Multispecies Coalescent Analyses Research Articles

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

Computational evolutionary biology, statistical phylogenetics and coalescent-based population genetics are becoming increasingly central to the analysis and understanding of molecular sequence data. We present the Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package version 1.7, which implements a family of Markov chain Monte Carlo (MCMC) algorithms for Bayesian phylogenetic inference, divergence time dating, coalescent analysis, phylogeography and related molecular evolutionary analyses. This package includes an enhanced graphical user interface program called Bayesian Evolutionary Analysis Utility (BEAUti) that enables access to advanced models for molecular sequence and phenotypic trait evolution that were previously available to developers only. The package also provides new tools for visualizing and summarizing multispecies coalescent and phylogeographic analyses. BEAUti and BEAST 1.7 are open source under the GNU lesser general public license and available at http://beast-mcmc.googlecode.com and http://beast.bio.ed.ac.uk

Molecular phylogeography reveals an antitropical distribution and local diversification of Solenogyne (Asteraceae) in the Ryukyu Archipelago of Japan and Australia

An antitropical distribution represents an intriguing disjunction, in which a given species or sister lineages occupy regions north and south of the tropics but are absent from the intervening areas. Solenogyne mikadoi endemic to the Ryukyu Archipelago is regarded as an Australian element. Testing the phylogenetic relationship with Australian congeners and discussing the onset timing and causes of the disjunction would potentially enhance the understanding of antitropical distribution. A nuclear ribosomal DNA phylogeny was reconstructed using Bayesian and most parsimonious criteria with allied genera. Solenogyne was monophyletic and clustered with Lagenophora huegelii endemic to Australia, indicating the antitropical distribution and Australian origin of Solenogyne. Multispecies coalescent analysis based on nuclear ribosomal DNA and chloroplast DNA indicated the divergence of S. mikadoi and Australian congeners in the Plio-Pleistocene. Phylogenetic network analyses suggested that the ancestral lineage of S. mikadoi first colonized the southernmost island in the archipelago and then dispersed northward. The migration to the archipelago likely followed the flourishing of Solenogyne in open vegetation communities that radiated in south-eastern Australia during the late Pliocene. This disjunction might arise through long-distance dispersal across the tropics or, alternatively, through extinction in the tropics as a result of unsuitably high temperatures during climate oscillation and/or competitions from diverse tropical flora surviving since the early Tertiary.

Molecular systematics of the neotropical shovelnose catfish genus Pseudoplatystoma Bleeker 1862 based on nuclear and mtDNA markers

Pseudoplatystoma is a commercially important genus of Neotropical migratory catfishes widely distributed in all major river basins of South America. Historically, only three species were recognized, but a recent revision proposed eight putative morphospecies for the genus. A molecular study based on mitochondria DNA (mtDNA) provided support for recognition of only some of the species and raised questions about species boundaries in this group. We present a more encompassing analysis based on mtDNA (cytochrome b, 818bp) and nuclear DNA-based phylogenies (Rag1 intron 1, 664bp and S7 intron 1, 635bp) for a more extensive sampling (279 individuals from 42 localities) of all putative species in all major river basins. Patterns generated by individual gene genealogies and a multispecies coalescent analysis provided evidence to suggest recognition of only four distinct species in this genus: Pseudoplatystoma magdaleniatum, Pseudoplatystoma corruscans, Pseudoplatystoma tigrimun (sensu lato) and Pseudoplatystoma fasciatum (sensu lato). The species phylogeny places P. magdaleniatum as the sister group to all the other species in the genus, but the relationships among P. fasciatum s.l, P. tigrimum s.l., and P. corruscans could not be resolved with confidence.