Maternal variation in Huichol and Mixtec populations from Mexico

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TABLE OF CONTENTS ABBREVIATIONS .................................................................................................................... 3 Definition of basic terms used in the thesis: ............................................................................... 3 INTRODUCTION ...................................................................................................................... 4 1. LITERATURE OVERVIEW ................................................................................................. 5 1.2 Mitochondrial molecular clock ......................................................................................... 6 1.3 Phylogenetic studies ......................................................................................................... 7 1.4 World mtDNA haplogroups ............................................................................................. 8 1.5 Native American mtDNA haplogroups ............................................................................ 8 1.4 Migration theories .......................................................................................................... 10 1.5 Minor founders ............................................................................................................... 11 1.6 Middle America .............................................................................................................. 12 2. EXPERIMENTAL STUDY ................................................................................................. 15 2.1 Aims of this study ........................................................................................................... 15 2.2 Materials and methods .................................................................................................... 16 2.2.1 Samples .................................................................................................................... 16 2.2.2 DNA amplification .................................................................................................. 16 2.2.3 Product purification ................................................................................................. 17 2.2.4. Sequencing reactions .............................................................................................. 18 2.2.5 Statistical analysis ................................................................................................... 19 2.3. RESULTS AND DISCUSSION ........................................................................................ 21 2.3.1. Phylogenetic network ................................................................................................. 21 2.3.2. C4c haplogroup .......................................................................................................... 29 CONCLUSIONS ...................................................................................................................... 33 KOKKUVÕTE ......................................................................................................................... 34 References ................................................................................................................................ 37 SUPPLEMENTARY MATERIALS ........................................................................................ 45 2
ABBREVIATIONS bp - base pair D-loop - displacement loop HVS - Hypervariable Segment LGM - Last Glacial Maximum MRCA - Most Recent Common Ancestor mtDNA - Mitochondrial DNA SNP - Single Nucleotide Polymorphism nps - nucleotide position PCR - polymerase chain reaction ybp - years before present BIM - Beringian incubation model aDNA - ancient DNA Definition of basic terms used in the thesis: Haplotype- a specific mitochondrial genotype defined by a characteristic collection of mtDNA polymorphisms Haplogroup- a group of similar haplotypes, that share a common ancestor LGM- a period in the Earth's climate history when ice sheets were at their maximum extension, between 26,500 and 19,000–20,000 years ago 3
Page 1: TARTU UNIVERSITY FACULTY OF SCIENCE
Page 5 and 6: 1. LITERATURE OVERVIEW 1.1 Mitochon
Page 7 and 8: One of the reasons may be, that ped
Page 9 and 10: Figure 2. Diagnostic markers of Nat
Page 11 and 12: According to it, only one small gro
Page 13 and 14: their way down to the South America
Page 15 and 16: 2. EXPERIMENTAL STUDY 2.1 Aims of t
Page 17 and 18: To determine possible contamination
Page 19 and 20: * let dry at 37ºC for 5 min *add 1
Page 21 and 22: 2.3 RESULTS AND DISCUSSION 2.3.1 Ph
Page 23 and 24: that populations have gone through
Page 25 and 26: Figure 5. Haplogroup A haplotype ne
Page 27 and 28: Figure 7. Haplogroup C haplotype ne
Page 29 and 30: 2.3.2 C4c haplogroup One Huichol in
Page 31 and 32: N 12705s 16223 R 73 11719s R0 14766
Page 33 and 34: CONCLUSIONS Mitochondrial DNA has b
Page 35 and 36: mitokondriaalne DNA. Huitšoli proo
Page 37 and 38: References Achilli, A, Perego, U. A
Page 39 and 40: Forster, P., Torroni, A., Renfrew,
Page 41 and 42: Loogvali, E. L., Kivisild, T., Marg
Page 43 and 44: Sandoval, K., Buentello-Malo, L., P
Page 45 and 46: SUPPLEMENTARY MATERIALS Tabel 1.1.
Page 47 and 48: Table 4.Data used for haplogroups f

Maternal variation in Huichol and Mixtec populations from Mexico

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