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

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

*BEAST species trees

The species tree resulting from the eight *BEAST runs

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

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

Input files

The input files for BAPS, MrBayes, BUCKy and *BEAST

SNP report

The SNP report produced with GS Amplicon Variant Analyzer 2.8

Individual gene trees

The individual gene trees resulting from MrBayes used in BUCKy

Alignments

The alignments (raw, with indels removed, and collapsed into haplotypes)

454 sequencing

The raw 454 reads (in SFF format)

Species trees resulting from the concatenation-based estimation in MrBayes for the genus <i>Triturus</i>, based on 38 nuclear markers positioned in 3′ untranslated regions, sequenced for 20 individuals.

<p>Internal branches supported with pp = 1.0 are marked with an asterisk. Analyses a and b reflect two different input files used which, for heterozygote marker-individual combinations, include either one or the other allele. The inferred position of the root for <i>Triturus</i> is shown. Background colors reflect variation in the number of rib-bearing pre-sacral vertebrae characterizing <i>Triturus</i> morphotypes as in Fig. 1 and the character stage changes required are noted in red.</p

Previously argued phylogenetic hypotheses for the genus <i>Triturus</i>.

<p>Background colors reflect the variation in the number of rib-bearing pre-sacral vertebrae (NRBV) characterizing the five <i>Triturus</i> morphotypes. The two species with a green background are marbled newts and the remaining species are crested newts. The MrBayes phylogeny (left) is based on full mitochondrial genomes <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111011#pone.0111011-Wielstra1" target="_blank">[19]</a>. Posterior probabilities for all internal branches are 0.95 or higher. Note that this phylogeny is concordant with the most parsimonious interpretation of the evolution of the number of rib-bearing pre-sacral vertebrae (with the required character state changes noted in red). The *BEAST coalescent-based estimation of the species tree (right) is based on three nuclear introns (adapted from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111011#pone.0111011-Wielstra2" target="_blank">[20]</a>). Posterior probabilities for internal branches are all below 0.95 and only those supported at over 0.75 are shown.</p