, and in theory,
this process is well‐understood. However, only rarely can we follow this process—whether
it originates from the spread of a new mutation, or by introgression from another
population. In this issue of Molecular Ecology, Hanemaaijer et al. (2018) report
on a 25‐year long study of the mosquitoes Anopheles gambiae (Figure 1) and Anopheles
coluzzi in Mali, based on genotypes at 15 single‐nucleotide polymorphism (SNP).
The species are usually reproductively isolated from each other, but in 2002 and
2006, bursts of hybridization were observed, when F1 hybrids became abundant.
Alleles backcrossed from A. gambiae into A. coluzzi, but after the first event,
these declined over the following years. In contrast, after 2006, an insecticide
resistance allele that had established in A. gambiae spread into A. coluzzi, and
rose to high frequency there, over 6 years (~75 generations). Whole genome sequences
of 74 individuals showed that A. gambiae SNP from across the genome had become
common in the A. coluzzi population, but that most of these were clustered in
34 genes around the resistance locus. A new set of SNP from 25 of these genes
were assayed over time; over the 4 years since near‐fixation of the resistance
allele; some remained common, whereas others declined. What do these patterns
tell us about this introgression event?
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. Data from: The consequences of an introgression event. 2019. doi:10.5061/dryad.2kb6fh4'
apa: 'Barton, N. H. (2019). Data from: The consequences of an introgression event.
Dryad. https://doi.org/10.5061/dryad.2kb6fh4'
chicago: 'Barton, Nicholas H. “Data from: The Consequences of an Introgression Event.”
Dryad, 2019. https://doi.org/10.5061/dryad.2kb6fh4.'
ieee: 'N. H. Barton, “Data from: The consequences of an introgression event.” Dryad,
2019.'
ista: 'Barton NH. 2019. Data from: The consequences of an introgression event, Dryad,
10.5061/dryad.2kb6fh4.'
mla: 'Barton, Nicholas H. Data from: The Consequences of an Introgression Event.
Dryad, 2019, doi:10.5061/dryad.2kb6fh4.'
short: N.H. Barton, (2019).
date_created: 2021-08-06T12:03:50Z
date_published: 2019-01-09T00:00:00Z
date_updated: 2023-09-19T10:06:07Z
day: '09'
department:
- _id: NiBa
doi: 10.5061/dryad.2kb6fh4
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.2kb6fh4
month: '01'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '40'
relation: used_in_publication
status: public
status: public
title: 'Data from: The consequences of an introgression event'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '6071'
abstract:
- lang: eng
text: 'Transcription factors, by binding to specific sequences on the DNA, control
the precise spatio-temporal expression of genes inside a cell. However, this specificity
is limited, leading to frequent incorrect binding of transcription factors that
might have deleterious consequences on the cell. By constructing a biophysical
model of TF-DNA binding in the context of gene regulation, I will first explore
how regulatory constraints can strongly shape the distribution of a population
in sequence space. Then, by directly linking this to a picture of multiple types
of transcription factors performing their functions simultaneously inside the
cell, I will explore the extent of regulatory crosstalk -- incorrect binding interactions
between transcription factors and binding sites that lead to erroneous regulatory
states -- and understand the constraints this places on the design of regulatory
systems. I will then develop a generic theoretical framework to investigate the
coevolution of multiple transcription factors and multiple binding sites, in the
context of a gene regulatory network that performs a certain function. As a particular
tractable version of this problem, I will consider the evolution of two transcription
factors when they transmit upstream signals to downstream target genes. Specifically,
I will describe the evolutionary steady states and the evolutionary pathways involved,
along with their timescales, of a system that initially undergoes a transcription
factor duplication event. To connect this important theoretical model to the prominent
biological event of transcription factor duplication giving rise to paralogous
families, I will then describe a bioinformatics analysis of C2H2 Zn-finger transcription
factors, a major family in humans, and focus on the patterns of evolution that
paralogs have undergone in their various protein domains in the recent past. '
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
citation:
ama: Prizak R. Coevolution of transcription factors and their binding sites in sequence
space. 2019. doi:10.15479/at:ista:th6071
apa: Prizak, R. (2019). Coevolution of transcription factors and their binding
sites in sequence space. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th6071
chicago: Prizak, Roshan. “Coevolution of Transcription Factors and Their Binding
Sites in Sequence Space.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:th6071.
ieee: R. Prizak, “Coevolution of transcription factors and their binding sites in
sequence space,” Institute of Science and Technology Austria, 2019.
ista: Prizak R. 2019. Coevolution of transcription factors and their binding sites
in sequence space. Institute of Science and Technology Austria.
