Maternal variation in Huichol and Mixtec populations from Mexico

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Thus, the new American maternal lineages were recognized, leading the number of founding lineages from 4 to 15: A2*, A2a, A2b, B2, C1b, C1c, C1d*, C1d1, C4c, D1, D2a, D3, Dd4h3a, X2a and X2g (Achilli et al., 2008; Tamm et al., 2007; Fagundes et al., 2008; Perego et al., 2009, 2010; Malhi et al., 2010; Hooshiar Kashani et al., 2012). The defining mutations for all 15 haplogroups are present in Figure 2. Haplogroups A2, B2, C1 (including it subgroups) and D1 are called major pan-American founder haplogroups because of their frequency and the distribution pattern all over the Americas. The rest are the minor founding haplogroups, which are present in a lower quantity and are geographically restricted. 1.4 Migration theories Although in the last decade the studies of Native American mtDNA have shed light to population movements into the Western Hemisphere, the arrival time(s), the migration routes and number of expansion events in the Americas remain controversial. After the discovery of the Clovis culture in New Mexico in 1929, there has for many years been a predominant hypothesis among archaeologists, that Clovis people were the first inhabitants of the Americas, living 11,500-10,900 ybp (Haynes et al., 1992, 2005). Clovis was the first well-established human culture in the Americas. The Clovis-first theory was supported with the discovery of a number of other Clovis sites in wide area from Southern Canada to Mexico, possibly to Southern America (Pearson and Ream, 2005). However, there have been found other ancient sites which indicated human presence in the Americas much earlier, for example: the Monte-Verde site in Chile with the estimated age of ~14,600 ybp (Dillehay, 2008), the Meadowcroft Rockshelter in Pennsylvania dating to 22,000-18,000 ybp (Adovasio and Pedler, 2004), the Buttermilk Creek Complex in Texas which shows that people already lived in North America 15,500 ybp (Waters et al., 2011). Findings over the past few years and a re-examination of old ones have convincingly shown that humans were present in the Americas before Clovis culture arose. Pre-Clovis occupation model is in agreement with genetic data. The high diversity level and the distribution pattern of the major Pan-American haplogroups together with their similar coalescence time estimates, has been used to support a singlemigration model (Forster et al.,1996; Bonatto and Salzano, 1997; Merriwether et al., 1995). 10
According to it, only one small group of people came from Asia to Beringia - a landbridge connecting Asian and American continents during the cold periods due to lowered see level - where it probably settled before the eventual expansion into the Americas, (Tamm et al., 2007; Fagundez et al., 2008). The „Beringian incubation model“ (BIM) (Tamm et al., 2007) and its variants (Bonatto and Solzano, 1997; Kitchen et al., 2008; Mulligan eta al., 2008) point out that American founding population could have reached Beringia by 30,000 ybp, supporting this with the evidence of the earliest human habitation signs in Yana Rhinoceros Horn Site in Northeastern Siberia (Pitulko et al., 2004). The founding populations remained in Beringian refugium for ~5,000-15,000 ybp leading to the separation of the American founder lineages from their Asian sister-clades. The autochthonous patterns of variation within the continental founder haplogroups testifies that after the retreat of the ice-sheets the expanding populations colonized the double continent around 14,000-16,000 ybp with a very rapid speed (Tamm et al., 2007; Kitchen et al., 2008; Mulligan eta al., 2008). The analysis of maternal variability in higher resolution (completely sequenced mitochondrial genomes), have revealed greater number of American founder haplogroups. Their distribution, frequency and age make us to reconsider the number and migrations routes into the Americas. 1.5 Minor founders Minor haplogroups A2a, A2b, D2a and D3 are restricted in arctic regions of the Siberia, Alaska, the Canada and the Greenland (Torroni et al, 1993; Helgason et al., 2006; Derenko et al., 2007; Tamm et al., 2007; Gilbert et al., 2008; Derbeneva et al., 2002; Volodko et al., 2008; Saillard et al., 2000; Starikovskaja et al., 2005). The proposed reason for the presence of partly different sub-haplogroups in arctic populations is that they diversified in Beringia after the initial migration into the Americas had occurred (Tamm et al., 2007). Recent years, a single-migration model of first humans coming to the North America through the ice-free corridor, is being changed to the other one: first Americans (Paleo-Indians) dispersal along the deglaciated Pacific coastline (Schurr and Sherry, 2004; Dillehay, 2008; Goebel et al., 2008; Gilbert et al., 2008). The theory is strongly supported by genetic evidence (founder haplogroups are autochthonous over continent) and archaeological discoveries (e.g. Monte-Verde site in Chile). The Pacific coastline migration model was confirmed while 11
Page 1 and 2: TARTU UNIVERSITY FACULTY OF SCIENCE
Page 3 and 4: ABBREVIATIONS bp - base pair D-loop
Page 5 and 6: 1. LITERATURE OVERVIEW 1.1 Mitochon
Page 7 and 8: One of the reasons may be, that ped
Page 9: Figure 2. Diagnostic markers of Nat
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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