Data from: Worldwide phylogeny of three-spined sticklebacks
Stickleback fishes in the family Gasterosteidae have become model organisms in ecology and evolutionary biology. However, even in the case of the most widely studied species in this family – the three-spined stickleback (Gasterosteus aculeatus) – the worldwide phylogenetic relationships and coloniza...
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Online Access: | https://doi.org/10.5061/dryad.2529hr1 |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::7b0f074ce39d1062a3ebc98ad7d8c970 2023-05-15T15:12:55+02:00 Data from: Worldwide phylogeny of three-spined sticklebacks Fang, Bohao Merilä, Juha Ribeiro, Filipe Alexandre, Carlos M. Momigliano, Paolo 2019-01-01 https://doi.org/10.5061/dryad.2529hr1 undefined unknown http://dx.doi.org/10.5061/dryad.2529hr1 https://dx.doi.org/10.5061/DRYAD.2529HR1 lic_creative-commons oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:108370 oai:easy.dans.knaw.nl:easy-dataset:108370 10.5061/DRYAD.2529HR1 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 re3data_____::r3d100000044 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f Life sciences medicine and health care Coalescent Gasterosteus phylogenomics RAD-seq SNP Global Pleistocene to Holocene Gasterosteus aculeatus anthro-se envir Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2019 fttriple https://doi.org/10.5061/dryad.2529hr1 https://doi.org/10.5061/DRYAD.2529HR1 2023-01-22T17:22:31Z Stickleback fishes in the family Gasterosteidae have become model organisms in ecology and evolutionary biology. However, even in the case of the most widely studied species in this family – the three-spined stickleback (Gasterosteus aculeatus) – the worldwide phylogenetic relationships and colonization history of the different populations and lineages remain poorly resolved. Using a large collection of samples covering most parts of the species distribution range, we subjected thousands of single nucleotide polymorphisms to coalescent analyses in order to reconstruct a robust worldwide phylogeny of extant G. aculeatus populations, as well their ancestral geographic distributions using Statistical-Dispersal Vicariance and Bayesian Binary MCMC analyses. The results suggest that contemporary populations originated from the Pacific Ocean in the late Pleistocene, and the Atlantic was colonized through the Arctic Ocean by a lineage that diverged from Pacific sticklebacks ca 44.6 Kya. This lineage contains two branches: one that is distributed in the Mediterranean area, from the Iberian Peninsula to the Black Sea (‘Southern European lineage’), and another that is comprised of populations from northern Europe and the east coast of North America (‘Trans-Atlantic lineage’). Hence, the results suggest that the North American East Coast was colonized by trans-Atlantic migration. Coalescence-based divergence time estimates suggest that divergence among major clades is much more recent than previously estimated. Worldwide phylogenetic tree of Gasterosteus aculeatusThe time-calibrated worldwide phylogenetic tree of Gasterosteus aculeatus.World_3sp.treeVCF file for all samplesVCF file for all samples. It consists of 126 Gasterosteus aculeatus and 2 individuals of G. nipponicus, a sister species of G. aculeatus.128IDs_full_chrs_ref.vcfAlignments_load_to_BEASTSequence alignments used for phylogenomic analyses. The alignments include 8079 concatenated SNPs.Assembly parameters for ipyrad programAssembly parameters for the ipyrad ... Dataset Arctic Arctic Ocean Unknown Arctic Arctic Ocean Pacific Kya ENVELOPE(8.308,8.308,63.772,63.772) |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
unknown |
topic |
Life sciences medicine and health care Coalescent Gasterosteus phylogenomics RAD-seq SNP Global Pleistocene to Holocene Gasterosteus aculeatus anthro-se envir |
spellingShingle |
