Phylogenetic Resolution with mtDNA D-loop vs. HVS 1: Methodological Approaches in Anthropological Genetics Utilizing Four Siberian Populations
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 h...
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ftunivkansas:oai:kuscholarworks.ku.edu:1808/12210 2023-05-15T16:09:09+02:00 Phylogenetic Resolution with mtDNA D-loop vs. HVS 1: Methodological Approaches in Anthropological Genetics Utilizing Four Siberian Populations Johnson, Stephen Michael Crawford, Michael H Dean, Bartholomew Mielke, James H 2013 120 pages http://hdl.handle.net/1808/12210 http://dissertations.umi.com/ku:12976 en eng University of Kansas http://dissertations.umi.com/ku:12976 http://hdl.handle.net/1808/12210 This item is protected by copyright and unless otherwise specified the copyright of this thesis/dissertation is held by the author. openAccess Physical anthropology Genetics Russian--History D-loop Hypervariable region Mitochondrial dna Phylogenetics Population genetics Siberia Thesis 2013 ftunivkansas 2022-08-26T13:13:27Z 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, ... Thesis Evenki Yakut Siberia The University of Kansas: KU ScholarWorks Evenki ENVELOPE(132.817,132.817,59.683,59.683) |
institution |
Open Polar |
collection |
The University of Kansas: KU ScholarWorks |
op_collection_id |
ftunivkansas |
language |
English |
topic |
Physical anthropology Genetics Russian--History D-loop Hypervariable region Mitochondrial dna Phylogenetics Population genetics Siberia |
spellingShingle |
Physical anthropology Genetics Russian--History D-loop Hypervariable region Mitochondrial dna Phylogenetics Population genetics Siberia Johnson, Stephen Michael Phylogenetic Resolution with mtDNA D-loop vs. HVS 1: Methodological Approaches in Anthropological Genetics Utilizing Four Siberian Populations |
topic_facet |
Physical anthropology Genetics Russian--History D-loop Hypervariable region Mitochondrial dna Phylogenetics Population genetics Siberia |
description |
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, ... |
author2 |
Crawford, Michael H Dean, Bartholomew Mielke, James H |
format |
Thesis |
author |
Johnson, Stephen Michael |
author_facet |
Johnson, Stephen Michael |
author_sort |
Johnson, Stephen Michael |
title |
Phylogenetic Resolution with mtDNA D-loop vs. HVS 1: Methodological Approaches in Anthropological Genetics Utilizing Four Siberian Populations |
title_short |
Phylogenetic Resolution with mtDNA D-loop vs. HVS 1: Methodological Approaches in Anthropological Genetics Utilizing Four Siberian Populations |
title_full |
Phylogenetic Resolution with mtDNA D-loop vs. HVS 1: Methodological Approaches in Anthropological Genetics Utilizing Four Siberian Populations |
title_fullStr |
Phylogenetic Resolution with mtDNA D-loop vs. HVS 1: Methodological Approaches in Anthropological Genetics Utilizing Four Siberian Populations |
title_full_unstemmed |
Phylogenetic Resolution with mtDNA D-loop vs. HVS 1: Methodological Approaches in Anthropological Genetics Utilizing Four Siberian Populations |
title_sort |
phylogenetic resolution with mtdna d-loop vs. hvs 1: methodological approaches in anthropological genetics utilizing four siberian populations |
publisher |
University of Kansas |
publishDate |
2013 |
url |
http://hdl.handle.net/1808/12210 http://dissertations.umi.com/ku:12976 |
long_lat |
ENVELOPE(132.817,132.817,59.683,59.683) |
geographic |
Evenki |
geographic_facet |
Evenki |
genre |
Evenki Yakut Siberia |
genre_facet |
Evenki Yakut Siberia |
op_relation |
http://dissertations.umi.com/ku:12976 http://hdl.handle.net/1808/12210 |
op_rights |
This item is protected by copyright and unless otherwise specified the copyright of this thesis/dissertation is held by the author. openAccess |
_version_ |
1766405088075579392 |