---
OA_place: publisher
OA_type: gold
_id: '18515'
abstract:
- lang: eng
text: "Understanding the role of evolutionary processes in shaping genetic variation
has been a\r\nprimary goal in evolutionary genetics. In this regard, a key question
is how genetically\r\ndistinct populations evolve in the face of gene flow, thereby
generating genetic and\r\nphenotypic divergence and reproductive isolation (RI).
This requires quantifying the role\r\nand relative contributions of prezygotic
and postzygotic isolating mechanisms on the\r\nreduction of gene exchange between
populations, and identifying regions in the genome\r\nthat mediate RI, which is
often polygenic. Further, this needs distinguishing neutral and\r\nselected regions
in the genome, and discerning how selection influences patterns of neutral\r\ndivergence.\r\nPopulation
structure, defined as any deviation from panmixia, such as geographic distribution,
movement and mating patterns of individuals, influences how genetic variation
is\r\nstructured in space and shapes the neutral null model. Availability of large
scale spatial\r\ngenomic datasets now enables us to detect signatures of population
structure in genetic\r\ndata and infer population genetic parameters. Such inferences
are crucial and have wide\r\napplications in biodiversity, conservation genetics,
population management and medical\r\ngenetics. However, inferences are based on
assumptions that do not always match the\r\ncomplex reality, thus leading to erroneous
conclusions. Moreover, the role and interaction\r\nof heterogeneous population
density and dispersal, which are ubiquitous in nature, has\r\nbeen challenging
to study owing to their mathematical complexity. In such scenarios,\r\nfeedback
between theory, data and simulations can prove to be useful.\r\nIn this thesis,
I examine the effect of population structure on neutral genetic variation\r\nand
barriers to gene exchange in hybridising populations, thereby bridging together
the\r\nfields of spatial population genetics and speciation.\r\nDespite being
a key concept in speciation, reproductive isolation (RI) lacks a quantitative\r\ndefinition
and has been used and measured differently across different fields. Chapter 2\r\ngives
a quantitative definition of RI, in terms of the effect of genetic differences
on gene\r\nflow. We give analytical predictions for RI in a range of scenarios,
in terms of effective migration rates for discrete populations and barrier strength
for continuous populations.\r\nIn addition to this, we discuss current measures
of RI and their limitations, and propose\r\nthe need for new measures that combine
organismal and genetic perspectives of RI.\r\nIn chapter 3, I examine the combined
effect of assortative mating, sexual selection\r\nand viability selection on RI.
For this, we consider a polygenic ‘magic’ trait under a\r\nmainland-island model.
We obtain novel theoretical predictions for molecular divergence\r\nin terms of
effective migration rates, which bears a simple relationship to measurable\r\nfitness
components of migrants and various early generation hybrids. We explore the\r\nconditions
under which local adaptation can be maintained despite maladaptive gene flow\r\nand
quantify the relative contributions of viability and sexual selection to genome-wide\r\nbarriers
to gene flow.\r\nThe next two chapters of the thesis focus on a hybrid zone of
Antirrhinum majus that\r\nconsist of two subspecies- the magenta flowered A. m.
pseudomajus and the yellow\r\nflowered A.m. striatum. Previous studies have suggested
that flower colour is target of\r\npollinator mediated selection and is influenced
only by few genes. While these regions\r\nshow high genetic differentiation between
the subspecies, the rest of the genome is seen\r\nto be well mixed. Chapter 4
examines the effects of heterogeneous population density\r\nand leptokurtic dispersal
on isolation by distance and the distribution of heterozygosity\r\nby focusing
on non-flower colour markers.\r\nChapter 5 analyses cline shapes and associations
among 6 focal flower colour markers to\r\nunderstand how selection and dispersal
maintain this hybrid zone. We see sharp coincident\r\nstepped clines at all loci
and positive associations throughout the hybrid zone, contrary to\r\nthe expected
patterns from diffusive gene flow. With a novel scheme of inferring dispersal\r\ncombined
with multilocus simulations, we show that stepped clines do not reflect genetic\r\nbarriers
to gene flow, but are rather a result of long-distance migration. This framework\r\nallows
us to get realistic estimates gene flow and selection and shows how traditional
cline\r\nanalysis may lead to inaccurate conclusions when assumptions of the theory
are not met.\r\nOverall, this thesis investigates how different features of population
structure leave\r\ndetectable signatures in genetic variation, namely in patterns
of isolation by distance,\r\nlinkage disequilibrium and genetic divergence. It
also highlights how effective migration\r\nrates provide useful way of analysing
polygenic architectures and shed new light into\r\nhybrid zones. In doing so,
I identify scenarios when simple models become insufficient\r\nand suggest possibe
directions by combining genetic data with simulations."
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "I also acknowledge the funding agencies Marie Curie COFUND Doctoral
Fellowship,\r\nAustrian Science Fund FWF (grant P32166) and ERC (grant PR1000ERC02)
for financially\r\nsupporting my research over the years."
alternative_title:
- ISTA Thesis
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
citation:
ama: Surendranadh P. Effect of population structure on neutral genetic variation
and barriers to gene exchange. 2024. doi:10.15479/at:ista:18515
apa: Surendranadh, P. (2024). Effect of population structure on neutral genetic
variation and barriers to gene exchange. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:18515
chicago: Surendranadh, Parvathy. “Effect of Population Structure on Neutral Genetic
Variation and Barriers to Gene Exchange.” Institute of Science and Technology
Austria, 2024. https://doi.org/10.15479/at:ista:18515.
ieee: P. Surendranadh, “Effect of population structure on neutral genetic variation
and barriers to gene exchange,” Institute of Science and Technology Austria, 2024.
ista: Surendranadh P. 2024. Effect of population structure on neutral genetic variation
and barriers to gene exchange. Institute of Science and Technology Austria.
mla: Surendranadh, Parvathy. Effect of Population Structure on Neutral Genetic
Variation and Barriers to Gene Exchange. Institute of Science and Technology
Austria, 2024, doi:10.15479/at:ista:18515.
short: P. Surendranadh, Effect of Population Structure on Neutral Genetic Variation
and Barriers to Gene Exchange, Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-11-06T21:25:37Z
date_published: 2024-11-07T00:00:00Z
date_updated: 2026-04-07T12:56:52Z
day: '07'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/at:ista:18515
file:
- access_level: open_access
checksum: c32cf7bc75748d9c551d8eb70178bbec
content_type: application/pdf
creator: psurendr
date_created: 2024-11-07T10:59:29Z
date_updated: 2024-11-07T10:59:29Z
file_id: '18519'
file_name: PhD_Thesis__Parvathy_071124_PDFA.pdf
file_size: 37019760
relation: main_file
success: 1
- access_level: closed
checksum: 4417e02d54084d89e75734e18caaa96d
content_type: application/zip
creator: psurendr
date_created: 2024-11-07T10:59:42Z
date_updated: 2024-11-07T10:59:42Z
file_id: '18520'
file_name: PhD Thesis- Parvathy_071124.zip
file_size: 41198857
relation: source_file
file_date_updated: 2024-11-07T10:59:42Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '11'
oa: 1
oa_version: Published Version
page: '219'
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: Snapdragon Speciation
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: Effect of population structure on neutral genetic variation and barriers to
gene exchange
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
OA_place: publisher
OA_type: gold
_id: '18908'
abstract:
- lang: eng
text: Chromosomal rearrangements can lead to the coupling of reproductive barriers,
but whether and how they contribute to the completion of speciation remains unclear.
Marine snails of the genus Littorina repeatedly form hybrid zones between populations
segregating for multiple inversion arrangements, providing opportunities to study
their barrier effects. Here, we analyzed 2 adjacent transects across hybrid zones
between 2 ecotypes of Littorina fabalis (“large” and “dwarf”) adapted to different
wave exposure conditions on a Swedish island. Applying whole-genome sequencing,
we found 12 putative inversions on 9 of 17 chromosomes. Nine of the putative inversions
reached near differential fixation between the 2 ecotypes, and all were in strong
linkage disequilibrium. These inversions cover 20% of the genome and carry 93%
of divergent single nucleotide polymorphisms (SNPs). Bimodal hybrid zones in both
transects indicated that the 2 ecotypes of Littorina fabalis maintain their genetic
and phenotypic integrity following contact. The bimodality reflects the strong
coupling between inversion clines and the extension of the barrier effect across
the whole genome. Demographic inference suggests that coupling arose during a
period of allopatry and has been maintained for > 1,000 generations after
secondary contact. Overall, this study shows that the coupling of multiple chromosomal
inversions contributes to strong reproductive isolation. Notably, 2 of the putative
inversions overlap with inverted genomic regions associated with ecotype differences
in a closely related species (Littorina saxatilis), suggesting the same regions,
with similar structural variants, repeatedly contribute to ecotype evolution in
distinct species.
acknowledgement: The computations and data handling were enabled by resources provided
by the Swedish National Infrastructure for Computing at UPPMAX partially funded
by the Swedish Research Council through grant agreement no. 2018-05973. We thank
all the member of the Littorina team for the stimulating discussions about the manuscripts,
James Reeves for his help the implementation of Hsplit, and Thomas Broquet for his
useful comments in the latter stage of manuscript revisions.
article_processing_charge: Yes
article_type: letter_note
author:
- first_name: Alan
full_name: Le Moan, Alan
last_name: Le Moan
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Marina
full_name: Rafajlović, Marina
last_name: Rafajlović
- first_name: Olga
full_name: Ortega-Martinez, Olga
last_name: Ortega-Martinez
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Roger K
full_name: Butlin, Roger K
last_name: Butlin
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
citation:
ama: Le Moan A, Stankowski S, Rafajlović M, et al. Coupling of twelve putative chromosomal
inversions maintains a strong barrier to gene flow between snail ecotypes. Evolution
Letters. 2024;8(4):575-586. doi:10.1093/evlett/qrae014
apa: Le Moan, A., Stankowski, S., Rafajlović, M., Ortega-Martinez, O., Faria, R.,
Butlin, R. K., & Johannesson, K. (2024). Coupling of twelve putative chromosomal
inversions maintains a strong barrier to gene flow between snail ecotypes. Evolution
Letters. Oxford University Press. https://doi.org/10.1093/evlett/qrae014
chicago: Le Moan, Alan, Sean Stankowski, Marina Rafajlović, Olga Ortega-Martinez,
Rui Faria, Roger K Butlin, and Kerstin Johannesson. “Coupling of Twelve Putative
Chromosomal Inversions Maintains a Strong Barrier to Gene Flow between Snail Ecotypes.”
