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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ftdoajarticles:oai:doaj.org/article:2f622fdeb7a245b2853bfc64966a8f4a 2023-05-15T14:47:05+02:00 Thousands of RAD-seq Loci Fully Resolve the Phylogeny of the Highly Disjunct Arctic-Alpine Genus Diapensia (Diapensiaceae). Yan Hou Michael D Nowak Virginia Mirré Charlotte S Bjorå Christian Brochmann Magnus Popp 2015-01-01T00:00:00Z https://doi.org/10.1371/journal.pone.0140175 https://doaj.org/article/2f622fdeb7a245b2853bfc64966a8f4a EN eng Public Library of Science (PLoS) http://europepmc.org/articles/PMC4598014?pdf=render https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0140175 https://doaj.org/article/2f622fdeb7a245b2853bfc64966a8f4a PLoS ONE, Vol 10, Iss 10, p e0140175 (2015) Medicine R Science Q article 2015 ftdoajarticles https://doi.org/10.1371/journal.pone.0140175 2022-12-30T21:36:19Z 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 Directory of Open Access Journals: DOAJ Articles Arctic PLOS ONE 10 10 e0140175 |
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Medicine R Science Q Yan Hou Michael D Nowak Virginia Mirré Charlotte S Bjorå Christian Brochmann Magnus Popp Thousands of RAD-seq Loci Fully Resolve the Phylogeny of the Highly Disjunct Arctic-Alpine Genus Diapensia (Diapensiaceae). |
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Medicine R Science Q |
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 |
Yan Hou Michael D Nowak Virginia Mirré Charlotte S Bjorå Christian Brochmann Magnus Popp |
author_facet |
Yan Hou Michael D Nowak Virginia Mirré Charlotte S Bjorå Christian Brochmann Magnus Popp |
author_sort |
Yan Hou |
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 |
2015 |
url |
https://doi.org/10.1371/journal.pone.0140175 https://doaj.org/article/2f622fdeb7a245b2853bfc64966a8f4a |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
PLoS ONE, Vol 10, Iss 10, p e0140175 (2015) |
op_relation |
http://europepmc.org/articles/PMC4598014?pdf=render https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0140175 https://doaj.org/article/2f622fdeb7a245b2853bfc64966a8f4a |
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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1766318216654618624 |