Related papers: Predicting the ancestral character changes in a tr…
In this paper, we consider a tree inference problem motivated by the critical problem in single-cell genomics of reconstructing dynamic cellular processes from sequencing data. In particular, given a population of cells sampled from such a…
Phylogenomics, even more so than traditional phylogenetics, needs to represent the uncertainty in evolutionary trees due to systematic error. Here we illustrate the analysis of genome-scale alignments of yeast, using robust measures of the…
In a deterministic or random tree, a notion of ancestral diversity can be defined as follows. Sample independently $n$ groups of $k$ leaves and count the number $N_n(k)$ of distinct most recent common ancestors of each of the groups. As $n$…
Tree-based networks are a class of phylogenetic networks that attempt to formally capture what is meant by "tree-like" evolution. A given non-tree-based phylogenetic network, however, might appear to be very close to being tree-based, or…
In evolutionary biology, genetic sequences carry with them a trace of the underlying tree that describes their evolution from a common ancestral sequence. The question of how many sequence sites are required to recover this evolutionary…
Genetic sequence data of pathogens are increasingly used to investigate transmission dynamics in both endemic diseases and disease outbreaks; such research can aid in development of appropriate interventions and in design of studies to…
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…
Recent theoretical work has demonstrated that Neighbor Joining applied to concatenated DNA sequences is a statistically consistent method of species tree reconstruction. This brief note compares the accuracy of this approach to other…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
Due to their long-standing reputation as excellent off-the-shelf predictors, random forests continue remain a go-to model of choice for applied statisticians and data scientists. Despite their widespread use, however, until recently, little…
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…
We consider the Moran model of population genetics with two types, mutation, and selection, and investigate the line of descent of a randomly-sampled individual from a contemporary population. We trace this ancestral line back into the…
Probability estimation is one of the fundamental tasks in statistics and machine learning. However, standard methods for probability estimation on discrete objects do not handle object structure in a satisfactory manner. In this paper, we…
Phylogenetic mixture models are statistical models of character evolution allowing for heterogeneity. Each of the classes in some unknown partition of the characters may evolve by different processes, or even along different trees. The…
We consider the transmission of a state from the root of a tree towards its leaves, assuming that each transmission occurs through a noisy channel. The states at the leaves are observed, while at deeper nodes we can compute the likelihood…
We consider a pruning of the inhomogeneous continuum random trees, as well as the cut trees that encode the genealogies of the fragmentations that come with the pruning. We propose a new approach to the reconstruction problem, which has…
The maximum parsimony phylogenetic tree reconstruction problem is NP-hard, presenting a computational bottleneck for classical computing and motivating the exploration of emerging paradigms like quantum computing. To this end, we design…
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…
We consider a broadcasting problem on a tree where a binary digit (e.g., a spin or a nucleotide's purine/pyrimidine type) is propagated from the root to the leaves through symmetric noisy channels on the edges that randomly flip the state…
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…