Thousands of RAD-seq Loci Fully Resolve the Phylogeny of the Highly Disjunct Arctic-Alpine Genus Diapensia (Diapensiaceae)
Restriction-site associated DNA sequencing (RAD-seq) has recently become an important method to generate genome-wide molecular data for species delimitation, phylogeography, and population genetic studies. However, very few empirical studies have so far tested its applicability in phylogenetic recon...
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ftoslouniv:oai:www.duo.uio.no:10852/48798 2023-05-15T14:27:31+02:00 Thousands of RAD-seq Loci Fully Resolve the Phylogeny of the Highly Disjunct Arctic-Alpine Genus Diapensia (Diapensiaceae) Hou, Yan Nowak, Michael Mirre, Virginia Bjorå, Charlotte Sletten Brochmann, Christian Popp, Magnus 2016-01-01T20:41:53Z http://hdl.handle.net/10852/48798 http://urn.nb.no/URN:NBN:no-52651 https://doi.org/10.1371/journal.pone.0140175 EN eng Public Library of Science (PLoS) http://urn.nb.no/URN:NBN:no-52651 Hou, Yan Nowak, Michael Mirre, Virginia Bjorå, Charlotte Sletten Brochmann, Christian Popp, Magnus . Thousands of RAD-seq Loci Fully Resolve the Phylogeny of the Highly Disjunct Arctic-Alpine Genus Diapensia (Diapensiaceae). PLoS ONE. 2015 http://hdl.handle.net/10852/48798 1305083 info:ofi/fmt:kev:mtx:ctx&ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=PLoS ONE&rft.volume=&rft.spage=&rft.date=2015 PLoS ONE 10 14 http://dx.doi.org/10.1371/journal.pone.0140175 URN:NBN:no-52651 Fulltext https://www.duo.uio.no/bitstream/handle/10852/48798/1/journal-pone-0140175.pdf Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/ CC-BY 1932-6203 Journal article Tidsskriftartikkel Peer reviewed PublishedVersion 2016 ftoslouniv https://doi.org/10.1371/journal.pone.0140175 2020-06-21T08:49:25Z Restriction-site associated DNA sequencing (RAD-seq) has recently become an important method to generate genome-wide molecular data for species delimitation, phylogeography, and population genetic studies. However, very few empirical studies have so far tested its applicability in phylogenetic reconstruction. The alpine-arctic genus Diapensia was selected to study the origin of the disjunction between the Arctic and the Himalayan-Hengduan Mountains (HHM). However, a previous phylogenetic analysis based on one nuclear and four plastid DNA regions failed to resolve the oldest divergences in Diapensia as well as the relationship between the two HHM species. Here we reconstruct a fully resolved phylogeny of Diapensia and address the conflict between the currently accepted taxonomy and the gene trees in the HHM species using RAD-seq. Based on a data set containing 2,650 loci selected to maximize the number of parsimony informative sites and allowing for a high level of missing data (51%), the phylogeny of Diapensia was fully resolved and each of the four species was reciprocally monophyletic. Whereas the arctic D. lapponica was inferred as sister to the HHM clade in the previous study, the RAD-seq data resolved the two arctic species as sisters to the HHM clade. Similar relationships were inferred from a differently filtered data set with far fewer loci (114) and less missing data (21%), but with lower support and with one of the two HHM species as non-monophyletic. Bayesian concordance analysis and Patterson’s D-statistic tests suggested that admixture has occurred between the two HHM species. Article in Journal/Newspaper Arctic Arctic Universitet i Oslo: Digitale utgivelser ved UiO (DUO) Arctic PLOS ONE 10 10 e0140175 |
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Open Polar |
collection |
Universitet i Oslo: Digitale utgivelser ved UiO (DUO) |
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ftoslouniv |
language |
English |
description |
