Related papers: Species tree estimation using ASTRAL: how many gen…
Most current methods for inferring species-level phylogenies under the coalescent model assume that no gene flow occurs following speciation. While some studies have examined the impact of gene flow on estimation accuracy for certain…
Poly-trees are singly connected causal networks in which variables may arise from multiple causes. This paper develops a method of recovering ply-trees from empirically measured probability distributions of pairs of variables. The method…
We analyse a maximum-likelihood approach for combining phylogenetic trees into a larger `supertree'. This is based on a simple exponential model of phylogenetic error, which ensures that ML supertrees have a simple combinatorial description…
Phylogenetic (i.e. leaf-labeled) trees play a fundamental role in evolutionary research. A typical problem is to reconstruct such trees from data like DNA alignments (whose columns are often referred to as characters), and a simple…
The rooted subtree prune and regraft (rSPR) distance between two rooted binary phylogenetic trees is a well-studied measure of topological dissimilarity that is NP-hard to compute. Here we describe an improved linear kernel for the problem.…
Reconstructing a parsimonious phylogenetic network that displays multiple phylogenetic trees is an important problem in theory of phylogenetics, where the complexity of the inferred networks is measured by reticulation numbers. The…
Ancestral state reconstruction is one of the most important tasks in evolutionary biology. Conditions under which we can reliably reconstruct the ancestral state have been studied for both discrete and continuous traits. However, the…
We study the problem of learning a node-labeled tree given independent traces from an appropriately defined deletion channel. This problem, tree trace reconstruction, generalizes string trace reconstruction, which corresponds to the tree…
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…
Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed to this purpose. Theoretical results are available that show…
In an extant population, how much information do extant individuals provide on the pedigree of their ancestors? Recent work by Kim, Mossel, Ramnarayan and Turner (2020) studied this question under a number of simplifying assumptions,…
In this study, we investigate the problem of comparing gene trees reconciled with the same species tree using a novel semi-metric, called the Path-Label Reconciliation (PLR) dissimilarity measure. This approach not only quantifies…
Phylogenetic trees are frequently used to model evolution. Such trees are typically reconstructed from data like DNA, RNA, or protein alignments using methods based on criteria like maximum parsimony (amongst others). Maximum parsimony has…
We consider the problem of estimating a large causal polytree from a relatively small i.i.d. sample. This is motivated by the problem of determining causal structure when the number of variables is very large compared to the sample size,…
The maximum agreement forest (MAF) problem in phylogenetics takes as input a set t >= 2 of binary phylogenetic trees T on the same set of taxa X. It asks for a partition of X into the smallest number of blocks such that the subtrees induced…
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…
The history of gene families - which are equivalent to \emph{event-labeled} gene trees - can be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes. The…
Recurrence formulas are presented for studying the accuracy of the Fitch method for reconstructing the ancestral states in a given phylogenetic tree. As their applications, we analyze the convergence of the accuracy of reconstructing the…
The recovery of an unknown signal from its linear measurements is a fundamental problem spanning numerous scientific and engineering disciplines. Commonly, prior knowledge suggests that the underlying signal resides within a known algebraic…
Modern biological techniques enable very dense genetic sampling of unfolding evolutionary histories, and thus frequently sample some genotypes multiple times. This motivates strategies to incorporate genotype abundance information in…