mla: Prizak, Roshan. Coevolution of Transcription Factors and Their Binding Sites
in Sequence Space. Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:th6071.
short: R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in
Sequence Space, Institute of Science and Technology Austria, 2019.
date_created: 2019-03-06T16:16:10Z
date_published: 2019-03-11T00:00:00Z
date_updated: 2023-09-22T10:00:48Z
day: '11'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: GaTk
- _id: NiBa
doi: 10.15479/at:ista:th6071
file:
- access_level: open_access
checksum: e60a72de35d270b31f1a23d50f224ec0
content_type: application/pdf
creator: rprizak
date_created: 2019-03-06T16:05:07Z
date_updated: 2020-07-14T12:47:18Z
file_id: '6072'
file_name: Thesis_final_PDFA_RoshanPrizak.pdf
file_size: 20995465
relation: main_file
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checksum: 67c2630333d05ebafef5f018863a8465
content_type: application/zip
creator: rprizak
date_created: 2019-03-06T16:09:39Z
date_updated: 2020-07-14T12:47:18Z
file_id: '6073'
file_name: thesis_v2_merge.zip
file_size: 85705272
relation: source_file
title: Latex files
file_date_updated: 2020-07-14T12:47:18Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '189'
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1358'
relation: part_of_dissertation
status: public
- id: '955'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
title: Coevolution of transcription factors and their binding sites in sequence space
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6856'
abstract:
- lang: eng
text: 'Plant mating systems play a key role in structuring genetic variation both
within and between species. In hybrid zones, the outcomes and dynamics of hybridization
are usually interpreted as the balance between gene flow and selection against
hybrids. Yet, mating systems can introduce selective forces that alter these expectations;
with diverse outcomes for the level and direction of gene flow depending on variation
in outcrossing and whether the mating systems of the species pair are the same
or divergent. We present a survey of hybridization in 133 species pairs from 41
plant families and examine how patterns of hybridization vary with mating system.
We examine if hybrid zone mode, level of gene flow, asymmetries in gene flow and
the frequency of reproductive isolating barriers vary in relation to mating system/s
of the species pair. We combine these results with a simulation model and examples
from the literature to address two general themes: (i) the two‐way interaction
between introgression and the evolution of reproductive systems, and (ii) how
mating system can facilitate or restrict interspecific gene flow. We conclude
that examining mating system with hybridization provides unique opportunities
to understand divergence and the processes underlying reproductive isolation.'
article_processing_charge: No
article_type: original
author:
- 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
- first_name: Yaniv
full_name: Brandvain, Yaniv
last_name: Brandvain
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Sarah
full_name: Yakimowski, Sarah
last_name: Yakimowski
- first_name: Tanmay
full_name: Dixit, Tanmay
last_name: Dixit
- first_name: Christian
full_name: Lexer, Christian
last_name: Lexer
- first_name: Eva
full_name: Cereghetti, Eva
id: 71AA91B4-05ED-11EA-8BEB-F5833E63BD63
last_name: Cereghetti
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
citation:
ama: 'Pickup M, Barton NH, Brandvain Y, et al. Mating system variation in hybrid
zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist.
2019;224(3):1035-1047. doi:10.1111/nph.16180'
apa: 'Pickup, M., Barton, N. H., Brandvain, Y., Fraisse, C., Yakimowski, S., Dixit,
T., … Field, D. (2019). Mating system variation in hybrid zones: Facilitation,
barriers and asymmetries to gene flow. New Phytologist. Wiley. https://doi.org/10.1111/nph.16180'
chicago: 'Pickup, Melinda, Nicholas H Barton, Yaniv Brandvain, Christelle Fraisse,
Sarah Yakimowski, Tanmay Dixit, Christian Lexer, Eva Cereghetti, and David Field.
“Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries
to Gene Flow.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.16180.'
ieee: 'M. Pickup et al., “Mating system variation in hybrid zones: Facilitation,
barriers and asymmetries to gene flow,” New Phytologist, vol. 224, no.
3. Wiley, pp. 1035–1047, 2019.'
ista: 'Pickup M, Barton NH, Brandvain Y, Fraisse C, Yakimowski S, Dixit T, Lexer
C, Cereghetti E, Field D. 2019. Mating system variation in hybrid zones: Facilitation,
barriers and asymmetries to gene flow. New Phytologist. 224(3), 1035–1047.'
mla: 'Pickup, Melinda, et al. “Mating System Variation in Hybrid Zones: Facilitation,
Barriers and Asymmetries to Gene Flow.” New Phytologist, vol. 224, no.