Restriction-site associated DNA sequencing (RAD-seq) has recently become an important method to generate genome-wide molecular data for species delimitation, phylogeography, and population genetic studies. However, very few empirical studies have so far tested its applicability in phylogenetic reconstruction. The alpine-arctic genus Diapensia was selected to study the origin of the disjunction between the Arctic and the Himalayan-Hengduan Mountains (HHM). However, a previous phylogenetic analysis based on one nuclear and four plastid DNA regions failed to resolve the oldest divergences in Diapensia as well as the relationship between the two HHM species. Here we reconstruct a fully resolved phylogeny of Diapensia and address the conflict between the currently accepted taxonomy and the gene trees in the HHM species using RAD-seq. Based on a data set containing 2,650 loci selected to maximize the number of parsimony informative sites and allowing for a high level of missing data (51%), the phylogeny of Diapensia was fully resolved and each of the four species was reciprocally monophyletic. Whereas the arctic D. lapponica was inferred as sister to the HHM clade in the previous study, the RAD-seq data resolved the two arctic species as sisters to the HHM clade. Similar relationships were inferred from a differently filtered data set with far fewer loci (114) and less missing data (21%), but with lower support and with one of the two HHM species as non-monophyletic. Bayesian concordance analysis and Patterson’s D-statistic tests suggested that admixture has occurred between the two HHM species. |
format |
Article in Journal/Newspaper |
author |
Hou, Yan Nowak, Michael Mirre, Virginia Bjorå, Charlotte Sletten Brochmann, Christian Popp, Magnus |
spellingShingle |
Hou, Yan Nowak, Michael Mirre, Virginia Bjorå, Charlotte Sletten Brochmann, Christian Popp, Magnus Thousands of RAD-seq Loci Fully Resolve the Phylogeny of the Highly Disjunct Arctic-Alpine Genus Diapensia (Diapensiaceae) |
author_facet |
Hou, Yan Nowak, Michael Mirre, Virginia Bjorå, Charlotte Sletten Brochmann, Christian Popp, Magnus |
author_sort |
Hou, Yan |
title |
Thousands of RAD-seq Loci Fully Resolve the Phylogeny of the Highly Disjunct Arctic-Alpine Genus Diapensia (Diapensiaceae) |
title_short |
Thousands of RAD-seq Loci Fully Resolve the Phylogeny of the Highly Disjunct Arctic-Alpine Genus Diapensia (Diapensiaceae) |
title_full |
Thousands of RAD-seq Loci Fully Resolve the Phylogeny of the Highly Disjunct Arctic-Alpine Genus Diapensia (Diapensiaceae) |
title_fullStr |
Thousands of RAD-seq Loci Fully Resolve the Phylogeny of the Highly Disjunct Arctic-Alpine Genus Diapensia (Diapensiaceae) |
title_full_unstemmed |
Thousands of RAD-seq Loci Fully Resolve the Phylogeny of the Highly Disjunct Arctic-Alpine Genus Diapensia (Diapensiaceae) |
title_sort |
thousands of rad-seq loci fully resolve the phylogeny of the highly disjunct arctic-alpine genus diapensia (diapensiaceae) |
publisher |
Public Library of Science (PLoS) |
publishDate |
2016 |
url |
http://hdl.handle.net/10852/48798 http://urn.nb.no/URN:NBN:no-52651 https://doi.org/10.1371/journal.pone.0140175 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic Arctic |
genre_facet |
Arctic Arctic |
op_source |
1932-6203 |
op_relation |
http://urn.nb.no/URN:NBN:no-52651 Hou, Yan Nowak, Michael Mirre, Virginia Bjorå, Charlotte Sletten Brochmann, Christian Popp, Magnus . Thousands of RAD-seq Loci Fully Resolve the Phylogeny of the Highly Disjunct Arctic-Alpine Genus Diapensia (Diapensiaceae). PLoS ONE. 2015 http://hdl.handle.net/10852/48798 1305083 info:ofi/fmt:kev:mtx:ctx&ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=PLoS ONE&rft.volume=&rft.spage=&rft.date=2015 PLoS ONE 10 14 http://dx.doi.org/10.1371/journal.pone.0140175 URN:NBN:no-52651 Fulltext https://www.duo.uio.no/bitstream/handle/10852/48798/1/journal-pone-0140175.pdf |
op_rights |
Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/ |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1371/journal.pone.0140175 |
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PLOS ONE |
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10 |
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10 |
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e0140175 |
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