Related papers: Registering the evolutionary history in individual…

Evolutionary models used for describing molecular sequence variation suppose that at a non-recombining genomic segment, sequences share ancestry that can be represented as a genealogy--a rooted, binary, timed tree, with tips corresponding…

Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…

Computational phylogenetics has become an established tool in historical linguistics, with many language families now analyzed using likelihood-based inference. However, standard approaches rely on expert-annotated cognate sets, which are…

We study a universal object for the genealogy of a sample in populations with mutations: the critical birth-death process with Poissonian mutations, conditioned on its population size at a fixed time horizon. We show how this process arises…

Differential evolution possesses a multitude of various strategies for generating new trial solutions. Unfortunately, the best strategy is not known in advance. Moreover, this strategy usually depends on the problem to be solved. This paper…

Comparisons of single-cell RNA sequencing (scRNA-seq) data across species can reveal links between cellular gene expression and the evolution of cell functions, features, and phenotypes. These comparisons invoke evolutionary histories, as…

This paper presents a procedure to add broader diversity at the beginning of the evolutionary process. It consists of creating two initial populations with different parameter settings, evolving them for a small number of generations,…

Ecological networks describe the interactions between different species, informing us of how they rely on one another for food, pollination and survival. If a species in an ecosystem is under threat of extinction, it can affect other…

We survey results on the description of stochastically evolving genealogies of populations and marked genealogies of multitype populations or spatial populations via tree-valued Markov processes on (marked) ultrametric measure spaces. In…

Phylogenetic trait evolution models allow for the estimation of evolutionary correlations between a set of traits observed in a sample of related organisms. By directly modeling the evolution of the traits along an estimable phylogenetic…

Phylogenetics, the inference of evolutionary trees from molecular sequence data such as DNA, is an enterprise that yields valuable evolutionary understanding of many biological systems. Bayesian phylogenetic algorithms, which approximate a…

A birth-death-sampling model gives rise to phylogenetic trees with samples from the past and the present. Interpreting "birth" as branching speciation, "death" as extinction, and "sampling" as fossil preservation and recovery, this model --…

We are interested in modeling some two-level population dynamics, resulting from the interplay of ecological interactions and phenotypic variation of individuals (or hosts) and the evolution of cells (or parasites) of two types living in…

In this paper we consider two continuous-mass population models as analogues of logistic branching random walks, one is supported on a finite trait space and the other one is supported on an infinite trait space. For the first model with…

Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…

How do phylogenetic reconstruction algorithms go astray when they return incorrect trees? This simple question has not been answered in detail, even for maximum parsimony (MP), the simplest phylogenetic criterion. Understanding MP has…

In this paper we consider a microscopic model of a simple ecosystem. The basic ingredients of this model are individuals, and both the phenotypic and genotypic levels are taken in account. The model is based on a long range cellular…

Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced…

In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…

Stochastic modeling of phylogenies raises five questions that have received varying levels of attention from quantitatively inclined biologists. 1) How large do we expect (from the model) the ration of maximum historical diversity to…