Evolution Letters. Oxford University Press, 2024. https://doi.org/10.1093/evlett/qrae014.
ieee: A. Le Moan et al., “Coupling of twelve putative chromosomal inversions
maintains a strong barrier to gene flow between snail ecotypes,” Evolution
Letters, vol. 8, no. 4. Oxford University Press, pp. 575–586, 2024.
ista: Le Moan A, Stankowski S, Rafajlović M, Ortega-Martinez O, Faria R, Butlin
RK, Johannesson K. 2024. Coupling of twelve putative chromosomal inversions maintains
a strong barrier to gene flow between snail ecotypes. Evolution Letters. 8(4),
575–586.
mla: Le Moan, Alan, et al. “Coupling of Twelve Putative Chromosomal Inversions Maintains
a Strong Barrier to Gene Flow between Snail Ecotypes.” Evolution Letters,
vol. 8, no. 4, Oxford University Press, 2024, pp. 575–86, doi:10.1093/evlett/qrae014.
short: A. Le Moan, S. Stankowski, M. Rafajlović, O. Ortega-Martinez, R. Faria, R.K.
Butlin, K. Johannesson, Evolution Letters 8 (2024) 575–586.
date_created: 2025-01-27T13:30:27Z
date_published: 2024-04-23T00:00:00Z
date_updated: 2025-09-09T12:05:51Z
day: '23'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/evlett/qrae014
external_id:
isi:
- '001206532900001'
pmid:
- '39479507'
file:
- access_level: open_access
checksum: 2f7780b7b6b3489755f1815f476639c6
content_type: application/pdf
creator: dernst
date_created: 2025-01-27T13:33:14Z
date_updated: 2025-01-27T13:33:14Z
file_id: '18909'
file_name: 2024_EvolutionLetter_Moan.pdf
file_size: 24356661
relation: main_file
success: 1
file_date_updated: 2025-01-27T13:33:14Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '4'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '04'
oa: 1
oa_version: Published Version
page: 575-586
pmid: 1
publication: Evolution Letters
publication_identifier:
issn:
- 2056-3744
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Coupling of twelve putative chromosomal inversions maintains a strong barrier
to gene flow between snail ecotypes
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: 8
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '18944'
abstract:
- lang: eng
text: 'Understanding connectivity patterns exhibited by endangered species living
in fragmented habitats is fundamental to improving management and conservation
actions. Such improvements can be particularly pressing at the trailing edges
of these habitats, where populations are facing the greatest challenges from climate
change, and appear even more crucial if the species is commercially harvested.
Seascape genetics have been increasingly used to meet these needs. In this study,
we examined connectivity patterns among 32 populations of the oarweed kelp Laminaria
digitata located at the species’ southern range limit. The distance
(or sampling gap) between neighboring populations ranged from a few km to a few
100s of km. By genotyping 11 microsatellite markers, we aimed to (1) refine analyses
of population structure; (2) test whether on-shelf islands are genetically more
differentiated than mainland populations; (3) evaluate the relative importance
of various abiotic conditions in shaping the genetic structure; and (4) evaluate
if the relative importance of each environmental factor varied according to sampling
schemes. Our analyses revealed a positive relationship between connectivity links
and genetic diversity: populations with high levels of connectivity were genetically
enriched while isolated populations showed signs of genetic erosion. The genetically
impoverished populations corresponded to the southernmost populations as well
as populations along the northern coast of Brittany (Locquirec, Saint-Malo Bay)
and the northernmost population in Pas-de-Calais. By performing distance-based
redundancy analysis on various sampling schemes, geographic distance appeared
as the dominant factor influencing connectivity between populations separated
by great distances, while hydrodynamic processes were the main factor when analyzing
at a final spatial resolution.'
article_processing_charge: No
article_type: original
author:
- first_name: Louise
full_name: Fouqueau, Louise
id: 1676e173-8143-11ed-8927-fe165216a93f
last_name: Fouqueau
orcid: 0000-0003-0371-9339
- first_name: L
full_name: Reynes, L
last_name: Reynes
- first_name: F
full_name: Tempera, F
last_name: Tempera
- first_name: T
full_name: Bajjouk, T
last_name: Bajjouk
- first_name: A
full_name: Blanfuné, A
last_name: Blanfuné
- first_name: C
full_name: Chevalier, C
last_name: Chevalier
- first_name: M
full_name: Laurans, M
last_name: Laurans
- first_name: S
full_name: Mauger, S
last_name: Mauger
- first_name: M
full_name: Sourisseau, M
last_name: Sourisseau
- first_name: J
full_name: Assis, J
last_name: Assis
- first_name: L
full_name: Lévêque, L
last_name: Lévêque
- first_name: M
full_name: Valero, M
last_name: Valero
citation:
ama: Fouqueau L, Reynes L, Tempera F, et al. Seascape genetic study on Laminaria
digitata underscores the critical role of sampling schemes. Marine Ecology
Progress Series. 2024;740:23-42. doi:10.3354/meps14640
apa: Fouqueau, L., Reynes, L., Tempera, F., Bajjouk, T., Blanfuné, A., Chevalier,
C., … Valero, M. (2024). Seascape genetic study on Laminaria digitata underscores
the critical role of sampling schemes. Marine Ecology Progress Series.
Inter-Research Science Center. https://doi.org/10.3354/meps14640
chicago: Fouqueau, Louise, L Reynes, F Tempera, T Bajjouk, A Blanfuné, C Chevalier,
M Laurans, et al. “Seascape Genetic Study on Laminaria Digitata Underscores the
Critical Role of Sampling Schemes.” Marine Ecology Progress Series. Inter-Research
Science Center, 2024. https://doi.org/10.3354/meps14640.
ieee: L. Fouqueau et al., “Seascape genetic study on Laminaria digitata underscores
the critical role of sampling schemes,” Marine Ecology Progress Series,
vol. 740. Inter-Research Science Center, pp. 23–42, 2024.
ista: Fouqueau L, Reynes L, Tempera F, Bajjouk T, Blanfuné A, Chevalier C, Laurans
M, Mauger S, Sourisseau M, Assis J, Lévêque L, Valero M. 2024. Seascape genetic
study on Laminaria digitata underscores the critical role of sampling schemes.
Marine Ecology Progress Series. 740, 23–42.
mla: Fouqueau, Louise, et al. “Seascape Genetic Study on Laminaria Digitata Underscores
the Critical Role of Sampling Schemes.” Marine Ecology Progress Series,
vol. 740, Inter-Research Science Center, 2024, pp. 23–42, doi:10.3354/meps14640.
short: L. Fouqueau, L. Reynes, F. Tempera, T. Bajjouk, A. Blanfuné, C. Chevalier,
M. Laurans, S. Mauger, M. Sourisseau, J. Assis, L. Lévêque, M. Valero, Marine
Ecology Progress Series 740 (2024) 23–42.
corr_author: '1'
date_created: 2025-01-29T09:09:10Z
date_published: 2024-07-25T00:00:00Z
date_updated: 2025-01-29T09:12:34Z
day: '25'
department:
- _id: NiBa
doi: 10.3354/meps14640
intvolume: ' 740'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://inria.hal.science/hal-04624490/
month: '07'
oa: 1
oa_version: Submitted Version
page: 23-42
publication: Marine Ecology Progress Series
publication_identifier:
eissn:
- 1616-1599
issn:
- 0171-8630
publication_status: published
publisher: Inter-Research Science Center
quality_controlled: '1'
scopus_import: '1'
status: public
title: Seascape genetic study on Laminaria digitata underscores the critical role
of sampling schemes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 740
year: '2024'
...
---
OA_place: publisher
OA_type: gold
_id: '18949'
abstract:
- lang: eng
text: 'Speciation research—the scientific field focused on understanding the origin
and diversity of species—has a long and complex history. While relevant to one
another, the specific goals and activities of speciation researchers are highly
diverse, and scattered across a collection of different perspectives. Thus, our
understanding of speciation will benefit from efforts to bridge scientific findings
and the diverse people who do the work. In this paper, we outline two ways of
integrating speciation research: (i) scientific integration, through the bringing
together of ideas, data, and approaches; and (ii) social integration, by creating
ways for a diversity of researchers to participate in the scientific process.
We then discuss five challenges to integration: (i) the multidisciplinary nature
of speciation research, (ii) the complex language of speciation; (iii) a bias
toward certain study systems; (iv) the challenges of working across scales; and
(v) inconsistent measures and reporting standards. We provide practical steps
that individuals and groups can take to help overcome these challenges, and argue
that integration is a team effort in which we all have a role to play.'
acknowledgement: "We thank the staff of the Tvärminne Zoological Station (University
of Helsinki) for their hospitality during the workshop. We are also grateful to
everyone who applied to attend the workshop.\r\nFunding for the workshop was provided
by the European Society for Evolutionary Biology through the Special Topic Network
(STN) funding scheme."
