---
OA_place: publisher
OA_type: hybrid
_id: '19438'
abstract:
- lang: eng
text: "Polymorphic short insertions and deletions (INDELs \r\n 50 bp) are abundant,
although less common than single nucleotide polymorphisms (SNPs). Evidence from
model organisms shows INDELs to be more strongly influenced by purifying selection
than SNPs. Partly for this reason, INDELs are rarely used as markers for demographic
processes or to detect divergent selection. Here, we compared INDELs and SNPs
in the intertidal snail Littorina saxatilis, focussing on hybrid zones between
ecotypes, in order to test the utility of INDELs in the detection of divergent
selection. We computed INDEL and SNP site frequency spectra using capture sequencing
data. We assessed the impact of divergent selection by analyzing allele frequency
clines across habitat boundaries. We also examined the influence of GC-biased
gene conversion because it may be confounded with signatures of selection. We
show evidence that short INDELs are affected more by purifying selection than
SNPs, but part of the observed site frequency spectra difference can be attributed
to GC-biased gene conversion. We did not find a difference in the impact of divergent
selection between short INDELs and SNPs. Short INDELs and SNPs were similarly
distributed across the genome and so are likely to respond to indirect selection
in the same way. A few regions likely affected by divergent selection were revealed
by INDELs and not by SNPs. Short INDELs can be useful (additional) genetic markers
helping to identify genomic regions important for adaptation and population divergence."
acknowledgement: "This work was supported by the Natural Environment Research Council
(NE/K014021/1), European Research Council (ERC-2015-AdG-693030- BARRIERS) and Swedish
Research Council VR (2018-03695) and we are also very grateful for the support of
the Linnaeus Centre for Marine Evolutionary Biology at the University of Gothenburg.\r\nWe
thank the Swedish Bioinformatics Advisory Program organized by SciLifeLab for feedback
and assistance on the variant calling pipeline and Alan Le Moan for helpful discussions.
R.K.B. and A.M.W. contributed equally to this work. We are also very grateful to
Tomas Larsson and Marina Panova for their bioinformatic analyses on the genome and
the annotation. The bioinformatic analyses were performed on resources at the University
of Sheffield’s High Performance Computing cluster, ShARC. We thank two anonymous
reviewers for helpful comments on a previous version."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Samuel
full_name: Perini, Samuel
last_name: Perini
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
- 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: Perini S, Johannesson K, Butlin RK, Westram AM. Short INDELs and SNPs as markers
of evolutionary processes in hybrid zones. Journal of Evolutionary Biology.
2025;38(3):367-378. doi:10.1093/jeb/voaf002
apa: Perini, S., Johannesson, K., Butlin, R. K., & Westram, A. M. (2025). Short
INDELs and SNPs as markers of evolutionary processes in hybrid zones. Journal
of Evolutionary Biology. Oxford University Press. https://doi.org/10.1093/jeb/voaf002
chicago: Perini, Samuel, Kerstin Johannesson, Roger K. Butlin, and Anja M Westram.
“Short INDELs and SNPs as Markers of Evolutionary Processes in Hybrid Zones.”
Journal of Evolutionary Biology. Oxford University Press, 2025. https://doi.org/10.1093/jeb/voaf002.
ieee: S. Perini, K. Johannesson, R. K. Butlin, and A. M. Westram, “Short INDELs
and SNPs as markers of evolutionary processes in hybrid zones,” Journal of
Evolutionary Biology, vol. 38, no. 3. Oxford University Press, pp. 367–378,
2025.
ista: Perini S, Johannesson K, Butlin RK, Westram AM. 2025. Short INDELs and SNPs
as markers of evolutionary processes in hybrid zones. Journal of Evolutionary
Biology. 38(3), 367–378.
mla: Perini, Samuel, et al. “Short INDELs and SNPs as Markers of Evolutionary Processes
in Hybrid Zones.” Journal of Evolutionary Biology, vol. 38, no. 3, Oxford
University Press, 2025, pp. 367–78, doi:10.1093/jeb/voaf002.
short: S. Perini, K. Johannesson, R.K. Butlin, A.M. Westram, Journal of Evolutionary
Biology 38 (2025) 367–378.
corr_author: '1'
date_created: 2025-03-23T23:01:25Z
date_published: 2025-03-01T00:00:00Z
date_updated: 2025-09-30T11:19:56Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/jeb/voaf002
external_id:
isi:
- '001415267900001'
pmid:
- '39803902'
file:
- access_level: open_access
checksum: 01408e626a4131bfec5ffc70b0af9129
content_type: application/pdf
creator: dernst
date_created: 2025-04-03T11:53:06Z
date_updated: 2025-04-03T11:53:06Z
file_id: '19469'
file_name: 2025_JourEvolBiology_Perini.pdf
file_size: 12826085
relation: main_file
success: 1
file_date_updated: 2025-04-03T11:53:06Z
has_accepted_license: '1'
intvolume: ' 38'
isi: 1
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '03'
oa: 1
oa_version: Published Version
page: 367-378
pmid: 1
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Short INDELs and SNPs as markers of evolutionary processes in hybrid zones
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 38
year: '2025'
...
