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

Abstract

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, and the Eastern Asian lineages of M, N, and Y. This is not surprising based their close geographical proximity to East Asian cultures. Results from this study indicate that the addition of the second and third hypervariable segment only sometimes aids in further characterizing the populations. In three of the four populations (Altai, Evenki, and Yakut), all of the haplotypes that were not characterized by HVS1 alone were resolved by adding HVS 2 and 3. However, no tangible differences were reported between the two sets of data for gene and nucleotide diversity. Likewise, no significant difference in results is gained from adding the HVS 2 and 3 data for AMOVA, Neighbor-joining trees based on population FSTs, neutrality tests or mismatch analysis. The addition of these extra genomic regions did, however, allow for a better resolution of population relatedness in multidimensional scaling, NJTs built directly from DNA sequences with bootstrapping (1000 replicates), and although it did not give higher correlation coefficients for mantel randomization tests, it did yield greater statistical significance. This study and the conflicting findings therein suggest that the debate over whether or not resources should be used to analyze the entire mitochondrial D-Loop or simply the seemingly standard HVS1 remains a valid query. It is not necessarily as dichotomous a question as whether one is better than the other, but it depends on the research questions, the types of analyses conducted, and the sample sizes of the populations of study.