Related papers: Large-scale Species Tree Estimation
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…
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…
Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly…
With advances in sequencing technologies, there are now massive amounts of genomic data from across all life, leading to the possibility that a robust Tree of Life can be constructed. However, "gene tree heterogeneity", which is when…
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…
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…
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…
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…
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…
We consider the problem of estimating the evolutionary history of a set of species (phylogeny or species tree) from several genes. It is known that the evolutionary history of individual genes (gene trees) might be topologically distinct…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
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…
We present an algorithm for classification tasks on big data. Experiments conducted as part of this study indicate that the algorithm can be as accurate as ensemble methods such as random forests or gradient boosted trees. Unlike ensemble…
Based on decision trees, many fields have arguably made tremendous progress in recent years. In simple words, decision trees use the strategy of "divide-and-conquer" to divide the complex problem on the dependency between input features and…
Connected acyclic graphs (trees) are data objects that hierarchically organize categories. Collections of trees arise in a diverse variety of fields, including evolutionary biology, public health, machine learning, social sciences and…
The reconstruction of a species tree from genomic data faces a double hurdle. First, the (gene) tree describing the evolution of each gene may differ from the species tree, for instance, due to incomplete lineage sorting. Second, the…
The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all…
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…
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…