---
_id: '17207'
acknowledgement: "This research was funded by the Austrian Science Fund (FWF), project
doi: 10.55776/P32896, Institutional Identifier: 501100002428, grant number: P32896
and L.F. acknowledges the support of the NOMIS-ISTA Fellowship Program.\r\nWe would
like to thank Nick Barton, Roger Butlin, Stuart Baird, Patrik Nosil, and Jason Sexton
for their insightful comments on the earlier drafts, and to John Carchrae for his
valuable contribution in refining phrasing and enhancing clarity. For open access
purposes, the author has applied a CC BY public copyright license to any author-accepted
manuscript version arising from this submission."
article_processing_charge: No
article_type: letter_note
author:
- first_name: Louise
full_name: Fouqueau, Louise
id: 1676e173-8143-11ed-8927-fe165216a93f
last_name: Fouqueau
orcid: 0000-0003-0371-9339
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
citation:
ama: 'Fouqueau L, Polechova J. Eco-evolutionary dynamics in changing environments:
Integrating theory with data. Journal of evolutionary biology. 2024;37(6):579-587.
doi:10.1093/jeb/voae067'
apa: 'Fouqueau, L., & Polechova, J. (2024). Eco-evolutionary dynamics in changing
environments: Integrating theory with data. Journal of Evolutionary Biology.
Oxford University Press. https://doi.org/10.1093/jeb/voae067'
chicago: 'Fouqueau, Louise, and Jitka Polechova. “Eco-Evolutionary Dynamics in Changing
Environments: Integrating Theory with Data.” Journal of Evolutionary Biology.
Oxford University Press, 2024. https://doi.org/10.1093/jeb/voae067.'
ieee: 'L. Fouqueau and J. Polechova, “Eco-evolutionary dynamics in changing environments:
Integrating theory with data,” Journal of evolutionary biology, vol. 37,
no. 6. Oxford University Press, pp. 579–587, 2024.'
ista: 'Fouqueau L, Polechova J. 2024. Eco-evolutionary dynamics in changing environments:
Integrating theory with data. Journal of evolutionary biology. 37(6), 579–587.'
mla: 'Fouqueau, Louise, and Jitka Polechova. “Eco-Evolutionary Dynamics in Changing
Environments: Integrating Theory with Data.” Journal of Evolutionary Biology,
vol. 37, no. 6, Oxford University Press, 2024, pp. 579–87, doi:10.1093/jeb/voae067.'
short: L. Fouqueau, J. Polechova, Journal of Evolutionary Biology 37 (2024) 579–587.
date_created: 2024-07-07T22:01:04Z
date_published: 2024-06-28T00:00:00Z
date_updated: 2025-09-08T08:08:00Z
day: '28'
department:
- _id: NiBa
doi: 10.1093/jeb/voae067
external_id:
isi:
- '001258359900001'
pmid:
- '38941551'
intvolume: ' 37'
isi: 1
issue: '6'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/jeb/voae067
month: '06'
oa: 1
oa_version: Published Version
page: 579-587
pmid: 1
project:
- _id: c08d3278-5a5b-11eb-8a69-fdb09b55f4b8
grant_number: P32896
name: Causes and consequences of population fragmentation
- _id: 9B861AAC-BA93-11EA-9121-9846C619BF3A
name: NOMIS Fellowship Program
publication: Journal of evolutionary biology
publication_identifier:
eissn:
- 1420-9101
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Eco-evolutionary dynamics in changing environments: Integrating theory with
data'
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 37
year: '2024'
...
---
_id: '17237'
abstract:
- lang: eng
text: 'The impact of climate change on populations will be contingent upon their
contemporary adaptive evolution. In this study, we investigated the contemporary
evolution of 4 populations of the cold-water kelp Laminaria digitata by analyzing
their spatial and temporal genomic variations using ddRAD-sequencing. These populations
were sampled from the center to the southern margin of its north-eastern Atlantic
distribution at 2 time points, spanning at least 2 generations. Through genome
scans for local adaptation at a single time point, we identified candidate loci
that showed clinal variation correlated with changes in sea surface temperature
(SST) along latitudinal gradients. This finding suggests that SST may drive the
adaptive response of these kelp populations, although factors such as species’
demographic history should also be considered. Additionally, we performed a simulation
approach to distinguish the effect of selection from genetic drift in allele frequency
changes over time. This enabled the detection of loci in the southernmost population
that exhibited temporal differentiation beyond what would be expected from genetic
drift alone: these are candidate loci which could have evolved under selection
over time. In contrast, we did not detect any outlier locus based on temporal
differentiation in the population from the North Sea, which also displayed low
and decreasing levels of genetic diversity. The diverse evolutionary scenarios
observed among populations can be attributed to variations in the prevalence of
selection relative to genetic drift across different environments. Therefore,
our study highlights the potential of temporal genomics to offer valuable insights
into the contemporary evolution of marine foundation species facing climate change.'
acknowledgement: "This work was funded by the EU project MARFOR Biodiversa/004/2015.
L.F. was additionally funded by the Region Bretagne (ARED 2017 REEALG) and the NOMIS
Foundation. The project leading to this publication has received funding from the
EC2CO (CNRS) fund and from the European FEDER Fund under project 1166-39417.\r\nThis
work is especially dedicated to the memory of Gernot Glöckner who contributed to
the sequencing of Laminaria digitata genome and passed away in very recent time.
The authors thank the ABiMS platform of the Roscoff biological station (http://abims.sb-roscoff.fr)
for providing the HPC resources that contributed to the search results reported
in this document. We also acknowledge the staff of the “Cluster de calcul intensif
HPC” Platform of the OSU Institut Pythéas (Aix-Marseille Université, INSU-CNRS)
for providing the computing facilities."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Lauric
full_name: Reynes, Lauric
last_name: Reynes
- first_name: Louise
full_name: Fouqueau, Louise
id: 1676e173-8143-11ed-8927-fe165216a93f
last_name: Fouqueau
orcid: 0000-0003-0371-9339
- first_name: Didier
full_name: Aurelle, Didier
last_name: Aurelle
- first_name: Stephane
full_name: Mauger, Stephane
last_name: Mauger
- first_name: Christophe
full_name: Destombe, Christophe
last_name: Destombe
- first_name: Myriam
full_name: Valero, Myriam
last_name: Valero
citation:
ama: Reynes L, Fouqueau L, Aurelle D, Mauger S, Destombe C, Valero M. Temporal genomics
help in deciphering neutral and adaptive patterns in the contemporary evolution
of kelp populations. Journal of Evolutionary Biology. 2024;37(6):677-692.
