---
_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
license: https://creativecommons.org/publicdomain/zero/1.0/
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: '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: 2025-06-11T13:45:56Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1002/evl3.270
external_id:
isi:
- '000754412600008'
pmid:
- '35127140'
file:
- access_level: open_access
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
pmid: 1
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
scopus_import: '1'
status: public
title: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics,
and disease control
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
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: 2026-04-07T12:54:28Z
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
checksum: 04ca9e2f0e344d680b947f2457df8d0a
content_type: application/pdf
creator: oolusany
date_created: 2022-01-24T10:34:45Z
date_updated: 2022-01-24T10:34:45Z
file_id: '10659'
file_name: rstb.2021.0010.pdf
file_size: 1845792
relation: main_file
file_date_updated: 2022-01-24T10:34:45Z
has_accepted_license: '1'
intvolume: ' 377'
isi: 1
issue: '1846'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '01'
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
publication_identifier:
eissn:
- 1471-2970
issn:
- 0962-8436
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
related_material:
link:
- relation: earlier_version
url: https://doi.org/10.1101/2021.08.05.455207
record:
- id: '14711'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Genetic load and extinction in peripheral populations: The roles of migration,
drift and demographic stochasticity'
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: '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: Steinrück, Magdalena
id: 2C023F40-F248-11E8-B48F-1D18A9856A87
last_name: Steinrück
orcid: 0000-0003-1229-9719
- 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, Steinrück 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., Steinrück, 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 Steinrück, 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, Steinrück 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. Steinrück, D. Toledo-Aparicio, J.P. Bollback,
C.C. Guet, G. Tkačik, ELife 11 (2022).
corr_author: '1'
date_created: 2022-02-06T23:01:32Z
date_published: 2022-01-26T00:00:00Z
date_updated: 2025-03-31T16:00:23Z
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
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).'
corr_author: '1'
date_created: 2022-02-21T16:08:10Z
date_published: 2022-04-11T00:00:00Z
date_updated: 2026-04-07T12:54:28Z
day: '11'
ddc:
- '570'
department:
- _id: GradSch
- _id: NiBa
doi: 10.1098/rstb.2021.0009
external_id:
isi:
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pmid:
- '35184588'
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date_created: 2022-08-02T06:14:32Z
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intvolume: ' 377'
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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'
...
---
OA_place: publisher
_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.
corr_author: '1'
date_created: 2022-05-16T16:49:18Z
date_published: 2022-05-18T00:00:00Z
date_updated: 2026-04-07T14:29:57Z
day: '18'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/at:ista:11388
file:
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creator: sbelohla
date_created: 2022-05-19T13:03:13Z
date_updated: 2023-05-20T22:30:03Z
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file_name: thesis_sb_final_pdfa.pdf
file_size: 8247240
relation: main_file
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has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2022'
...
---
OA_place: publisher
_id: '12987'
abstract:
- lang: eng
text: Chromosomal inversion polymorphisms, segments of chromosomes that are flipped
in orientation and occur in reversed order in some individuals, have long been
recognized to play an important role in local adaptation. They can reduce recombination
in heterozygous individuals and thus help to maintain sets of locally adapted
alleles. In a wide range of organisms, populations adapted to different habitats
differ in frequency of inversion arrangements. However, getting a full understanding
of the importance of inversions for adaptation requires confirmation of their
influence on traits under divergent selection. Here, we studied a marine snail,
Littorina saxatilis, that has evolved ecotypes adapted to wave exposure or crab
predation. These two types occur in close proximity on different parts of the
shore. Gene flow between them exists in contact zones. However, they exhibit strong
phenotypic divergence in several traits under habitat-specific selection, including
size, shape and behaviour. We used crosses between these ecotypes to identify
genomic regions that explain variation in these traits by using QTL analysis and
variance partitioning across linkage groups. We could show that previously detected
inversion regions contribute to adaptive divergence. Some inversions influenced
multiple traits suggesting that they contain sets of locally adaptive alleles.
