Phylogeny estimation is difficult for closely related populations and species, especially if
they have been exchanging genes. We present a hierarchical Bayesian, Markov-chain …

We review recent trends in phylogeography and phylogenetics and argue that these two
fields stand to be reunited by the common yardstick provided by sequence and SNP data …

An intricate relation exists between gene trees and species phylogenies, due to evolutionary
processes that act on the genes within and across the branches of the species phylogeny …

Gene tree topologies have proven a powerful data source for various tasks, including
species tree inference and species delimitation. Consequently, methods for computing …

The molecular era has fundamentally reshaped our knowledge of the evolution and
diversification of angiosperms. One outstanding question is the phylogenetic placement of …

One of the longstanding questions in phylogenetic systematics is how to address
incongruence among phylogenies obtained from multiple markers and how to determine the …

Numerous simulation studies have investigated the accuracy of phylogenetic inference of
gene trees under maximum parsimony, maximum likelihood, and Bayesian techniques. The …

Gene trees record the combination of gene-level events, such as duplication, transfer and
loss (DTL), and species-level events, such as speciation and extinction. Gene tree–species …

We describe a software package (SpedeSTEM) that allows researchers to conduct a species
delimitation analysis using intraspecific genetic data. Our method operates under the …

The multispecies coalescent (MSC) model has emerged as a powerful framework for
inferring species phylogenies while accounting for ancestral polymorphism and gene tree …