doi:10.1093/jeb/voae048
apa: Reynes, L., Fouqueau, L., Aurelle, D., Mauger, S., Destombe, C., & Valero,
M. (2024). Temporal genomics help in deciphering neutral and adaptive patterns
in the contemporary evolution of kelp populations. Journal of Evolutionary
Biology. Oxford University Press. https://doi.org/10.1093/jeb/voae048
chicago: Reynes, Lauric, Louise Fouqueau, Didier Aurelle, Stephane Mauger, Christophe
Destombe, and Myriam Valero. “Temporal Genomics Help in Deciphering Neutral and
Adaptive Patterns in the Contemporary Evolution of Kelp Populations.” Journal
of Evolutionary Biology. Oxford University Press, 2024. https://doi.org/10.1093/jeb/voae048.
ieee: L. Reynes, L. Fouqueau, D. Aurelle, S. Mauger, C. Destombe, and M. Valero,
“Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary
evolution of kelp populations,” Journal of Evolutionary Biology, vol. 37,
no. 6. Oxford University Press, pp. 677–692, 2024.
ista: Reynes L, Fouqueau L, Aurelle D, Mauger S, Destombe C, Valero M. 2024. Temporal
genomics help in deciphering neutral and adaptive patterns in the contemporary
evolution of kelp populations. Journal of Evolutionary Biology. 37(6), 677–692.
mla: Reynes, Lauric, et al. “Temporal Genomics Help in Deciphering Neutral and Adaptive
Patterns in the Contemporary Evolution of Kelp Populations.” Journal of Evolutionary
Biology, vol. 37, no. 6, Oxford University Press, 2024, pp. 677–92, doi:10.1093/jeb/voae048.
short: L. Reynes, L. Fouqueau, D. Aurelle, S. Mauger, C. Destombe, M. Valero, Journal
of Evolutionary Biology 37 (2024) 677–692.
date_created: 2024-07-14T22:01:12Z
date_published: 2024-06-01T00:00:00Z
date_updated: 2025-06-04T07:23:23Z
day: '01'
department:
- _id: NiBa
doi: 10.1093/jeb/voae048
external_id:
arxiv:
- '2404.14003'
pmid:
- '38629140'
intvolume: ' 37'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2404.14003
month: '06'
oa: 1
oa_version: Preprint
page: 677-692
pmid: 1
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Temporal genomics help in deciphering neutral and adaptive patterns in the
contemporary evolution of kelp populations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2024'
...
---
_id: '17238'
abstract:
- lang: eng
text: We know that heritable variation is abundant, and that selection causes all
but the smallest populations to rapidly shift beyond their original trait distribution.
So then, what limits the range of a species? There are physical constraints and
also population genetic limits to the effectiveness of selection, ultimately set
by population size. Global adaptation, where the same genotype is favoured over
the whole range, is most efficient when based on a multitude of weakly selected
alleles and is effective even when local demes are small, provided that there
is some gene flow. In contrast, local adaptation is sensitive to gene flow and
may require alleles with substantial effect. How can populations combine the advantages
of large effective size with the ability to specialise into local niches? To what
extent does reproductive isolation help resolve this tension? I address these
questions using eco-evolutionary models of polygenic adaptation, contrasting discrete
demes with continuousspace.
acknowledgement: This work was supported by a grant from the ERC, 101055327, “HaplotypeStructure”.
I thank Himani Sachdeva, Michal Hledik, Jitka Polechova, and the reviewers for their
helpful comments.
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Limits to species’ range: The tension between local and global
adaptation. Journal of Evolutionary Biology. 2024;37(6):605-615. doi:10.1093/jeb/voae052'
apa: 'Barton, N. H. (2024). Limits to species’ range: The tension between local
and global adaptation. Journal of Evolutionary Biology. Oxford University
Press. https://doi.org/10.1093/jeb/voae052'
chicago: 'Barton, Nicholas H. “Limits to Species’ Range: The Tension between Local
and Global Adaptation.” Journal of Evolutionary Biology. Oxford University
Press, 2024. https://doi.org/10.1093/jeb/voae052.'
ieee: 'N. H. Barton, “Limits to species’ range: The tension between local and global
adaptation,” Journal of Evolutionary Biology, vol. 37, no. 6. Oxford University
Press, pp. 605–615, 2024.'
ista: 'Barton NH. 2024. Limits to species’ range: The tension between local and
global adaptation. Journal of Evolutionary Biology. 37(6), 605–615.'
mla: 'Barton, Nicholas H. “Limits to Species’ Range: The Tension between Local and
Global Adaptation.” Journal of Evolutionary Biology, vol. 37, no. 6, Oxford
University Press, 2024, pp. 605–15, doi:10.1093/jeb/voae052.'
short: N.H. Barton, Journal of Evolutionary Biology 37 (2024) 605–615.
corr_author: '1'
date_created: 2024-07-14T22:01:12Z
date_published: 2024-06-01T00:00:00Z
date_updated: 2025-09-08T08:08:41Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/jeb/voae052
external_id:
isi:
- '001225323900001'
pmid:
- '38683160'
file:
- access_level: open_access
checksum: 94e6b68bddf6cadcec29c7f41647359f
content_type: application/pdf
creator: dernst
date_created: 2024-07-15T09:45:25Z
date_updated: 2024-07-15T09:45:25Z
file_id: '17241'
file_name: 2024_JourEvolutionaryBiology_Barton.pdf
file_size: 1194263
relation: main_file
success: 1
file_date_updated: 2024-07-15T09:45:25Z
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 605-615
pmid: 1
project:
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Limits to species'' range: The tension between local and global adaptation'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 37
year: '2024'
...
