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Ancient, Modern Exomes of Native American Group Shed Light on Genomic Effects of Colonization

NEW YORK (GenomeWeb) – Researchers have teased out how European colonization affected variation within the genomes of a Native American group living in what is now British Columbia.

The Tsimshian people have lived in coastal British Columbia and southern Alaska for thousands of years and suffered an extreme population decline — a reduction in effective population size of 57 percent — following European contact and smallpox epidemics.

Using exome sequencing data from both ancient and modern Tsimshian individuals, researchers from the US and Canada examined how this event influenced genomic patterns within this indigenous group. As the researchers reported in the American Journal of Human Genetics, they found that while population collapses are expected to lead to an increase in deleterious alleles, this did not occur among the Tsimshian, possibly due to subsequent admixture with other native and non-native groups.

"We find a more nuanced story, that despite the population collapse, the genetic diversity of modern Tsimshian people varies significantly," first author John Lindo from Emory University said in a statement.

For their analyses, Lindo and his colleagues turned to exome sequencing data they previously collected from 24 modern and 24 ancient Tsimshian individuals living in Prince Rupert Harbour, BC. The ancient Tsimshian individuals in this analysis lived between 6,000 years and 500 years ago. The researchers' earlier study found that the modern and ancient individuals there formed a continuous population that experienced a population bottleneck about 175 years ago, around the time of a smallpox epidemic.

For this new study, the researchers also folded in data from two other ancient individuals who lived on the nearby Lucy Island, BC, and Prince of Wales Island, Alaska.

Within the targeted regions, the researchers uncovered nearly 60,000 high-confidence SNPs within the modern individuals and almost 63,000 high-confidence SNPs within the ancient Prince Rupert Harbour and Lucy Island samples. The ancient individuals, the researchers reported, had higher levels of mean observed heterozygosity than the modern individuals, which they noted was consistent with a population that has undergone a recent population collapse.

They further noted a correlation between increasing heterozygosity and time before present. After masking European contributions to the modern population as well as accounting for variability in genotype calling, the researchers noted that the trend of older samples harboring higher heterozygosity persisted. This, the researchers said, could be due either to population decline prior to European contact or to the decline sparked by European contact.

Similarly, ancient Tsimshianindividuals harbored increased numbers of rare and novel variants, as compared to modern individuals, which the researchers also said supported the idea that the population underwent an expansion following the peopling of the Americas and a population collapse following European contact, leading to the removal of low-frequency variants among modern Tsimshian.

Lindo and his colleagues also surmised that the ancient Tsimshian were already undergoing a steady decline in population prior to the arrival of Europeans.

Admixture following the steep population decline the Tsimshian experienced after European arrival also left its mark on their genomes, the researchers reported. They estimated that modern Tsimshian individuals harbor about 30 percent European admixture.

This admixture, the researchers reported, increased the genetic diversity within modern Tsimshian individuals. When they compared the genetic diversity of ancient and modern Tsimshian individuals, the researchers noted that it was fairly similar. But when they masked the contribution of Europeans to modern Tsimshian individuals' genomes, they found that the modern Tsimshian individuals' genomes harbored less diversity than the ancient individuals, suggesting that post- population decline admixture bolstered the genetic diversity of the modern Tsimshian population.

"A population with relatively high genetic diversity has a greater potential to fight off pathogens and avoid recessive traits," Lindo said. "It exemplifies the benefits of gene flow between populations, especially following catastrophic events such as the smallpox epidemics that the Tsimshian endured."