The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.

Tibetans have lived at very high altitudes for thousands of years, and they have a distinctive suite of physiological traits that enable them to tolerate environmental hypoxia. These phenotypes are clearly the result of adaptation to this environment, but their genetic basis remains unknown. We report genome-wide scans that reveal positive selection in several regions that contain genes whose products are likely involved in high-altitude adaptation. Positively selected haplotypes of EGLN1 and PPARA were significantly associated with the decreased hemoglobin phenotype that is unique to this highland population. Identification of these genes provides support for previously hypothesized mechanisms of high-altitude adaptation and illuminates the complexity of hypoxia-response pathways in humans.

Accurate estimation of recent shared ancestry is important for genetics, evolution, medicine, conservation biology, and forensics. Established methods estimate kinship accurately for first-degree through third-degree relatives. We demonstrate that chromosomal segments shared by two individuals due to identity by descent (IBD) provide much additional information about shared ancestry. We developed a maximum-likelihood method for the estimation of recent shared ancestry (ERSA) from the number and lengths of IBD segments derived from high-density SNP or whole-genome sequence data. We used ERSA to estimate relationships from SNP genotypes in 169 individuals from three large, well-defined human pedigrees. ERSA is accurate to within one degree of relationship for 97% of first-degree through fifth-degree relatives and 80% of sixthdegree and seventh-degree relatives. We demonstrate that ERSA's statistical power approaches the maximum theoretical limit imposed by the fact that distant relatives frequently share no DNA through a common ancestor. ERSA greatly expands the range of relationships that can be estimated from genetic data and is implemented in a freely available software package.[Supplemental material is available for this article. The software program ERSA is freely available for academic use at http://jorde-lab.genetics.utah.edu/ersa.]Knowledge about the recent shared ancestry between individuals is fundamental to a wide variety of genetic studies. Detecting cryptic relatedness is a valuable technique for mapping diseasesusceptibility loci and for identifying other at-risk individuals (Neklason et al. 2008;Thomas et al. 2008). For case-control association studies and population-based genetic analyses, related individuals must be identified and removed from samples that are intended to be random representatives of their populations (Voight and Pritchard 2005;Pemberton et al. 2010;Simonson et al. 2010;Xing et al. 2010). Using genetic data to correct pedigree errors increases the power of disease mapping in families (Cherny et al. 2001). Genetic identification of relatives has also proven invaluable in forensic identification of missing persons, victims of mass disasters, and suspects in criminal investigations (Biesecker et al. 2005;Bieber et al. 2006;Zupanic Pajnic et al. 2010). Studies of conservation biology, quantitative genetics, and evolutionary biology are greatly illuminated when the recent shared ancestry between individuals can be reconstructed, especially in agricultural and wild populations (DeWoody 2005;Slate et al. 2010).Most established methods for detecting and estimating genetic relationships are based on genome-wide averages of the estimated number of alleles shared identically by descent (IBD) between two individuals (Weir et al. 2006). These methods are accurate and efficient for relationships as distant as third-degree relatives (e.g., first cousins) but cannot identify more distant relationships. Here we present ERSA, a novel method for estimation of recent shared ancestry. Our method build...

Alu elements have inserted in primate genomes throughout the evolution of the order. One particular Alu lineage (Ye) began amplifying relatively early in hominid evolution and continued propagating at a low level as many of its members are found in a variety of hominid genomes. This study represents the first conclusive application of short interspersed elements, which are considered nearly homoplasy-free, to elucidate the phylogeny of hominids. Phylogenetic analysis of Alu Ye5 elements and elements from several other subfamilies reveals high levels of support for monophyly of Hominidae, tribe Hominini and subtribe Hominina. Here we present the strongest evidence reported to date for a sister relationship between humans and chimpanzees while clearly distinguishing the chimpanzee and human lineages.mobile elements ͉ short interspersed elements ͉ trichotomy ͉ primates