---
_id: '14556'
abstract:
- lang: eng
text: Inversions are structural mutations that reverse the sequence of a chromosome
segment and reduce the effective rate of recombination in the heterozygous state.
They play a major role in adaptation, as well as in other evolutionary processes
such as speciation. Although inversions have been studied since the 1920s, they
remain difficult to investigate because the reduced recombination conferred by
them strengthens the effects of drift and hitchhiking, which in turn can obscure
signatures of selection. Nonetheless, numerous inversions have been found to be
under selection. Given recent advances in population genetic theory and empirical
study, here we review how different mechanisms of selection affect the evolution
of inversions. A key difference between inversions and other mutations, such as
single nucleotide variants, is that the fitness of an inversion may be affected
by a larger number of frequently interacting processes. This considerably complicates
the analysis of the causes underlying the evolution of inversions. We discuss
the extent to which these mechanisms can be disentangled, and by which approach.
acknowledgement: 'We are grateful to two referees and Luke Holman for valuable comments
on a previous version of our manuscript. This paper was conceived at the ESEB Progress
Meeting ‘Disentangling neutral versus adaptive evolution in chromosomal inversions’,
organized by ELB, KJ and TF and held at Tjärnö Marine Laboratory (Sweden) between
28 February and 3 March 2022. We are indebted to ESEB for sponsoring our workshop
and to the following funding bodies for supporting our research: ERC AdG 101055327
to NHB; Swedish Research Council (VR) 2018-03695 and Leverhulme Trust RPG-2021-141
to RKB; Fundação para a Ciência e a Tecnologia (FCT) contract 2020.00275.CEECIND
and research project PTDC/BIA-1232 EVL/1614/2021 to RF; Fundação para a Ciência
e a Tecnologia (FCT) junior researcher contract CEECIND/02616/2018 to IF; Swiss
National Science Foundation (SNSF) Ambizione #PZ00P3_185952 to KJG; National Science
Foundation NSF-OCE 2043905 and NSF-DEB 1655701 to KEL; Swiss National Science Foundation
(SNSF) 310030_204681 to CLP; Swedish Research Council (VR) 2021-05243 to MR; Norwegian
Research Council grant 315287 to AMW; Swiss National Science Foundation (SNSF) 31003A-182262
and FZEB-0-214654 to TF. We also thank Luca Ferretti for the discussion and Eliane
Zinn (Flatt lab) for help with reference formatting.'
article_number: '14242'
article_processing_charge: Yes (in subscription journal)
article_type: review
author:
- first_name: Emma L.
full_name: Berdan, Emma L.
last_name: Berdan
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
- first_name: Brian
full_name: Charlesworth, Brian
last_name: Charlesworth
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Inês
full_name: Fragata, Inês
last_name: Fragata
- first_name: Kimberly J.
full_name: Gilbert, Kimberly J.
last_name: Gilbert
- first_name: Paul
full_name: Jay, Paul
last_name: Jay
- first_name: Martin
full_name: Kapun, Martin
last_name: Kapun
- first_name: Katie E.
full_name: Lotterhos, Katie E.
last_name: Lotterhos
- first_name: Claire
full_name: Mérot, Claire
last_name: Mérot
- first_name: Esra
full_name: Durmaz Mitchell, Esra
last_name: Durmaz Mitchell
- first_name: Marta
full_name: Pascual, Marta
last_name: Pascual
- first_name: Catherine L.
full_name: Peichel, Catherine L.
last_name: Peichel
- first_name: Marina
full_name: Rafajlović, Marina
last_name: Rafajlović
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Stephen W.
full_name: Schaeffer, Stephen W.
last_name: Schaeffer
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Thomas
full_name: Flatt, Thomas
last_name: Flatt
citation:
ama: Berdan EL, Barton NH, Butlin R, et al. How chromosomal inversions reorient
the evolutionary process. Journal of Evolutionary Biology. 2023;36(12).
doi:10.1111/jeb.14242
apa: Berdan, E. L., Barton, N. H., Butlin, R., Charlesworth, B., Faria, R., Fragata,
I., … Flatt, T. (2023). How chromosomal inversions reorient the evolutionary process.
Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.14242
chicago: Berdan, Emma L., Nicholas H Barton, Roger Butlin, Brian Charlesworth, Rui
Faria, Inês Fragata, Kimberly J. Gilbert, et al. “How Chromosomal Inversions Reorient
the Evolutionary Process.” Journal of Evolutionary Biology. Wiley, 2023.
https://doi.org/10.1111/jeb.14242.
ieee: E. L. Berdan et al., “How chromosomal inversions reorient the evolutionary
process,” Journal of Evolutionary Biology, vol. 36, no. 12. Wiley, 2023.
ista: Berdan EL, Barton NH, Butlin R, Charlesworth B, Faria R, Fragata I, Gilbert
KJ, Jay P, Kapun M, Lotterhos KE, Mérot C, Durmaz Mitchell E, Pascual M, Peichel
CL, Rafajlović M, Westram AM, Schaeffer SW, Johannesson K, Flatt T. 2023. How
chromosomal inversions reorient the evolutionary process. Journal of Evolutionary
Biology. 36(12), 14242.
mla: Berdan, Emma L., et al. “How Chromosomal Inversions Reorient the Evolutionary
Process.” Journal of Evolutionary Biology, vol. 36, no. 12, 14242, Wiley,
2023, doi:10.1111/jeb.14242.