3, Wiley, 2019, pp. 1035–47, doi:10.1111/nph.16180.'
short: M. Pickup, N.H. Barton, Y. Brandvain, C. Fraisse, S. Yakimowski, T. Dixit,
C. Lexer, E. Cereghetti, D. Field, New Phytologist 224 (2019) 1035–1047.
date_created: 2019-09-07T14:35:40Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-10-18T08:47:08Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/nph.16180
ec_funded: 1
external_id:
pmid:
- '31505037'
file:
- access_level: open_access
checksum: 21e4c95599bbcaf7c483b89954658672
content_type: application/pdf
creator: dernst
date_created: 2019-11-13T08:15:05Z
date_updated: 2020-07-14T12:47:42Z
file_id: '7011'
file_name: 2019_NewPhytologist_Pickup.pdf
file_size: 1511958
relation: main_file
file_date_updated: 2020-07-14T12:47:42Z
has_accepted_license: '1'
intvolume: ' 224'
issue: '3'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 1035-1047
pmid: 1
project:
- _id: 25B36484-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '329960'
name: Mating system and the evolutionary dynamics of hybrid zones
- _id: 2662AADE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02463
name: Sex chromosomes and species barriers
publication: New Phytologist
publication_identifier:
eissn:
- 1469-8137
issn:
- 0028-646X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Mating system variation in hybrid zones: Facilitation, barriers and asymmetries
to gene flow'
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: 224
year: '2019'
...
---
_id: '6089'
abstract:
- lang: eng
text: Pleiotropy is the well-established idea that a single mutation affects multiple
phenotypes. If a mutation has opposite effects on fitness when expressed in different
contexts, then genetic conflict arises. Pleiotropic conflict is expected to reduce
the efficacy of selection by limiting the fixation of beneficial mutations through
adaptation, and the removal of deleterious mutations through purifying selection.
Although this has been widely discussed, in particular in the context of a putative
“gender load,” it has yet to be systematically quantified. In this work, we empirically
estimate to which extent different pleiotropic regimes impede the efficacy of
selection in Drosophila melanogaster. We use whole-genome polymorphism data from
a single African population and divergence data from D. simulans to estimate the
fraction of adaptive fixations (α), the rate of adaptation (ωA), and the direction
of selection (DoS). After controlling for confounding covariates, we find that
the different pleiotropic regimes have a relatively small, but significant, effect
on selection efficacy. Specifically, our results suggest that pleiotropic sexual
antagonism may restrict the efficacy of selection, but that this conflict can
be resolved by limiting the expression of genes to the sex where they are beneficial.
Intermediate levels of pleiotropy across tissues and life stages can also lead
to maladaptation in D. melanogaster, due to inefficient purifying selection combined
with low frequency of mutations that confer a selective advantage. Thus, our study
highlights the need to consider the efficacy of selection in the context of antagonistic
pleiotropy, and of genetic conflict in general.
article_processing_charge: No
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- 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: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Fraisse C, Puixeu Sala G, Vicoso B. Pleiotropy modulates the efficacy of selection
in drosophila melanogaster. Molecular biology and evolution. 2019;36(3):500-515.
doi:10.1093/molbev/msy246
apa: Fraisse, C., Puixeu Sala, G., & Vicoso, B. (2019). Pleiotropy modulates
the efficacy of selection in drosophila melanogaster. Molecular Biology and
Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msy246
chicago: Fraisse, Christelle, Gemma Puixeu Sala, and Beatriz Vicoso. “Pleiotropy
Modulates the Efficacy of Selection in Drosophila Melanogaster.” Molecular
Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/molbev/msy246.
ieee: C. Fraisse, G. Puixeu Sala, and B. Vicoso, “Pleiotropy modulates the efficacy
of selection in drosophila melanogaster,” Molecular biology and evolution,
vol. 36, no. 3. Oxford University Press, pp. 500–515, 2019.
ista: Fraisse C, Puixeu Sala G, Vicoso B. 2019. Pleiotropy modulates the efficacy
of selection in drosophila melanogaster. Molecular biology and evolution. 36(3),
500–515.
mla: Fraisse, Christelle, et al. “Pleiotropy Modulates the Efficacy of Selection
in Drosophila Melanogaster.” Molecular Biology and Evolution, vol. 36,
no. 3, Oxford University Press, 2019, pp. 500–15, doi:10.1093/molbev/msy246.
short: C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36
(2019) 500–515.
date_created: 2019-03-10T22:59:19Z
date_published: 2019-03-01T00:00:00Z
date_updated: 2024-02-21T13:59:17Z
day: '01'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1093/molbev/msy246
external_id:
isi:
- '000462585100006'
pmid:
- '30590559'
intvolume: ' 36'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30590559
month: '03'
oa: 1
oa_version: Submitted Version
page: 500-515
pmid: 1
project:
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28842-B22
name: Sex chromosome evolution under male- and female- heterogamety
publication: Molecular biology and evolution
publication_identifier:
eissn:
- 1537-1719
issn:
- 0737-4038
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
record:
- id: '5757'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Pleiotropy modulates the efficacy of selection in drosophila melanogaster
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 36
year: '2019'
...
