Clustering of 770,000 genomes reveals post-colonial population structure of North America.

Despite strides in characterizing human history from genetic polymorphism data, progress in identifying genetic signatures of recent demography has been limited. Here we identify very recent fine-scale population structure in North America from a network of over 500 million genetic (identity-by-descent, IBD) connections among 770,000 genotyped individuals of US origin. We detect densely connected clusters within the network and annotate these clusters using a database of over 20 million genealogical records.

Evolutionary history inferred from the de novo assembly of a nonmodel organism, the blue-eyed black lemur.

Lemurs, the living primates most distantly related to humans, demonstrate incredible diversity in behaviour, life history patterns and adaptive traits. Although many lemur species are endangered within their native Madagascar, there is no high-quality genome assembly from this taxon, limiting population and conservation genetic studies. One critically endangered lemur is the blue-eyed black lemur Eulemur flavifrons.

TroX: a new method to learn about the genesis of aneuploidy from trisomic products of conception.

Motivation: An estimated 10-30% of clinically recognized conceptions are aneuploid, leading to spontaneous miscarriages, in vitro fertilization failures and, when viable, severe developmental disabilities. With the ongoing reduction in the cost of genotyping and DNA sequencing, the use of high-density single nucleotide polymorphism (SNP) markers for clinical diagnosis of aneuploidy and biomedical research into its causes is becoming common practice. A reliable, flexible and computationally feasible method for inferring the sources of aneuploidy is thus crucial.

Effect of epistasis and linkage on fixation probability in three-locus models: an ancestral recombination-selection graph approach.

We study the probability of ultimate fixation of a single new mutant arising in an individual chosen at random at a locus linked to two other loci carrying previously arisen mutations. This is done using the Ancestral Recombination-Selection Graph (ARSG) in a finite population in the limit of a large population size, which is also known as the Ancestral Influence Graph (AIG). An analytical expansion of the fixation probability with respect to population-scaled recombination rates and selection intensities is obtained.

Fixation probability in a two-locus model by the ancestral recombination-selection graph.

We use the ancestral influence graph (AIG) for a two-locus, two-allele selection model in the limit of a large population size to obtain an analytic approximation for the probability of ultimate fixation of a single mutant allele A. We assume that this new mutant is introduced at a given locus into a finite population in which a previous mutant allele B is already segregating with a wild type at another linked locus. We deduce that the fixation probability increases as the recombination rate increases if allele A is either in positive epistatic interaction with B and allele B is beneficial or in no epistatic interaction with B and then allele A itself is beneficial.

Finite populations, finite resources, and the evolutionary maintenance of genetic recombination.

Most previous models for the evolution of sex implicitly assume infinite population sizes and limitless resources. However, because favorable mutations are very rare and eukaryotic populations are finite, it has already been shown that multiple favorable mutants virtually never occur by chance. Therefore, sex is required to combine different favorable mutations into a single lineage.

Joint stationary moments of a two-island diffusion model of population subdivision.

An expression for joint stationary moments of a diffusion approximation to a generalized Wright-Fisher model, corresponding to two finite populations of equal sizes, with migration and mutation, is derived. This gives a complete description of the stationary distribution of allele frequencies in the balance between migration, mutation and genetic drift. We derive the sampling formula in terms of the joint stationary moments, and we also prove that the diffusion process corresponding to this model of population division is not reversible.