This article reviews the various models that have been used to describe the relationships
between gene trees and species trees. Molecular phylogeny has focused mainly on …

Phylogenomics refers to the inference of historical relationships among species using
genome-scale sequence data and to the use of phylogenetic analysis to infer protein …

Current sequencing methods produce large amounts of data, but genome assemblies
constructed from these data are often fragmented and incomplete. Incomplete and error …

Comparisons of gene trees and species trees are key to understanding major processes of
genome evolution such as gene duplication and loss. Because current methods to …

Motivation: Gene family evolution is driven by evolutionary events such as speciation, gene
duplication, horizontal gene transfer and gene loss, and inferring these events in the …

The availability of whole genome sequences was expected to supply essentially unlimited
data for phylogenetics. However, strict reliance on single-copy genes for this purpose has …

Gene phylogenies provide a rich source of information about the way evolution shapes
genomes, populations, and phenotypes. In addition to substitutions, evolutionary events …

Carnivorous plants exploit animals as a nutritional source and have inspired long-standing
questions about the origin and evolution of carnivory-related traits. To investigate the …

Gene sequences contain a gold mine of phylogenetic information. But unfortunately for
taxonomists this information does not only tell the story of the species from which it was …

Many recent phylogenetic methods have focused on accurately inferring species trees when
there is gene tree discordance due to incomplete lineage sorting (ILS). For almost all of …