Related papers: Fast coalescent-based computation of local branch …
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…
The reconstruction of large phylogenetic trees from data that violates clocklike evolution (or as a supertree constructed from any m input trees) raises a difficult question for biologists - how can one assign relative dates to the vertices…
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…
We present the first sub-quadratic time algorithm that with high probability correctly reconstructs phylogenetic trees for short sequences generated by a Markov model of evolution. Due to rapid expansion in sequence databases, such very…
We present an algorithm for phylogenetic reconstruction using quartets that returns the correct topology for $n$ taxa in $O(n \log n)$ time with high probability, in a probabilistic model where a quartet is not consistent with the true…
Topological phylogenetic trees can be assigned edge weights in several natural ways, highlighting different aspects of the tree. Here the rooted triple and quartet metrizations are introduced, and applied to formulate novel fast methods of…
The kernel method is a potential approach to analyzing structured data such as sequences, trees, and graphs; however, unordered trees have not been investigated extensively. Kimura et al. (2011) proposed a kernel function for unordered…
A popular line of research in evolutionary biology is the use of time-calibrated phylogenies for the inference of diversification processes. This requires computing the likelihood of a given ultrametric tree as the reconstructed tree…
We consider the reconstruction of a phylogeny from multiple genes under the multispecies coalescent. We establish a connection with the sparse signal detection problem, where one seeks to distinguish between a distribution and a mixture of…
In many interesting cases the reconstruction of a correct phylogeny is blurred by high mutation rates and/or horizontal transfer events. As a consequence a divergence arises between the true evolutionary distances and the differences…
Statistical inference of evolutionary parameters from molecular sequence data relies on coalescent models to account for the shared genealogical ancestry of the samples. However, inferential algorithms do not scale to available data sets. A…
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 propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…
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…
In population genetics, there is often interest in inferring selection coefficients. This task becomes more challenging if multiple linked selected loci are considered simultaneously. For such a situation, we propose a novel generalized…
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…
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…
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…
Background: The reconstruction of the phylogenetic tree topology of four taxa is, still nowadays, one of the main challenges in phylogenetics. Its difficulties lie in considering not too restrictive evolutionary models, and correctly…
This work considers the problem of learning the structure of multivariate linear tree models, which include a variety of directed tree graphical models with continuous, discrete, and mixed latent variables such as linear-Gaussian models,…