Our study also identified regions without known inversions that are important
for phenotypic divergence. Thus, we provide a more complete overview of the importance
of inversions in relation to the remaining genome.
article_processing_charge: No
author:
- first_name: Eva
full_name: Koch, Eva
last_name: Koch
- first_name: Hernán E.
full_name: Morales, Hernán E.
last_name: Morales
- first_name: Jenny
full_name: Larsson, Jenny
last_name: Larsson
- 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: Alan R.
full_name: Lemmon, Alan R.
last_name: Lemmon
- first_name: E. Moriarty
full_name: Lemmon, E. Moriarty
last_name: Lemmon
- 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 E, Morales HE, Larsson J, et al. Data from: Genetic variation for adaptive
traits is associated with polymorphic inversions in Littorina saxatilis. 2021.
doi:10.5061/DRYAD.ZGMSBCCB4'
apa: 'Koch, E., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon,
A. R., … Butlin, R. K. (2021). Data from: Genetic variation for adaptive traits
is associated with polymorphic inversions in Littorina saxatilis. Dryad. https://doi.org/10.5061/DRYAD.ZGMSBCCB4'
chicago: 'Koch, Eva, Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria,
Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin.
“Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic
Inversions in Littorina Saxatilis.” Dryad, 2021. https://doi.org/10.5061/DRYAD.ZGMSBCCB4.'
ieee: 'E. Koch et al., “Data from: Genetic variation for adaptive traits
is associated with polymorphic inversions in Littorina saxatilis.” Dryad, 2021.'
ista: 'Koch E, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM,
Johannesson K, Butlin RK. 2021. Data from: Genetic variation for adaptive traits
is associated with polymorphic inversions in Littorina saxatilis, Dryad, 10.5061/DRYAD.ZGMSBCCB4.'
mla: 'Koch, Eva, et al. Data from: Genetic Variation for Adaptive Traits Is Associated
with Polymorphic Inversions in Littorina Saxatilis. Dryad, 2021, doi:10.5061/DRYAD.ZGMSBCCB4.'
short: E. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M.
Lemmon, K. Johannesson, R.K. Butlin, (2021).
date_created: 2023-05-16T12:34:09Z
date_published: 2021-04-10T00:00:00Z
date_updated: 2026-04-07T14:01:30Z
day: '10'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5061/DRYAD.ZGMSBCCB4
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.zgmsbccb4
month: '04'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '9394'
relation: used_in_publication
status: public
status: public
title: 'Data from: Genetic variation for adaptive traits is associated with polymorphic
inversions in Littorina saxatilis'
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2021'
...
---
_id: '13062'
abstract:
- lang: eng
text: 'This paper analyzes the conditions for local adaptation in a metapopulation
with infinitely many islands under a model of hard selection, where population
size depends on local fitness. Each island belongs to one of two distinct ecological
niches or habitats. Fitness is influenced by an additive trait which is under
habitat-dependent directional selection. Our analysis is based on the diffusion
approximation and accounts for both genetic drift and demographic stochasticity.
By neglecting linkage disequilibria, it yields the joint distribution of allele
frequencies and population size on each island. We find that under hard selection,
the conditions for local adaptation in a rare habitat are more restrictive for
more polygenic traits: even moderate migration load per locus at very many loci
is sufficient for population sizes to decline. This further reduces the efficacy
of selection at individual loci due to increased drift and because smaller populations
are more prone to swamping due to migration, causing a positive feedback between
increasing maladaptation and declining population sizes. Our analysis also highlights
the importance of demographic stochasticity, which exacerbates the decline in
numbers of maladapted populations, leading to population collapse in the rare
habitat at significantly lower migration than predicted by deterministic arguments.'
article_processing_charge: No
author:
- first_name: Eniko
full_name: Szep, Eniko
id: 485BB5A4-F248-11E8-B48F-1D18A9856A87
last_name: Szep
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
- 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: 'Szep E, Sachdeva H, Barton NH. Supplementary code for: Polygenic local adaptation
in metapopulations: A stochastic eco-evolutionary model. 2021. doi:10.5061/DRYAD.8GTHT76P1'
apa: 'Szep, E., Sachdeva, H., & Barton, N. H. (2021). Supplementary code for:
Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model.
