Related papers: Relative Timing Information and Orthology in Evolu…
The evolution of two species with different fitness is investigated on degree-heterogeneous graphs. The population evolves either by one individual dying and being replaced by the offspring of a random neighbor (voter model (VM) dynamics)…
Estimating the phylogeny of the genus Homo is entering a new phase of vastly improved data and methodology. There is increasing evidence of 6 to 10 competing species/lineages at any point in the last half million years, making the…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…
Research shows that gene duplication followed by either repurposing or removal of duplicated genes is an important contributor to evolution of gene and protein interaction networks. We aim to identify which characteristics of a network can…
Many of the commonly used methods for orthology detection start from mutually most similar pairs of genes (reciprocal best hits) as an approximation for evolutionary most closely related pairs of genes (reciprocal best matches). This…
Directed cographs (di-cographs) play a crucial role in the reconstruction of evolutionary histories of genes based on homology relations which are binary relations between genes. A variety of methods based on pairwise sequence comparisons…
Understanding the dynamic transition of motifs in temporal graphs is essential for revealing how graph structures evolve over time, identifying critical patterns, and predicting future behaviors, yet existing methods often focus on…
Genome-scale orthology assignments are usually based on reciprocal best matches. In the absence of horizontal gene transfer (HGT), every pair of orthologs forms a reciprocal best match. Incorrect orthology assignments therefore are always…
A graph $G$ is a \emph{max point-tolerance (MPT)} graph if each vertex $v$ of $G$ can be mapped to a \emph{pointed-interval} $(I_v, p_v)$ where $I_v$ is an interval of $\mathbb{R}$ and $p_v \in I_v$ such that $uv$ is an edge of $G$ iff $I_u…
Divergence time estimation requires the reconciliation of two major sources of data. These are fossil and/or biogeographic evidence that give estimates of the absolute age of nodes (ancestors) and molecular estimates that give us estimates…
An evolutionary tree is a rooted tree where each internal vertex has at least two children and where the leaves are labeled with distinct symbols representing species. Evolutionary trees are useful for modeling the evolutionary history of…
Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…
Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…
Threshold graphs are recursive deterministic network models that have been proposed for describing certain economic and social interactions. One drawback of this graph family is that it has limited generative attachment rules. To mitigate…
Comparative and evolutive ecologists are interested in the distribution of quantitative traits among related species. The classical framework for these distributions consists of a random process running along the branches of a phylogenetic…
Consider a graph $G$ where each vertex is visibly labelled as a member of a distinct class, but also has a hidden binary state: wild or tame. Edges with end points in the same class are called agreement edges. Premise: an edge connecting…
Evolutionary events such as incomplete lineage sorting and lateral gene transfer constitute major problems for inferring species trees from gene trees, as they can sometimes lead to gene trees which conflict with the underlying species…
This paper explores the application of a new algebraic method of color exchanges to the edge coloring of simple graphs. Vizing's theorem states that the edge coloring of a simple graph $G$ requires either $\Delta$ or $\Delta+1$ colors,…
Horizontal gene transfer inference approaches are usually based on gene sequences: parametric methods search for patterns that deviate from a particular genomic signature, while phylogenetic methods use sequences to reconstruct the gene and…
In this paper we study two natural models of \textit{random temporal} graphs. In the first, the \textit{continuous} model, each edge $e$ is assigned $l_e$ labels, each drawn uniformly at random from $(0,1]$, where the numbers $l_e$ are…