Novel mtDNA and Y-DNA Haplogroups and Polymorphisms in South American Indians
DNA in Forensics 2012, Sep 06-08 2012
Below are some of the more interesting findings related to New World genetics reported at the recent “DNA in Forensics 2012” conference held at the University of Innsbruck, Austria (via Dienekes).
The detection of mtDNA hg D4g in several Mataco-Guaycurú populations in South America contributes to the growing number of D4 lineages reported from the Americas. Perego et al. (“Distinctive Paleo-Indian Migration Routes from Beringia Marked by Two Rare mtDNA Haplogroups,” Curr Biol 19 (1):1-8, 2009) reported novel hg D4h3 in western North and South America. Kumar et al. (“Large Scale Mitochondrial Sequencing in Mexican Americans Suggests a Reappraisal of Native American Origins,” BMC Evol Biol 11:293, 2011) described hg D4e1c in Mexico. Hg D4e1c is a sister lineage to hg D2, which is found in Eskimo-Aleuts, southern Na-Dene, Paleoasiatic peoples, in Tibet and in South Siberia. It was famously detected in the prehistoric Saqqaq individual from Greenland. Although there is a chance that hg D4e1c is of recent Asian American origin, the overall pattern seems to be clear: the number of founding American Indian haplogroups is growing and an increasing number of D4 lineages are being described. If hg D1 is specific to the Americas, its sister D4 haplogroups are mostly concentrated in Asia. But now it appears that American Indians have lineages from two most wide-spread and internally differentiated D clades – D1 and D4, whereas only D4 lineages are found in Asia. The fact that American Indian D4 lineages are found sporadically in the overall D4 phylogeny suggests that lineage extinction may have been common in the Americas.
Roewer et al. reported Y-DNA C3* (M-217) in northwest South America, which is a different clade from the North America-specific C3b. This finding undermines the theory that hg C3 was brought to the Americas from Siberia as part of a later wave of migration associated with the spread of Na-Dene languages. It further supports the observation that hg C3 is found all over the New World from Eskimos in the north to, now, northwest South America, in the south.
MtDNA Analysis of Mocoví Population, Southernmost Guaycurú Speakers in South America
Sala, A., M. C. Martí, M. C. Bobillo, and D. Corach
Mocoví is the south most ethnicity, linguistically associated to Pilagá, Toba and Wichi tribes, representing the Mataco-Guaycurú speakers group. Mocoví inhabit Chaco and Santa Fe provinces and amounts over 15.000 people. Aiming to increase the knowledge of Guaycurú speakers, Mocoví individuals (N= 27) and additional Tobas (N= 47) from Santa Fe province were analyzed by means mitochondrial DNA Control Region sequencing under EMPOP guidelines. The results were compared with previously obtained sequence data of three ethnic groups that inhabit the area of Argentinean Gran Chaco: Pilagá (N=55, from Formosa province), Toba (N=64), from Formosa and Chaco provinces and Wichi (N= 48) from Formosa. The entire mtDNA Control Region (16024 to 576) was sequenced in a total of 241 unrelated individuals. Sequencing strategy included the use of at least six primers for each sample in order to obtain unambiguous sequences. The four Native American haplogroups (Hgs) were present in these groups, with diverse frequencies. Hgs B2 and D (subhaplogroups D1 and D4g) are well represented in Pilagá, Toba and Wichi. Mocoví showed high frequency in HgA (52%) meanwhile the frequency of HgD is very low (7%). Haplogroup C is absent in Tobas and Wichi, whereas is present in Pilagá and Mocoví with a frequency around of 17%. The haplotype diversity in Mocoví sample was higher than the rest of the groups and highest genetic distances were observed when this group was compared with Toba, Pilagá and Wichi. Genetic distances were all significant, except between Toba ́s groups. This work allowed us to analyze the spread of mitochondrial lineages from Mataco-Guaycurú speakers and to find the relationship between the individuals that inhabit nowadays the Argentinean Gran Chaco.