Dryad. https://doi.org/10.5061/DRYAD.8GTHT76P1'
chicago: 'Szep, Eniko, Himani Sachdeva, and Nicholas H Barton. “Supplementary Code
for: Polygenic Local Adaptation in Metapopulations: A Stochastic Eco-Evolutionary
Model.” Dryad, 2021. https://doi.org/10.5061/DRYAD.8GTHT76P1.'
ieee: 'E. Szep, H. Sachdeva, and N. H. Barton, “Supplementary code for: Polygenic
local adaptation in metapopulations: A stochastic eco-evolutionary model.” Dryad,
2021.'
ista: 'Szep E, Sachdeva H, Barton NH. 2021. Supplementary code for: Polygenic local
adaptation in metapopulations: A stochastic eco-evolutionary model, Dryad, 10.5061/DRYAD.8GTHT76P1.'
mla: 'Szep, Eniko, et al. Supplementary Code for: Polygenic Local Adaptation
in Metapopulations: A Stochastic Eco-Evolutionary Model. Dryad, 2021, doi:10.5061/DRYAD.8GTHT76P1.'
short: E. Szep, H. Sachdeva, N.H. Barton, (2021).
corr_author: '1'
date_created: 2023-05-23T16:17:02Z
date_published: 2021-03-02T00:00:00Z
date_updated: 2025-06-12T06:35:39Z
day: '02'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5061/DRYAD.8GTHT76P1
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.8gtht76p1
month: '03'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '9252'
relation: used_in_publication
status: public
status: public
title: 'Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic
eco-evolutionary model'
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: '2021'
...
---
_id: '14984'
abstract:
- lang: eng
text: Hybrid zones are narrow geographic regions where different populations, races
or interbreeding species meet and mate, producing mixed ‘hybrid’ offspring. They
are relatively common and can be found in a diverse range of organisms and environments.
The study of hybrid zones has played an important role in our understanding of
the origin of species, with hybrid zones having been described as ‘natural laboratories’.
This is because they allow us to study,in situ, the conditions and evolutionary
forces that enable divergent taxa to remain distinct despite some ongoing gene
exchange between them.
article_processing_charge: No
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Daria
full_name: Shipilina, Daria
id: 428A94B0-F248-11E8-B48F-1D18A9856A87
last_name: Shipilina
orcid: 0000-0002-1145-9226
- 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: 'Stankowski S, Shipilina D, Westram AM. Hybrid Zones. In: Encyclopedia of
Life Sciences. Vol 2. eLS. Wiley; 2021. doi:10.1002/9780470015902.a0029355'
apa: Stankowski, S., Shipilina, D., & Westram, A. M. (2021). Hybrid Zones. In
Encyclopedia of Life Sciences (Vol. 2). Wiley. https://doi.org/10.1002/9780470015902.a0029355
chicago: Stankowski, Sean, Daria Shipilina, and Anja M Westram. “Hybrid Zones.”
In Encyclopedia of Life Sciences, Vol. 2. ELS. Wiley, 2021. https://doi.org/10.1002/9780470015902.a0029355.
ieee: S. Stankowski, D. Shipilina, and A. M. Westram, “Hybrid Zones,” in Encyclopedia
of Life Sciences, vol. 2, Wiley, 2021.
ista: 'Stankowski S, Shipilina D, Westram AM. 2021.Hybrid Zones. In: Encyclopedia
of Life Sciences. vol. 2.'
mla: Stankowski, Sean, et al. “Hybrid Zones.” Encyclopedia of Life Sciences,
vol. 2, Wiley, 2021, doi:10.1002/9780470015902.a0029355.
short: S. Stankowski, D. Shipilina, A.M. Westram, in:, Encyclopedia of Life Sciences,
Wiley, 2021.
corr_author: '1'
date_created: 2024-02-14T12:05:50Z
date_published: 2021-05-28T00:00:00Z
date_updated: 2024-10-09T21:08:11Z
day: '28'
department:
- _id: NiBa
doi: 10.1002/9780470015902.a0029355
intvolume: ' 2'
language:
- iso: eng
month: '05'
oa_version: None
publication: Encyclopedia of Life Sciences
publication_identifier:
eisbn:
- '9780470015902'
isbn:
- '9780470016176'
publication_status: published
publisher: Wiley
quality_controlled: '1'
series_title: eLS
status: public
title: Hybrid Zones
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2021'
...
