Related papers: General triallelic frequency spectrum under demogr…
The sample frequency spectrum of a segregating site is the probability distribution of a sample of alleles from a genetic locus, conditional on observing the sample to have more than one clearly different phenotypes. We present a model for…
The differences between DNA-sequences within a population are the basis to infer the ancestral relationship of the individuals. Within the classical infinitely many sites model, it is possible to estimate the mutation rate based on the site…
We consider neutral evolution of a large population subject to changes in its population size. For a population with a time-variable carrying capacity we have computed the distributions of the total branch lengths of its sample genealogies.…
Consider a supercritical birth and death process where the children acquire mutations. We study the mutation rates along the ancestral lineages in a sample of size $n$ from the population at time $T$. The mutation rate is time-inhomogenous…
Assume that individuals alive at time $t$ in some population can be ranked in such a way that the coalescence times between consecutive individuals are i.i.d. The ranked sequence of these branches is called a coalescent point process. We…
The site frequency spectrum describes variation among a set of n DNA sequences. Its i'th entry (i=1,2,...,n-1) is the number of nucleotide sites at which the mutant allele is present in i copies. Under selective neutrality, random mating,…
We consider an expanding population on the plane. The genealogy of a sample from the population is modelled by coalescing Brownian motion on the circle. We establish a weak law of large numbers for the site frequency spectrum in this model.…
The rapid development of sequencing technologies represents new opportunities for population genetics research. It is expected that genomic data will increase our ability to reconstruct the history of populations. While this increase in…
Consider a population that is expanding in two-dimensional space. Suppose we collect data from a sample of individuals taken at random either from the entire population, or from near the outer boundary of the population. A quantity of…
Natural populations often show enhanced genetic drift consistent with a strong skew in their offspring number distribution. The skew arises because the variability of family sizes is either inherently strong or amplified by population…
Coalescent theory combined with statistical modeling allows us to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. When sequences are sampled serially through…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…
The site frequency spectrum (SFS) is a popular summary statistic of genomic data. While the SFS of a constant-sized population undergoing neutral mutations has been extensively studied in population genetics, the rapidly growing amount of…
In this article, discrete and stochastic changes in (effective) population size are incorporated into the spectral representation of a biallelic diffusion process for drift and small mutation rates. A forward algorithm inspired by…
We derive exact formulae for the allele frequency spectrum under the coalescent with mutation, conditioned on allele counts at some fixed time in the past. We consider unlinked biallelic markers mutating according to a finite sites, or…
We present a robust method which translates information on the speed of coming down from infinity of a genealogical tree into sampling formulae for the underlying population. We apply these results to population dynamics where the genealogy…
Demographic models built from genetic data play important roles in illuminating prehistorical events and serving as null models in genome scans for selection. We introduce an inference method based on the joint frequency spectrum of genetic…
In forensic DNA calculations of relatedness of individuals and in DNA mixture analyses, two sources of uncertainty are present concerning the allele frequencies used for evaluating genotype probabilities when evaluating likelihoods. They…
The sample frequency spectrum (SFS) of DNA sequences from a collection of individuals is a summary statistic which is commonly used for parametric inference in population genetics. Despite the popularity of SFS-based inference methods,…
The sample frequency spectrum (SFS), which describes the distribution of mutant alleles in a sample of DNA sequences, is a widely used summary statistic in population genetics. The expected SFS has a strong dependence on the historical…