Species networks generalize the notion of species trees to allow for hybridization or other
lateral gene transfer. Under the network multispecies coalescent model, individual gene …

If all nucleotide sites evolved at the same rate within molecules and throughout the history of
lineages, if all nucleotides were in equal proportion, if any nucleotide or amino acid evolved …

Hybridization events complicate the accurate reconstruction of phylogenies, as they lead to
patterns of genetic heritability that are unexpected under traditional, bifurcating models of …

We consider the evolution of phylogenetic gene trees along phylogenetic species networks,
according to the network multispecies coalescent process, and introduce a new network …

MSCquartets is an R package for species tree hypothesis testing, inference of species trees
and inference of species networks under the Multispecies Coalescent model of incomplete …

Identifying the footprints of selection in coding sequences can inform about the importance
and function of individual sites. Analyses of the ratio of nonsynonymous to synonymous …

The likelihood ratio test (LRT) is widely used for comparing the relative fit of nested latent
variable models. Following Wilks' theorem, the LRT is conducted by comparing the LRT …

Inference of network-like evolutionary relationships between species from genomic data
must address the interwoven signals from both gene flow and incomplete lineage sorting …

A simple graphical device, the simplex plot of quartet concordance factors, is introduced to
aid in the exploration of a collection of gene trees on a common set of taxa. A single plot …

Inference of species networks from genomic data under the Network Multispecies
Coalescent Model is currently severely limited by heavy computational demands. It also …