Novel Y Chromosome Polymorphisms in Native American Haplogroup Q1a3a1
Alechine, E., and D. Corach
Since 1996, when DYS199 marker was first described on the Y chromosome (Underhill et al), Native American populations have been characterized by DYS199/M3 polymorphism. The high frequency of its derived state, attaining 77% in Native American males (Bortolini et al. 2003), might be explained by: (a) an extremely reduced number of colonists carrying this marker or (b) increased reproductive fitness. Y-chromosome characteristics related to male fertility may influence the high prevalence of haplogroup Q1a3a1 within Native Americans. Therefore, the aim of this work was to analyze STS markers on the Y chromosome linked to fertility in samples from confirmed fathers belonging to haplogroup (hg) Q1a3a1 and reference hg R1b1a2. Unrelated male samples from routine paternity casework have been analyzed including those belonging either to hg Q1a3a1 or R1b1a2. Paternity was assessed by PowerPlex®16 and Y-chromosome haplogroups by Real Time PCR followed by HRM. Afterwards, sY1261, sY1191, sY1291, sY1206 and sY1201 STS markers located in AZFb/c regions have been amplified and analyzed by capillary electrophoresis. A novel SNP variant was found on the distal copy of the sY1206 marker showing a G>T variation exclusively in haplogroup Q1a3a1. Moreover, marker sY1291 showed a 21bp size difference between haplogroup Q1a3a1 (517pb) and R1b1a2 (538pb) due to a homopolymeric T track. This last finding is in concordance with previously published results (Lin et al. 2006), where a length difference was first characterized for this marker but not linked to any haplogroup or population. Nevertheless, no differential deletions of the Y-STSs markers analyzed were found between haplogroup Q1a3a1 and R1b1a2, conversely to what has been previously described (Repping et al. 2004, 2006). These results were consistent within all the analyzed samples. The present results describe two novel Y chromosome polymorphisms and disprove the presence of the b2/b3 deletion as a characteristic of hg Q1a3a1.
Identification of a Novel Native American Y Chromosome Founding Lineage in Northwest South America
Roewer, L., M. Nothnagel, L. Gusmão, V. Gomes, M. González, D. Corach, A. Sala, E. Alechine, T. Palha, N. Santos, A. Ribeiro-dos-Santos, M. Geppert, S. Willuweit, M. Nagy, S. Zweynert, M. Baeta, C. Núñez, B. Martínez-Jarreta, F. González-Andrade, E. Fagundes de Carvalho, D. Aparecida da Silva, J. Jose Builes, D. Turbon, A. M. Lopez Parra, E. Arroyo-Pardo, U. Toscanini, L. Borjas, C. Barletta, E. Ewart, S. Santos, and M. Krawczak
For the first time, we could identify a novel Native American founding lineage C-M217 (C3*) within a restricted area of North-west South America. This finding is intriguing in view of the high prevalence of the same haplogroup in Central, East and North East Asia, and its concurrent absence from North America. Possible scenarios include (i) later migratory waves that quickly passed the existing populations in North America, and (ii) long-distance trade or contact with East Asia. Fifty years after Estrada, Meggers and Evans (1962) suggested trans-Pacific connections between the middle Jōmon culture of Kyushu (Japan) and the littoral Valdivia culture in Ecuador (6400-5300 YBP), based upon cultural similarity, it is indeed tempting to speculate that C-M217 (C3*) was introduced into South America from Eastern Asia by sea, either along the American West coast or across the Pacific (with some help by major currents). The striking differences observed between the Y-STR haplotypes of Ecuadorian and Asian C-M217 (C3*) carriers would be explicable in terms of a long divergence time after the arrival (although a more recent introduction cannot be excluded).
Because the highest frequency (22%) of maternally-inherited mtDNA D4h3 sequences were found in Ecuador (Rickards et al., 1999), I can’t think of a better location, in South America, to find a paternally-inherited Y chromosome haplotype which may have been brought at the same time (re: NRY C*).
With regards to, “now it appears that American Indians have lineages from two most wide-spread and internally differentiated D clades – D1 and D4,”. Take another look at Phylotree. D1 is a subset of Asian D4.
Non-D1 ‘D’ sequences have been reported previously in Argentina including the Misiones province and Gran Chaco region. None have withstood the test of time for ‘founding haplogroup status’. Most have not even been claimed to be new founding haplotypes (like the abstract you provided). From Bobillo et al. (2009):
“The analysis of positions 8383, 8419 and 9431 revealed the hg D4c2 status of sample AMI038; moreover, the CR sequence nearly matched (except for the insertion of two cytosines at 309) three Japanese hg D4c2 sequences . The detection of this haplogroup is concordant with the demographic characteristics of the province of Misiones, where this sample was obtained. In this province, the most relevant Asian immigration waves occurred during the early twentieth century .”
D4h3 sequences are found from southern Alaska (On Your Knees Cave) to southern Chile. That is the difference between legitimate founding haplotypes and isolate instances of admixture (or even sequencing errors).
These are fair points, Gisele, and we’ll have to see what happens to those other ones with more localized distributions. But we can’t be assumptive about the fact that all of those isolated instances are admixture or sequence error until they are shown to be such. Just like you did with D1 vs. D2 in that other paper on mtDNA in Mexico or in Bobillo et al. (2009).
Regarding D1 being a subset of D4, it’s a matter of labels. All D4 haplogroups (a through s) are in sister relationship to D1. D1 is not a subset of any of them. One could just as easily call the whole clade D1 and then all D4s would look like subsets of D1.