---
_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
arxiv: 1
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).
corr_author: '1'
date_created: 2021-12-12T23:01:27Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2024-10-09T21:01:16Z
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: 2025-07-10T12:01:23Z
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:
- 1420-9101
issn:
- 1010-061X
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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: 2026-06-18T19:37:17Z
day: '01'
ddc:
- '570'
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:
- 1420-9101
issn:
- 1010-061X
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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: 2025-07-10T12:01:37Z
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:
- 1420-9101
issn:
- 1010-061X
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
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.
corr_author: '1'
date_created: 2021-02-14T23:01:14Z
date_published: 2021-01-15T00:00:00Z
date_updated: 2025-06-12T06:34:23Z
day: '15'
department:
- _id: NiBa
doi: 10.1111/1755-0998.13323
external_id:
isi:
- '000614183100001'
pmid:
- '33448666'
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
pmid: 1
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: 'DILS: Demographic inferences with linked selection by using ABC'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
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).
corr_author: '1'
date_created: 2021-02-18T14:41:30Z
date_published: 2021-02-01T00:00:00Z
date_updated: 2026-06-18T19:40:39Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/genetics/iyaa025
external_id:
isi:
- '000637218100005'
pmid:
- '33724409'
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
pmid: 1
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'
scopus_import: '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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 217
year: '2021'
...
---
_id: '9192'
abstract:
- lang: eng
text: Here are the research data underlying the publication " Effects of fine-scale
population structure on inbreeding in a long-term study of snapdragons (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
orcid: 0000-0001-6395-386X
- 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. 2021. doi:10.15479/AT:ISTA:9192
apa: Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., &
Barton, N. H. (2021). 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:9192
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, 2021. https://doi.org/10.15479/AT:ISTA:9192.
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, 2021.
ista: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2021.
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:9192.
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, 2021, doi:10.15479/AT:ISTA:9192.
short: P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton,
(2021).
contributor:
- contributor_type: project_member
first_name: Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
- 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
- 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_leader
first_name: Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
date_created: 2021-02-24T17:49:21Z
date_published: 2021-02-26T00:00:00Z
date_updated: 2025-04-15T08:20:40Z
day: '26'
ddc:
- '576'
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/AT:ISTA:9192
file:
- access_level: open_access
checksum: f85537815809a8a4b7da9d01163f88c0
content_type: application/x-zip-compressed
creator: larathoo
date_created: 2021-02-24T17:45:13Z
date_updated: 2021-02-24T17:45:13Z
file_id: '9193'
file_name: Data_Code.zip
file_size: 5934452
relation: main_file
success: 1
file_date_updated: 2021-02-24T17:45:13Z
has_accepted_license: '1'
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8254'
relation: earlier_version
status: public
- id: '11321'
relation: later_version
status: public
- id: '11411'
relation: used_in_publication
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: '2021'
...
---
_id: '9252'
abstract:
- lang: eng
text: 'This paper analyses the conditions for local adaptation in a metapopulation
with infinitely many islands under a model of hard selection, where population
size depends on local fitness. Each island belongs to one of two distinct ecological
niches or habitats. Fitness is influenced by an additive trait which is under
habitat‐dependent directional selection. Our analysis is based on the diffusion
approximation and accounts for both genetic drift and demographic stochasticity.
By neglecting linkage disequilibria, it yields the joint distribution of allele
frequencies and population size on each island. We find that under hard selection,
the conditions for local adaptation in a rare habitat are more restrictive for
more polygenic traits: even moderate migration load per locus at very many loci
is sufficient for population sizes to decline. This further reduces the efficacy
of selection at individual loci due to increased drift and because smaller populations
are more prone to swamping due to migration, causing a positive feedback between
increasing maladaptation and declining population sizes. Our analysis also highlights
the importance of demographic stochasticity, which exacerbates the decline in
numbers of maladapted populations, leading to population collapse in the rare
habitat at significantly lower migration than predicted by deterministic arguments.'
acknowledgement: We thank the reviewers for their helpful comments, and also our colleagues,
for illuminating discussions over the long gestation of this paper.
