Knowing phylogenetic relationships among species is fundamental for many studies in
biology. An accurate phylogenetic tree underpins our understanding of the major transitions …

As more complete genomes are sequenced, phylogenetic analysis is entering a new era—
that of phylogenomics. One branch of this expanding field aims to reconstruct the …

Phylogenetic analysis has entered the genomics (multilocus) era. For less experienced
researchers, conquering the large number of software programs required for a multilocus …

Budding yeasts (subphylum Saccharomycotina) are found in every biome and are as
genetically diverse as plants or animals. To understand budding yeast evolution, we …

Background Next-generation sequencing has provided a wealth of plastid genome
sequence data from an increasingly diverse set of green plants (Viridiplantae). Although …

Motivation Diverse disciplines in biology process and analyze multiple sequence alignments
(MSAs) and phylogenetic trees to evaluate their information content, infer evolutionary …

The appearance of photosynthetic eukaryotes (algae and plants) dramatically altered the
Earth's ecosystem, making possible all vertebrate life on land, including humans. Dating …

It is thought that speciation in phytophagous insects is often due to colonization of novel host
plants, because radiations of plant and insect lineages are typically asynchronous. Recent …

Phylogenomic subsampling is a procedure by which small sets of loci are selected from
large genome-scale data sets and used for phylogenetic inference. This step is often …

The origins and the divergence times of the most basal lineages within primates have been
difficult to resolve mainly due to the incomplete sampling of early fossil taxa. The main …