article_number: kzae001
article_processing_charge: Yes
article_type: original
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Asher D
full_name: Cutter, Asher D
last_name: Cutter
- first_name: Ina
full_name: Satokangas, Ina
last_name: Satokangas
- first_name: Brian A
full_name: Lerch, Brian A
last_name: Lerch
- first_name: Jonathan
full_name: Rolland, Jonathan
last_name: Rolland
- first_name: Carole M
full_name: Smadja, Carole M
last_name: Smadja
- first_name: J Carolina
full_name: Segami Marzal, J Carolina
last_name: Segami Marzal
- first_name: Christopher R
full_name: Cooney, Christopher R
last_name: Cooney
- first_name: Philine G D
full_name: Feulner, Philine G D
last_name: Feulner
- first_name: Fabricius Maia Chaves Bicalho
full_name: Domingos, Fabricius Maia Chaves Bicalho
last_name: Domingos
- first_name: Henry L
full_name: North, Henry L
last_name: North
- first_name: Ryo
full_name: Yamaguchi, Ryo
last_name: Yamaguchi
- first_name: Roger K
full_name: Butlin, Roger K
last_name: Butlin
- first_name: Jochen B W
full_name: Wolf, Jochen B W
last_name: Wolf
- first_name: Jenn
full_name: Coughlan, Jenn
last_name: Coughlan
- first_name: Patrick
full_name: Heidbreder, Patrick
last_name: Heidbreder
- first_name: Rebeca
full_name: Hernández-Gutiérrez, Rebeca
last_name: Hernández-Gutiérrez
- first_name: Karen B
full_name: Barnard-Kubow, Karen B
last_name: Barnard-Kubow
- first_name: David
full_name: Peede, David
last_name: Peede
- first_name: Loïs
full_name: Rancilhac, Loïs
last_name: Rancilhac
- first_name: Rodrigo Brincalepe
full_name: Salvador, Rodrigo Brincalepe
last_name: Salvador
- first_name: Ken A
full_name: Thompson, Ken A
last_name: Thompson
- first_name: Elizabeth A
full_name: Stacy, Elizabeth A
last_name: Stacy
- first_name: Leonie C
full_name: Moyle, Leonie C
last_name: Moyle
- first_name: Martin D
full_name: Garlovsky, Martin D
last_name: Garlovsky
- first_name: Arif
full_name: Maulana, Arif
last_name: Maulana
- first_name: Annina
full_name: Kantelinen, Annina
last_name: Kantelinen
- first_name: N Ivalú
full_name: Cacho, N Ivalú
last_name: Cacho
- first_name: Hilde
full_name: Schneemann, Hilde
last_name: Schneemann
- first_name: Marisol
full_name: Domínguez, Marisol
last_name: Domínguez
- first_name: Erik B
full_name: Dopman, Erik B
last_name: Dopman
- first_name: Konrad
full_name: Lohse, Konrad
last_name: Lohse
- first_name: Sina J
full_name: Rometsch, Sina J
last_name: Rometsch
- first_name: Aaron A
full_name: Comeault, Aaron A
last_name: Comeault
- first_name: Richard M
full_name: Merrill, Richard M
last_name: Merrill
- first_name: Elizabeth S C
full_name: Scordato, Elizabeth S C
last_name: Scordato
- first_name: Sonal
full_name: Singhal, Sonal
last_name: Singhal
- first_name: Varpu
full_name: Pärssinen, Varpu
last_name: Pärssinen
- first_name: Alycia C R
full_name: Lackey, Alycia C R
last_name: Lackey
- first_name: Sanghamitra
full_name: Kumar, Sanghamitra
last_name: Kumar
- first_name: Joana I
full_name: Meier, Joana I
last_name: Meier
- 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: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Mark
full_name: Ravinet, Mark
last_name: Ravinet
- first_name: Jonna
full_name: Kulmuni, Jonna
last_name: Kulmuni
citation:
ama: Stankowski S, Cutter AD, Satokangas I, et al. Toward the integration of speciation
research. Evolutionary Journal of the Linnean Society. 2024;3(1). doi:10.1093/evolinnean/kzae001
apa: Stankowski, S., Cutter, A. D., Satokangas, I., Lerch, B. A., Rolland, J., Smadja,
C. M., … Kulmuni, J. (2024). Toward the integration of speciation research. Evolutionary
Journal of the Linnean Society. Oxford University Press. https://doi.org/10.1093/evolinnean/kzae001
chicago: Stankowski, Sean, Asher D Cutter, Ina Satokangas, Brian A Lerch, Jonathan
Rolland, Carole M Smadja, J Carolina Segami Marzal, et al. “Toward the Integration
of Speciation Research.” Evolutionary Journal of the Linnean Society. Oxford
University Press, 2024. https://doi.org/10.1093/evolinnean/kzae001.
ieee: S. Stankowski et al., “Toward the integration of speciation research,”
Evolutionary Journal of the Linnean Society, vol. 3, no. 1. Oxford University
Press, 2024.
ista: Stankowski S, Cutter AD, Satokangas I, Lerch BA, Rolland J, Smadja CM, Segami
Marzal JC, Cooney CR, Feulner PGD, Domingos FMCB, North HL, Yamaguchi R, Butlin
RK, Wolf JBW, Coughlan J, Heidbreder P, Hernández-Gutiérrez R, Barnard-Kubow KB,
Peede D, Rancilhac L, Salvador RB, Thompson KA, Stacy EA, Moyle LC, Garlovsky
MD, Maulana A, Kantelinen A, Cacho NI, Schneemann H, Domínguez M, Dopman EB, Lohse
K, Rometsch SJ, Comeault AA, Merrill RM, Scordato ESC, Singhal S, Pärssinen V,
Lackey ACR, Kumar S, Meier JI, Barton NH, Fraisse C, Ravinet M, Kulmuni J. 2024.
Toward the integration of speciation research. Evolutionary Journal of the Linnean
Society. 3(1), kzae001.
mla: Stankowski, Sean, et al. “Toward the Integration of Speciation Research.” Evolutionary
Journal of the Linnean Society, vol. 3, no. 1, kzae001, Oxford University
Press, 2024, doi:10.1093/evolinnean/kzae001.
short: S. Stankowski, A.D. Cutter, I. Satokangas, B.A. Lerch, J. Rolland, C.M. Smadja,
J.C. Segami Marzal, C.R. Cooney, P.G.D. Feulner, F.M.C.B. Domingos, H.L. North,
R. Yamaguchi, R.K. Butlin, J.B.W. Wolf, J. Coughlan, P. Heidbreder, R. Hernández-Gutiérrez,
K.B. Barnard-Kubow, D. Peede, L. Rancilhac, R.B. Salvador, K.A. Thompson, E.A.
Stacy, L.C. Moyle, M.D. Garlovsky, A. Maulana, A. Kantelinen, N.I. Cacho, H. Schneemann,
M. Domínguez, E.B. Dopman, K. Lohse, S.J. Rometsch, A.A. Comeault, R.M. Merrill,
E.S.C. Scordato, S. Singhal, V. Pärssinen, A.C.R. Lackey, S. Kumar, J.I. Meier,
N.H. Barton, C. Fraisse, M. Ravinet, J. Kulmuni, Evolutionary Journal of the Linnean
Society 3 (2024).
corr_author: '1'
date_created: 2025-01-29T10:38:17Z
date_published: 2024-02-16T00:00:00Z
date_updated: 2025-01-29T10:55:54Z
day: '16'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/evolinnean/kzae001
file:
- access_level: open_access
checksum: db08120a92527acaef476bd93f2b87f9
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creator: dernst
date_created: 2025-01-29T10:52:40Z
date_updated: 2025-01-29T10:52:40Z
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file_name: 2024_EvolJourLinneanSoc_Stankowski.pdf
file_size: 3935454
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intvolume: ' 3'
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language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: Evolutionary Journal of the Linnean Society
publication_identifier:
issn:
- 2752-938X
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Toward the integration of speciation research
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '19520'
abstract:
- lang: eng
text: Vertebrates exhibit a wide range of motor behaviors, ranging from swimming
to complex limb-based movements. Here we take advantage of frog metamorphosis,
which captures a swim-to-limb-based movement transformation during the development
of a single organism, to explore changes in the underlying spinal circuits. We
find that the tadpole spinal cord contains small and largely homogeneous populations
of motor neurons (MNs) and V1 interneurons (V1s) at early escape swimming stages.
These neuronal populations only modestly increase in number and subtype heterogeneity
with the emergence of free swimming. In contrast, during frog metamorphosis and
the emergence of limb movement, there is a dramatic expansion of MN and V1 interneuron
number and transcriptional heterogeneity, culminating in cohorts of neurons that
exhibit striking molecular similarity to mammalian motor circuits. CRISPR/Cas9-mediated
gene disruption of the limb MN and V1 determinants FoxP1 and Engrailed-1, respectively,
results in severe but selective deficits in tail and limb function. Our work thus
demonstrates that neural diversity scales exponentially with increasing behavioral
complexity and illustrates striking evolutionary conservation in the molecular
organization and function of motor circuits across species.
acknowledged_ssus:
- _id: Bio
acknowledgement: "We would like to thank the members of the Sweeney Lab (especially
Stavros Papadopoulos and\r\nSophie Gobeil) for their contributions to this project
and, in addition to the lab, Graziana Gatto\r\nand Mario de Bono, for discussion,
and support. We are also grateful to Tom Jessell and Chris\r\nKintner for their
scientific insight and mentorship during the conception of this project. This\r\nproject
would also not have been possible with the technical support of the Matthias Nowak,\r\nVerena
Mayer and the Aquatics as well as the Imaging and Optics Facility support teams\r\n(ISTA).
In addition, we thank our funding sources for providing the resources to do these\r\nexperiments:
FTI Strategy Lower Austria Dissertation Grant Number FT121-D-046 (D.V.);\r\nHorizon
Europe ERC Starting Grant Number 101041551 (L.B.S., F.A.T. and D.V); Special\r\nResearch
Program (SFB) of the Austrian Science Fund (FWF) Project number F7814-B (L.B.S);\r\nNINDS
5R35NS116858 (J.S.D); CZI grant DAF2020-225401 (DOI): 10.37921/120055ratwvi\r\n(R.H.);
NIH grant number R01NS123116 (J.B.B); American Lebanese Syrian Associated\r\nCharities
(ALSAC) (J.B.B.); German Academic Exchange Service (DAAD) IFI Grant Number\r\n57515251-91853472
(Z.H.); and Project A.L.S. (S.B-M.). "
article_processing_charge: No
author:
- first_name: David
full_name: Vijatovic, David
id: cf391e77-ec3c-11ea-a124-d69323410b58
last_name: Vijatovic
- first_name: 'Florina Alexandra '
full_name: 'Toma, Florina Alexandra '
id: 2f73f876-f128-11eb-9611-b96b5a30cb0e
last_name: Toma
- first_name: Zoe P
full_name: Harrington, Zoe P
id: a8144562-32c9-11ee-b5ce-d9800628bda2
last_name: Harrington
orcid: 0009-0008-0158-4032
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Alexandra J.
full_name: Trevisan, Alexandra J.
last_name: Trevisan
- first_name: Phillip
full_name: Chapman, Phillip
last_name: Chapman
- first_name: Mara
full_name: Julseth, Mara
id: 1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1
last_name: Julseth
- first_name: Susan
full_name: Brenner-Morton, Susan
last_name: Brenner-Morton
- first_name: Mariano I.
full_name: Gabitto, Mariano I.
last_name: Gabitto
- first_name: Jeremy S.
full_name: Dasen, Jeremy S.
last_name: Dasen
- first_name: Jay B.
full_name: Bikoff, Jay B.
last_name: Bikoff
- first_name: Lora Beatrice Jaeger
full_name: Sweeney, Lora Beatrice Jaeger
id: 56BE8254-C4F0-11E9-8E45-0B23E6697425
last_name: Sweeney
orcid: 0000-0001-9242-5601
citation:
ama: Vijatovic D, Toma FA, Harrington ZP, et al. Spinal neuron diversity scales
exponentially with swim-to-limb transformation during frog metamorphosis. bioRxiv.
doi:10.1101/2024.09.20.614050
apa: Vijatovic, D., Toma, F. A., Harrington, Z. P., Sommer, C. M., Hauschild, R.,
Trevisan, A. J., … Sweeney, L. B. (n.d.). Spinal neuron diversity scales exponentially
with swim-to-limb transformation during frog metamorphosis. bioRxiv. https://doi.org/10.1101/2024.09.20.614050
chicago: Vijatovic, David, Florina Alexandra Toma, Zoe P Harrington, Christoph
M Sommer, Robert Hauschild, Alexandra J. Trevisan, Phillip Chapman, et al. “Spinal
Neuron Diversity Scales Exponentially with Swim-to-Limb Transformation during
Frog Metamorphosis.” BioRxiv, n.d. https://doi.org/10.1101/2024.09.20.614050.
ieee: D. Vijatovic et al., “Spinal neuron diversity scales exponentially
with swim-to-limb transformation during frog metamorphosis,” bioRxiv. .
ista: Vijatovic D, Toma FA, Harrington ZP, Sommer CM, Hauschild R, Trevisan AJ,
Chapman P, Julseth M, Brenner-Morton S, Gabitto MI, Dasen JS, Bikoff JB, Sweeney
LB. Spinal neuron diversity scales exponentially with swim-to-limb transformation
during frog metamorphosis. bioRxiv, 10.1101/2024.09.20.614050.
mla: Vijatovic, David, et al. “Spinal Neuron Diversity Scales Exponentially with
Swim-to-Limb Transformation during Frog Metamorphosis.” BioRxiv, doi:10.1101/2024.09.20.614050.
short: D. Vijatovic, F.A. Toma, Z.P. Harrington, C.M. Sommer, R. Hauschild, A.J.