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: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
- 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: 'Szep E, Sachdeva H, Barton NH. Polygenic local adaptation in metapopulations:
A stochastic eco‐evolutionary model. Evolution. 2021;75(5):1030-1045. doi:10.1111/evo.14210'
apa: 'Szep, E., Sachdeva, H., & Barton, N. H. (2021). Polygenic local adaptation
in metapopulations: A stochastic eco‐evolutionary model. Evolution. Wiley.
https://doi.org/10.1111/evo.14210'
chicago: 'Szep, Eniko, Himani Sachdeva, and Nicholas H Barton. “Polygenic Local
Adaptation in Metapopulations: A Stochastic Eco‐evolutionary Model.” Evolution.
Wiley, 2021. https://doi.org/10.1111/evo.14210.'
ieee: 'E. Szep, H. Sachdeva, and N. H. Barton, “Polygenic local adaptation in metapopulations:
A stochastic eco‐evolutionary model,” Evolution, vol. 75, no. 5. Wiley,
pp. 1030–1045, 2021.'
ista: 'Szep E, Sachdeva H, Barton NH. 2021. Polygenic local adaptation in metapopulations:
A stochastic eco‐evolutionary model. Evolution. 75(5), 1030–1045.'
mla: 'Szep, Eniko, et al. “Polygenic Local Adaptation in Metapopulations: A Stochastic
Eco‐evolutionary Model.” Evolution, vol. 75, no. 5, Wiley, 2021, pp. 1030–45,
doi:10.1111/evo.14210.'
short: E. Szep, H. Sachdeva, N.H. Barton, Evolution 75 (2021) 1030–1045.
corr_author: '1'
date_created: 2021-03-20T08:22:10Z
date_published: 2021-05-01T00:00:00Z
date_updated: 2025-06-12T06:35:39Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/evo.14210
external_id:
isi:
- '000636966300001'
pmid:
- '33742441'
file:
- access_level: open_access
checksum: b90fb5767d623602046fed03725e16ca
content_type: application/pdf
creator: kschuh
date_created: 2021-08-11T13:39:19Z
date_updated: 2021-08-11T13:39:19Z
file_id: '9886'
file_name: 2021_Evolution_Szep.pdf
file_size: 734102
relation: main_file
success: 1
file_date_updated: 2021-08-11T13:39:19Z
has_accepted_license: '1'
intvolume: ' 75'
isi: 1
issue: '5'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
- General Agricultural and Biological Sciences
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '05'
oa: 1
oa_version: Published Version
page: 1030-1045
pmid: 1
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '13062'
relation: research_data
status: public
scopus_import: '1'
status: public
title: 'Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary
model'
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 75
year: '2021'
...
---
_id: '9374'
abstract:
- lang: eng
text: If there are no constraints on the process of speciation, then the number
of species might be expected to match the number of available niches and this
number might be indefinitely large. One possible constraint is the opportunity
for allopatric divergence. In 1981, Felsenstein used a simple and elegant model
to ask if there might also be genetic constraints. He showed that progress towards
speciation could be described by the build‐up of linkage disequilibrium among
divergently selected loci and between these loci and those contributing to other
forms of reproductive isolation. Therefore, speciation is opposed by recombination,
because it tends to break down linkage disequilibria. Felsenstein then introduced
a crucial distinction between “two‐allele” models, which are subject to this effect,
and “one‐allele” models, which are free from the recombination constraint. These
fundamentally important insights have been the foundation for both empirical and
theoretical studies of speciation ever since.
acknowledgement: RKB was funded by the Natural Environment Research Council (NE/P012272/1
& NE/P001610/1), the European Research Council (693030 BARRIERS), and the Swedish
Research Council (VR) (2018‐03695). MRS was funded by the National Science Foundation
(Grant No. DEB1939290).
article_processing_charge: No
article_type: original
author:
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
- first_name: Maria R.
full_name: Servedio, Maria R.
last_name: Servedio
- first_name: Carole M.
full_name: Smadja, Carole M.
last_name: Smadja
- first_name: Claudia
full_name: Bank, Claudia
last_name: Bank
- 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: Samuel M.
full_name: Flaxman, Samuel M.
last_name: Flaxman
- first_name: Tatiana
full_name: Giraud, Tatiana
last_name: Giraud
- first_name: Robin
full_name: Hopkins, Robin
last_name: Hopkins
- first_name: Erica L.
full_name: Larson, Erica L.
last_name: Larson
- first_name: Martine E.
full_name: Maan, Martine E.
