---
OA_place: publisher
_id: '20694'
abstract:
- lang: eng
text: "Understanding the mechanisms underlying speciation is a central aim of evolutionary
biology.\r\nA persistent challenge in the field is to identify loci that contribute
to reproductive isolation,\r\nwhile disentangling signals of selection from demography,
linkage and intrinsic genomic\r\nfeatures. Traditional population genomic approaches
that rely on site-based statistics in\r\narbitrary fixed windows face inherent
limitations, as they conflate historical and\r\ncontemporary processes of divergence
and overlook haplotype structure. Recent advances in\r\nwhole-genome sequencing
and methods to infer ancestral recombination graphs (ARGs) now\r\noffer the opportunity
to study genealogical relationships explicitly, revealing how lineages\r\ncoalesce
and recombine through time. By directly analysing haplotype clustering by species\r\nor
phenotype and their patterns of coalescence, ARG-based methods show promise for\r\ndiagnosing
sweeps, identifying barrier loci maintained under divergent selection amid gene\r\nflow,
and tracing their evolutionary history.\r\nIn this thesis, I explore the utility
of genealogical approaches for studying species\r\ndivergence. In chapter 2, I
propose a conceptual framework for defining haplotype blocks\r\nthrough the structure
of the ARG, using simulations and empirical data to highlight how\r\ngenealogical
processes generate rich and often overlooked haplotypic patterns.\r\nIn chapter
3, I examine the genomic basis of a key evolutionary innovation in marine\r\nsnails
Littorina. These snails offer a unique opportunity to study an innovation because
they\r\ninclude a very recent transition from egg-laying to live bearing, yet
snails with the different\r\nreproductive modes are not reciprocally monophyletic.
I exploited this by using topology\r\nclustering in ARG-derived local genealogical
trees to pinpoint narrow genomic regions or\r\nhaplotype blocks that carry swept
alleles, thus revealing that the transition from egg-laying\r\nto live-bearing
involves multiple, live-bearer-specific sweeps.\r\nChapter 4 establishes a population-scale,
phased genomic resource for Antirrhinum\r\nmajus, using cost-effective haplotagging,
then optimizes imputation from low-coverage data\r\nagainst high-accuracy KASP
sequencing to maximize sequence completeness with modest\r\naccuracy trade-offs
against a traditional short-read sequence pipeline. A hybrid phasing\r\nstrategy
combines molecular phasing with statistical phasing to generate phased whole\r\ngenome
sequences of 1084 Antirrhinum individuals at a fraction of long-read sequencing\r\ncosts.\r\nIn
chapter 5, I analyse hybridising populations from two replicate hybrid zones to
find\r\na parallel genetic basis of flower colour, amidst the noise in genomic
differentiation landscape\r\ndriven by variation in demographic history. While
outlier genome scans of FST failed to dissect\r\nthe causes of differentiation,
ARG-based topology clustering revealed a reuse of colour\r\nassociated haplotypes
across hybrid zones. In addition to the biological insight, this chapter\r\nalso
presents a comparison of the latest ARG inference tools, showing that signals
of\r\nAbstract\r\nviii\r\ntopological clustering qualitatively agree between methods,
despite differences in the tree\r\nsequences.\r\nNext, in chapter 6, by leveraging
~1000 individuals in one of the hybrid zones, I\r\nintegrated genome-wide association
studies of floral pigmentation with genealogical\r\ninference, to test for additional
colour loci, and confirm the effect of previously described loci.\r\nThis work
demonstrates that flower colour variation is driven by a small number of large
effect\r\nloci, while also hinting at the presence of a new candidate regulatory
factor.\r\nFinally in chapter 7, in a preliminary analysis, I begin to dissect
the genomic island of\r\nspeciation around Rosea/Eluta to understand its evolutionary
origins. My results show that it\r\nconsists of 5 highly divergent loci, each
of which is associated with flower colour. Using\r\npatterns of coalescence in
genealogical trees, I find evidence of staggered selective sweeps\r\nand a persistent
localized barrier to gene flow within an otherwise permeable genome.\r\nTogether,
these chapters add to the increasing pool of studies using genealogical\r\napproaches
to complement and extend site-based statistics to use haplotype structures in\r\nspeciation
research. By tracking haplotypes directly and connecting genealogical clustering
to\r\npopulation processes, ARG-based inference promises to provide new insights
into how local\r\nselective pressures, demographic history, and long-term barriers
interact to shape the\r\ngenomic architecture of divergence. By underscoring the
value of ARGs in revealing the finescale origins and maintenance of biodiversity,
this thesis presents cautious optimism about\r\nthe benefits of using genealogical
inference to learn more than what site-based statistics\r\ncould tell us."
