Related papers: Identifying species network features from gene tre…
When hybridization or other forms of lateral gene transfer have occurred, evolutionary relationships of species are better represented by phylogenetic networks than by trees. While inference of such networks remains challenging, several…
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…
Inference of species networks from genomic data under the Network Multispecies Coalescent Model is currently severely limited by heavy computational demands. It also remains unclear how complicated networks can be for consistent inference…
Inference of phylogenetic networks is of increasing interest in the genomic era. However, the extent to which phylogenetic networks are identifiable from various types of data remains poorly understood, despite its crucial role in…
The inference of phylogenetic networks, which model complex evolutionary processes including hybridization and gene flow, remains a central challenge in evolutionary biology. Until now, statistically consistent inference methods have been…
Inference of network-like evolutionary relationships between species from genomic data must address the interwoven signals from both gene flow and incomplete lineage sorting. The heavy computational demands of standard approaches to this…
Motivation: The abundance of gene flow in the Tree of Life challenges the notion that evolution can be represented with a fully bifurcating process, as this process cannot capture important biological realities like hybridization,…
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…
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…
An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic tree with leaves consisting of a set $X$ of species from a…
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…
Phylogenetic networks are mathematical structures for modeling and visualization of reticulation processes in the study of evolution. Galled networks, reticulation visible networks, nearly-stable networks and stable-child networks are the…
In phylogenetics, it is important for the phylogenetic network model parameters to be identifiable so that the evolutionary histories of a group of species can be consistently inferred. However, as the complexity of the phylogenetic network…
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…
Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…
We study the problem of identifying different behaviors occurring in different parts of a large heterogenous network. We zoom in to the network using lenses of different sizes to capture the local structure of the network. These network…
Phylogenetic networks can represent evolutionary events that cannot be described by phylogenetic trees, such as hybridization, introgression, and lateral gene transfer. Studying phylogenetic networks under a statistical model of DNA…
The Tree of Life is the graphical structure that represents the evolutionary process from single-cell organisms at the origin of life to the vast biodiversity we see today. Reconstructing this tree from genomic sequences is challenging due…
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…