short: E.L. Berdan, N.H. Barton, R. Butlin, B. Charlesworth, R. Faria, I. Fragata,
K.J. Gilbert, P. Jay, M. Kapun, K.E. Lotterhos, C. Mérot, E. Durmaz Mitchell,
M. Pascual, C.L. Peichel, M. Rafajlović, A.M. Westram, S.W. Schaeffer, K. Johannesson,
T. Flatt, Journal of Evolutionary Biology 36 (2023).
date_created: 2023-11-19T23:00:55Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2025-09-09T13:22:35Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/jeb.14242
external_id:
isi:
- '001098690500001'
pmid:
- '37942504'
file:
- access_level: open_access
checksum: 93ae4fa700aab8646bc62f0adeed8f8f
content_type: application/pdf
creator: dernst
date_created: 2024-07-16T08:16:31Z
date_updated: 2024-07-16T08:16:31Z
file_id: '17253'
file_name: 2023_JourEvolutionaryBio_Berdan.pdf
file_size: 1401726
relation: main_file
success: 1
file_date_updated: 2024-07-16T08:16:31Z
has_accepted_license: '1'
intvolume: ' 36'
isi: 1
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
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: How chromosomal inversions reorient the evolutionary process
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 36
year: '2023'
...
---
_id: '12264'
abstract:
- lang: eng
text: Reproductive isolation (RI) is a core concept in evolutionary biology. It
has been the central focus of speciation research since the modern synthesis and
is the basis by which biological species are defined. Despite this, the term is
used in seemingly different ways, and attempts to quantify RI have used very different
approaches. After showing that the field lacks a clear definition of the term,
we attempt to clarify key issues, including what RI is, how it can be quantified
in principle, and how it can be measured in practice. Following other definitions
with a genetic focus, we propose that RI is a quantitative measure of the effect
that genetic differences between populations have on gene flow. Specifically,
RI compares the flow of neutral alleles in the presence of these genetic differences
to the flow without any such differences. RI is thus greater than zero when genetic
differences between populations reduce the flow of neutral alleles between populations.
We show how RI can be quantified in a range of scenarios. A key conclusion is
that RI depends strongly on circumstances—including the spatial, temporal and
genomic context—making it difficult to compare across systems. After reviewing
methods for estimating RI from data, we conclude that it is difficult to measure
in practice. We discuss our findings in light of the goals of speciation research
and encourage the use of methods for estimating RI that integrate organismal and
genetic approaches.
acknowledgement: 'We are grateful to the participants of the ESEB satellite symposium
‘Understanding reproductive isolation: bridging conceptual barriers in speciation research’ in 2021 for the interesting discussions that helped us clarify the thoughts presented in this article. We thank Roger
Butlin, Michael Turelli and two anonymous reviewers for their thoughtful comments
on this manuscript. We are also very grateful to Roger Butlin and the Barton Group
for the continued conversa-tions about RI. In addition, we thank all participants
of the speciation survey. Part of this work was funded by the Austrian Science Fund
FWF (grant P 32166)'
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Parvathy
full_name: Surendranadh, Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
orcid: 0000-0001-6395-386X
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Westram AM, Stankowski S, Surendranadh P, Barton NH. What is reproductive isolation?
Journal of Evolutionary Biology. 2022;35(9):1143-1164. doi:10.1111/jeb.14005
apa: Westram, A. M., Stankowski, S., Surendranadh, P., & Barton, N. H. (2022).
What is reproductive isolation? Journal of Evolutionary Biology. Wiley.
https://doi.org/10.1111/jeb.14005
chicago: Westram, Anja M, Sean Stankowski, Parvathy Surendranadh, and Nicholas H
Barton. “What Is Reproductive Isolation?” Journal of Evolutionary Biology.
Wiley, 2022. https://doi.org/10.1111/jeb.14005.
ieee: A. M. Westram, S. Stankowski, P. Surendranadh, and N. H. Barton, “What is
reproductive isolation?,” Journal of Evolutionary Biology, vol. 35, no.
9. Wiley, pp. 1143–1164, 2022.
ista: Westram AM, Stankowski S, Surendranadh P, Barton NH. 2022. What is reproductive
isolation? Journal of Evolutionary Biology. 35(9), 1143–1164.
mla: Westram, Anja M., et al. “What Is Reproductive Isolation?” Journal of Evolutionary
Biology, vol. 35, no. 9, Wiley, 2022, pp. 1143–64, doi:10.1111/jeb.14005.
short: A.M. Westram, S. Stankowski, P. Surendranadh, N.H. Barton, Journal of Evolutionary
Biology 35 (2022) 1143–1164.
corr_author: '1'
date_created: 2023-01-16T09:59:24Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2025-04-15T08:20:40Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/jeb.14005
external_id:
isi:
- '000849851100002'
pmid:
- '36063156'
file:
- access_level: open_access
checksum: f08de57112330a7ee88d2e1b20576a1e
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T10:05:31Z
date_updated: 2023-01-30T10:05:31Z
file_id: '12448'
file_name: 2022_JourEvoBiology_Westram.pdf
file_size: 3146793
relation: main_file
success: 1
file_date_updated: 2023-01-30T10:05:31Z
has_accepted_license: '1'
intvolume: ' 35'
isi: 1
issue: '9'
keyword:
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1143-1164
pmid: 1
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: Snapdragon Speciation
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '12265'
relation: other
status: public
scopus_import: '1'
status: public
title: What is reproductive isolation?
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 35
year: '2022'
...
