Genomic analyses inform on migration events during the peopling of Eurasia.

High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.

The influences of genes, the environment, and social factors on the evolution of skin color diversity in India.

OBJECTIVES: Skin color is a highly visible and variable trait across human populations. It is not yet clear how evolutionary forces interact to generate phenotypic diversity. Here, we sought to unravel through an integrative framework the role played by three factors-demography and migration, sexual selection, and natural selection-in driving skin color diversity in India. METHODS: Skin reflectance data were collected from 10 diverse socio-cultural populations along the latitudinal expanse of India, including both sexes. We first looked at how skin color varies within and between these populations. Second, we compared patterns of sexual dimorphism in skin color. Third, we studied the influence of ultraviolet radiation on skin color throughout India. Finally, we attempted to disentangle the interactions between these factors in the context of available genetic data. RESULTS: We found that the relative importance of these forces varied between populations. Social factors and population structure have played a stronger role than natural selection in shaping skin color diversity across India. Phenotypic overprinting resulted from additional genetic mutations overriding the skin lightening effect of variants such as the SLC24A5 rs1426654-A allele in some populations, in the context of the variable influence of sexual selection. Furthermore, specific genotypes are not associated reliably with specific skin color phenotypes. This result has relevance for DNA forensics and ancient DNA research. CONCLUSIONS: India is a crucible of macro- and micro-evolutionary forces, and the complex interactions of physical and social forces are visible in the patterns of skin color seen today in the country.

The light skin allele of SLC24A5 in South Asians and Europeans shares identity by descent.

Skin pigmentation is one of the most variable phenotypic traits in humans. A non-synonymous substitution (rs1426654) in the third exon of SLC24A5 accounts for lighter skin in Europeans but not in East Asians. A previous genome-wide association study carried out in a heterogeneous sample of UK immigrants of South Asian descent suggested that this gene also contributes significantly to skin pigmentation variation among South Asians. In the present study, we have quantitatively assessed skin pigmentation for a largely homogeneous cohort of 1228 individuals from the Southern region of the Indian subcontinent. Our data confirm significant association of rs1426654 SNP with skin pigmentation, explaining about 27% of total phenotypic variation in the cohort studied. Our extensive survey of the polymorphism in 1573 individuals from 54 ethnic populations across the Indian subcontinent reveals wide presence of the derived-A allele, although the frequencies vary substantially among populations. We also show that the geospatial pattern of this allele is complex, but most importantly, reflects strong influence of language, geography and demographic history of the populations. Sequencing 11.74 kb of SLC24A5 in 95 individuals worldwide reveals that the rs1426654-A alleles in South Asian and West Eurasian populations are monophyletic and occur on the background of a common haplotype that is characterized by low genetic diversity. We date the coalescence of the light skin associated allele at 22-28 KYA. Both our sequence and genome-wide genotype data confirm that this gene has been a target for positive selection among Europeans. However, the latter also shows additional evidence of selection in populations of the Middle East, Central Asia, Pakistan and North India but not in South India.

Ancient mtDNA from the extinct Indian cheetah supports unexpectedly deep divergence from African cheetahs.

The Indian cheetah was hunted to extinction by the mid-20th century. While analysis of 139 bp of mitochondrial DNA (mtDNA) has confirmed that the Indian cheetah was part of the Asiatic subspecies (Acinonyx jubatus venaticus), the detailed relationships between cheetah populations remains unclear due to limited genetic data. We clarify these relationships by studying larger fragments of cheetah mtDNA, both from an Indian cheetah museum specimen and two African cheetah, one modern and one historic, imported into India at different times. Our results suggest that the most recent common ancestor of cheetah mtDNA is approximately twice as ancient as currently recognised. The Indian and Southeast African (Acinonyx jubatus jubatus) cheetah mtDNA diverged approximately 72 kya, while the Southeast and Northeast African (Acinonyx jubatus soemmeringii) cheetah mtDNA diverged around 139 kya. Additionally, the historic African cheetah sampled from India proved to have an A. j. jubatus haplotype, suggesting a hitherto unrecognised South African route of cheetah importation into India in the 19th century. Together, our results provide a deeper understanding of the relationships between cheetah subspecies, and have important implications for the conservation of A. j. venaticus and potential reintroduction of cheetahs into India.