相关论文: Quantifying the accuracy of ancestral state predic…

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…

Statistical consistency in phylogenetics has traditionally referred to the accuracy of estimating phylogenetic parameters for a fixed number of species as we increase the number of characters. However, as sequences are often of fixed length…

The reconstruction of phylogenetic trees from mixed populations has become important in the study of cancer evolution, as sequencing is often performed on bulk tumor tissue containing mixed populations of cells. Recent work has shown how to…

Given two phylogenetic trees on the same set of taxa X, the maximum parsimony distance d_MP is defined as the maximum, ranging over all characters c on X, of the absolute difference in parsimony score induced by c on the two trees. In this…

This paper studies a Markov chain for phylogenetic reconstruction which uses a popular transition between tree topologies known as subtree pruning-and-regrafting (SPR). We analyze the Markov chain in the simpler setting that the generating…

The standard models of sequence evolution on a tree determine probabilities for every character or site pattern. A flattening is an arrangement of these probabilities into a matrix, with rows corresponding to all possible site patterns for…

The ancestral maximum-likelihood and phylogeography problems are two fundamental problems involving evolutionary studies. The ancestral maximum-likelihood problem involves identifying a rooted tree alongside internal node sequences that…

One of the main aims of phylogenetics is to reconstruct the \enquote{Tree of Life}. In this respect, different methods and criteria are used to analyze DNA sequences of different species and to compare them in order to derive the…

The so-called binary perfect phylogeny with persistent characters has recently been thoroughly studied in computational biology as it is less restrictive than the well known binary perfect phylogeny. Here, we focus on the notion of (binary)…

Inferences about the evolution of continuous traits based on reconstruction of ancestral states has often been considered more error-prone than analysis of independent contrasts. Here we show that both methods in fact yield identical…

Phylogenetic trees represent evolutionary relationships and can be uniquely defined by sets of finite-state biological characteristics. Despite prior work showing that sufficiently large trees can be determined by $r$-state character sets,…

Phylogenetic inference aims to reconstruct the evolutionary relationships of different species based on genetic (or other) data. Discrete characters are a particular type of data, which contain information on how the species should be…

Finding optimal evolutionary trees from sequence data is typically an intractable problem, and there is usually no way of knowing how close to optimal the best tree from some search truly is. The problem would seem to be particularly acute…

In evolutionary biology, the speciation history of living organisms is represented graphically by a phylogeny, that is, a rooted tree whose leaves correspond to current species and branchings indicate past speciation events. Phylogenies are…

Bayesian inference is now a leading technique for reconstructing phylogenetic trees from aligned sequence data. In this short note, we formally show that the maximum posterior tree topology provides a statistically consistent estimate of a…

Phylogenetic trees are used to model evolution: leaves are labelled to represent contemporary species ("taxa") and interior vertices represent extinct ancestors. Informally, convex characters are measurements on the contemporary species in…

Phylogenetic networks are used to display the relationship of different species whose evolution is not treelike, which is the case, for instance, in the presence of hybridization events or horizontal gene transfers. Tree inference methods…

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…

Perfect phylogenies are fundamental in the study of evolutionary trees because they capture the situation when each evolutionary trait emerges only once in history; if such events are believed to be rare, then by Occam's Razor such…

Phylogenetic trees play a key role in the reconstruction of evolutionary relationships. Typically, they are derived from aligned sequence data (like DNA, RNA, or proteins) by using optimization criteria like, e.g., maximum parsimony (MP).…