---
_id: '6090'
abstract:
- lang: eng
text: Cells need to reliably sense external ligand concentrations to achieve various
biological functions such as chemotaxis or signaling. The molecular recognition
of ligands by surface receptors is degenerate in many systems, leading to crosstalk
between ligand-receptor pairs. Crosstalk is often thought of as a deviation from
optimal specific recognition, as the binding of noncognate ligands can interfere
with the detection of the receptor's cognate ligand, possibly leading to a false
triggering of a downstream signaling pathway. Here we quantify the optimal precision
of sensing the concentrations of multiple ligands by a collection of promiscuous
receptors. We demonstrate that crosstalk can improve precision in concentration
sensing and discrimination tasks. To achieve superior precision, the additional
information about ligand concentrations contained in short binding events of the
noncognate ligand should be exploited. We present a proofreading scheme to realize
an approximate estimation of multiple ligand concentrations that reaches a precision
close to the derived optimal bounds. Our results help rationalize the observed
ubiquity of receptor crosstalk in molecular sensing.
article_number: '022423'
article_processing_charge: No
author:
- first_name: Martín
full_name: Carballo-Pacheco, Martín
last_name: Carballo-Pacheco
- first_name: Jonathan
full_name: Desponds, Jonathan
last_name: Desponds
- first_name: Tatyana
full_name: Gavrilchenko, Tatyana
last_name: Gavrilchenko
- first_name: Andreas
full_name: Mayer, Andreas
last_name: Mayer
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
- first_name: Gautam
full_name: Reddy, Gautam
last_name: Reddy
- first_name: Ilya
full_name: Nemenman, Ilya
last_name: Nemenman
- first_name: Thierry
full_name: Mora, Thierry
last_name: Mora
citation:
ama: Carballo-Pacheco M, Desponds J, Gavrilchenko T, et al. Receptor crosstalk improves
concentration sensing of multiple ligands. Physical Review E. 2019;99(2).
doi:10.1103/PhysRevE.99.022423
apa: Carballo-Pacheco, M., Desponds, J., Gavrilchenko, T., Mayer, A., Prizak, R.,
Reddy, G., … Mora, T. (2019). Receptor crosstalk improves concentration sensing
of multiple ligands. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.99.022423
chicago: Carballo-Pacheco, Martín, Jonathan Desponds, Tatyana Gavrilchenko, Andreas
Mayer, Roshan Prizak, Gautam Reddy, Ilya Nemenman, and Thierry Mora. “Receptor
Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review
E. American Physical Society, 2019. https://doi.org/10.1103/PhysRevE.99.022423.
ieee: M. Carballo-Pacheco et al., “Receptor crosstalk improves concentration
sensing of multiple ligands,” Physical Review E, vol. 99, no. 2. American
Physical Society, 2019.
ista: Carballo-Pacheco M, Desponds J, Gavrilchenko T, Mayer A, Prizak R, Reddy G,
Nemenman I, Mora T. 2019. Receptor crosstalk improves concentration sensing of
multiple ligands. Physical Review E. 99(2), 022423.
mla: Carballo-Pacheco, Martín, et al. “Receptor Crosstalk Improves Concentration
Sensing of Multiple Ligands.” Physical Review E, vol. 99, no. 2, 022423,
American Physical Society, 2019, doi:10.1103/PhysRevE.99.022423.
short: M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G.
Reddy, I. Nemenman, T. Mora, Physical Review E 99 (2019).
date_created: 2019-03-10T22:59:20Z
date_published: 2019-02-26T00:00:00Z
date_updated: 2024-02-28T13:12:06Z
day: '26'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1103/PhysRevE.99.022423
external_id:
isi:
- '000459916500007'
intvolume: ' 99'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/448118v1.abstract
month: '02'
oa: 1
oa_version: Preprint
publication: Physical Review E
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Receptor crosstalk improves concentration sensing of multiple ligands
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 99
year: '2019'
...