Trevisan, P. Chapman, M. Julseth, S. Brenner-Morton, M.I. Gabitto, J.S. Dasen,
J.B. Bikoff, L.B. Sweeney, BioRxiv (n.d.).
corr_author: '1'
date_created: 2025-04-07T08:48:28Z
date_published: 2024-09-27T00:00:00Z
date_updated: 2025-05-14T11:40:13Z
day: '27'
department:
- _id: LoSw
- _id: TiVo
- _id: Bio
- _id: NiBa
doi: 10.1101/2024.09.20.614050
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2024.09.20.614050
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: bd73af52-d553-11ed-ba76-912049f0ac7a
grant_number: FTI21-D-046
name: Development of V1 interneuron diversity during swim-to-walk transition of
Xenopus metamorphosis
- _id: ebb66355-77a9-11ec-83b8-b8ac210a4dae
grant_number: '101041551'
name: Development and Evolution of Tetrapod Motor Circuits
- _id: c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473
grant_number: CZI01
name: Tools for automation and feedback microscopy
publication: bioRxiv
publication_status: submitted
status: public
title: Spinal neuron diversity scales exponentially with swim-to-limb transformation
during frog metamorphosis
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
_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: 2026-06-18T17:53:35Z
day: '28'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/jeb/voae067
external_id:
isi:
- '001258359900001'
pmid:
- '38941551'
intvolume: ' 37'
isi: 1
issue: '6'
language:
- iso: eng
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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:
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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
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success: 1
file_date_updated: 2024-07-15T09:45:25Z
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language:
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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: '17344'
abstract:
- lang: eng
text: 'This file contains the Mathematica notebook associated with the paper Effect
of assortative mating and sexual selection on polygenic barriers to gene flow.
It contains the numerical approximations, analyses, and simulations used in the
study. '
acknowledged_ssus:
- _id: ScienComp
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: Himani
full_name: Sachdeva, Himani
last_name: Sachdeva
citation:
ama: Surendranadh P, Sachdeva H. Mathematica notebook for “Effect of assortative
mating and sexual selection on polygenic barriers to gene flow.” 2024. doi:10.15479/AT:ISTA:17344
apa: Surendranadh, P., & Sachdeva, H. (2024). Mathematica notebook for “Effect
of assortative mating and sexual selection on polygenic barriers to gene flow.”
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:17344
chicago: Surendranadh, Parvathy, and Himani Sachdeva. “Mathematica Notebook for
‘Effect of Assortative Mating and Sexual Selection on Polygenic Barriers to Gene
Flow.’” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:17344.
ieee: P. Surendranadh and H. Sachdeva, “Mathematica notebook for ‘Effect of assortative
mating and sexual selection on polygenic barriers to gene flow.’” Institute of
Science and Technology Austria, 2024.
ista: Surendranadh P, Sachdeva H. 2024. Mathematica notebook for ‘Effect of assortative
mating and sexual selection on polygenic barriers to gene flow’, Institute of
Science and Technology Austria, 10.15479/AT:ISTA:17344.
mla: Surendranadh, Parvathy, and Himani Sachdeva. Mathematica Notebook for “Effect
of Assortative Mating and Sexual Selection on Polygenic Barriers to Gene Flow.”
Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:17344.
short: P. Surendranadh, H. Sachdeva, (2024).
date_created: 2024-07-29T14:01:43Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2025-01-14T13:02:59Z
ddc:
- '576'
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/AT:ISTA:17344
file:
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checksum: 75bdbc7ad7cc6afe4459bc4a8824a302
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creator: psurendr
date_created: 2024-07-29T13:51:11Z
date_updated: 2024-07-29T13:51:11Z
file_id: '17345'
file_name: Submission.nb
file_size: 726132
relation: main_file
success: 1
file_date_updated: 2024-07-29T13:51:11Z
has_accepted_license: '1'
month: '07'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
status: public
title: Mathematica notebook for 'Effect of assortative mating and sexual selection
on polygenic barriers to gene flow'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
_id: '17888'
abstract:
- lang: eng
text: "Context: Biotic resource exploitation is a critical determinant of species’
distributions. However, quantifying resource exploitation patterns through space
and time can be difficult, complicating their incorporation in spatial ecology
studies. Therefore, understanding the local drivers of spatial patterns of resource
exploitation may contribute to better large-scale species distribution models.\r\nObjectives:
We investigated (1) how the resource exploitation patterns of two trophic interactions
(plant–insect) are explained by insect behaviour, resource aggregation, and potential
insect-insect interactions. We also analyzed how (2) resource patch size and (3)
resource accessibility in a heterogeneous landscape affected host exploitation
patterns.\r\nMethods: We quantified nectar robbing by insects in the genus Bombus
(bumblebees) and seed predation by Brachypterolus vestitus larvae (Antirrhinum
beetle) on Antirrhinum majus L. (wild snapdragons) in the Pyrenees Mountains,
Catalonia, Spain. We tested hypotheses about resource exploitation by integrating
spatial analyses at multiple scales.\r\nResults: Both trophic interactions were
aggregated, explained by the aggregation of their resource. At some scales, nectar
robbing is more aggregated than the resource. Trophic interaction abundance is
proportional to resource patch size, following the ideal free distribution model.
Landscape features do not explain the locations exploited. Nectar robbing and
seed predation occur together more often than expected.\r\nConclusions: Our findings
suggest that multiple biotic and ecological spatial factors may simultaneously
affect resource exploitation at a local scale. These findings should be considered
when developing agricultural projects, management plans and conservation policies."
acknowledgement: "For the beetle barcoding, we are very thankful to Brent Emerson’s
laboratory at the Consejo Superior de Investigaciones Científicas (CSIC) at the
Instituto de Productos Naturales y Agrobiología (IPNA) in La Laguna, Tenerife. Many
thanks to numerous field assistants, especially Sandra Cuevas Gallego, Beatriz Pablo
Carmona, Luís Santos Cid and Alex Fuster, for their assistance in data collection.
Finally, we thank Jesús Muñoz, Virgilio Gómez-Rubio, and two anonymous reviewers
for comments that greatly improved the quality of the manuscript.\r\nOpen access
funding provided by Institute of Science and Technology (IST Austria). CB received
funding from the European Union’s Horizon 2020 research and innovation programme
under the Marie Skłodowska-Curie Grant Agreement No. 754411. NB was funded by the
FWF grant “Löwenmaul speciation” P 32166-B32."
article_number: '172'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Guillem
full_name: Pocull Belles, Guillem
id: 54359172-700c-11ef-a103-c1d91ceac6d6
last_name: Pocull Belles
- first_name: Carina
full_name: Baskett, Carina
id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87
last_name: Baskett
orcid: 0000-0002-7354-8574
- 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: 'Pocull Belles G, Baskett C, Barton NH. Multiscale spatial analysis of two
plant–insect interactions: Effects of landscape, resource distribution, and other
insects. Landscape Ecology. 2024;39(9). doi:10.1007/s10980-024-01899-9'
apa: 'Pocull Belles, G., Baskett, C., & Barton, N. H. (2024). Multiscale spatial
analysis of two plant–insect interactions: Effects of landscape, resource distribution,
and other insects. Landscape Ecology. Springer Nature. https://doi.org/10.1007/s10980-024-01899-9'
chicago: 'Pocull Belles, Guillem, Carina Baskett, and Nicholas H Barton. “Multiscale
Spatial Analysis of Two Plant–Insect Interactions: Effects of Landscape, Resource
Distribution, and Other Insects.” Landscape Ecology. Springer Nature, 2024.
https://doi.org/10.1007/s10980-024-01899-9.'
ieee: 'G. Pocull Belles, C. Baskett, and N. H. Barton, “Multiscale spatial analysis
of two plant–insect interactions: Effects of landscape, resource distribution,
and other insects,” Landscape Ecology, vol. 39, no. 9. Springer Nature,
2024.'
ista: 'Pocull Belles G, Baskett C, Barton NH. 2024. Multiscale spatial analysis
of two plant–insect interactions: Effects of landscape, resource distribution,
and other insects. Landscape Ecology. 39(9), 172.'
mla: 'Pocull Belles, Guillem, et al. “Multiscale Spatial Analysis of Two Plant–Insect
Interactions: Effects of Landscape, Resource Distribution, and Other Insects.”
Landscape Ecology, vol. 39, no. 9, 172, Springer Nature, 2024, doi:10.1007/s10980-024-01899-9.'
short: G. Pocull Belles, C. Baskett, N.H. Barton, Landscape Ecology 39 (2024).
corr_author: '1'
date_created: 2024-09-08T22:01:11Z
date_published: 2024-09-01T00:00:00Z
date_updated: 2025-09-08T09:20:11Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1007/s10980-024-01899-9
ec_funded: 1
external_id:
isi:
- '001304011900001'
file:
- access_level: open_access
checksum: 2e1cbc320ec1b4447a5a8562a90bcbc3
content_type: application/pdf
creator: dernst
date_created: 2024-09-11T07:14:03Z
date_updated: 2024-09-11T07:14:03Z
file_id: '18054'
file_name: 2024_LandscapeEcology_Pocull.pdf
file_size: 1494987
relation: main_file
success: 1
file_date_updated: 2024-09-11T07:14:03Z
has_accepted_license: '1'
intvolume: ' 39'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: Snapdragon Speciation
publication: Landscape Ecology
publication_identifier:
eissn:
- 1572-9761
issn:
- 0921-2973
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Multiscale spatial analysis of two plant–insect interactions: Effects of landscape,
resource distribution, and other insects'
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: 39
year: '2024'
...
