Related papers: A mixing tree-valued process arising under neutral…
Species tree estimation is a complex problem, due to the fact that different parts of the genome can have different evolutionary histories than the genome itself. One of the causes for this discord is incomplete lineage sorting (also called…
Galled trees are widely studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into galled networks by relaxing a structural condition. In this work, a linear recurrence formula is given…
We consider the genealogy of a sample of individuals taken from a spatially structured population when the variance of the offspring distribution is relatively large. The space is structured into discrete sites of a graph G. If the…
Evolutionary models for populations of constant size are frequently studied using the Moran model, the Wright-Fisher model, or their diffusion limits. When evolution is neutral, a random genealogy given through Kingman's coalescent is used…
The reconstruction of phylogenies from DNA or protein sequences is a major task of computational evolutionary biology. Common phenomena, notably variations in mutation rates across genomes and incongruences between gene lineage histories,…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
We study coalescent processes conditional on the population pedigree under the exchangeable diploid bi-parental population model of \citet{BirknerEtAl2018}. While classical coalescent models average over all reproductive histories, thereby…
We consider the Wright-Fisher model for a population of $N$ individuals, each identified with a sequence of a finite number of sites, and single-crossover recombination between them. We trace back the ancestry of single individuals from the…
This paper gives a new flavor of what Peter Jagers and his co-authors call `the path to extinction'. In a neutral population with constant size $N$, we assume that each individual at time $0$ carries a distinct type, or allele. We consider…
The reconstruction of a species tree from genomic data faces a double hurdle. First, the (gene) tree describing the evolution of each gene may differ from the species tree, for instance, due to incomplete lineage sorting. Second, the…
We consider the compact space of pairs of nested partitions of $\mathbb N$, where by analogy with models used in molecular evolution, we call "gene partition" the finer partition and "species partition" the coarser one. We introduce the…
We introduce a generalization of Kingman's coalescent on $[n]$ that we call the Kingman coalescent on a graph $G = ([n],E)$. Specifically, we generalize a forest valued representation of the coalescent introduced in Addario-Berry and Eslava…
In sexual populations, selection operates neither on the whole genome, which is repeatedly taken apart and reassembled by recombination, nor on individual alleles that are tightly linked to the chromosomal neighborhood. The resulting…
We introduce a stochastic model of a population with overlapping generations and arbitrary levels of self-fertilization versus outcrossing. We study how the global graph of reproductive relationships, or population pedigree, influences the…
This paper extends earlier work by Cox and Durrett, who studied the coalescence times for two lineages in the stepping stone model on the two-dimensional torus. We show that the genealogy of a sample of size n is given by a time change of…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
To learn about the past from a sample of genomic sequences, one needs to understand how evolutionary processes shape genetic diversity. Most population genetic inference is based on frameworks assuming adaptive evolution is rare. But if…
Consider an arbitrary large population at the present time, originated at an unspecified arbitrary large time in the past, where individuals in the same generation reproduce independently, forward in time, with the same offspring…
We consider the range $R^{(n)}$, the tree made up of visited vertices by a diffusive null-recurrent randomly biased walk $\mathbb{X}$ on a Galton-Watson tree $\mathbb{T}$ up to the $n$-th return time to its root and we consider the…
The Ancestral Selection Graph (ASG) is an important genealogical process which extends the well-known Kingman coalescent to incorporate natural selection. We show that the number of lineages of the ASG with and without mutation is…