---
_id: '12265'
acknowledgement: We are very grateful to the authors of the commentaries for the interesting
discussion and to Luke Holman for handling this set of manuscripts. Part of this
work was funded by the Austrian Science Fund FWF (grant P 32166).
article_processing_charge: Yes (via OA deal)
article_type: letter_note
author:
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Parvathy
full_name: Surendranadh, Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
orcid: 0000-0001-6395-386X
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Westram AM, Stankowski S, Surendranadh P, Barton NH. Reproductive isolation,
speciation, and the value of disagreement: A reply to the commentaries on ‘What
is reproductive isolation?’ Journal of Evolutionary Biology. 2022;35(9):1200-1205.
doi:10.1111/jeb.14082'
apa: 'Westram, A. M., Stankowski, S., Surendranadh, P., & Barton, N. H. (2022).
Reproductive isolation, speciation, and the value of disagreement: A reply to
the commentaries on ‘What is reproductive isolation?’ Journal of Evolutionary
Biology. Wiley. https://doi.org/10.1111/jeb.14082'
chicago: 'Westram, Anja M, Sean Stankowski, Parvathy Surendranadh, and Nicholas
H Barton. “Reproductive Isolation, Speciation, and the Value of Disagreement:
A Reply to the Commentaries on ‘What Is Reproductive Isolation?’” Journal of
Evolutionary Biology. Wiley, 2022. https://doi.org/10.1111/jeb.14082.'
ieee: 'A. M. Westram, S. Stankowski, P. Surendranadh, and N. H. Barton, “Reproductive
isolation, speciation, and the value of disagreement: A reply to the commentaries
on ‘What is reproductive isolation?,’” Journal of Evolutionary Biology,
vol. 35, no. 9. Wiley, pp. 1200–1205, 2022.'
ista: 'Westram AM, Stankowski S, Surendranadh P, Barton NH. 2022. Reproductive isolation,
speciation, and the value of disagreement: A reply to the commentaries on ‘What
is reproductive isolation?’ Journal of Evolutionary Biology. 35(9), 1200–1205.'
mla: 'Westram, Anja M., et al. “Reproductive Isolation, Speciation, and the Value
of Disagreement: A Reply to the Commentaries on ‘What Is Reproductive Isolation?’”
Journal of Evolutionary Biology, vol. 35, no. 9, Wiley, 2022, pp. 1200–05,
doi:10.1111/jeb.14082.'
short: A.M. Westram, S. Stankowski, P. Surendranadh, N.H. Barton, Journal of Evolutionary
Biology 35 (2022) 1200–1205.
corr_author: '1'
date_created: 2023-01-16T09:59:37Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2025-04-15T08:20:40Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/jeb.14082
external_id:
isi:
- '000849851100009'
file:
- access_level: open_access
checksum: 27268009e5eec030bc10667a4ac5ed4c
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T10:14:09Z
date_updated: 2023-01-30T10:14:09Z
file_id: '12449'
file_name: 2022_JourEvoBiology_Westram_Response.pdf
file_size: 349603
relation: main_file
success: 1
file_date_updated: 2023-01-30T10:14:09Z
has_accepted_license: '1'
intvolume: ' 35'
isi: 1
issue: '9'
keyword:
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1200-1205
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: Snapdragon Speciation
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '12264'
relation: other
status: public
scopus_import: '1'
status: public
title: 'Reproductive isolation, speciation, and the value of disagreement: A reply
to the commentaries on ‘What is reproductive isolation?’'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 35
year: '2022'
...
---
_id: '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: '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: 2025-07-10T12:01:26Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/jeb.13723
external_id:
isi:
- '000587769700001'
pmid:
- '33107098'
intvolume: ' 34'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/jeb.13723
month: '02'
oa: 1
oa_version: Published Version
page: 270-283
pmid: 1
project:
- _id: 2662AADE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02463
name: Sex chromosomes and species barriers
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 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: '7205'
abstract:
- lang: eng
text: Genetic incompatibilities contribute to reproductive isolation between many
diverging populations, but it is still unclear to what extent they play a role
if divergence happens with gene flow. In contact zones between the "Crab" and
"Wave" ecotypes of the snail Littorina saxatilis, divergent selection forms strong
barriers to gene flow, while the role of post‐zygotic barriers due to selection
against hybrids remains unclear. High embryo abortion rates in this species could
indicate the presence of such barriers. Post‐zygotic barriers might include genetic
incompatibilities (e.g. Dobzhansky–Muller incompatibilities) but also maladaptation,
both expected to be most pronounced in contact zones. In addition, embryo abortion
might reflect physiological stress on females and embryos independent of any genetic
stress. We examined all embryos of >500 females sampled outside and inside contact
zones of three populations in Sweden. Females' clutch size ranged from 0 to 1,011
embryos (mean 130 ± 123), and abortion rates varied between 0% and 100% (mean
12%). We described female genotypes by using a hybrid index based on hundreds
of SNPs differentiated between ecotypes with which we characterized female genotypes.
We also calculated female SNP heterozygosity and inversion karyotype. Clutch size
did not vary with female hybrid index, and abortion rates were only weakly related
to hybrid index in two sites but not at all in a third site. No additional variation
in abortion rate was explained by female SNP heterozygosity, but increased female
inversion heterozygosity added slightly to increased abortion. Our results show
only weak and probably biologically insignificant post‐zygotic barriers contributing
to ecotype divergence, and the high and variable abortion rates were marginally,
if at all, explained by hybrid index of females.
article_processing_charge: No
article_type: original
author:
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Zuzanna
full_name: Zagrodzka, Zuzanna
last_name: Zagrodzka
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin RK. Is embryo abortion
a post-zygotic barrier to gene flow between Littorina ecotypes? Journal of
Evolutionary Biology. 2020;33(3):342-351. doi:10.1111/jeb.13570
apa: Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R.
