Related papers: Testing for polytomies in phylogenetic species tre…
Compared to a neutral model, purifying selection distorts the structure of genealogies and hence alters the patterns of sampled genetic variation. Although these distortions may be common in nature, our understanding of how we expect…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
The Sackin and Colless indices are two widely-used metrics for measuring the balance of trees and for testing evolutionary models in phylogenetics. This short paper contributes two results about the Sackin and Colless indices of trees. One…
A phylogenetic tree is an edge-weighted binary tree, with leaves labelled by a collection of species, that represents the evolutionary relationships between those species. For such a tree, a phylogenetic diversity index is a function that…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
Spontaneous symmetry breaking plays a fundamental role in many areas of condensed matter and particle physics. A fundamental problem in ecology is the elucidation of the mechanisms responsible for biodiversity and stability. Neutral theory,…
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 ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
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…
A labeled gene tree topology that is more probable than the labeled gene tree topology matching a species tree is called \textit{anomalous}. Species trees that can generate such anomalous gene trees are said to be in the \textit{anomaly…
Samples of phylogenetic trees arise in a variety of evolutionary and biomedical applications, and the Fr\'echet mean in Billera-Holmes-Vogtmann tree space is a summary tree shown to have advantages over other mean or consensus trees.…
Phylogenetic networks are a generalization of phylogenetic trees to leaf-labeled directed acyclic graphs that represent ancestral relationships between species whose past includes non-tree-like events such as hybridization and horizontal…
Many biological studies involve inferring the evolutionary history of a sample of individuals from a large population and interpreting the reconstructed tree. Such an ascertained tree typically represents only a small part of a…
Species trees represent the historical divergences of populations or species, while gene trees trace the ancestry of individual gene copies sampled within those populations. In cases involving rapid speciation, gene trees with topologies…
The delimitation of biological species, i.e., deciding which individuals belong to the same species and whether and how many different species are represented in a data set, is key to the conservation of biodiversity. Much existing work…
Bipartition cover probabilities quantify whether a collection of gene trees contains every bipartition of the underlying species tree, a condition that underlies finite-sample guarantees for summary methods such as ASTRAL. We study this…
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…
We study the effect of biological confounders on the model selection problem between Kingman coalescents with population growth, and Xi-coalescents involving simultaneous multiple mergers. We use a low dimensional, computationally tractable…
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…
Understanding which phenotypic traits are consistently correlated throughout evolution is a highly pertinent problem in modern evolutionary biology. Here, we propose a multivariate phylogenetic latent liability model for assessing the…