The widespread application of high-throughput sequencing in studying evolutionary
processes and patterns of diversification has led to many important discoveries. However …

Abstract During the last 15–20 years, phylogenetic, phylogeographic, paleontological,
geological, and habitat modeling studies have improved our knowledge of Sundaic …

Production of massive DNA sequence data sets is transforming phylogenetic inference, but
best practices for analyzing such data sets are not well established. One uncertainty is …

Targeted sequence capture is becoming a widespread tool for generating large
phylogenomic data sets to address difficult phylogenetic problems. However, this …

It has long been appreciated that analyses of genomic data (eg, whole genome sequencing
or sequence capture) have the potential to reveal the tree of life, but it remains challenging …

A comprehensive account of both basic and advanced material in phylogeny estimation,
focusing on computational and statistical issues. No background in biology or computer …

Rapid evolutionary radiations are expected to require large amounts of sequence data to
resolve. To resolve these types of relationships many systematists believe that it will be …

Background Divergence time estimation is fundamental to understanding many aspects of
the evolution of organisms, such as character evolution, diversification, and biogeography …

Building taxon-rich phylogenies is foundational for macroevolutionary studies. One
approach to improve taxon sampling beyond individual studies is to build supermatricies of …

Reconstructing relationships among extant birds (Neornithes) has been one of the most
difficult problems in phylogenetics, and, despite intensive effort, the avian tree of life remains …