Life sciences medicine and health care Coalescent Gasterosteus phylogenomics RAD-seq SNP Global Pleistocene to Holocene Gasterosteus aculeatus anthro-se envir Fang, Bohao Merilä, Juha Ribeiro, Filipe Alexandre, Carlos M. Momigliano, Paolo Data from: Worldwide phylogeny of three-spined sticklebacks |
topic_facet |
Life sciences medicine and health care Coalescent Gasterosteus phylogenomics RAD-seq SNP Global Pleistocene to Holocene Gasterosteus aculeatus anthro-se envir |
description |
Stickleback fishes in the family Gasterosteidae have become model organisms in ecology and evolutionary biology. However, even in the case of the most widely studied species in this family – the three-spined stickleback (Gasterosteus aculeatus) – the worldwide phylogenetic relationships and colonization history of the different populations and lineages remain poorly resolved. Using a large collection of samples covering most parts of the species distribution range, we subjected thousands of single nucleotide polymorphisms to coalescent analyses in order to reconstruct a robust worldwide phylogeny of extant G. aculeatus populations, as well their ancestral geographic distributions using Statistical-Dispersal Vicariance and Bayesian Binary MCMC analyses. The results suggest that contemporary populations originated from the Pacific Ocean in the late Pleistocene, and the Atlantic was colonized through the Arctic Ocean by a lineage that diverged from Pacific sticklebacks ca 44.6 Kya. This lineage contains two branches: one that is distributed in the Mediterranean area, from the Iberian Peninsula to the Black Sea (‘Southern European lineage’), and another that is comprised of populations from northern Europe and the east coast of North America (‘Trans-Atlantic lineage’). Hence, the results suggest that the North American East Coast was colonized by trans-Atlantic migration. Coalescence-based divergence time estimates suggest that divergence among major clades is much more recent than previously estimated. Worldwide phylogenetic tree of Gasterosteus aculeatusThe time-calibrated worldwide phylogenetic tree of Gasterosteus aculeatus.World_3sp.treeVCF file for all samplesVCF file for all samples. It consists of 126 Gasterosteus aculeatus and 2 individuals of G. nipponicus, a sister species of G. aculeatus.128IDs_full_chrs_ref.vcfAlignments_load_to_BEASTSequence alignments used for phylogenomic analyses. The alignments include 8079 concatenated SNPs.Assembly parameters for ipyrad programAssembly parameters for the ipyrad ... |
format |
Dataset |
author |
Fang, Bohao Merilä, Juha Ribeiro, Filipe Alexandre, Carlos M. Momigliano, Paolo |
author_facet |
Fang, Bohao Merilä, Juha Ribeiro, Filipe Alexandre, Carlos M. Momigliano, Paolo |
author_sort |
Fang, Bohao |
title |
Data from: Worldwide phylogeny of three-spined sticklebacks |
title_short |
Data from: Worldwide phylogeny of three-spined sticklebacks |
title_full |
Data from: Worldwide phylogeny of three-spined sticklebacks |
title_fullStr |
Data from: Worldwide phylogeny of three-spined sticklebacks |
title_full_unstemmed |
Data from: Worldwide phylogeny of three-spined sticklebacks |
title_sort |
data from: worldwide phylogeny of three-spined sticklebacks |
publishDate |
2019 |
url |
https://doi.org/10.5061/dryad.2529hr1 |
long_lat |
ENVELOPE(8.308,8.308,63.772,63.772) |
geographic |
Arctic Arctic Ocean Pacific Kya |
geographic_facet |
Arctic Arctic Ocean Pacific Kya |
genre |
Arctic Arctic Ocean |
genre_facet |
Arctic Arctic Ocean |
op_source |
oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:108370 oai:easy.dans.knaw.nl:easy-dataset:108370 10.5061/DRYAD.2529HR1 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 re3data_____::r3d100000044 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f |
op_relation |
http://dx.doi.org/10.5061/dryad.2529hr1 https://dx.doi.org/10.5061/DRYAD.2529HR1 |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.2529hr1 https://doi.org/10.5061/DRYAD.2529HR1 |
_version_ |
1766343545854099456 |