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

Ben Wielstra,Maciej Pabijan,Kristiaan J Van Der Gaag,Jan W Arntzen,Wieslaw Babik,Helge Thorsten Lumbsch

doi:10.1371/journal.pone.0111011

Abstract

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.

Highlights

The importance of molecular data in biological systematics can hardly be overstated, but potential pitfalls should be considered
The average number of alleles per marker within individuals ranges from 1.0 to 1.6, with T. dobrogicus showing the highest heterozygosity of all species
BAPS partitions the dataset into nine gene pools, corresponding to the nine Triturus species

Summary

Introduction

The importance of molecular data in biological systematics can hardly be overstated, but potential pitfalls should be considered. A single gene tree does not necessarily reflect the phylogenetic relationships among species – hereafter referred to as the species tree – as phenomena like incomplete lineage sorting and introgression cloud the pattern of descent [1]. The mitochondrial genome is inherited as a single unit and gives rise to a single gene tree. The nuclear genome, due to its recombining nature, represents a collection of gene trees embedded in the species tree. To distill the species tree, a multitude of nuclear genes should be employed [2]. The progress in next-generation sequencing facilitates the production of large datasets and the use of multilocus datasets in systematics will soon become the norm [3,4]

Methods

Results

Conclusion