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...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2015-01-01
|
| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC4598014?pdf=render |
| _version_ | 1811242623639224320 |
|---|---|
| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-04-12T13:53:46Z |
| format | Article |
| id | doaj.art-2f622fdeb7a245b2853bfc64966a8f4a |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-12T13:53:46Z |
| publishDate | 2015-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-2f622fdeb7a245b2853bfc64966a8f4a2022-12-22T03:30:26ZengPublic Library of Science (PLoS)PLoS ONE1932-62032015-01-011010e014017510.1371/journal.pone.0140175Thousands of RAD-seq Loci Fully Resolve the Phylogeny of the Highly Disjunct Arctic-Alpine Genus Diapensia (Diapensiaceae).Yan HouMichael D NowakVirginia MirréCharlotte S BjoråChristian BrochmannMagnus PoppRestriction-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.http://europepmc.org/articles/PMC4598014?pdf=render |
| spellingShingle | 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). PLoS ONE |
| title | 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_short | 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 |
| url | http://europepmc.org/articles/PMC4598014?pdf=render |
| work_keys_str_mv | AT yanhou thousandsofradseqlocifullyresolvethephylogenyofthehighlydisjunctarcticalpinegenusdiapensiadiapensiaceae AT michaeldnowak thousandsofradseqlocifullyresolvethephylogenyofthehighlydisjunctarcticalpinegenusdiapensiadiapensiaceae AT virginiamirre thousandsofradseqlocifullyresolvethephylogenyofthehighlydisjunctarcticalpinegenusdiapensiadiapensiaceae AT charlottesbjora thousandsofradseqlocifullyresolvethephylogenyofthehighlydisjunctarcticalpinegenusdiapensiadiapensiaceae AT christianbrochmann thousandsofradseqlocifullyresolvethephylogenyofthehighlydisjunctarcticalpinegenusdiapensiadiapensiaceae AT magnuspopp thousandsofradseqlocifullyresolvethephylogenyofthehighlydisjunctarcticalpinegenusdiapensiadiapensiaceae |