Related papers: Ancestral diversity in fragmentation trees
Phylogenetic networks generalize phylogenetic trees, and have been introduced in order to describe evolution in the case of transfer of genetic material between coexisting species. There are many classes of phylogenetic networks, which can…
We ask the question "when will natural selection on a gene in a spatially structured population cause a detectable trace in the patterns of genetic variation observed in the contemporary population?". We focus on the situation in which…
If one goes backward in time, the number of ancestors of an individual doubles at each generation. This exponential growth very quickly exceeds the population size, when this size is finite. As a consequence, the ancestors of a given…
Generating function equation has been derived for the probability distribution of the number of nodes with $k \ge 0$ outgoing lines in randomly evolving special trees. The stochastic properties of end-nodes (k=0) have been analyzed, and it…
The branching structure of biological evolution confers statistical dependencies on phenotypic trait values in related organisms. For this reason, comparative macroevolutionary studies usually begin with an inferred phylogeny that describes…
Let $t$ be a rooted tree and $n_i(t)$ the number of nodes in $t$ having $i$ children. The degree sequence $(n_i(t),i\geq 0)$ of $t$ satisfies $\sum_{i\ge 0} n_i(t)=1+\sum_{i\ge 0} in_i(t)=|t|$, where $|t|$ denotes the number of nodes in…
By unifying three foundational principles of modern biology, we develop a mathematical framework to analyze the growing tree of life. Contrary to the static case, where the analogy between phylogenetic trees and the tree that grows in soil…
Binary trees are fundamental objects in models of evolutionary biology and population genetics. Here, we discuss some of their combinatorial and structural properties as they depend on the tree class considered. Furthermore, the process by…
Consider a family of random ordered graph trees $(T_n)_{n\geq 1}$, where $T_n$ has $n$ vertices. It has previously been established that if the associated search-depth processes converge to the normalised Brownian excursion when rescaled…
We present a graph theoretical approach to the configurational statistics of random tree-like objects, such as randomly branching polymers. In particular, for ideal trees we show that Pr\"ufer labelling provides: (i) direct access to the…
Recently, much attention has been given to understanding recombination events along a chromosome in a variety of field. For instance, many population genetics problems are limited by the inaccuracy of inferred evolutionary histories of…
By introducing the notions of living and dead nodes a new model of random tree evolution with continuous time parameter has been constructed. It is assumed that two random variables, the lifetime and the offspring number of living nodes…
We consider Galton-Watson trees associated with a critical offspring distribution and conditioned to have exactly $n$ vertices. These trees are embedded in the real line by affecting spatial positions to the vertices, in such a way that the…
We reconsider the deterministic haploid mutation-selection equation with two types. This is an ordinary differential equation that describes the type distribution (forward in time) in a population of infinite size. This paper establishes…
Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed to this purpose. Theoretical results are available that show…
We consider a model of random tree growth, where at each time unit a new vertex is added and attached to an already existing vertex chosen at random. The probability with which a vertex with degree $k$ is chosen is proportional to $w(k)$,…
Phylogenetic diversity is a measure for describing how much of an evolutionary tree is spanned by a subset of species. If one applies this to the (unknown) subset of current species that will still be present at some future time, then this…
The spread of infectious disease in a human community or the proliferation of fake news on social media can be modeled as a randomly growing tree-shaped graph. The history of the random growth process is often unobserved but contains…
Given a gene-tree labeled topology $G$ and a species tree $S$, the "ancestral configurations" at an internal node $k$ of $S$ represent the combinatorially different sets of gene lineages that can be present at $k$ when all possible…
Phylogenetic trees represent the evolutionary relationships between extant lineages, where extinct or non-sampled lineages are omitted. Extending the work of Stadler and collaborators, this paper focuses on the branch lengths in…