---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20190'
abstract:
- lang: eng
text: 'A major goal of speciation research is identifying loci that underpin barriers
to gene flow. Population genomics takes a ‘bottom-up’ approach, scanning the genome
for molecular signatures of processes that drive or maintain divergence. However,
interpreting the ‘genomic landscape’ of speciation is complicated, because genome
scans conflate multiple processes, most of which are not informative about gene
flow. However, studying replicated population contrasts, including multiple incidences
of secondary contact, can strengthen inferences. In this paper, we use linked-read
sequencing (haplotagging), FST scans and genealogical methods to characterise
the genomic landscape associated with replicate hybrid zone formation. We studied
two flower colour varieties of the common snapdragon, Antirrhinum majus subspecies
majus, that form secondary hybrid zones in multiple independent valleys in the
Pyrenees. Consistent with past work, we found very low differentiation at one
well-studied zone (Planoles). However, at a second zone (Avellanet), we found
stronger differentiation and greater heterogeneity, which we argue is due to differences
in the amount of introgression following secondary contact. Topology weighting
of genealogical trees identified loci where haplotype diversity was associated
with the two snapdragon varieties. Two of the strongest associations were at previously
identified flower colour loci: Flavia, that affects yellow pigmentation, and Rosea/Eluta,
two linked loci that affect magenta pigmentation. Preliminary analysis of coalescence
times provides additional evidence for selective sweeps at these loci and barriers
to gene flow. Our study highlights the impact of demographic history on the differentiation
landscape, emphasising the need to distinguish between historical divergence and
recent introgression.'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: 'We thank ESEB Godfrey Hewitt Mobility Award for supporting AP’s
research stay at UC Davis. We thank Tom Ellis, Parvathy Surendranadh, and other
Barton Group and Coop Lab members for stimulating discussions. We are grateful to
all the interns and volunteers who have helped us with fieldwork. We thank Eva Salmerón
Mateu for her assistance in fieldwork logistics at the field station, El Serrat.
We are grateful to Enrico Coen and his research group for providing the Antirrhinum
molle PoolSeq data used in the allele polarisation. We are also thankful to Enrico
Coen and Cristophe Thébaud for discovering the Avellanet hybrid zone, followed up
with sampling led by D.L.F. in 2017. The study was supported by Austrian Science
Fund (FWF) Grant (Snapdragon Speciation P32166, awarded to D.L.F.); ERC (Advanced
Grant HaplotypeStructure 101055327, awarded to NHB); ERC (POC Grant 101069216, awarded
to Y.F.C.) and the National Institutes of Health (NIH R35 GM136290, awarded to G.C.).
Y.F.C. was supported by the Max Planck Society. Computing infrastructure for bioinformatics
and analyses was provided by ISTA High Performance Cluster. '
article_number: e70067
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- 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: Alan
full_name: Le Moan, Alan
last_name: Le Moan
- first_name: Adrian J.
full_name: Mcnairn, Adrian J.
last_name: Mcnairn
- first_name: Jennifer K.
full_name: Grenier, Jennifer K.
last_name: Grenier
- first_name: Marek
full_name: Kucka, Marek
last_name: Kucka
- first_name: Graham
full_name: Coop, Graham
last_name: Coop
- first_name: Yingguang Frank
full_name: Chan, Yingguang Frank
last_name: Chan
- 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: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
citation:
ama: Pal A, Shipilina D, Le Moan A, et al. Genealogical analysis of replicate flower
colour hybrid zones in Antirrhinum. Molecular Ecology. 2025;34(22). doi:10.1111/mec.70067
apa: Pal, A., Shipilina, D., Le Moan, A., Mcnairn, A. J., Grenier, J. K., Kucka,
M., … Stankowski, S. (2025). Genealogical analysis of replicate flower colour
hybrid zones in Antirrhinum. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.70067
chicago: Pal, Arka, Daria Shipilina, Alan Le Moan, Adrian J. Mcnairn, Jennifer K.
