Gene flow among populations or species and incomplete lineage sorting (ILS) are two
evolutionary processes responsible for generating gene tree discordance and therefore …

Large phylogeny estimation is a combinatorial optimization problem that no future computer
will ever be able to solve exactly in practical computing time. The difficulty of the problem is …

This paper will attempt to resolve some controversies about the effects of missing data on
phylogenetic analysis. Whether missing data are generally problematic is a critical issue in …

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

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 …

The sizes of the data matrices assembled to resolve branches of the tree of life have
increased dramatically, motivating the development of programs for fast, yet accurate …

A number of approaches for studying macroevolution using phylogenetic trees have been
developed in the last few years. Here, we present RPANDA, an R package that implements …

We propose a model based approach to use multiple gene trees to estimate the species
tree. The coalescent process requires that gene divergences occur earlier than species …

Genome‐scale sequence data have become increasingly available in the phylogenetic
studies for understanding the evolutionary histories of species. However, it is challenging to …

The development and application of coalescent methods are undergoing rapid changes.
One little explored area that bears on the application of gene-tree-based coalescent …