K. (2020). Is embryo abortion a post-zygotic barrier to gene flow between Littorina
ecotypes? Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13570
chicago: Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and
Roger K. Butlin. “Is Embryo Abortion a Post-Zygotic Barrier to Gene Flow between
Littorina Ecotypes?” Journal of Evolutionary Biology. Wiley, 2020. https://doi.org/10.1111/jeb.13570.
ieee: K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. K. Butlin, “Is
embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes?,”
Journal of Evolutionary Biology, vol. 33, no. 3. Wiley, pp. 342–351, 2020.
ista: Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin RK. 2020. Is embryo
abortion a post-zygotic barrier to gene flow between Littorina ecotypes? Journal
of Evolutionary Biology. 33(3), 342–351.
mla: Johannesson, Kerstin, et al. “Is Embryo Abortion a Post-Zygotic Barrier to
Gene Flow between Littorina Ecotypes?” Journal of Evolutionary Biology,
vol. 33, no. 3, Wiley, 2020, pp. 342–51, doi:10.1111/jeb.13570.
short: K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R.K. Butlin, Journal
of Evolutionary Biology 33 (2020) 342–351.
date_created: 2019-12-22T23:00:43Z
date_published: 2020-03-01T00:00:00Z
date_updated: 2025-07-10T11:54:22Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/jeb.13570
external_id:
isi:
- '000500954800001'
pmid:
- '31724256'
file:
- access_level: open_access
checksum: 7534ff0839709c0c5265c12d29432f03
content_type: application/pdf
creator: dernst
date_created: 2020-09-22T09:42:18Z
date_updated: 2020-09-22T09:42:18Z
file_id: '8553'
file_name: 2020_EvolBiology_Johannesson.pdf
file_size: 885611
relation: main_file
success: 1
file_date_updated: 2020-09-22T09:42:18Z
has_accepted_license: '1'
intvolume: ' 33'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 342-351
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: '13067'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes?
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: 33
year: '2020'
...
---
_id: '617'
abstract:
- lang: eng
text: Insects are exposed to a variety of potential pathogens in their environment,
many of which can severely impact fitness and health. Consequently, hosts have
evolved resistance and tolerance strategies to suppress or cope with infections.
Hosts utilizing resistance improve fitness by clearing or reducing pathogen loads,
and hosts utilizing tolerance reduce harmful fitness effects per pathogen load.
To understand variation in, and selective pressures on, resistance and tolerance,
we asked to what degree they are shaped by host genetic background, whether plasticity
in these responses depends upon dietary environment, and whether there are interactions
between these two factors. Females from ten wild-type Drosophila melanogaster
genotypes were kept on high- or low-protein (yeast) diets and infected with one
of two opportunistic bacterial pathogens, Lactococcus lactis or Pseudomonas entomophila.
We measured host resistance as the inverse of bacterial load in the early infection
phase. The relationship (slope) between fly fecundity and individual-level bacteria
load provided our fecundity tolerance measure. Genotype and dietary yeast determined
host fecundity and strongly affected survival after infection with pathogenic
P. entomophila. There was considerable genetic variation in host resistance, a
commonly found phenomenon resulting from for example varying resistance costs
or frequency-dependent selection. Despite this variation and the reproductive
cost of higher P. entomophila loads, fecundity tolerance did not vary across genotypes.
The absence of genetic variation in tolerance may suggest that at this early infection
stage, fecundity tolerance is fixed or that any evolved tolerance mechanisms are
not expressed under these infection conditions.
acknowledgement: 'We would like to thank Susann Wicke for performing the genome-wide
SNP/indel analyses, as well as Veronica Alves, Kevin Ferro, Momir Futo, Barbara
Hasert, Dafne Maximo, Nora Schulz, Marlene Sroka, and Barth Wieczorek for technical
help. We thank Brian Lazzaro for the L. lactis strain and Bruno Lemaitre for the
Pseudomonas entomophila strain. We would like to thank two anonymous reviewers for
their helpful comments. We are grateful to the Deutsche Forschungsgemeinschaft (DFG)
priority programme 1399 ‘Host parasite coevolution’ for funding this project (AR
872/1-1). '
article_processing_charge: No
article_type: original
author:
- first_name: Megan
full_name: Kutzer, Megan
id: 29D0B332-F248-11E8-B48F-1D18A9856A87
last_name: Kutzer
orcid: 0000-0002-8696-6978
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
- first_name: Sophie
full_name: Armitage, Sophie
last_name: Armitage
citation:
ama: Kutzer M, Kurtz J, Armitage S. Genotype and diet affect resistance, survival,
and fecundity but not fecundity tolerance. Journal of Evolutionary Biology.
2018;31(1):159-171. doi:10.1111/jeb.13211
apa: Kutzer, M., Kurtz, J., & Armitage, S. (2018). Genotype and diet affect
resistance, survival, and fecundity but not fecundity tolerance. Journal of
Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13211
chicago: Kutzer, Megan, Joachim Kurtz, and Sophie Armitage. “Genotype and Diet Affect
Resistance, Survival, and Fecundity but Not Fecundity Tolerance.” Journal of
Evolutionary Biology. Wiley, 2018. https://doi.org/10.1111/jeb.13211.
ieee: M. Kutzer, J. Kurtz, and S. Armitage, “Genotype and diet affect resistance,
survival, and fecundity but not fecundity tolerance,” Journal of Evolutionary
Biology, vol. 31, no. 1. Wiley, pp. 159–171, 2018.
ista: Kutzer M, Kurtz J, Armitage S. 2018. Genotype and diet affect resistance,
survival, and fecundity but not fecundity tolerance. Journal of Evolutionary Biology.