---
APC_amount: 3062,93 EUR
OA_place: publisher
OA_type: hybrid
_id: '18525'
abstract:
- lang: eng
text: As their statistical power grows, genome-wide association studies (GWAS) have
identified an increasing number of loci underlying quantitative traits of interest.
These loci are scattered throughout the genome and are individually responsible
only for small fractions of the total heritable trait variance. The recently proposed
omnigenic model provides a conceptual framework to explain these observations
by postulating that numerous distant loci contribute to each complex trait via
effect propagation through intracellular regulatory networks. We formalize this
conceptual framework by proposing the “quantitative omnigenic model” (QOM), a
statistical model that combines prior knowledge of the regulatory network topology
with genomic data. By applying our model to gene expression traits in yeast, we
demonstrate that QOM achieves similar gene expression prediction performance to
traditional GWAS with hundreds of times less parameters, while simultaneously
extracting candidate causal and quantitative chains of effect propagation through
the regulatory network for every individual gene. We estimate the fraction of
heritable trait variance in cis- and in trans-, break the latter down by effect
propagation order, assess the trans- variance not attributable to transcriptional
regulation, and show that QOM correctly accounts for the low-dimensional structure
of gene expression covariance. We furthermore demonstrate the relevance of QOM
for systems biology, by employing it as a statistical test for the quality of
regulatory network reconstructions, and linking it to the propagation of nontranscriptional
(including environmental) effects.
acknowledgement: N.R.acknowledges the support of the Austrian Academy of Sciences
through the Doctoral Fellowship Programme (DOC) of the Austrian Academy of Sciences
26917. M.H. and G.T. were supported in part by the Human Frontiers Science Program
Grant RGP0034/2018. We thank Nicholas H. Barton, Fyodor Kondrashov, and Matthew
R. Robinson for fruitful discussions.
article_number: e2402340121
article_processing_charge: Yes
article_type: original
author:
- first_name: Natalia
full_name: Ruzickova, Natalia
id: D2761128-D73D-11E9-A1BF-BA0DE6697425
last_name: Ruzickova
- first_name: Michal
full_name: Hledik, Michal
id: 4171253A-F248-11E8-B48F-1D18A9856A87
last_name: Hledik
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Ruzickova N, Hledik M, Tkačik G. Quantitative omnigenic model discovers interpretable
genome-wide associations. Proceedings of the National Academy of Sciences of
the United States of America. 2024;121(44). doi:10.1073/pnas.2402340121
apa: Ruzickova, N., Hledik, M., & Tkačik, G. (2024). Quantitative omnigenic
model discovers interpretable genome-wide associations. Proceedings of the
National Academy of Sciences of the United States of America. National Academy
of Sciences. https://doi.org/10.1073/pnas.2402340121
chicago: Ruzickova, Natalia, Michal Hledik, and Gašper Tkačik. “Quantitative Omnigenic
Model Discovers Interpretable Genome-Wide Associations.” Proceedings of the
National Academy of Sciences of the United States of America. National Academy
of Sciences, 2024. https://doi.org/10.1073/pnas.2402340121.
ieee: N. Ruzickova, M. Hledik, and G. Tkačik, “Quantitative omnigenic model discovers
interpretable genome-wide associations,” Proceedings of the National Academy
of Sciences of the United States of America, vol. 121, no. 44. National Academy
of Sciences, 2024.
ista: Ruzickova N, Hledik M, Tkačik G. 2024. Quantitative omnigenic model discovers
interpretable genome-wide associations. Proceedings of the National Academy of
Sciences of the United States of America. 121(44), e2402340121.
mla: Ruzickova, Natalia, et al. “Quantitative Omnigenic Model Discovers Interpretable
Genome-Wide Associations.” Proceedings of the National Academy of Sciences
of the United States of America, vol. 121, no. 44, e2402340121, National Academy
of Sciences, 2024, doi:10.1073/pnas.2402340121.
short: N. Ruzickova, M. Hledik, G. Tkačik, Proceedings of the National Academy of
Sciences of the United States of America 121 (2024).
corr_author: '1'
date_created: 2024-11-10T23:01:59Z
date_published: 2024-10-29T00:00:00Z
date_updated: 2026-08-10T07:47:55Z
day: '29'
ddc:
- '570'
department:
- _id: GaTk
- _id: NiBa
doi: 10.1073/pnas.2402340121
external_id:
isi:
- '001349462600001'
pmid:
- '39441639'
file:
- access_level: open_access
checksum: d930e2ccf9ec900c7d7509a78cfb3564
content_type: application/pdf
creator: dernst
date_created: 2024-11-11T09:31:00Z
date_updated: 2024-11-11T09:31:00Z
file_id: '18536'
file_name: 2024_PNAS_Ruzickova.pdf
file_size: 25529709
relation: main_file
success: 1
file_date_updated: 2024-11-11T09:31:00Z
has_accepted_license: '1'
intvolume: ' 121'
isi: 1
issue: '44'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 7bec9174-9f16-11ee-852c-ded9fe5f810e
name: Collective behaviour of cells in pancreatic Islets of Langerhans
- _id: 2665AAFE-B435-11E9-9278-68D0E5697425
grant_number: RGP0034/2018
name: Can evolution minimize spurious signaling crosstalk to reach optimal performance?
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
record:
- id: '20357'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Quantitative omnigenic model discovers interpretable genome-wide associations
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
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(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 121
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '14796'
abstract:
- lang: eng
text: Key innovations are fundamental to biological diversification, but their genetic
basis is poorly understood. A recent transition from egg-laying to live-bearing
in marine snails (Littorina spp.) provides the opportunity to study the genetic
architecture of an innovation that has evolved repeatedly across animals. Individuals
do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical
analysis revealed numerous small genomic regions where all live-bearers carry
the same core haplotype. Candidate regions show evidence for live-bearer–specific
positive selection and are enriched for genes that are differentially expressed
between egg-laying and live-bearing reproductive systems. Ages of selective sweeps
suggest that live-bearer–specific alleles accumulated over more than 200,000 generations.
Our results suggest that new functions evolve through the recruitment of many
alleles rather than in a single evolutionary step.
acknowledgement: "We thank J. Galindo, M. Montaño-Rendón, N. Mikhailova, A. Blakeslee,
E. Arnason, and P. Kemppainen for providing samples; R. Turney, G. Sotelo, J. Larsson,
T. Broquet, and S. Loisel for help collecting samples; Science Animated for providing
the snail cartoons shown in Fig. 1; M. Dunning for help in developing bioinformatic
pipelines; R. Faria, H. Morales, and V. Sousa for advice; and M. Hahn, J. Slate,
M. Ravinet, J. Raeymaekers, A. Comeault, and N. Barton for feedback on a draft manuscript.\r\nThis
work was supported by the Natural Environment Research Council (grant NE/P001610/1
to R.K.B.), the European Research Council (grant ERC-2015-AdG693030-BARRIERS to
R.K.B.), the Norwegian Research Council (RCN Project 315287 to A.M.W.), and the
Swedish Research Council (grant 2020-05385 to E.L.)."
article_processing_charge: No
article_type: original
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Zuzanna B.
full_name: Zagrodzka, Zuzanna B.
last_name: Zagrodzka
- first_name: Martin D.
full_name: Garlovsky, Martin D.
last_name: Garlovsky
- first_name: Arka
full_name: Pal, Arka
id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425
last_name: Pal
orcid: 0000-0002-4530-8469
- first_name: Daria
full_name: Shipilina, Daria
id: 428A94B0-F248-11E8-B48F-1D18A9856A87
last_name: Shipilina
orcid: 0000-0002-1145-9226
- first_name: Diego Fernando
full_name: Garcia Castillo, Diego Fernando
id: ae681a14-dc74-11ea-a0a7-c6ef18161701
last_name: Garcia Castillo
- first_name: Hila
full_name: Lifchitz, Hila
id: d6ab5470-2fb3-11ed-8633-986a9b84edac
last_name: Lifchitz
- first_name: Alan
full_name: Le Moan, Alan
last_name: Le Moan
- first_name: Erica
full_name: Leder, Erica
last_name: Leder
- first_name: James
full_name: Reeve, James
last_name: Reeve
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: Stankowski S, Zagrodzka ZB, Garlovsky MD, et al. The genetic basis of a recent
transition to live-bearing in marine snails. Science. 2024;383(6678):114-119.
doi:10.1126/science.adi2982
apa: Stankowski, S., Zagrodzka, Z. B., Garlovsky, M. D., Pal, A., Shipilina, D.,
Garcia Castillo, D. F., … Butlin, R. K. (2024). The genetic basis of a recent
transition to live-bearing in marine snails. Science. American Association
for the Advancement of Science. https://doi.org/10.1126/science.adi2982
chicago: Stankowski, Sean, Zuzanna B. Zagrodzka, Martin D. Garlovsky, Arka Pal,
Daria Shipilina, Diego Fernando Garcia Castillo, Hila Lifchitz, et al. “The Genetic
Basis of a Recent Transition to Live-Bearing in Marine Snails.” Science.
American Association for the Advancement of Science, 2024. https://doi.org/10.1126/science.adi2982.
ieee: S. Stankowski et al., “The genetic basis of a recent transition to
live-bearing in marine snails,” Science, vol. 383, no. 6678. American Association
for the Advancement of Science, pp. 114–119, 2024.
ista: Stankowski S, Zagrodzka ZB, Garlovsky MD, Pal A, Shipilina D, Garcia Castillo
DF, Lifchitz H, Le Moan A, Leder E, Reeve J, Johannesson K, Westram AM, Butlin
RK. 2024. The genetic basis of a recent transition to live-bearing in marine snails.
Science. 383(6678), 114–119.
mla: Stankowski, Sean, et al. “The Genetic Basis of a Recent Transition to Live-Bearing
in Marine Snails.” Science, vol. 383, no. 6678, American Association for
the Advancement of Science, 2024, pp. 114–19, doi:10.1126/science.adi2982.
short: S. Stankowski, Z.B. Zagrodzka, M.D. Garlovsky, A. Pal, D. Shipilina, D.F.
Garcia Castillo, H. Lifchitz, A. Le Moan, E. Leder, J. Reeve, K. Johannesson,
A.M. Westram, R.K. Butlin, Science 383 (2024) 114–119.
corr_author: '1'
date_created: 2024-01-14T23:00:56Z
date_published: 2024-01-05T00:00:00Z
date_updated: 2026-08-12T22:30:40Z
day: '05'
department:
- _id: NiBa
- _id: GradSch
doi: 10.1126/science.adi2982
external_id:
isi:
- '001138156400003'
pmid:
- '38175895'
intvolume: ' 383'
isi: 1
issue: '6678'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://figshare.com/articles/journal_contribution/The_genetic_basis_of_a_recent_transition_to_live-bearing_in_marine_snails/26356054?file=47868241
month: '01'
oa: 1
oa_version: Submitted Version
page: 114-119
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
link:
- description: News on ISTA Website
relation: press_release
url: https://ista.ac.at/en/news/the-snail-or-the-egg/
record:
- id: '14812'
relation: research_data
status: public
- id: '20694'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: The genetic basis of a recent transition to live-bearing in marine snails
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 383
year: '2024'
...
