50 ancient and modern exomes from the Northwest Coast of North America

**ArmandoR1b** · 04-30-2016, 12:26 PM

Demographic and immune-based selection shifts before and after European contact inferred from 50 ancient and modern exomes from the Northwest Coast of North America
John Lindo, Emilia Huerta-Sanchez, Shigeki Nakagome, Morten Rasmussen, Barbara Petzelt, Joycellyn Mitchell, Jerome S Cybulski, Eske Willerslev, Michael DeGiorgio, Ripan S Malhi

The susceptibility of Native Americans to infectious disease has been postulated as a major factor for their population decline after European contact. To investigate if a preexisting genetic component contributed to this phenomenon, we analyzed 50 exomes of both ancient and modern individuals from the Northwest Coast of North America, dating from before and after European contact. We confirmed the genetic continuity between the ancient and modern individuals and modeled the population collapse after European contact, inferring a 57% reduction in effective population size. We also identified signatures of positive selection on immune-related genes in the ancient but not the modern group. The strongest selection signal in the ancients came from the human leukocyte antigen (HLA) gene HLA-DQA1, with alleles that are close to fixation. The important immune function of HLA-DQA1 supports an ancient adaptation to the environments of the Americas. The modern individuals show a marked decrease in the frequency of the associated alleles (the most pronounced variant showing a 64% difference). This decrease is likely due to the environmental change associated with European colonization, which resulted in a shift of selection pressures, whereby negative selection may have acted on the same gene after contact. Furthermore, the selection pressure shift could correlate to the European-borne epidemics of the 1800s, suffered in the Northwest Coast region. This is among the first studies to examine a single population through time and exemplifies the power of such studies in uncovering nuanced demographic and adaptive histories.

http://biorxiv.org/content/early/2016/04/29/051078

A big thanks to Shaikorth for alerting us to this: http://www.anthrogenica.com/showthre...l=1#post153947

Link to the PDF

**ArmandoR1b** · 04-30-2016, 12:59 PM

There were 25 modern Native Americans and 25 ancient Native Americans from the Northwest Coast of North America with an adequate amount of sequencing in comparison to other studies of ancients (9.66x and 7.97x respectively) and were compared to "Native American populations sampled from the Karitiana, Surui, and Maya Native American populations sampled from the Karitiana, Surui, and Maya21, and two ancient samples from the Americas—the Saqqaq22 and Anzick-123. The Native American (Surui, Mayan, and Karitiana) populations fall with the PRH Ancients and the Anzick-1 ancient sample from Montana. The modern Tsimshian fall along the gradient leading from the Native Americans and the Europeans, reflecting their admixed history with Europeans."

Northwest NA Admixture.jpg

Northwest NA PCA.jpg

At k=4 the ancients are very similar to Anzick and Mayans. At k=5 there is about a 30% difference with more gray in most of the Northwest ancients than in Anzick and the Mayans. Too bad we can't get a hold of the ancients to see how they look with Gedmatch calculators.

Samples and sequencing. To investigate possible immune-related genes under selection before
European contact, we sequenced the exomes of ancient and modern First Nations individuals of
the Prince Rupert Harbour (PRH) region of British Columbia, Canada (Supplementary Fig. 1).
We then performed genomic scans for positive selection and functional characterization of genes
exhibiting the strongest signals. Exomes of 25 modern individuals from two Coast Tsimshian
communities, Metlakatla and Lax Kw’alaams (henceforth referred to as “Tsimshian”), were
sequenced to a mean depth of 9.66x. The exomes of 25 ancient individuals from archaeological
sites in the PRH region (henceforth referred to as “PRH Ancients”; Supplementary Fig. 1) were
sequenced to a mean depth of 7.97x. Contamination estimates using the exome-wide data
revealed a mean contamination of 0.94% with a 95% CI: 0.83-1.10 16 (Supplementary Table 3).
All 25 ancient individuals exhibited patterns of C→T and G→A transitions consistent with
deamination due to post-mortem DNA damage17,18 (Supplementary Fig. 3). Mitochondrial
haplogroups were determined for each ancient individual, all showing haplotypes previously
identified in Native Americans19 (Supplementary Table 1).