acknowledged_ssus:
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Arka
full_name: Pal, Arka
id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425
last_name: Pal
orcid: 0000-0002-4530-8469
citation:
ama: Pal A. Using genealogies to study the genomic basis of species divergence.
2025. doi:10.15479/AT-ISTA-20694
apa: Pal, A. (2025). Using genealogies to study the genomic basis of species
divergence. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20694
chicago: Pal, Arka. “Using Genealogies to Study the Genomic Basis of Species Divergence.”
Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20694.
ieee: A. Pal, “Using genealogies to study the genomic basis of species divergence,”
Institute of Science and Technology Austria, 2025.
ista: Pal A. 2025. Using genealogies to study the genomic basis of species divergence.
Institute of Science and Technology Austria.
mla: Pal, Arka. Using Genealogies to Study the Genomic Basis of Species Divergence.
Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20694.
short: A. Pal, Using Genealogies to Study the Genomic Basis of Species Divergence,
Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-11-25T13:19:11Z
date_published: 2025-11-25T00:00:00Z
date_updated: 2026-04-28T13:20:36Z
day: '25'
ddc:
- '576'
- '578'
degree_awarded: PhD
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/AT-ISTA-20694
file:
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checksum: 7a10a738d58524aebb5dcbd9b34c21c5
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creator: apal
date_created: 2025-12-01T13:53:36Z
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language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '11'
oa: 1
oa_version: Published Version
page: '268'
project:
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: Snapdragon Speciation
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
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relation: part_of_dissertation
status: public
- id: '14796'
relation: part_of_dissertation
status: public
- id: '20190'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: Using genealogies to study the genomic basis of species divergence
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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: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
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: 2026-05-05T22:31:12Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/mec.70067
external_id:
isi:
- '001546622100001'
file:
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checksum: c586fc674df4e7dd6e43aef87a52c6f6
content_type: application/pdf
creator: dernst
date_created: 2026-01-05T13:47:47Z
date_updated: 2026-01-05T13:47:47Z
file_id: '20958'
file_name: 2025_MolecEcology_Pal.pdf
file_size: 9886694
relation: main_file
success: 1
file_date_updated: 2026-01-05T13:47:47Z
has_accepted_license: '1'
intvolume: ' 34'
isi: 1
issue: '22'
language:
- iso: eng
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/
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relation: dissertation_contains
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'
...
---
_id: '14850'
abstract:
- lang: eng
text: Elaborate sexual signals are thought to have evolved and be maintained to
serve as honest indicators of signaller quality. One measure of quality is health,
which can be affected by parasite infection. Cnemaspis mysoriensis is a diurnal
gecko that is often infested with ectoparasites in the wild, and males of this
species express visual (coloured gular patches) and chemical (femoral gland secretions)
traits that receivers could assess during social interactions. In this paper,
we tested whether ectoparasites affect individual health, and whether signal quality
is an indicator of ectoparasite levels. In wild lizards, we found that ectoparasite
level was negatively correlated with body condition in both sexes. Moreover, some
characteristics of both visual and chemical traits in males were strongly associated
with ectoparasite levels. Specifically, males with higher ectoparasite levels
had yellow gular patches with lower brightness and chroma, and chemical secretions
with a lower proportion of aromatic compounds. We then determined whether ectoparasite
levels in males influence female behaviour. Using sequential choice trials, wherein
females were provided with either the visual or the chemical signals of wild-caught
males that varied in ectoparasite level, we found that only chemical secretions
evoked an elevated female response towards less parasitised males. Simultaneous
choice trials in which females were exposed to the chemical secretions from males
that varied in parasite level further confirmed a preference for males with lower
parasites loads. Overall, we find that although health (body condition) or ectoparasite
load can be honestly advertised through multiple modalities, the parasite-mediated
female response is exclusively driven by chemical signals.
