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The classic multispecies coalescent (MSC) model provides the means for theoretical justification of incomplete lineage sorting-aware species tree inference methods. A large body of work in phylogenetics is dedicated to the design of…
Incomplete lineage sorting (ILS) is a common source of gene tree incongruence in multilocus analyses. A large number of methods have been developed to infer species trees in the presence of ILS. Here we provide a mathematical analysis of…
Under the multispecies coalescent model of molecular evolution, gene trees have independent evolutionary histories within a shared species tree. In comparison, supermatrix concatenation methods assume that gene trees share a single common…
We consider species tree estimation under a standard stochastic model of gene tree evolution that incorporates incomplete lineage sorting (as modeled by a coalescent process) and gene duplication and loss (as modeled by a branching…
Because biological processes can make different loci have different evolutionary histories, species tree estimation requires multiple loci from across the genome. While many processes can result in discord between gene trees and species…
A method was developed for Bayesian inference of species phylogeny using the multi-species coalescent model. To improve the mixing properties of the Markov chain Monte Carlo (MCMC) algorithm that traverses the space of species trees, we…
Species tree estimation is a complex problem, due to the fact that different parts of the genome can have different evolutionary histories than the genome itself. One of the causes for this discord is incomplete lineage sorting (also called…
Species tree reconstruction is complicated by effects of Incomplete Lineage Sorting (ILS), commonly modeled by the multi-species coalescent model. While there has been substantial progress in developing methods that estimate a species tree…
Species tree estimation from multi-locus datasets is statistically challenging for multiple reasons, including gene tree heterogeneity across the genome due to incomplete lineage sorting (ILS). Species tree estimation methods have been…
The multi-species coalescent provides an elegant theoretical framework for estimating species trees and species demographics from genetic markers. Practical applications of the multi-species coalescent model are, however, limited by the…
Species networks generalize the notion of species trees to allow for hybridization or other lateral gene transfer. Under the Network Multispecies Coalescent Model, individual gene trees arising from a network can have any topology, but…
Most current methods for inferring species-level phylogenies under the coalescent model assume that no gene flow occurs following speciation. While some studies have examined the impact of gene flow on estimation accuracy for certain…
The reconstruction of a species phylogeny from genomic data faces two significant hurdles: 1) the trees describing the evolution of each individual gene--i.e., the gene trees--may differ from the species phylogeny and 2) the molecular…
The multispecies coalescent model describes the generation of gene trees from a rooted metric species tree, and thus provides a framework for the inference of species trees from sampled gene trees. We prove that the STAR method of Liu et…
In this article we propose a new method, which we name 'quartet neighbor joining', or 'quartet-NJ', to infer an unrooted species tree on a given set of taxa T from empirical distributions of unrooted quartet gene trees on all four-taxon…
ASTRAL is a method for reconstructing species trees after inferring a set of gene trees and is increasingly used in phylogenomic analyses. It is statistically consistent under the multi-species coalescent model, is scalable, and has shown…
Polyploidy is an important speciation mechanism, particularly in land plants. Allopolyploid species are formed after hybridization between otherwise intersterile parental species. Recent theoretical progress has led to successful…
Gene trees are evolutionary trees representing the ancestry of genes sampled from multiple populations. Species trees represent populations of individuals -- each with many genes -- splitting into new populations or species. The coalescent…
Coalescent models of evolution account for incomplete lineage sorting by specifying a species tree parameter which determines a distribution on gene trees. It has been shown that the unrooted topology of the species tree parameter of the…
In phylogenomics, species-tree methods must contend with two major sources of noise; stochastic gene-tree variation under the multispecies coalescent model (MSC) and finite-sequence substitutional noise. Fast agglomerative methods such as…