Related papers: Ancestral reproductive bias in branching processes
Coalescent processes, including mutation, are derived from Moran type population models admitting large offspring numbers. Including mutation in the coalescent process allows for quantifying the turnover of alleles by computing the…
Repetitions within a given genealogical tree provides some information about the degree of consanguineity of a population. They can be analyzed with techniques usually employed in statistical physics when dealing with fixed point…
We investigate two stochastic models of a growing population subject to selection and mutation. In our models each individual carries a fitness which determines its mean offspring number. Many of these offspring inherit their parent's…
Migrations have played an important role in shaping the genetic diversity of human populations. Understanding genomic data thus requires careful modeling of historical gene flow. Here we consider the effect of relatively recent population…
This article evaluates bias in one class of methods used to estimate archaic admixture in modern humans. These methods study the pattern of allele sharing among modern and archaic genomes. They are sensitive to "ghost" admixture, which…
We introduce a general diploid population model with self-fertilization and possible overlapping generations, and study the genealogy of a sample of $n$ genes as the population size $N$ tends to infinity. Unlike traditional approach in…
How does social complexity depend on population size and cultural transmission? Kinship structures in traditional societies provide a fundamental illustration, where cultural rules between clans determine people's marriage possibilities.…
Recent studies at individual cell resolution have revealed phenotypic heterogeneity in nominally clonal tumor cell populations. The heterogeneity affects cell growth behaviors, which can result in departure from the idealized uniform…
Modern biological techniques enable very dense genetic sampling of unfolding evolutionary histories, and thus frequently sample some genotypes multiple times. This motivates strategies to incorporate genotype abundance information in…
Consider a continuous-time binary branching process conditioned to have population size n at some time t, and with a chance p for recording each extinct individual in the process. Within the family tree of this process, we consider the…
Life forms exhibit such a degree of exquisite organization that it seems impossible that they could have developed out of a process of trial and error, as intimated by the theory of Darwinian evolution. In this general public paper I…
Stem cell heterogeneity is essential for the homeostasis in tissue development. This paper established a general formulation for understanding the dynamics of stem cell regeneration with cell heterogeneity and random transitions of…
Understanding the patterns and processes of diversification of life in the planet is a key challenge of science. The Tree of Life represents such diversification processes through the evolutionary relationships among the different taxa, and…
Our purpose is to estimate the posterior distribution of the parameters of interest for controlled branching processes (CBPs) without prior knowledge of the maximum number of offspring that an individual can give birth to and without…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
The modeling of time series is becoming increasingly critical in a wide variety of applications. Overall, data evolves by following different patterns, which are generally caused by different user behaviors. Given a time series, we define…
The cell cycle duration is a variable cellular phenotype that underlies long-term population growth and age structures. By analyzing the stationary solutions of a branching process with heritable cell division times, we demonstrate…
In this article, we focus on Bienaym\'e-Galton-Watson processes with linear-fractional offspring distributions. At a fixed generation, we consider a sample of the individuals alive, drawn in two different ways: either through Bernoulli…
Given a sample of genome sequences from an asexual population, can one predict its evolutionary future? Here we demonstrate that the branching patterns of reconstructed genealogical trees contains information about the relative fitness of…
With advances in sequencing technologies, there are now massive amounts of genomic data from across all life, leading to the possibility that a robust Tree of Life can be constructed. However, "gene tree heterogeneity", which is when…