---
_id: '11479'
abstract:
- lang: eng
text: Understanding population divergence that eventually leads to speciation is
essential for evolutionary biology. High species diversity in the sea was regarded
as a paradox when strict allopatry was considered necessary for most speciation
events because geographical barriers seemed largely absent in the sea, and many
marine species have high dispersal capacities. Combining genome-wide data with
demographic modelling to infer the demographic history of divergence has introduced
new ways to address this classical issue. These models assume an ancestral population
that splits into two subpopulations diverging according to different scenarios
that allow tests for periods of gene flow. Models can also test for heterogeneities
in population sizes and migration rates along the genome to account, respectively,
for background selection and selection against introgressed ancestry. To investigate
how barriers to gene flow arise in the sea, we compiled studies modelling the
demographic history of divergence in marine organisms and extracted preferred
demographic scenarios together with estimates of demographic parameters. These
studies show that geographical barriers to gene flow do exist in the sea but that
divergence can also occur without strict isolation. Heterogeneity of gene flow
was detected in most population pairs suggesting the predominance of semipermeable
barriers during divergence. We found a weak positive relationship between the
fraction of the genome experiencing reduced gene flow and levels of genome-wide
differentiation. Furthermore, we found that the upper bound of the ‘grey zone
of speciation’ for our dataset extended beyond that found before, implying that
gene flow between diverging taxa is possible at higher levels of divergence than
previously thought. Finally, we list recommendations for further strengthening
the use of demographic modelling in speciation research. These include a more
balanced representation of taxa, more consistent and comprehensive modelling,
clear reporting of results and simulation studies to rule out nonbiological explanations
for general results.
acknowledgement: 'We greatly thank all the corresponding authors of the studies that
were included in our synthesis for the sharing of additional data: Thomas Broquet,
Dmitry Filatov, Quentin Rougemont, Paolo Momigliano, Pierre-Alexandre Gagnaire,
Carlos Prada, Ahmed Souissi, Michael Møller Hansen, Sylvie Lapègue, Joseph Di Battista,
Michael Hellberg and Carlos Prada. RKB and ADJ were supported by the European Research
Council. MR was supported by the Swedish Research Council Vetenskapsrådet (grant
number 2021-05243; to MR) and Formas (grant number 2019-00882; to KJ and MR), and
by additional grants from the European Research Council (to RKB) and Vetenskapsrådet
(to KJ) through the Centre for Marine Evolutionary Biology (https://www.gu.se/en/cemeb-marine-evolutionary-biology).'
article_processing_charge: No
article_type: original
author:
- first_name: Aurélien
full_name: De Jode, Aurélien
last_name: De Jode
- first_name: Alan
full_name: Le Moan, Alan
last_name: Le Moan
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
- first_name: Marina
full_name: Rafajlović, Marina
last_name: Rafajlović
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
citation:
ama: De Jode A, Le Moan A, Johannesson K, et al. Ten years of demographic modelling
of divergence and speciation in the sea. Evolutionary Applications. 2023;16(2):542-559.
doi:10.1111/eva.13428
apa: De Jode, A., Le Moan, A., Johannesson, K., Faria, R., Stankowski, S., Westram,
A. M., … Fraisse, C. (2023). Ten years of demographic modelling of divergence
and speciation in the sea. Evolutionary Applications. Wiley. https://doi.org/10.1111/eva.13428
chicago: De Jode, Aurélien, Alan Le Moan, Kerstin Johannesson, Rui Faria, Sean Stankowski,
Anja M Westram, Roger K. Butlin, Marina Rafajlović, and Christelle Fraisse. “Ten
Years of Demographic Modelling of Divergence and Speciation in the Sea.” Evolutionary
Applications. Wiley, 2023. https://doi.org/10.1111/eva.13428.
ieee: A. De Jode et al., “Ten years of demographic modelling of divergence
and speciation in the sea,” Evolutionary Applications, vol. 16, no. 2.
Wiley, pp. 542–559, 2023.
ista: De Jode A, Le Moan A, Johannesson K, Faria R, Stankowski S, Westram AM, Butlin
RK, Rafajlović M, Fraisse C. 2023. Ten years of demographic modelling of divergence
and speciation in the sea. Evolutionary Applications. 16(2), 542–559.
mla: De Jode, Aurélien, et al. “Ten Years of Demographic Modelling of Divergence
and Speciation in the Sea.” Evolutionary Applications, vol. 16, no. 2,
Wiley, 2023, pp. 542–59, doi:10.1111/eva.13428.
short: A. De Jode, A. Le Moan, K. Johannesson, R. Faria, S. Stankowski, A.M. Westram,
R.K. Butlin, M. Rafajlović, C. Fraisse, Evolutionary Applications 16 (2023) 542–559.
date_created: 2022-07-03T22:01:33Z
date_published: 2023-02-01T00:00:00Z
date_updated: 2025-04-23T08:49:14Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
- _id: BeVi
doi: 10.1111/eva.13428
external_id:
isi:
- '000815663700001'
pmid:
- '36793688'
file:
- access_level: open_access
checksum: d4d6fa9ddf36643af994a6a757919afb
content_type: application/pdf
creator: dernst
date_created: 2023-02-27T07:10:17Z
date_updated: 2023-02-27T07:10:17Z
file_id: '12685'
file_name: 2023_EvolutionaryApplications_DeJode.pdf
file_size: 2269822
relation: main_file
success: 1
file_date_updated: 2023-02-27T07:10:17Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 542-559
pmid: 1
publication: Evolutionary Applications
publication_identifier:
eissn:
- 1752-4571
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ten years of demographic modelling of divergence and speciation in the sea
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2023'
...
---
OA_type: free access
_id: '12166'
abstract:
- lang: eng
text: Kerstin Johannesson is a marine ecologist and evolutionary biologist based
at the Tjärnö Marine Laboratory of the University of Gothenburg, which is situated
in the beautiful Kosterhavet National Park on the Swedish west coast. Her work,
using marine periwinkles (especially Littorina saxatilis and L. fabalis) as main
model systems, has made a remarkable contribution to marine evolutionary biology
and our understanding of local adaptation and its genetic underpinnings.
article_processing_charge: No
article_type: editorial
author:
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
citation:
ama: Westram AM, Butlin R. Professor Kerstin Johannesson–winner of the 2022 Molecular
Ecology Prize. Molecular Ecology. 2023;32(1):26-29. doi:10.1111/mec.16779
apa: Westram, A. M., & Butlin, R. (2023). Professor Kerstin Johannesson–winner
of the 2022 Molecular Ecology Prize. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.16779
chicago: Westram, Anja M, and Roger Butlin. “Professor Kerstin Johannesson–Winner
of the 2022 Molecular Ecology Prize.” Molecular Ecology. Wiley, 2023. https://doi.org/10.1111/mec.16779.
ieee: A. M. Westram and R. Butlin, “Professor Kerstin Johannesson–winner of the
2022 Molecular Ecology Prize,” Molecular Ecology, vol. 32, no. 1. Wiley,
pp. 26–29, 2023.
ista: Westram AM, Butlin R. 2023. Professor Kerstin Johannesson–winner of the 2022
Molecular Ecology Prize. Molecular Ecology. 32(1), 26–29.
mla: Westram, Anja M., and Roger Butlin. “Professor Kerstin Johannesson–Winner of
the 2022 Molecular Ecology Prize.” Molecular Ecology, vol. 32, no. 1, Wiley,
2023, pp. 26–29, doi:10.1111/mec.16779.
short: A.M. Westram, R. Butlin, Molecular Ecology 32 (2023) 26–29.
corr_author: '1'
date_created: 2023-01-12T12:10:28Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2026-06-18T17:24:18Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/mec.16779
external_id:
isi:
- '000892168800001'
pmid:
- '36443277'
intvolume: ' 32'
isi: 1
issue: '1'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/mec.16779
month: '01'
oa: 1
oa_version: Published Version
page: 26-29
pmid: 1
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2023'
...
---
_id: '12514'
abstract:
- lang: eng
text: The concept of a “speciation continuum” has gained popularity in recent decades.
It emphasizes speciation as a continuous process that may be studied by comparing
contemporary population pairs that show differing levels of divergence. In their
recent perspective article in Evolution, Stankowski and Ravinet provided a valuable
service by formally defining the speciation continuum as a continuum of reproductive
isolation, based on opinions gathered from a survey of speciation researchers.
While we agree that the speciation continuum has been a useful concept to advance
the understanding of the speciation process, some intrinsic limitations exist.
Here, we advocate for a multivariate extension, the speciation hypercube, first
proposed by Dieckmann et al. in 2004, but rarely used since. We extend the idea
of the speciation cube and suggest it has strong conceptual and practical advantages
over a one-dimensional model. We illustrate how the speciation hypercube can be
used to visualize and compare different speciation trajectories, providing new
insights into the processes and mechanisms of speciation. A key strength of the
speciation hypercube is that it provides a unifying framework for speciation research,
as it allows questions from apparently disparate subfields to be addressed in
a single conceptual model.
acknowledgement: "The authors of this article were supported by LMU Munich (J.B.W.W.),
a James S. McDonnell Foundation postdoctoral fellowship (A.K.H.). P.N. received
funding from the European Research Council (ERC) under the European Union’s Horizon
2020 research and innovation program (Grant agreement No. 770826 EE-Dynamics).\r\nWe
thank participants in the 2019 Gordon Conference on Speciation for the extensive
conversation on this topic. Thanks to Dan Funk for providing permission to use data
from Funk et al. 2006, and for comments on the manuscript."
article_processing_charge: No
article_type: original
author:
- first_name: Daniel I.
full_name: Bolnick, Daniel I.
last_name: Bolnick
- first_name: Amanda K.
full_name: Hund, Amanda K.
last_name: Hund
- first_name: Patrik
full_name: Nosil, Patrik
last_name: Nosil
- first_name: Foen
full_name: Peng, Foen
last_name: Peng
- first_name: Mark
full_name: Ravinet, Mark
last_name: Ravinet
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Swapna
full_name: Subramanian, Swapna
last_name: Subramanian
- first_name: Jochen B.W.
full_name: Wolf, Jochen B.W.
last_name: Wolf
- first_name: Roman
full_name: Yukilevich, Roman
last_name: Yukilevich
citation:
ama: 'Bolnick DI, Hund AK, Nosil P, et al. A multivariate view of the speciation
continuum. Evolution: International journal of organic evolution. 2023;77(1):318-328.
doi:10.1093/evolut/qpac004'
apa: 'Bolnick, D. I., Hund, A. K., Nosil, P., Peng, F., Ravinet, M., Stankowski,
S., … Yukilevich, R. (2023). A multivariate view of the speciation continuum.