acknowledgement: "We thank Anuradha Batabyal and Shakilur Kabir for scientific discussions,
and help with sampling and colour analyses. We thank Muralidhar and the central
LCMS facility of the IISc for their technical support with the GCMS.\r\nResearch
funding was provided by the Department of Science and Technology Fund for Improvement
of S&T Infrastructure (DST-FIST), the Department of Biotechnology-Indian Institute
of Science (DBT-IISc) partnership program and a Science and Engineering Research
Board (SERB) grant to M.T. (EMR/2017/002228). Open Access funding provided by Indian
Institute of Science. Deposited in PMC for immediate release."
article_number: jeb246217
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: Mihir
full_name: Joshi, Mihir
last_name: Joshi
- first_name: Maria
full_name: Thaker, Maria
last_name: Thaker
citation:
ama: Pal A, Joshi M, Thaker M. Too much information? Males convey parasite levels
using more signal modalities than females utilise. Journal of Experimental
Biology. 2024;227(1). doi:10.1242/jeb.246217
apa: Pal, A., Joshi, M., & Thaker, M. (2024). Too much information? Males convey
parasite levels using more signal modalities than females utilise. Journal
of Experimental Biology. The Company of Biologists. https://doi.org/10.1242/jeb.246217
chicago: Pal, Arka, Mihir Joshi, and Maria Thaker. “Too Much Information? Males
Convey Parasite Levels Using More Signal Modalities than Females Utilise.” Journal
of Experimental Biology. The Company of Biologists, 2024. https://doi.org/10.1242/jeb.246217.
ieee: A. Pal, M. Joshi, and M. Thaker, “Too much information? Males convey parasite
levels using more signal modalities than females utilise,” Journal of Experimental
Biology, vol. 227, no. 1. The Company of Biologists, 2024.
ista: Pal A, Joshi M, Thaker M. 2024. Too much information? Males convey parasite
levels using more signal modalities than females utilise. Journal of Experimental
Biology. 227(1), jeb246217.
mla: Pal, Arka, et al. “Too Much Information? Males Convey Parasite Levels Using
More Signal Modalities than Females Utilise.” Journal of Experimental Biology,
vol. 227, no. 1, jeb246217, The Company of Biologists, 2024, doi:10.1242/jeb.246217.
short: A. Pal, M. Joshi, M. Thaker, Journal of Experimental Biology 227 (2024).
corr_author: '1'
date_created: 2024-01-22T08:14:49Z
date_published: 2024-01-10T00:00:00Z
date_updated: 2025-09-04T11:50:21Z
day: '10'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1242/jeb.246217
external_id:
isi:
- '001214515700016'
pmid:
- '38054353'
file:
- access_level: open_access
checksum: 136325372f6f45abaa62a71e2d23bfb6
content_type: application/pdf
creator: dernst
date_created: 2024-01-23T12:08:24Z
date_updated: 2024-01-23T12:08:24Z
file_id: '14877'
file_name: 2024_JourExperimBiology_Pal.pdf
file_size: 594128
relation: main_file
success: 1
file_date_updated: 2024-01-23T12:08:24Z
has_accepted_license: '1'
intvolume: ' 227'
isi: 1
issue: '1'
keyword:
- Insect Science
- Molecular Biology
- Animal Science and Zoology
- Aquatic Science
- Physiology
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Journal of Experimental Biology
publication_identifier:
eissn:
- 0022-0949
issn:
- 1477-9145
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/arka-pal/Cnemaspis-SexualSignaling
scopus_import: '1'
status: public
title: Too much information? Males convey parasite levels using more signal modalities
than females utilise
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: 227
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: 2026-05-05T22:31:12Z
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:
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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: 2026-05-05T22:31:12Z
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
content_type: application/pdf
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:
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- id: '20694'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: On the origin and structure of haplotype blocks
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: 32
year: '2023'
...
