Genome-scale data and the development of novel statistical phylogenetic approaches have
greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its …

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 …

Motivation Phylogenies are important for fundamental biological research, but also have
numerous applications in biotechnology, agriculture and medicine. Finding the optimal tree …

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

INTRODUCTION The ruminants are one of the most successful mammalian lineages,
exhibiting extensive morphological and ecological diversity and containing several key …

To better determine the history of modern birds, we performed a genome-scale phylogenetic
analysis of 48 species representing all orders of Neoaves using phylogenomic methods …

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

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

The precise pattern and timing of speciation events that gave rise to all living placental
mammals remain controversial. We provide a comprehensive phylogenetic analysis of …

Background Sequence data used in reconstructing phylogenetic trees may include various
sources of error. Typically errors are detected at the sequence level, but when missed, the …