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.