---
_id: '1513'
abstract:
- lang: eng
text: "Insects of the order Hemiptera (true bugs) use a wide range of mechanisms
of sex determination, including genetic sex determination, paternal genome elimination,
and haplodiploidy. Genetic sex determination, the prevalent mode, is generally
controlled by a pair of XY sex chromosomes or by an XX/X0 system, but different
configurations that include additional sex chromosomes are also present. Although
this diversity of sex determining systems has been extensively studied at the
cytogenetic level, only the X chromosome of the model pea aphid Acyrthosiphon
pisum has been analyzed at the genomic level, and little is known about X chromosome
biology in the rest of the order.\r\n\r\nIn this study, we take advantage of published
DNA- and RNA-seq data from three additional Hemiptera species to perform a comparative
analysis of the gene content and expression of the X chromosome throughout this
clade. We find that, despite showing evidence of dosage compensation, the X chromosomes
of these species show female-biased expression, and a deficit of male-biased genes,
in direct contrast to the pea aphid X. We further detect an excess of shared gene
content between these very distant species, suggesting that despite the diversity
of sex determining systems, the same chromosomal element is used as the X throughout
a large portion of the order. "
article_processing_charge: No
author:
- first_name: Arka
full_name: Pal, Arka
id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425
last_name: Pal
orcid: 0000-0002-4530-8469
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: 'Pal A, Vicoso B. The X chromosome of hemipteran insects: Conservation, dosage
compensation and sex-biased expression. Genome Biology and Evolution. 2015;7(12):3259-3268.
doi:10.1093/gbe/evv215'
apa: 'Pal, A., & Vicoso, B. (2015). The X chromosome of hemipteran insects:
Conservation, dosage compensation and sex-biased expression. Genome Biology
and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evv215'
chicago: 'Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects:
Conservation, Dosage Compensation and Sex-Biased Expression.” Genome Biology
and Evolution. Oxford University Press, 2015. https://doi.org/10.1093/gbe/evv215.'
ieee: 'A. Pal and B. Vicoso, “The X chromosome of hemipteran insects: Conservation,
dosage compensation and sex-biased expression,” Genome Biology and Evolution,
vol. 7, no. 12. Oxford University Press, pp. 3259–3268, 2015.'
ista: 'Pal A, Vicoso B. 2015. The X chromosome of hemipteran insects: Conservation,
dosage compensation and sex-biased expression. Genome Biology and Evolution. 7(12),
3259–3268.'
mla: 'Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects: Conservation,
Dosage Compensation and Sex-Biased Expression.” Genome Biology and Evolution,
vol. 7, no. 12, Oxford University Press, 2015, pp. 3259–68, doi:10.1093/gbe/evv215.'
short: A. Pal, B. Vicoso, Genome Biology and Evolution 7 (2015) 3259–3268.
corr_author: '1'
date_created: 2018-12-11T11:52:27Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2025-09-23T14:18:15Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/gbe/evv215
ec_funded: 1
external_id:
isi:
- '000366498700008'
file:
- access_level: open_access
checksum: 2b56b8c2e2a1d4cc3c9cb8daba26dd9b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:29Z
date_updated: 2020-07-14T12:45:00Z
file_id: '5284'
file_name: IST-2016-496-v1+1_Genome_Biol_Evol-2015-Pal-3259-68.pdf
file_size: 858027
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 3259 - 3268
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Genome Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '5664'
pubrep_id: '496'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The X chromosome of hemipteran insects: Conservation, dosage compensation
and sex-biased expression'
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: 7
year: '2015'
...