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 …

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 …

Motivation: Species trees provide insight into basic biology, including the mechanisms of
evolution and how it modifies biomolecular function and structure, biodiversity and co …

Background The use of transcriptomic and genomic datasets for phylogenetic reconstruction
has become increasingly common as researchers attempt to resolve recalcitrant nodes with …

There is a lack of consensus on how next-generation sequence (NGS) data should be
considered for phylogenetic and phylogeographic estimates, with some studies excluding …

Phylogenomic analyses routinely estimate species trees using methods that account for
gene tree discordance. However, the most scalable species tree inference methods, which …

Large datasets are required to solve difficult phylogenetic problems that are deep in the Tree
of Life. Currently, two divergent systematic methods are commonly applied to such datasets …

Species tree estimation is complicated by processes, such as gene duplication and loss and
incomplete lineage sorting (ILS), that cause discordance between gene trees and the …

Genome-wide phylogeny reconstruction is becoming increasingly common, and one driving
factor behind these phylogenomic studies is the promise that the potential discordance …

The heterogeneity of signals in the genomes of diverse organisms poses challenges for
traditional phylogenetic analysis. Phylogenetic methods known as “species tree” methods …