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Population stratification has long been recognized as a confounding factor in genetic association studies. Estimated ancestries, derived from multi-locus genotype data, can be used to perform a statistical correction for population stratification. One popular technique for estimation of ancestry is the model-based approach embodied by the widely applied(More)
Understanding the genetic structure of human populations is of fundamental interest to medical, forensic and anthropological sciences. Advances in high-throughput genotyping technology have markedly improved our understanding of global patterns of human genetic variation and suggest the potential to use large samples to uncover variation among closely(More)
Genome-wide scans for recent positive selection in humans have yielded insight into the mechanisms underlying the extensive phenotypic diversity in our species, but have focused on a limited number of populations. Here, we present an analysis of recent selection in a global sample of 53 populations, using genotype data from the Human Genome Diversity-CEPH(More)
Advances in genome technology have facilitated a new understanding of the historical and genetic processes crucial to rapid phenotypic evolution under domestication. To understand the process of dog diversification better, we conducted an extensive genome-wide survey of more than 48,000 single nucleotide polymorphisms in dogs and their wild progenitor, the(More)
The phenomenon of codon usage bias has been important in the study of evolution because it provides examples of weak selection working at the molecular level. During the last two decades, evidence has accumulated that some examples of codon usage bias are driven by selection, particularly for species of fungi connection between codon usage bias and(More)
SIMCOAL (version 1.0) is a computer program for the simulation of molecular genetic diversity in an arbitrary number of haploid populations examined for a set of fully linked loci. It is based on the retrospective coalescent approach initially described by Kingman (1982a,b), and clearly exposed in a series of other articles (Don-nelly and Tavaré 1995; Ewens(More)
We present a method for detecting haplotype blocks that simultaneously uses information about linkage-disequilibrium decay between the blocks and the diversity of haplotypes within the blocks. By use of phased single-nucleotide polymorphism data, our method partitions a chromosome into a series of adjacent, nonoverlapping blocks. The partition is made by(More)
Rare genetic variants contribute to complex disease risk; however, the abundance of rare variants in human populations remains unknown. We explored this spectrum of variation by sequencing 202 genes encoding drug targets in 14,002 individuals. We find rare variants are abundant (1 every 17 bases) and geographically localized, so that even with large sample(More)
Domestic dogs exhibit tremendous phenotypic diversity, including a greater variation in body size than any other terrestrial mammal. Here, we generate a high density map of canine genetic variation by genotyping 915 dogs from 80 domestic dog breeds, 83 wild canids, and 10 outbred African shelter dogs across 60,968 single-nucleotide polymorphisms (SNPs).(More)