Grenier, Marek Kucka, Graham Coop, et al. “Genealogical Analysis of Replicate
Flower Colour Hybrid Zones in Antirrhinum.” Molecular Ecology. Wiley, 2025.
https://doi.org/10.1111/mec.70067.
ieee: A. Pal et al., “Genealogical analysis of replicate flower colour hybrid
zones in Antirrhinum,” Molecular Ecology, vol. 34, no. 22. Wiley, 2025.
ista: Pal A, Shipilina D, Le Moan A, Mcnairn AJ, Grenier JK, Kucka M, Coop G, Chan
YF, Barton NH, Field D, Stankowski S. 2025. Genealogical analysis of replicate
flower colour hybrid zones in Antirrhinum. Molecular Ecology. 34(22), e70067.
mla: Pal, Arka, et al. “Genealogical Analysis of Replicate Flower Colour Hybrid
Zones in Antirrhinum.” Molecular Ecology, vol. 34, no. 22, e70067, Wiley,
2025, doi:10.1111/mec.70067.
short: A. Pal, D. Shipilina, A. Le Moan, A.J. Mcnairn, J.K. Grenier, M. Kucka, G.
Coop, Y.F. Chan, N.H. Barton, D. Field, S. Stankowski, Molecular Ecology 34 (2025).
corr_author: '1'
date_created: 2025-08-17T22:01:37Z
date_published: 2025-11-01T00:00:00Z
date_updated: 2026-06-04T22:31:19Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/mec.70067
external_id:
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- '001546622100001'
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creator: dernst
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date_updated: 2026-01-05T13:47:47Z
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file_size: 9886694
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success: 1
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has_accepted_license: '1'
intvolume: ' 34'
isi: 1
issue: '22'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '11'
oa: 1
oa_version: Published Version
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: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/snapdragon-secrets/
record:
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status: public
scopus_import: '1'
status: public
title: Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 34
year: '2025'
...
---
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: 2026-06-04T22:31:19Z
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: '12159'
abstract:
- lang: eng
text: The term “haplotype block” is commonly used in the developing field of haplotype-based
inference methods. We argue that the term should be defined based on the structure
of the Ancestral Recombination Graph (ARG), which contains complete information
on the ancestry of a sample. We use simulated examples to demonstrate key features
of the relationship between haplotype blocks and ancestral structure, emphasizing
the stochasticity of the processes that generate them. Even the simplest cases
of neutrality or of a “hard” selective sweep produce a rich structure, often missed
by commonly used statistics. We highlight a number of novel methods for inferring
haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate
how they can be used to define haplotype blocks using an empirical data set. While
the advent of new, computationally efficient methods makes it possible to apply
these concepts broadly, they (and additional new methods) could benefit from adding
features to explore haplotype blocks, as we define them. Understanding and applying
the concept of the haplotype block will be essential to fully exploit long and
linked-read sequencing technologies.
acknowledgement: 'We thank the Barton group for useful discussion and feedback during
the writing of this article. Comments from Roger Butlin, Molly Schumer''s Group,
the tskit development team, editors and three reviewers greatly improved the manuscript.
Funding was provided by SCAS (Natural Sciences Programme, Knut and Alice Wallenberg
Foundation), an FWF Wittgenstein grant (PT1001Z211), an FWF standalone grant (grant
P 32166), and an ERC Advanced Grant. YFC was supported by the Max Planck Society
and an ERC Proof of Concept Grant #101069216 (HAPLOTAGGING).'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Daria
full_name: Shipilina, Daria
id: 428A94B0-F248-11E8-B48F-1D18A9856A87
last_name: Shipilina
orcid: 0000-0002-1145-9226
- first_name: Arka
full_name: Pal, Arka
id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425
last_name: Pal
orcid: 0000-0002-4530-8469
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Yingguang Frank
full_name: Chan, Yingguang Frank
last_name: Chan
- 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: Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure
of haplotype blocks. Molecular Ecology. 2023;32(6):1441-1457. doi:10.1111/mec.16793
apa: Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., & Barton, N. H. (2023).
