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Ancient Indigenous Exomes Reveal History, Post-Colonization Immune Selection Shift

NEW YORK (GenomeWeb) – Ancient and modern day sequences from indigenous individuals from northwestern North America suggest contact with European colonizers altered the selective pressure on immune-related genes in the Native American populations.

Researchers from the University of Illinois and elsewhere performed exome sequencing on more than two dozen ancient indigenous samples from British Columbia, Canada that came from as far back as 6,000 years ago. They also sequenced contemporary Coast Tsimshian individuals from the Metlakatla and Lax Kw'alaams First Nations, uncovering genetic evidence to support the group's long history in the region. The results appeared online today in Nature Communications.

"Oral traditions and archaeological evidence to date have shown that there has been continuous aboriginal occupation of this region for more than 9,000 years. This study adds another layer of scientific data linking the actual ancestral human remains to their modern descendants through their DNA over a span of 6,000 years," co-author Barbara Petzelt, a representative from the Metlakatla Treaty Office, said in a statement. 

Compared with samples from indigenous individuals living in the region today, however, the team saw distinct selective pressures and frequency patterns for the human leucocyte antigen gene HLA-DQA1. In the oldest samples, for example, the immune gene appeared to be under positive selection — a situation that changed after European colonization when the indigenous group experienced a 57 percent population dip, in part due to exposure to new infectious diseases.

Past studies suggest that indigenous populations migrated into and across the Americas some 15,000 to 20,000 years ago, the authors explained, presumably encountering and adapting to pathogens from new environments along the way. They reasoned that "[i]f the indigenous people of America adapted to local pathogens, those adaptations would have proven useful in ancient times but not necessarily after European colonialists altered the environment with their pathogens, some of which may have been novel."

With that in mind, the researchers used TruSeq exome enrichment kits to capture protein-coding sequences from the genomes of 25 ancient and 25 modern-day indigenous individuals, and sequenced them on the Illumina HiSeq 2000. The ancient samples — which came from the Canadian Museum of History and were originally obtained from archeological sites near British Columbia's Prince Rupert Harbour — ranged in age from 1,036 to 6,260 years old. The modern individuals came from the Metlakatla and Lax Kw'alaams communities in the same area, which approved analyses of the ancient samples.

The team generated almost 10-fold average coverage of the contemporary indigenous exomes and nearly 8-fold average coverage of protein-coding sequences in the ancient samples. When it analyzed these sequences alongside data from other Native American populations or 1000 Genomes Project sequences, the group found that the present-day Tsimshian individuals had ancestry from both the ancient indigenous group and from Europeans.

From their demographic models, the researchers estimated that the Prince Rupert Harbour population experienced a population bottleneck roughly 175 years ago, around the time that smallpox epidemics ravaged the region. Meanwhile a search for selection signals in the sequences suggested that the HLA-DQA1 gene was prominent in ancient indigenous individuals, but less common in Tsimshian individuals today — a shift they scrutinized for its relationship to selective pressures after exposure to Europeans and the pathogens they brought with them. 

"The immune-related alleles that exhibit strong signals of positive selection in the ancient Native Americans from the Northwest Coast likely correlate to an adaptation to pathogens that were present in the ancient environments of the region," the study's authors concluded. "Our results also suggest that the indigenous population may have experienced negative selection on the same immune-related genetic component after European contact and the ensuing population collapse."