Related papers: An analytical comparison of coalescent-based multi…
Inference of the evolutionary histories of species, commonly represented by a species tree, is complicated by the divergent evolutionary history of different parts of the genome. Different loci on the genome can have different histories…
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…
A major problem for inferring species trees from gene trees is that evolutionary processes can sometimes favour gene tree topologies that conflict with an underlying species tree. In the case of incomplete lineage sorting, this phenomenon…
We introduce a simple algorithm for reconstructing phylogenies from multiple gene trees in the presence of incomplete lineage sorting, that is, when the topology of the gene trees may differ from that of the species tree. We show that our…
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…
Evolutionary events such as incomplete lineage sorting and lateral gene transfer constitute major problems for inferring species trees from gene trees, as they can sometimes lead to gene trees which conflict with the underlying species…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
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…
One approach to estimating a species tree from a collection of gene trees is to first estimate probabilities of clades from the gene trees, and then to construct the species tree from the estimated clade probabilities. While a greedy…
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…
Using topological summaries of gene trees as a basis for species tree inference is a promising approach to obtain acceptable speed on genomic-scale datasets, and to avoid some undesirable modeling assumptions. Here we study the…
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…
When gene copies are sampled from various species, the resulting gene tree might disagree with the containing species tree. The primary causes of gene tree and species tree discord include lineage sorting, horizontal gene transfer, and gene…
We consider the problem of estimating species trees from unrooted gene tree topologies in the presence of incomplete lineage sorting, a common phenomenon that creates gene tree heterogeneity in multilocus datasets. One popular class of…
The inference of the evolutionary history of a collection of organisms is a problem of fundamental importance in evolutionary biology. The abundance of DNA sequence data arising from genome sequencing projects has led to significant…
We consider the problem of drawing multiple gene trees inside a single species tree in order to visualize multispecies coalescent trees. Specifically, the drawing of the species tree fills a rectangle in which each of its edges is…
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…
The multispecies coalescent process models the genealogical relationships of genes sampled from several species, enabling useful predictions about phenomena such as the discordance between the gene tree and the species phylogeny due to…
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…
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…