Identifying the ancestral components of genomes of admixed individuals helps uncovering the genetic basis of diseases and understanding the demographic history of populations. We estimate local ancestry on 313 Chileans and assess the contribution from three continental populations. The distribution of ancestry block-length suggests an average admixing time around 10 generations ago. Sex-chromosome analyses confirm imbalanced contribution of European men and Native-American women. Previously known genes under selection contain SNPs showing large difference in allele frequencies. Furthermore, we show that assessing ancestry is harder at SNPs with higher recombination rates and easier at SNPs with large difference in allele frequencies at the ancestral populations. Two observations, that African ancestry proportions systematically decrease from North to South, and that European ancestry proportions are highest in central regions, show that the genetic structure of Chileans is under the influence of a diffusion process leading to an ancestry gradient related to geography.

No abstract

The East African Rift System (EARS) has played a central role in our understanding of human origins and vertebrate evolution in the late Cenozoic of Africa. However, the distribution of fossil sites along 3 the rift is highly biased toward its northern extent, and the types of paleoenvironments are primarily restricted to fluvial and lacustrine settings. Here we report the discovery of the first fossil sites from the Urema Rift at Gorongosa National Park (central Mozambique) at the southern end of the EARS, and reconstruct environmental contexts of the fossils. In situ and surface fossils from the lower member of the Mazamba Formation, estimated to be of Miocene age, comprise mammals, reptiles, fishes, invertebrates, palms, and dicot trees. Fossil and geological evidence indicates a coastal-plain paleoenvironmental mosaic of riverine forest/woodland and estuarine habitats that represent the first coastal biomes identified in the Neogene EARS context. Receiving continental sediment from source terranes west of today's Urema Graben, estuarine sequences accumulated prior to rifting as compound incised-valley fills on a low-gradient coastal plain following transgression. Modern environmental analogues are extremely productive habitats for marine and terrestrial fauna, including primates. Thus, our discoveries raise the possibility that the Miocene coastal landscapes of Gorongosa were ecologically-favorable habitats for primates, providing relatively stable maritime climate and ecosystem conditions, year-round freshwater availability, and food both from terrestrial and marine sources. The emerging fossil record from Gorongosa is beginning to fill an important gap in the paleobiogeography of Africa as no fossil sites of Neogene age have previously been reported from the southernmost part of the EARS. Furthermore, this unique window into past continentalmargin ecosystems of central Mozambique may allow us to test key paleobiogeographic hypotheses during critical periods of primate evolution.

No abstract

Abstract Detection of positive selection signatures in populations around the world is helping to uncover recent human evolutionary history as well as the genetic basis of diseases. Most human evolutionary genomic studies have been performed in European, African and Asian populations. However, populations with Native American ancestry have been largely underrepresented. Here, we used a genome-wide local ancestry enrichment approach complemented with neutral simulations to identify post-admixture adaptations underwent by admixed Chileans through gene flow from Europeans into local Native Americans. The top significant hits (P = 2.4 x 10−7) are variants in a region on chromosome 12 comprising multiple regulatory elements. This region includes rs12821256, which regulates the expression of KITLG, a well-known gene involved in lighter hair and skin pigmentation in Europeans. Another variant from that region is associated with the long noncoding RNA RP11-13A1.1, which has been specifically involved in the innate immune response against infectious pathogens (Riege, et al. 2017). Our results suggest that these genes were relevant for adaption in Chileans following the Columbian exchange.