Evolution: International Journal of Organic Evolution. Oxford University
Press. https://doi.org/10.1093/evolut/qpac004'
chicago: 'Bolnick, Daniel I., Amanda K. Hund, Patrik Nosil, Foen Peng, Mark Ravinet,
Sean Stankowski, Swapna Subramanian, Jochen B.W. Wolf, and Roman Yukilevich. “A
Multivariate View of the Speciation Continuum.” Evolution: International Journal
of Organic Evolution. Oxford University Press, 2023. https://doi.org/10.1093/evolut/qpac004.'
ieee: 'D. I. Bolnick et al., “A multivariate view of the speciation continuum,”
Evolution: International journal of organic evolution, vol. 77, no. 1.
Oxford University Press, pp. 318–328, 2023.'
ista: 'Bolnick DI, Hund AK, Nosil P, Peng F, Ravinet M, Stankowski S, Subramanian
S, Wolf JBW, Yukilevich R. 2023. A multivariate view of the speciation continuum.
Evolution: International journal of organic evolution. 77(1), 318–328.'
mla: 'Bolnick, Daniel I., et al. “A Multivariate View of the Speciation Continuum.”
Evolution: International Journal of Organic Evolution, vol. 77, no. 1,
Oxford University Press, 2023, pp. 318–28, doi:10.1093/evolut/qpac004.'
short: 'D.I. Bolnick, A.K. Hund, P. Nosil, F. Peng, M. Ravinet, S. Stankowski, S.
Subramanian, J.B.W. Wolf, R. Yukilevich, Evolution: International Journal of Organic
Evolution 77 (2023) 318–328.'
date_created: 2023-02-05T23:00:59Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2026-06-18T17:26:56Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/evolut/qpac004
external_id:
isi:
- '001021686300024'
pmid:
- '36622661'
intvolume: ' 77'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/evolut/qpac004
month: '01'
oa: 1
oa_version: Published Version
page: 318-328
pmid: 1
publication: 'Evolution: International journal of organic evolution'
publication_identifier:
eissn:
- 1558-5646
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: A multivariate view of the speciation continuum
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 77
year: '2023'
...
---
_id: '12933'
abstract:
- lang: eng
text: Datasets of the publication "Sex-specific estimation of cis and trans regulation
of gene expression in heads and gonads of Drosophila melanogaster".
article_processing_charge: No
author:
- first_name: Gemma
full_name: Puixeu Sala, Gemma
id: 33AB266C-F248-11E8-B48F-1D18A9856A87
last_name: Puixeu Sala
orcid: 0000-0001-8330-1754
citation:
ama: 'Puixeu Sala G. Data from: Sex-specific estimation of cis and trans regulation
of gene expression in heads and gonads of Drosophila melanogaster. 2023. doi:10.15479/AT:ISTA:12933'
apa: 'Puixeu Sala, G. (2023). Data from: Sex-specific estimation of cis and trans
regulation of gene expression in heads and gonads of Drosophila melanogaster.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12933'
chicago: 'Puixeu Sala, Gemma. “Data from: Sex-Specific Estimation of Cis and Trans
Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12933.'
ieee: 'G. Puixeu Sala, “Data from: Sex-specific estimation of cis and trans regulation
of gene expression in heads and gonads of Drosophila melanogaster.” Institute
of Science and Technology Austria, 2023.'
ista: 'Puixeu Sala G. 2023. Data from: Sex-specific estimation of cis and trans
regulation of gene expression in heads and gonads of Drosophila melanogaster,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:12933.'
mla: 'Puixeu Sala, Gemma. Data from: Sex-Specific Estimation of Cis and Trans
Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.
Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12933.'
short: G. Puixeu Sala, (2023).
contributor:
- first_name: Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
corr_author: '1'
date_created: 2023-05-10T10:00:49Z
date_published: 2023-05-15T00:00:00Z
date_updated: 2026-04-07T13:25:33Z
day: '15'
ddc:
- '570'
department:
- _id: GradSch
- _id: NiBa
- _id: BeVi
doi: 10.15479/AT:ISTA:12933
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file_size: 19543247
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date_updated: 2023-05-11T12:50:18Z
file_id: '12944'
file_name: readme.txt
file_size: 4566
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file_date_updated: 2023-05-11T12:50:18Z
has_accepted_license: '1'
month: '05'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '14077'
relation: used_in_publication
status: public
- id: '14058'
relation: used_in_publication
status: public
status: public
title: 'Data from: Sex-specific estimation of cis and trans regulation of gene expression
in heads and gonads of Drosophila melanogaster'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12949'
abstract:
- lang: eng
text: The classical infinitesimal model is a simple and robust model for the inheritance
of quantitative traits. In this model, a quantitative trait is expressed as the
sum of a genetic and a non-genetic (environmental) component and the genetic component
of offspring traits within a family follows a normal distribution around the average
of the parents’ trait values, and has a variance that is independent of the trait
values of the parents. Although the trait distribution across the whole population
can be far from normal, the trait distributions within families are normally distributed
with a variance-covariance matrix that is determined entirely by that in the
ancestral population and the probabilities of identity determined by the pedigree.
Moreover, conditioning on some of the trait values within the pedigree has predictable
effects on the mean and variance within and between families. In previous work,
Barton et al. (2017), we showed that when trait values are determined by the sum
of a large number of Mendelian factors, each of small effect, one can justify
the infinitesimal model as limit of Mendelian inheritance. It was also shown that
under some forms of epistasis, trait values within a family are still normally
distributed.
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. The infinitesimal model with dominance. 2023. doi:10.15479/AT:ISTA:12949
apa: Barton, N. H. (2023). The infinitesimal model with dominance. Institute of
Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12949
chicago: Barton, Nicholas H. “The Infinitesimal Model with Dominance.” Institute
of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12949.
ieee: N. H. Barton, “The infinitesimal model with dominance.” Institute of Science
and Technology Austria, 2023.
ista: Barton NH. 2023. The infinitesimal model with dominance, Institute of Science
and Technology Austria, 10.15479/AT:ISTA:12949.
mla: Barton, Nicholas H. The Infinitesimal Model with Dominance. Institute
of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12949.
short: N.H. Barton, (2023).
contributor:
- contributor_type: researcher
first_name: Amandine
last_name: Veber
- contributor_type: researcher
first_name: Alison
last_name: Etheridge
corr_author: '1'
date_created: 2023-05-13T09:49:09Z
date_published: 2023-05-13T00:00:00Z
date_updated: 2025-09-09T13:07:07Z
day: '13'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:12949
file:
- access_level: open_access
checksum: b0ce7d4b1ee7e7265430ceed36fc3336
content_type: application/octet-stream
creator: nbarton
date_created: 2023-05-13T09:36:33Z
date_updated: 2023-05-13T09:36:33Z
file_id: '12950'
file_name: Neutral identities 16th Jan
file_size: 13662
relation: main_file
success: 1
- access_level: open_access
checksum: ad5035ad4f7d3b150a252c79884f6a83
content_type: application/octet-stream
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keyword:
- Quantitative genetics
- infinitesimal model
month: '05'
oa: 1
oa_version: Published Version
project:
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grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publisher: Institute of Science and Technology Austria
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title: The infinitesimal model with dominance
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...
---
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_id: '14058'
abstract:
- lang: eng
text: "Females and males across species are subject to divergent selective pressures
arising\r\nfrom di↵erent reproductive interests and ecological niches. This often
translates into a\r\nintricate array of sex-specific natural and sexual selection
on traits that have a shared\r\ngenetic basis between both sexes, causing a genetic
sexual conflict. The resolution of\r\nthis conflict mostly relies on the evolution
of sex-specific expression of the shared genes,\r\nleading to phenotypic sexual
dimorphism. Such sex-specific gene expression is thought\r\nto evolve via modifications
of the genetic networks ultimately linked to sex-determining\r\ntranscription
factors. Although much empirical and theoretical evidence supports this\r\nstandard
picture of the molecular basis of sexual conflict resolution, there still are
a\r\nfew open questions regarding the complex array of selective forces driving
phenotypic\r\ndi↵erentiation between the sexes, as well as the molecular mechanisms
underlying sexspecific adaptation. I address some of these open questions in my
PhD thesis.\r\nFirst, how do patterns of phenotypic sexual dimorphism vary within
populations,\r\nas a response to the temporal and spatial changes in sex-specific
selective forces? To\r\ntackle this question, I analyze the patterns of sex-specific
phenotypic variation along\r\nthree life stages and across populations spanning
the whole geographical range of Rumex\r\nhastatulus, a wind-pollinated angiosperm,
in the first Chapter of the thesis.\r\nSecond, how do gene expression patterns
lead to phenotypic dimorphism, and what\r\nare the molecular mechanisms underlying
the observed transcriptomic variation? I\r\naddress this question by examining
the sex- and tissue-specific expression variation in\r\nnewly-generated datasets
of sex-specific expression in heads and gonads of Drosophila\r\nmelanogaster.
