Related papers: Approximating genealogies for partially linked neu…
In large populations, multiple beneficial mutations may be simultaneously spreading. In asexual populations, these mutations must either arise on the same background or compete against each other. In sexual populations, recombination can…
We consider a biological population in which a beneficial mutation is undergoing a selective sweep when a second beneficial mutation arises at a linked locus and we investigate the probability that both mutations will eventually fix in the…
A large offspring number diploid biparental multilocus population model of Moran type is our object of study. At each timestep, a pair of diploid individuals drawn uniformly at random contribute offspring to the population. The number of…
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…
Gene duplications are one of major primary driving forces for evolutionary novelty. We took population genetics models of genes duplicate to study how evolutionary forces acting during the fixation of mutant allele at duplicate loci. We…
Recurrent mutations are a common phenomenon in population genetics. They may be at the origin of the fixation of a new genotype, if they give a phenotypic advantage to the carriers of the new mutation. In this paper, we are interested in…
The genealogy at a single locus of a constant size $N$ population in equilibrium is given by the well-known Kingman's coalescent. When considering multiple loci under recombination, the ancestral recombination graph encodes the genealogies…
Our models for detecting the effect of adaptation on population genomic diversity are often predicated on a single newly arisen mutation sweeping rapidly to fixation. However, a population can also adapt to a new situation by multiple…
A probabilistic reconstruction of genealogies in a polyploid population (from 2x to 4x) is investigated, by considering genetic data analyzed as the probability of allele presence in a given genotype. Based on the likelihood of all possible…
Interacting particle systems undergoing repeated mutation and selection steps model genetic evolution, and also describe a broad class of sequential Monte Carlo methods. The genealogical tree embedded into the system is important in both…
Weak purifying selection, acting on many linked mutations, may play a major role in shaping patterns of molecular evolution in natural populations. Yet efforts to infer these effects from DNA sequence data are limited by our incomplete…
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…
The advent of modern genome sequencing techniques allows for a more stringent test of the neutrality hypothesis of Darwinian evolution, where all individuals have the same fitness. Using the individual based model of Wright and Fisher, we…
We have used the sexual Penna ageing model to show that the relation between dominance and recessiveness could be a force which optimizes the genome size. While the possibility of complementation of the damaged allele by its functional…
The domestication and subsequent selection by humans to create breeds of cattle undoubtedly altered the patterning of variation within their genomes. Strong selection to fix advantageous large-effect mutations underlying domesticability,…
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,…
The genetic diversity of a species is shaped by its recent evolutionary history and can be used to infer demographic events or selective sweeps. Most inference methods are based on the null hypothesis that natural selection is a weak or…
Genomic regions (or loci) displaying outstanding correlation with some environmental variables are likely to be under selection and this is the rationale of recent methods of identifying selected loci and retrieving functional information…
We consider a single genetic locus which carries two alleles, labelled P and Q. This locus experiences selection and mutation. It is linked to a second neutral locus with recombination rate r. If r=0, this reduces to the study of a single…
Compared to a neutral model, purifying selection distorts the structure of genealogies and hence alters the patterns of sampled genetic variation. Although these distortions may be common in nature, our understanding of how we expect…