31(1), 159–171.
mla: Kutzer, Megan, et al. “Genotype and Diet Affect Resistance, Survival, and Fecundity
but Not Fecundity Tolerance.” Journal of Evolutionary Biology, vol. 31,
no. 1, Wiley, 2018, pp. 159–71, doi:10.1111/jeb.13211.
short: M. Kutzer, J. Kurtz, S. Armitage, Journal of Evolutionary Biology 31 (2018)
159–171.
date_created: 2018-12-11T11:47:31Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-09-11T14:06:04Z
day: '01'
department:
- _id: SyCr
doi: 10.1111/jeb.13211
external_id:
isi:
- '000419307000014'
pmid:
- '29150962'
intvolume: ' 31'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/jeb.13211
month: '01'
oa: 1
oa_version: Published Version
page: 159 - 171
pmid: 1
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: published
publisher: Wiley
publist_id: '7187'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genotype and diet affect resistance, survival, and fecundity but not fecundity
tolerance
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 31
year: '2018'
...
---
OA_type: free access
_id: '1905'
abstract:
- lang: eng
text: The unprecedented polymorphism in the major histocompatibility complex (MHC)
genes is thought to be maintained by balancing selection from parasites. However,
do parasites also drive divergence at MHC loci between host populations, or do
the effects of balancing selection maintain similarities among populations? We
examined MHC variation in populations of the livebearing fish Poecilia mexicana
and characterized their parasite communities. Poecilia mexicana populations in
the Cueva del Azufre system are locally adapted to darkness and the presence of
toxic hydrogen sulphide, representing highly divergent ecotypes or incipient species.
Parasite communities differed significantly across populations, and populations
with higher parasite loads had higher levels of diversity at class II MHC genes.
However, despite different parasite communities, marked divergence in adaptive
traits and in neutral genetic markers, we found MHC alleles to be remarkably similar
among host populations. Our findings indicate that balancing selection from parasites
maintains immunogenetic diversity of hosts, but this process does not promote
MHC divergence in this system. On the contrary, we suggest that balancing selection
on immunogenetic loci may outweigh divergent selection causing divergence, thereby
hindering host divergence and speciation. Our findings support the hypothesis
that balancing selection maintains MHC similarities among lineages during and
after speciation (trans-species evolution).
acknowledgement: This study was funded by grants from the National Science Foundation
(NSF) to MT (IOS-1121832) and IS (DEB-0743406) and from the German Science Foundation
(DFG; PL 470/1-2) and ‘LOEWE − Landesoffensive zur Entwicklung wissenschaftlich-ökonomischer
Exzellenz’ of Hesse's Ministry of Higher Education, Research, and the Arts, to MP.
article_processing_charge: No
article_type: original
author:
- first_name: Michael
full_name: Tobler, Michael
last_name: Tobler
- first_name: Martin
full_name: Plath, Martin
last_name: Plath
- first_name: Rüdiger
full_name: Riesch, Rüdiger
last_name: Riesch
- first_name: Ingo
full_name: Schlupp, Ingo
last_name: Schlupp
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Gopi
full_name: Munimanda, Gopi
last_name: Munimanda
- first_name: C
full_name: Setzer, C
last_name: Setzer
- first_name: Dustin
full_name: Penn, Dustin
last_name: Penn
- first_name: Yoshan
full_name: Moodley, Yoshan
last_name: Moodley
citation:
ama: Tobler M, Plath M, Riesch R, et al. Selection from parasites favours immunogenetic
diversity but not divergence among locally adapted host populations. Journal
of Evolutionary Biology. 2014;27(5):960-974. doi:10.1111/jeb.12370
apa: Tobler, M., Plath, M., Riesch, R., Schlupp, I., Grasse, A. V., Munimanda, G.,
… Moodley, Y. (2014). Selection from parasites favours immunogenetic diversity
but not divergence among locally adapted host populations. Journal of Evolutionary
Biology. Wiley. https://doi.org/10.1111/jeb.12370
chicago: Tobler, Michael, Martin Plath, Rüdiger Riesch, Ingo Schlupp, Anna V Grasse,
Gopi Munimanda, C Setzer, Dustin Penn, and Yoshan Moodley. “Selection from Parasites
Favours Immunogenetic Diversity but Not Divergence among Locally Adapted Host
Populations.” Journal of Evolutionary Biology. Wiley, 2014. https://doi.org/10.1111/jeb.12370.
ieee: M. Tobler et al., “Selection from parasites favours immunogenetic diversity
but not divergence among locally adapted host populations,” Journal of Evolutionary
Biology, vol. 27, no. 5. Wiley, pp. 960–974, 2014.
ista: Tobler M, Plath M, Riesch R, Schlupp I, Grasse AV, Munimanda G, Setzer C,
Penn D, Moodley Y. 2014. Selection from parasites favours immunogenetic diversity
but not divergence among locally adapted host populations. Journal of Evolutionary
Biology. 27(5), 960–974.
mla: Tobler, Michael, et al. “Selection from Parasites Favours Immunogenetic Diversity
but Not Divergence among Locally Adapted Host Populations.” Journal of Evolutionary
Biology, vol. 27, no. 5, Wiley, 2014, pp. 960–74, doi:10.1111/jeb.12370.
short: M. Tobler, M. Plath, R. Riesch, I. Schlupp, A.V. Grasse, G. Munimanda, C.
Setzer, D. Penn, Y. Moodley, Journal of Evolutionary Biology 27 (2014) 960–974.
date_created: 2018-12-11T11:54:38Z
date_published: 2014-04-12T00:00:00Z
date_updated: 2025-09-29T12:28:21Z
day: '12'
department:
- _id: SyCr
doi: 10.1111/jeb.12370
external_id:
isi:
- '000334966800015'
pmid:
- '24725091'
intvolume: ' 27'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/jeb.12370
month: '04'
oa: 1
oa_version: None
page: 960 - 974
pmid: 1
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: published
publisher: Wiley
publist_id: '5190'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Selection from parasites favours immunogenetic diversity but not divergence
among locally adapted host populations
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 27
year: '2014'
...