Knowing phylogenetic relationships among species is fundamental for many studies in
biology. An accurate phylogenetic tree underpins our understanding of the major transitions …

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 …

Stochastic simulation is a key tool in population genetics, since the models involved are
often analytically intractable and simulation is usually the only way of obtaining ground-truth …

Phylogenetic analysis has entered the genomics (multilocus) era. For less experienced
researchers, conquering the large number of software programs required for a multilocus …

Background Evolutionary histories can be discordant across the genome, and such
discordances need to be considered in reconstructing the species phylogeny. ASTRAL is …

Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent
years with major new advances in nearly all aspects of the joint modelling of evolutionary …

Species tree reconstruction is complicated by effects of incomplete lineage sorting,
commonly modeled by the multi-species coalescent model (MSC). While there has been …

The hundreds of cichlid fish species in Lake Malawi constitute the most extensive recent
vertebrate adaptive radiation. Here we characterize its genomic diversity by sequencing 134 …

Species are fundamental units in biological research and can be defined on the basis of
various operational criteria. There has been growing use of molecular approaches for …

Motivation: The estimation of species phylogenies requires multiple loci, since different loci
can have different trees due to incomplete lineage sorting, modeled by the multi-species …