On the origin and structure of haplotype blocks. Molecular Ecology. Wiley.
https://doi.org/10.1111/mec.16793
chicago: Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and
Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” Molecular
Ecology. Wiley, 2023. https://doi.org/10.1111/mec.16793.
ieee: D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the
origin and structure of haplotype blocks,” Molecular Ecology, vol. 32,
no. 6. Wiley, pp. 1441–1457, 2023.
ista: Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. 2023. On the origin
and structure of haplotype blocks. Molecular Ecology. 32(6), 1441–1457.
mla: Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.”
Molecular Ecology, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:10.1111/mec.16793.
short: D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology
32 (2023) 1441–1457.
corr_author: '1'
date_created: 2023-01-12T12:09:17Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2026-06-04T22:31:19Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/mec.16793
external_id:
isi:
- '000900762000001'
pmid:
- '36433653'
file:
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checksum: b10e0f8fa3dc4d72aaf77a557200978a
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creator: dernst
date_created: 2023-08-16T08:15:41Z
date_updated: 2023-08-16T08:15:41Z
file_id: '14062'
file_name: 2023_MolecularEcology_Shipilina.pdf
file_size: 7144607
relation: main_file
success: 1
file_date_updated: 2023-08-16T08:15:41Z
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
issue: '6'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 1441-1457
pmid: 1
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: Snapdragon Speciation
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '20694'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: On the origin and structure of haplotype blocks
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: 32
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...
---
_id: '14984'
abstract:
- lang: eng
text: Hybrid zones are narrow geographic regions where different populations, races
or interbreeding species meet and mate, producing mixed ‘hybrid’ offspring. They
are relatively common and can be found in a diverse range of organisms and environments.
The study of hybrid zones has played an important role in our understanding of
the origin of species, with hybrid zones having been described as ‘natural laboratories’.
This is because they allow us to study,in situ, the conditions and evolutionary
forces that enable divergent taxa to remain distinct despite some ongoing gene
exchange between them.
article_processing_charge: No
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Daria
full_name: Shipilina, Daria
id: 428A94B0-F248-11E8-B48F-1D18A9856A87
last_name: Shipilina
orcid: 0000-0002-1145-9226
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
citation:
ama: 'Stankowski S, Shipilina D, Westram AM. Hybrid Zones. In: Encyclopedia of
Life Sciences. Vol 2. eLS. Wiley; 2021. doi:10.1002/9780470015902.a0029355'
apa: Stankowski, S., Shipilina, D., & Westram, A. M. (2021). Hybrid Zones. In
Encyclopedia of Life Sciences (Vol. 2). Wiley. https://doi.org/10.1002/9780470015902.a0029355
chicago: Stankowski, Sean, Daria Shipilina, and Anja M Westram. “Hybrid Zones.”
In Encyclopedia of Life Sciences, Vol. 2. ELS. Wiley, 2021. https://doi.org/10.1002/9780470015902.a0029355.
ieee: S. Stankowski, D. Shipilina, and A. M. Westram, “Hybrid Zones,” in Encyclopedia
of Life Sciences, vol. 2, Wiley, 2021.
ista: 'Stankowski S, Shipilina D, Westram AM. 2021.Hybrid Zones. In: Encyclopedia
of Life Sciences. vol. 2.'
mla: Stankowski, Sean, et al. “Hybrid Zones.” Encyclopedia of Life Sciences,
vol. 2, Wiley, 2021, doi:10.1002/9780470015902.a0029355.
short: S. Stankowski, D. Shipilina, A.M. Westram, in:, Encyclopedia of Life Sciences,
Wiley, 2021.
corr_author: '1'
date_created: 2024-02-14T12:05:50Z
date_published: 2021-05-28T00:00:00Z
date_updated: 2024-10-09T21:08:11Z
day: '28'
department:
- _id: NiBa
doi: 10.1002/9780470015902.a0029355
intvolume: ' 2'
language:
- iso: eng
month: '05'
oa_version: None
publication: Encyclopedia of Life Sciences
publication_identifier:
eisbn:
- '9780470015902'
isbn:
- '9780470016176'
publication_status: published
publisher: Wiley
quality_controlled: '1'
series_title: eLS
status: public
title: Hybrid Zones
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2021'
...