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Data concatenation, Bayesian concordance and coalescent-based analyses of the species tree for the rapid radiation of Triturus newts

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Data concatenation, Bayesian concordance and coalescent-based analyses of the species tree for the rapid radiation of Triturus newts

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dc.contributor.author Wielstra, Ben pl
dc.contributor.author Arntzen, Jan W. pl
dc.contributor.author van der Gaag, Kristiaan J. pl
dc.contributor.author Pabijan, Maciej [SAP11018728] pl
dc.contributor.author Babik, Wiesław [SAP11018324] pl
dc.date.accessioned 2015-04-30T07:19:27Z
dc.date.available 2015-04-30T07:19:27Z
dc.date.issued 2014 pl
dc.identifier.uri http://ruj.uj.edu.pl/xmlui/handle/item/6221
dc.language eng pl
dc.rights Udzielam licencji. Uznanie autorstwa 4.0 Międzynarodowa *
dc.rights.uri http://creativecommons.org/licenses/by/4.0/pl/legalcode *
dc.title Data concatenation, Bayesian concordance and coalescent-based analyses of the species tree for the rapid radiation of Triturus newts pl
dc.type JournalArticle pl
dc.abstract.en The phylogenetic relationships for rapid species radiations are difficult to disentangle. Here we study one such case, namely the genus Triturus, which is composed of the marbled and crested newts. We analyze data for 38 genetic markers, positioned in 3-prime untranslated regions of protein-coding genes, obtained with 454 sequencing. Our dataset includes twenty Triturus newts and represents all nine species. Bayesian analysis of population structure allocates all individuals to their respective species. The branching patterns obtained by data concatenation, Bayesian concordance analysis and coalescent-based estimations of the species tree differ from one another. The data concatenation based species tree shows high branch support but branching order is considerably affected by allele choice in the case of heterozygotes in the concatenation process. Bayesian concordance analysis expresses the conflict between individual gene trees for part of the Triturus species tree as low concordance factors. The coalescent-based species tree is relatively similar to a previously published species tree based upon morphology and full mtDNA and any conflicting internal branches are not highly supported. Our findings reflect high gene tree discordance due to incomplete lineage sorting (possibly aggravated by hybridization) in combination with low information content of the markers employed (as can be expected for relatively recent species radiations). This case study highlights the complexity of resolving rapid radiations and we acknowledge that to convincingly resolve the Triturus species tree even more genes will have to be consulted. pl
dc.subject.en crested newts pl
dc.subject.en gene flow pl
dc.subject.en mitochondrial-DNA pl
dc.subject.en multiple nuclear pl
dc.subject.en Cristatus pl
dc.subject.en phylogeography pl
dc.subject.en phylogenetics pl
dc.subject.en inference pl
dc.subject.en accuracy pl
dc.subject.en reconstruction pl
dc.description.volume 9 pl
dc.description.number 10 pl
dc.identifier.doi 10.1371/journal.pone.0111011 pl
dc.identifier.eissn 1932-6203 pl
dc.title.journal PLoS ONE pl
dc.language.container eng pl
dc.affiliation Wydział Biologii i Nauk o Ziemi : Instytut Nauk o Środowisku pl
dc.affiliation Wydział Biologii i Nauk o Ziemi : Instytut Zoologii pl
dc.subtype Article pl
dc.identifier.articleid e111011 pl
dc.rights.original CC-BY; otwarte czasopismo; ostateczna wersja wydawcy; w momencie opublikowania; 0; pl
dc.identifier.project ROD UJ / P pl
.pointsMNiSW [2014 A]: 40


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Udzielam licencji. Uznanie autorstwa 4.0 Międzynarodowa Except where otherwise noted, this item's license is described as Udzielam licencji. Uznanie autorstwa 4.0 Międzynarodowa