Related papers: Invertibility of the TKF model of sequence evoluti…

Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…

The analysis of DNA sequences has become critical in numerous fields, from evolutionary biology to understanding gene regulation and disease mechanisms. While deep neural networks can achieve remarkable predictive performance, they…

Horizontal gene transfer events partition a gene tree $T$ and thus, its leaf set into subsets of genes whose evolutionary history is described by speciation and duplication events alone. Indirect phylogenetic methods can be used to infer…

Phylogenetic diversity indices such as the Fair Proportion (FP) index are frequently discussed as prioritization criteria in biodiversity conservation. They rank species according to their contribution to overall diversity by taking into…

Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…

Phylogenetic networks are directed acyclic graphs that depict the genomic evolution of related taxa. Reticulation nodes in such networks (nodes with more than one parent) represent reticulate evolutionary events, such as recombination,…

Stochastic models of evolution (Markov random fields on trivalent trees) generally assume that different characters (different runs of the stochastic process) are independent and identically distributed. In this paper we take the first…

Large sets of genotypes give rise to the same phenotype because phenotypic expression is highly redundant. Accordingly, a population can accept mutations without altering its phenotype, as long as thegenotype mutates into another one on the…

Reconstructing evolutionary trees from molecular sequence data is a fundamental problem in computational biology. Stochastic models of sequence evolution are closely related to spin systems that have been extensively studied in statistical…

The sequence of amino acids in a protein is believed to determine its native state structure, which in turn is related to the functionality of the protein. In addition, information pertaining to evolutionary relationships is contained in…

Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…

Consider a population that is expanding in two-dimensional space. Suppose we collect data from a sample of individuals taken at random either from the entire population, or from near the outer boundary of the population. A quantity of…

Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…

In phylogenetic studies, the evolution of molecular sequences is assumed to have taken place along the phylogeny traced by the ancestors of extant species. In the presence of lateral gene transfer (LGT), however, this may not be the case,…

Phylogenetic networks are used to represent the evolutionary history of species. They are versatile when compared to traditional phylogenetic trees, as they capture more complex evolutionary events such as hybridization and horizontal gene…

We study the role of phylogenetic trees on correlations in mutation processes. Generally, correlations decay exponentially with the generation number. We find that two distinct regimes of behavior exist. For mutation rates smaller than a…

The properties of randomly evolving special trees having defined and analyzed already in two earlier papers (arXiv:cond-mat/0205650 and arXiv:cond-mat/0211092) have been investigated in the case when the continuous time parameter converges…

Structural information of phylogenetic tree topologies plays an important role in phylogenetic inference. However, finding appropriate topological structures for specific phylogenetic inference tasks often requires significant design effort…

Likelihood-based methods are widely considered the best approaches for reconstructing ancestral states. Although much effort has been made to study properties of these methods, previous works often assume that both the tree topology and…

Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…