Using ancient DNA to infer impacts of European colonization on first nations populations in coastal British Columbia, Canada

More than 270 individuals from about the last 6000 years have been unearthed from the Prince Rupert Harbour (PRH) archaeological sites in British Columbia (BC), Canada. Their descendants, the Coast Tsimshian, still reside in BC and partnered with the Malhi lab to explore their population history and the genetic effects of colonization on BC First Nations populations. In this dissertation, I sequenced the hypervariable segment (HVS1) of mitochondrial DNA (mtDNA) of 61 ancient PRH individuals and compared them to the descendant groups, the Lax Kw’alaams First Nation and Metlakatla First Nation. For context, I also compared the PRH individuals to the Nisga’a First Nation, the Stswecem’c Xgat’tem First Nation, and the Splatsin First Nation. There were haplotypes shared between these ancient and present-day individuals, and with the exception of the Metlakatla, genetic diversity in the present-day populations was less than that of the ancient population. This suggests a detrimental effect of European colonization, which would be expected given several factors including the spread of diseases by Europeans, forced migrations, and the stress of colonization. Additionally, the PRH population is not only related to these present-day coastal BC First Nations groups, but also to Alaskan Haida and Tlingit Indigenous groups as well. The Y-chromosome population history was also explored using high-resolution Y-STR data sets and SNPs. No STR haplotypes were shared between any present-day and ancient population, and the majority of present-day Y-chromosome haplogroups belong to those commonly found today in European populations. Since the mtDNA of present-day individuals exhibited a very low frequency of haplogroups commonly found in Europe, this indicates a sex-biased effect of colonization where the majority of the Indigenous Y-chromosome variation appears to have been replaced with European Y-chromosome variation. Since the whole mitochondrial genome (mitogenome) provides more information than the HVS1, I sequenced the mitogenome of 103 ancient and present-day BC individuals. Some of the HVS1 haplotypes that appeared to be the same, were no longer the same when mitogenome haplotypes were generated. There are three mitogenome haplotypes that are shared between at least one ancient individual and a member of a present-day First Nation population, further demonstrating genetic continuity of the BC populations. Since this is one of the largest ancient populations that has been studied and has present-day descendants, these BC populations are ideal for examining genetic continuity during European colonization. This could provide insight into other populations in the Americas as some of these ancient mitogenomes could represent founding lineages to this part of BC