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

• Type of Material: Article
• Authors: John Lindo, Emory University; Emilia Huerta-Sanchez, University of California Merced; Shigeki Nakagome, University of Chicago; Morten Rasmussen, University of Copenhagen; Barbara Petzelt, Metlakatla Treaty Office; Joycellyn Mitchell, Metlakatla Treaty Office; Jerome S. Cybulski, Canadian Museum of History; Eske Willerslev, University of Copenhagen; Michael DeGiorgio, Pennsylvania State University; Ripan S. Malhi, University of Chicago
• Language: English
• Date: 2016-04-29
• Publisher: Cold Spring Harbot Laboratory
• Publication Version: Preprint (Prior to Peer Review)
• Copyright Statement: The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
• License: Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International
• Final Published Version (URL): https://doi.org/10.1101/051078
• Title of Journal or Parent Work: bioRxiv
• Grant/Funding Information: This project was made possible through the active collaboration of the Lax Kw’alaams and Metlakatla First Nations. We would also like to thank Jun Li for furnishing comparative exome data from contemporary Native American populations. The research was funded by the National Science Foundation (#BCS-1413551) and by the Office of the Vice Chancellor of Research, University of Illinois at Urbana-Champaign, by the Canadian Museum of History, Gatineau, Quebec, Canada, and by Pennsylvania State University startup funds. Portions of this research were conducted with the Advanced CyberInfrastructure computational resources provided by The Institute for CyberScience at Pennsylvania State University.
• Keywords: genetic component; exomes; human leukocyte antigen (HLA); infectious disease; HLA-DQA1; population decline; immuse-related genes; adaptation; Northwest Coast of North America; Native Americans
• Research Categories: Biology, Genetics; Native American Studies

Abstract

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.