This is the opening paper in the special issue of Fungal Diversity, which collates the data on
defining species. Defining and recognizing species has long been a controversial issue …

Phylogenetic analysis of 11 genetic loci and results from many genoty** studies revealed
significant genetic diversity with the pathogenic Cryptococcus gattii/Cryptococcus …

Motivation: Increasing attention has been devoted to estimation of species-level
phylogenetic relationships under the coalescent model. However, existing methods either …

This paper provides an overview and a tutorial of the BPP program, which is a Bayesian
MCMC program for analyzing multi-locus genomic sequence data under the multispecies …

Species delimitation is the act of identifying species‐level biological diversity. In recent
years, the field has witnessed a dramatic increase in the number of methods available for …

The tree of life of fishes is in a state of flux because we still lack a comprehensive phylogeny
that includes all major groups. The situation is most critical for a large clade of spiny-finned …

In recent articles published in Molecular Phylogenetics and Evolution, Mark Springer and
John Gatesy (S&G) present numerous criticisms of recent implementations and testing of the …

Until recently, it has been common practice for a phylogenetic analysis to use a single gene
sequence from a single individual organism as a proxy for an entire species. With …

Phylogenetic relationships among recently diverged species are often difficult to resolve due
to insufficient phylogenetic signal in available markers and/or conflict among gene trees …

This is a time of unprecedented transition in DNA sequencing technologies. Next-generation
sequencing (NGS) clearly holds promise for fast and cost-effective generation of multilocus …