Siberia is an ideal region for exploring population histories from a molecular anthropological perspective given the diverse human populations, in terms of linguistic affiliation and lifestyle, currently inhabiting this geographically large region. As such, this thesis explores new methodologies for the investigation of the genetic histories of Siberian populations. While previous genetic work in this area of the world was able to provide detailed insights into paternal histories based on Y chromosomal data, it was not as successful on the maternal side. There existed difficulties in exploring the complex maternal demographic histories due to high levels of sequence identity between individuals in different populations when using only a very small region of the mitochondrial DNA (mtDNA), known as the hypervariable region I (HV1). This realization led to the initial focus of this dissertation which was to identify and test improved methods of sequencing entire mtDNA genomes. This was necessary because the mtDNA genomes that were published for human Siberian populations and across the globe prior to the work described here were chosen based on specific sub-sample selection criteria that introduced an ascertainment bias rendering them unusable for population-wide analyses. After testing multiple next generation DNA sequencing methods, I helped develop a sequencing library preparation method based on multiplexing and hybridization enrichment of mtDNAs for sequencing by synthesis that has since become widely used in labs across the globe. Comparing the same samples sequenced by both the traditional and new methods for five ethnolinguistic populations showed that these new methods were robust and could lead to different inferences about population histories while avoiding a sampling bias. Based on the results of this thesis it is now recommended for researchers to sequence complete mtDNA genomes for all relevant samples within a collection. By applying these methods to additional Siberian populations it was possible to better describe maternal population contact and identify demographic changes over time. This additional information allowed for the identification of putative drops in the maternal effective population sizes in the Siberian populations examined here. When examining the potential migrations and population contact between Turkic-speaking Yakuts and the Tungusic-speaking Even and Evenks, there exists a differential sharing of haplotypes suggesting that the Tungusic speaking populations herein were already in the northern region and split prior to the expansion of the Yakuts into their territory. The putative origin of the Yakuts as being around Lake Baikal was given additional support from the analyses included in this study and the origins of the Dolgans were shown to predominately include the admixture of Yakuts and Evenks.

Siberia is an ideal region for exploring population histories from a molecular anthropological perspective given the diverse human populations, in terms of linguistic affiliation and lifestyle, currently inhabiting this geographically large region. As such, this thesis explores new methodologies for the investigation of the genetic histories of Siberian populations. While previous genetic work in this area of the world was able to provide detailed insights into paternal histories based on Y chromosomal data, it was not as successful on the maternal side. There existed difficulties in exploring the complex maternal demographic histories due to high levels of sequence identity between individuals in different populations when using only a very small region of the mitochondrial DNA (mtDNA), known as the hypervariable region I (HV1). This realization led to the initial focus of this dissertation which was to identify and test improved methods of sequencing entire mtDNA genomes. This was necessary because the mtDNA genomes that were published for human Siberian populations and across the globe prior to the work described here were chosen based on specific sub-sample selection criteria that introduced an ascertainment bias rendering them unusable for population-wide analyses. After testing multiple next generation DNA sequencing methods, I helped develop a sequencing library preparation method based on multiplexing and hybridization enrichment of mtDNAs for sequencing by synthesis that has since become widely used in labs across the globe. Comparing the same samples sequenced by both the traditional and new methods for five ethnolinguistic populations showed that these new methods were robust and could lead to different inferences about population histories while avoiding a sampling bias. Based on the results of this thesis it is now recommended for researchers to sequence complete mtDNA genomes for all relevant samples within a collection. By applying these methods to additional Siberian populations it was possible to better describe maternal population contact and identify demographic changes over time. This additional information allowed for the identification of putative drops in the maternal effective population sizes in the Siberian populations examined here. When examining the potential migrations and population contact between Turkic-speaking Yakuts and the Tungusic-speaking Even and Evenks, there exists a differential sharing of haplotypes suggesting that the Tungusic speaking populations herein were already in the northern region and split prior to the expansion of the Yakuts into their territory. The putative origin of the Yakuts as being around Lake Baikal was given additional support from the analyses included in this study and the origins of the Dolgans were shown to predominately include the admixture of Yakuts and Evenks.