I additionally used two complementary approaches for the study of the\r\ngenetic
basis of sex di↵erences in gene expression in the second and third Chapters of\r\nthe
thesis.\r\nThird, how does intersex correlation, thought to be one of the main
aspects constraining the ability for the two sexes to decouple, interact with
the evolution of sexual\r\ndimorphism? I develop models of sex-specific stabilizing
selection, mutation and drift\r\nto formalize common intuition regarding the patterns
of covariation between intersex\r\ncorrelation and sexual dimorphism in the fourth
Chapter of the thesis.\r\nAlltogether, the work described in this PhD thesis provides
useful insights into the\r\nlinks between genetic, transcriptomic and phenotypic
layers of sex-specific variation,\r\nand contributes to our general understanding
of the dynamics of sexual dimorphism\r\nevolution."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Gemma
full_name: Puixeu Sala, Gemma
id: 33AB266C-F248-11E8-B48F-1D18A9856A87
last_name: Puixeu Sala
orcid: 0000-0001-8330-1754
citation:
ama: 'Puixeu Sala G. The molecular basis of sexual dimorphism: Experimental and
theoretical characterization of phenotypic, transcriptomic and genetic patterns
of sex-specific adaptation. 2023. doi:10.15479/at:ista:14058'
apa: 'Puixeu Sala, G. (2023). The molecular basis of sexual dimorphism: Experimental
and theoretical characterization of phenotypic, transcriptomic and genetic patterns
of sex-specific adaptation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14058'
chicago: 'Puixeu Sala, Gemma. “The Molecular Basis of Sexual Dimorphism: Experimental
and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns
of Sex-Specific Adaptation.” Institute of Science and Technology Austria, 2023.
https://doi.org/10.15479/at:ista:14058.'
ieee: 'G. Puixeu Sala, “The molecular basis of sexual dimorphism: Experimental and
theoretical characterization of phenotypic, transcriptomic and genetic patterns
of sex-specific adaptation,” Institute of Science and Technology Austria, 2023.'
ista: 'Puixeu Sala G. 2023. The molecular basis of sexual dimorphism: Experimental
and theoretical characterization of phenotypic, transcriptomic and genetic patterns
of sex-specific adaptation. Institute of Science and Technology Austria.'
mla: 'Puixeu Sala, Gemma. The Molecular Basis of Sexual Dimorphism: Experimental
and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns
of Sex-Specific Adaptation. Institute of Science and Technology Austria, 2023,
doi:10.15479/at:ista:14058.'
short: 'G. Puixeu Sala, The Molecular Basis of Sexual Dimorphism: Experimental and
Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns
of Sex-Specific Adaptation, Institute of Science and Technology Austria, 2023.'
corr_author: '1'
date_created: 2023-08-15T10:20:40Z
date_published: 2023-08-15T00:00:00Z
date_updated: 2026-04-07T13:25:34Z
day: '15'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: GradSch
- _id: NiBa
- _id: BeVi
doi: 10.15479/at:ista:14058
ec_funded: 1
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date_updated: 2023-08-17T06:55:24Z
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file_name: PhDThesis_PuixeuG.pdf
file_size: 19856686
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language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '230'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 9B9DFC9E-BA93-11EA-9121-9846C619BF3A
grant_number: '25817'
name: 'Sexual conflict: resolution, constraints and biomedical implications'
publication_identifier:
isbn:
- 978-3-99078-035-0
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
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- id: '9803'
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status: public
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- id: '14077'
relation: part_of_dissertation
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status: public
supervisor:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: 'The molecular basis of sexual dimorphism: Experimental and theoretical characterization
of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2023'
...
---
_id: '14077'
abstract:
- lang: eng
text: "The regulatory architecture of gene expression is known to differ substantially
between sexes in Drosophila, but most studies performed\r\nso far used whole-body
data and only single crosses, which may have limited their scope to detect patterns
that are robust across tissues\r\nand biological replicates. Here, we use allele-specific
gene expression of parental and reciprocal hybrid crosses between 6 Drosophila\r\nmelanogaster
inbred lines to quantify cis- and trans-regulatory variation in heads and gonads
of both sexes separately across 3 replicate\r\ncrosses. Our results suggest that
female and male heads, as well as ovaries, have a similar regulatory architecture.
On the other hand,\r\ntestes display more and substantially different cis-regulatory
effects, suggesting that sex differences in the regulatory architecture that\r\nhave
been previously observed may largely derive from testis-specific effects. We also
examine the difference in cis-regulatory variation\r\nof genes across different
levels of sex bias in gonads and heads. Consistent with the idea that intersex
correlations constrain expression\r\nand can lead to sexual antagonism, we find
more cis variation in unbiased and moderately biased genes in heads. In ovaries,
reduced cis\r\nvariation is observed for male-biased genes, suggesting that cis
variants acting on these genes in males do not lead to changes in ovary\r\nexpression.
Finally, we examine the dominance patterns of gene expression and find that sex-
and tissue-specific patterns of inheritance\r\nas well as trans-regulatory variation
are highly variable across biological crosses, although these were performed in
highly controlled\r\nexperimental conditions. This highlights the importance of
using various genetic backgrounds to infer generalizable patterns."
acknowledged_ssus:
- _id: ScienComp
acknowledgement: We thank members of the Vicoso Group for comments on the manuscript,
the Scientific Computing Unit at ISTA for technical support, and 2 anonymous reviewers
for useful feedback. GP is the recipient of a DOC Fellowship of the Austrian Academy
of Sciences at the Institute of Science and Technology Austria (DOC 25817) and received
funding from the European Union’s Horizon 2020 research and innovation program under
the Marie Skłodowska-Curie Grant (agreement no. 665385).
article_processing_charge: Yes
article_type: original
author:
- first_name: Gemma
full_name: Puixeu Sala, Gemma
id: 33AB266C-F248-11E8-B48F-1D18A9856A87
last_name: Puixeu Sala
orcid: 0000-0001-8330-1754
- first_name: Ariana
full_name: Macon, Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: 'Puixeu Sala G, Macon A, Vicoso B. Sex-specific estimation of cis and trans
regulation of gene expression in heads and gonads of Drosophila melanogaster.
G3: Genes, Genomes, Genetics. 2023;13(8). doi:10.1093/g3journal/jkad121'
apa: 'Puixeu Sala, G., Macon, A., & Vicoso, B. (2023). Sex-specific estimation
of cis and trans regulation of gene expression in heads and gonads of Drosophila
melanogaster. G3: Genes, Genomes, Genetics. Oxford University Press. https://doi.org/10.1093/g3journal/jkad121'
chicago: 'Puixeu Sala, Gemma, Ariana Macon, and Beatriz Vicoso. “Sex-Specific Estimation
of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila
Melanogaster.” G3: Genes, Genomes, Genetics. Oxford University Press, 2023.
https://doi.org/10.1093/g3journal/jkad121.'
ieee: 'G. Puixeu Sala, A. Macon, and B. Vicoso, “Sex-specific estimation of cis
and trans regulation of gene expression in heads and gonads of Drosophila melanogaster,”
G3: Genes, Genomes, Genetics, vol. 13, no. 8. Oxford University Press,
2023.'
ista: 'Puixeu Sala G, Macon A, Vicoso B. 2023. Sex-specific estimation of cis and
trans regulation of gene expression in heads and gonads of Drosophila melanogaster.
G3: Genes, Genomes, Genetics. 13(8).'
mla: 'Puixeu Sala, Gemma, et al. “Sex-Specific Estimation of Cis and Trans Regulation
of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” G3: Genes,
Genomes, Genetics, vol. 13, no. 8, Oxford University Press, 2023, doi:10.1093/g3journal/jkad121.'
short: 'G. Puixeu Sala, A. Macon, B. Vicoso, G3: Genes, Genomes, Genetics 13 (2023).'
corr_author: '1'
date_created: 2023-08-18T06:52:14Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2026-04-07T13:25:34Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
- _id: NiBa
- _id: GradSch
doi: 10.1093/g3journal/jkad121
ec_funded: 1
external_id:
isi:
- '001002997200001'
pmid:
- '37259621'
file:
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checksum: c62e29fc7c5efbf8356f4c60cab4a2d1
content_type: application/pdf
creator: dernst
date_created: 2023-11-07T09:00:19Z
date_updated: 2023-11-07T09:00:19Z
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file_name: 2023_G3_Puixeu.pdf
file_size: 845642
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success: 1
file_date_updated: 2023-11-07T09:00:19Z
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intvolume: ' 13'
isi: 1
issue: '8'
keyword:
- Genetics (clinical)
- Genetics
- Molecular Biology
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 9B9DFC9E-BA93-11EA-9121-9846C619BF3A
grant_number: '25817'
name: 'Sexual conflict: resolution, constraints and biomedical implications'
publication: 'G3: Genes, Genomes, Genetics'
publication_identifier:
issn:
- 2160-1836
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
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title: Sex-specific estimation of cis and trans regulation of gene expression in heads
and gonads of Drosophila melanogaster
tmp:
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legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
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type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2023'
...
---
_id: '14452'
abstract:
- lang: eng
text: The classical infinitesimal model is a simple and robust model for the inheritance
of quantitative traits. In this model, a quantitative trait is expressed as the
sum of a genetic and an environmental component, and the genetic component of
offspring traits within a family follows a normal distribution around the average
of the parents’ trait values, and has a variance that is independent of the parental
traits. In previous work, we showed that when trait values are determined by the
sum of a large number of additive Mendelian factors, each of small effect, one
can justify the infinitesimal model as a limit of Mendelian inheritance. In this
paper, we show that this result extends to include dominance. We define the model
in terms of classical quantities of quantitative genetics, before justifying it
as a limit of Mendelian inheritance as the number, M, of underlying loci tends
to infinity. As in the additive case, the multivariate normal distribution of
trait values across the pedigree can be expressed in terms of variance components
in an ancestral population and probabilities of identity by descent determined
by the pedigree. Now, with just first-order dominance effects, we require two-,
three-, and four-way identities. We also show that, even if we condition on parental
trait values, the “shared” and “residual” components of trait values within each
family will be asymptotically normally distributed as the number of loci tends
to infinity, with an error of order 1/M−−√. We illustrate our results with some
numerical examples.
acknowledgement: NHB was supported in part by ERC Grants 250152 and 101055327. AV
was partly supported by the chaire Modélisation Mathématique et Biodiversité of
Veolia Environment—Ecole Polytechnique—Museum National d’Histoire Naturelle—Fondation
X.
article_number: iyad133
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison M.
full_name: Etheridge, Alison M.
last_name: Etheridge
- first_name: Amandine
full_name: Véber, Amandine
last_name: Véber
citation:
ama: Barton NH, Etheridge AM, Véber A. The infinitesimal model with dominance. Genetics.
2023;225(2). doi:10.1093/genetics/iyad133
apa: Barton, N. H., Etheridge, A. M., & Véber, A. (2023). The infinitesimal
model with dominance. Genetics. Oxford University Press. https://doi.org/10.1093/genetics/iyad133
chicago: Barton, Nicholas H, Alison M. Etheridge, and Amandine Véber. “The Infinitesimal
Model with Dominance.” Genetics. Oxford University Press, 2023. https://doi.org/10.1093/genetics/iyad133.
ieee: N. H. Barton, A. M. Etheridge, and A. Véber, “The infinitesimal model with
dominance,” Genetics, vol. 225, no. 2. Oxford University Press, 2023.
ista: Barton NH, Etheridge AM, Véber A. 2023. The infinitesimal model with dominance.
Genetics. 225(2), iyad133.
mla: Barton, Nicholas H., et al. “The Infinitesimal Model with Dominance.” Genetics,
vol. 225, no. 2, iyad133, Oxford University Press, 2023, doi:10.1093/genetics/iyad133.
short: N.H. Barton, A.M. Etheridge, A. Véber, Genetics 225 (2023).
date_created: 2023-10-29T23:01:15Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2025-09-09T13:07:07Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/genetics/iyad133
ec_funded: 1
external_id:
arxiv:
- '2211.03515'
isi:
- '001148042000008'
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issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication: Genetics
publication_identifier:
eissn:
- 1943-2631
issn:
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publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
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title: The infinitesimal model with dominance
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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: 225
year: '2023'
...