Related papers: Bias in Estimators of Archaic Admixture
Although there has been much interest in estimating divergence and admixture from genomic data, it has proven difficult to distinguish gene flow after divergence from alternative histories involving structure in the ancestral population.…
Admixed populations are formed by the merging of two or more ancestral populations, and the ancestry of each locus in an admixed genome derives from either source. Consider a simple "pulse" admixture model, where populations A and B merged…
Following genetic ancestry in eukaryote populations poses several open problems due to sexual reproduction and recombination. The history of extant genetic material is usually modeled backwards in time, but tracking chromosomes at a large…
Ancestral inference for branching processes in random environments involves determining the ancestor distribution parameters using the population sizes of descendant generations. In this paper, we introduce a new methodology for ancestral…
We investigate through numerical simulations the effect of selection on two summary statistics for nucleotide variation in a sample of two genes from a population of N asexually reproducing haploid individuals. One is the mean time since…
Over the last fifty years, geneticists have made great strides in understanding how our species' evolutionary history gave rise to current patterns of human genetic diversity classically summarized by Lewontin in his 1972 paper, 'The…
Consider a branching process with a homogeneous reproduction law. Sampling a single cell uniformly from the population at a time $T > 0$ and looking along the sampled cell's ancestral lineage, we find that the reproduction law is…
Population genetic studies have found evidence for dramatic population growth in recent human history. It is unclear how this recent population growth, combined with the effects of negative natural selection, has affected patterns of…
In genetically admixed populations, admixed individuals possess ancestry from multiple source groups. Studies of human genetic admixture frequently estimate ancestry components corresponding to fractions of individual genomes that trace to…
We consider the Moran model of population genetics with two types, mutation, and selection, and investigate the line of descent of a randomly-sampled individual from a contemporary population. We trace this ancestral line back into the…
The genetic structure of human populations is extraordinarily complex and of fundamental importance to studies of anthropology, evolution, and medicine. As increasingly many individuals are of mixed origin, there is an unmet need for tools…
Additive genetic variance in natural populations is commonly estimated using mixed models, in which the covariance of the genetic effects is modeled by a genetic similarity matrix derived from a dense set of markers. An important but…
The current state-of-the-art of population synthesis is reviewed. The field is currently undergoing major revisions with the recognition of several key processes as new critical ingredients. Stochastic effects can artificially enhance or…
The aim of this paper is to propose a novel estimation method of using genetic-predicted observations to estimate trans-ancestry genetic correlations, which describes how genetic architecture of complex traits varies among populations, in…
We consider two versions of stochastic population models with mutation and selection. The first approach relies on a multitype branching process; here, individuals reproduce and change type (i.e., mutate) independently of each other,…
Human populations have a complex history of introgression and of changing population size. Human genetic variation has been affected by both these processes, so that inference of past population size depends upon the pattern of gene flow…
We propose a hierarchical Bayesian model to estimate the proportional contribution of source populations to a newly founded colony. Samples are derived from the first generation offspring in the colony, but mating may occur preferentially…
It is increasingly recognized that participation bias can pose problems for genetic studies. Recently, to overcome the challenge that genetic information of non-participants is unavailable, it is shown that by comparing the IBD (identity by…
When long-lived, balancing selection can lead to trans-species polymorphisms that are shared by two or more species identical by descent. In this case, the gene genealogies at the selected sites cluster by allele instead of by species and,…
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…