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 …

Green plants (Viridiplantae) include around 450,000–500,000 species, of great diversity and
have important roles in terrestrial and aquatic ecosystems. Here, as part of the One …

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

The unprecedented amount of data resulting from next-generation sequencing has opened
a new era in phylogenetic estimation. Although large datasets should, in theory, increase …

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

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

Summary The stinging wasps (Hymenoptera: Aculeata) are an extremely diverse lineage of
hymenopteran insects, encompassing over 70,000 described species and a diversity of life …

Discordances between species trees and gene trees can complicate phylogenetics
reconstruction. ASTRAL is a leading method for inferring species trees given gene trees …

Restriction-site associated DNA (RAD) sequencing and related methods rely on the
conservation of enzyme recognition sites to isolate homologous DNA fragments for …

With the increasing availability of whole genome data, many species trees are being
constructed from hundreds to thousands of loci. Although concatenation analysis using …