Phylogenetic Resolution with mtDNA D-loop vs. HVS 1: Methodological Approaches in Anthropological Genetics Utilizing Four Siberian Populations

• Main Author: Johnson, Stephen Michael
• Other Authors: Crawford, Michael H, Dean, Bartholomew, Mielke, James H
• Format: Thesis
• Language: English
• Published: University of Kansas 2013
• Subjects: Physical anthropology; Genetics; Russian > History; D-loop; Hypervariable region; Mitochondrial dna; Phylogenetics; Population genetics; Siberia; Evenki; Yakut
• Online Access: http://hdl.handle.net/1808/12210; http://dissertations.umi.com/ku:12976

Mitochondrial DNA is a useful genetic marker for answering evolutionary questions due to its high copy number, maternal mode of inheritance, and its high rate of evolution (Stoneking and Soodyall, 1996). The vast majority of research on mitochondrial DNA in anthropological studies has utilized the hypervariable segment 1 (HVS 1) to reconstruct population history and structure, explore population ancestry, construct phylogenies, and answer questions about the origins of prehistoric populations. A common debate in this field is whether better phylogenetic resolution can be obtained by the use of additional sequence data or genomic regions. If only the hypervariable segment is under scrutiny, does adding all three regions provide the same results or does it provide a deeper resolution, conveying a better understanding of populations of inquiry? Sequence data from the D-loop of four Siberian populations: Altai, Evenki, Yakut, and Udehe have been analyzed using multivariate statistics in order to gain insight on evolutionary questions about these populations, and to investigate the utility and efficacy of sequencing the entire D-loop (HVS 1,2,and3 combined) versus sequencing solely the HVS 1. By comparing sequence data from the HVS1 to the whole D-Loop, this project investigated: 1.) if the increase in the number of SNPs sequenced revealed different phylogenetic relationships between Siberian populations; 2.) if additional genetic variation can be revealed by the addition of more genomic regions; and 3.) whether additional SNPs reveal stronger relationships between genetics, linguistics, and geography than using the HVS1 alone. Results of these statistics are consistent with previously reported findings for these populations based on HVS1 sequences data. The Altai, Evenki, and Yakut are predominately characterized by mtDNA lineages C and D, with various other Eurasian and East Asian lineages influencing their gene pool, whereas the Udehe from this study are solely characterized by the Native Siberian haplogroup C, ...