Related papers: Detection of selective sweeps in cattle using geno…
Selective sweeps are typically associated with a local reduction of genetic diversity around the adaptive site. However, selective sweeps can also quickly carry neutral mutations to observable population frequencies if they arise early in a…
We consider applying Bayesian Variable Selection Regression, or BVSR, to genome-wide association studies and similar large-scale regression problems. Currently, typical genome-wide association studies measure hundreds of thousands, or…
A panel of large number of common Single Nucleotide Polymorphisms (SNPs) distributed across an entire porcine genome has been widely used to represent genetic variability of pig. With the advent of SNP-array technology, a genome-wide…
A selective sweep describes the reduction of linked genetic variation due to strong positive selection. If s is the fitness advantage of a homozygote for the beneficial allele and h its dominance coefficient, it is usually assumed that…
Two major sources of stochasticity in the dynamics of neutral alleles result from resampling of finite populations (genetic drift) and the random genetic background of nearby selected alleles on which the neutral alleles are found (linked…
Many experimental and field studies have shown that adaptation can occur very rapidly. Two qualitatively different modes of fast adaptation have been proposed: selective sweeps wherein large shifts in the allele frequencies occur at a few…
Rapid adaptation has been observed in numerous organisms in response to selective pressures, such as the application of pesticides and the presence of pathogens. When rapid adaptation is driven by rare alleles from the standing genetic…
Consider a genetic locus carrying a strongly beneficial allele which has recently fixed in a large population. As strongly beneficial alleles fix quickly, sequence diversity at partially linked neutral loci is reduced. This phenomenon is…
Natural selection at one site shapes patterns of genetic variation at linked sites. Quantifying the effects of 'linked selection' on levels of genetic diversity is key to making reliable inference about demography, building a null model in…
The domestication and development of cattle has considerably impacted human societies, but the histories of cattle breeds have been poorly understood especially for African, Asian, and American breeds. Using genotypes from 43,043 autosomal…
We use a microscopic model of population dynamics, a modified version of the well known Penna model, to study some aspects of microevolution. This research is motivated by recent reports on the effect of selective hunting on the gene pool…
The detection of molecular signatures of selection is one of the major concerns of modern population genetics. A widely used strategy in this context is to compare samples from several populations, and to look for genomic regions with…
To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we analyzed novel high-quality genome sequences of three gray wolves, one from each of three putative centers of dog domestication,…
Suppose that the only available information in a multi-class problem are expert estimates of the conditional probabilities of occurrence for a set of binary features. The aim is to select a subset of features to be measured in subsequent…
The unique inheritance pattern of X chromosomes makes them preferential targets of adaptive evolution. We here investigate natural selection on the X chromosome in all species of great apes. We find that diversity is more strongly reduced…
We study the impact of a hard selective sweep on the genealogy of partially linked neutral loci in the vicinity of the positively selected allele. We consider a sexual population of stochastically varying size and, focusing on two…
Haplotypes, the global patterns of DNA sequence variation, have important implications for identifying complex traits. Recently, blocks of limited haplotype diversity have been discovered in human chromosomes, intensifying the research on…
Selective sweeps affect neutral genetic diversity through hitchhiking. While this effect is limited to the local genomic region of the sweep in panmictic populations, we find that in spatially-extended populations the combined effects of…
Recruitment dynamics, or the distribution of the number of offspring among individuals, is central for understanding ecology and evolution. Sweepstakes reproduction (heavy right-tailed offspring number distribution) is central for…
Genomic selection has increased genetic gain in several livestock species, but due to the complicated genetics and reproduction biology not yet in honey bees. Recently, 2 970 queens were genotyped to gather a reference population. For the…