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 …

The availability of phylogenetic data has greatly expanded in recent years. As a result, a
new era in phylogenetic analysis is dawning—one in which the methods we use to analyse …

The timing of early cellular evolution, from the divergence of Archaea and Bacteria to the
origin of eukaryotes, is poorly constrained. The ATP synthase complex is thought to have …

Core gene phylogenies provide a window into early evolution, but different gene sets and
analytical methods have yielded substantially different views of the tree of life. Trees inferred …

ALE and GeneRax are tools for probabilistic gene tree–species tree reconciliation. Based on
a common underlying statistical model of how gene trees evolve along species trees, these …

Species tree inference from gene family trees is a significant problem in computational
biology. However, gene tree heterogeneity, which can be caused by several factors …

Motivation Missing data and incomplete lineage sorting (ILS) are two major obstacles to
accurate species tree inference. Gene tree summary methods such as ASTRAL and ASTRID …

Target enrichment is becoming increasingly popular for phylogenomic studies. Although
baits for enrichment are typically designed to target single-copy genes, paralogs are often …

Whole-genome duplication (WGD) occurs broadly and repeatedly across the history of
eukaryotes and is recognized as a prominent evolutionary force, especially in plants …

Motivation Genomes are a rich source of information on the pattern and process of evolution
across biological scales. How best to make use of that information is an active area of …