last_name: Maan
- first_name: Joana
full_name: Meier, Joana
last_name: Meier
- first_name: Richard
full_name: Merrill, Richard
last_name: Merrill
- first_name: Mohamed A. F.
full_name: Noor, Mohamed A. F.
last_name: Noor
- first_name: Daniel
full_name: Ortiz‐Barrientos, Daniel
last_name: Ortiz‐Barrientos
- first_name: Anna
full_name: Qvarnström, Anna
last_name: Qvarnström
citation:
ama: Butlin RK, Servedio MR, Smadja CM, et al. Homage to Felsenstein 1981, or why
are there so few/many species? Evolution. 2021;75(5):978-988. doi:10.1111/evo.14235
apa: Butlin, R. K., Servedio, M. R., Smadja, C. M., Bank, C., Barton, N. H., Flaxman,
S. M., … Qvarnström, A. (2021). Homage to Felsenstein 1981, or why are there so
few/many species? Evolution. Wiley. https://doi.org/10.1111/evo.14235
chicago: Butlin, Roger K., Maria R. Servedio, Carole M. Smadja, Claudia Bank, Nicholas
H Barton, Samuel M. Flaxman, Tatiana Giraud, et al. “Homage to Felsenstein 1981,
or Why Are There so Few/Many Species?” Evolution. Wiley, 2021. https://doi.org/10.1111/evo.14235.
ieee: R. K. Butlin et al., “Homage to Felsenstein 1981, or why are there
so few/many species?,” Evolution, vol. 75, no. 5. Wiley, pp. 978–988, 2021.
ista: Butlin RK, Servedio MR, Smadja CM, Bank C, Barton NH, Flaxman SM, Giraud T,
Hopkins R, Larson EL, Maan ME, Meier J, Merrill R, Noor MAF, Ortiz‐Barrientos
D, Qvarnström A. 2021. Homage to Felsenstein 1981, or why are there so few/many
species? Evolution. 75(5), 978–988.
mla: Butlin, Roger K., et al. “Homage to Felsenstein 1981, or Why Are There so Few/Many
Species?” Evolution, vol. 75, no. 5, Wiley, 2021, pp. 978–88, doi:10.1111/evo.14235.
short: R.K. Butlin, M.R. Servedio, C.M. Smadja, C. Bank, N.H. Barton, S.M. Flaxman,
T. Giraud, R. Hopkins, E.L. Larson, M.E. Maan, J. Meier, R. Merrill, M.A.F. Noor,
D. Ortiz‐Barrientos, A. Qvarnström, Evolution 75 (2021) 978–988.
date_created: 2021-05-06T04:34:47Z
date_published: 2021-04-19T00:00:00Z
date_updated: 2026-06-18T19:48:42Z
day: '19'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/evo.14235
external_id:
isi:
- '000647224000001'
intvolume: ' 75'
isi: 1
issue: '5'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
- General Agricultural and Biological Sciences
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://onlinelibrary.wiley.com/doi/10.1111/evo.14235
month: '04'
oa: 1
oa_version: Published Version
page: 978-988
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Homage to Felsenstein 1981, or why are there so few/many species?
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: 75
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. Proceedings of the National Academy
of Sciences of the United States of America. 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. Proceedings of the National Academy of Sciences of
the United States of America. 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.” Proceedings of
the National Academy of Sciences of the United States of America. 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,” Proceedings of the National Academy
of Sciences of the United States of America, vol. 118, no. 25. 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. Proceedings
of the National Academy of Sciences of the United States of America. 118(25),
e2015005118.
mla: Meier, Joana I., et al. “Haplotype Tagging Reveals Parallel Formation of Hybrid
Races in Two Butterfly Species.” Proceedings of the National Academy of Sciences
of the United States of America, vol. 118, no. 25, e2015005118, 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, Proceedings of the National Academy of Sciences of the United States
of America 118 (2021).
date_created: 2021-05-07T17:10:21Z
date_published: 2021-06-21T00:00:00Z
date_updated: 2025-05-14T10:58:04Z
day: '21'
ddc:
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department:
- _id: NiBa
doi: 10.1073/pnas.2015005118
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title: Haplotype tagging reveals parallel formation of hybrid races in two butterfly
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