Identification of Native American Founder mtDNAs Through the Analysis of Complete mtDNA Sequences: Some Caveats

Abstract

SummaryIn this study, a detailed analysis of both previously published and new data was performed to determine whether complete, or almost complete, mtDNA sequences can resolve the long-debated issue of which Asian mtDNAs were founder sequences for the Native American mtDNA pool. Unfortunately, we now know that coding region data and their analysis are not without problems. To obtain and report reasonably correct sequences does not seem to be a trivial task, and to discriminate between Asian and Native American mtDNA ancestries may be more complex than previously believed. It is essential to take into account the effects of mutational hot spots in both the control and coding regions, so that the number of apparent Native American mtDNA founder sequences is not erroneously inflated. As we report here, a careful analysis of all available data indicates that there is very little evidence that more than five founder mtDNA sequences entered Beringia before the Last Glacial Maximum and left their traces in the current Native American mtDNA pool.

Gender bias in the multiethnic genetic composition of central Argentina

“…Nomenclature of African haplotypes follows Salas et al (2002Salas et al ( , 2004Salas et al ( ), with updates in Č erný et al (2007, Kivisild et al (2004), and Torroni et al (2006). For Native American haplogroups, we use the most updated nomenclature from Bandelt et al (2003) and Kong et al (2006), and for the European profiles, Achilli et al (2005Achilli et al ( , 2004, Loogväli et al (2004), and Sun et al (2006), among others. DnaSP 4.10.3 software (Rozas et al 2003) was used for computation of different diversity indices.…”

Phylogeographic analysis of mitochondrial DNA haplogroup F2 in China reveals T12338C in the initiation codon of the ND5 gene not to be pathogenic

“…The haplogroup status was further confirmed by detecting additional variations in other regions as described in our previous studies (Yao et al 2002aKong et al 2003a). A segment covering region 10171-10659 of the rCRS, which was suggested to be informative in defining East Asian specific haplogroups (Yao et al 2002a), was adopted to specify the phylogenetic status of the F* or R9* mtDNAs (the asterisk attached to haplogroups indicates that the sample was not able to be further classified into the sub-clade(s) of the haplogroup) in our previous studies (Yao et al 2000(Yao et al , 2002a(Yao et al ,c, 2003Yao and Zhang 2002;Kong et al 2003a) and unpublished data. For those published data sets (not from our laboratory) with only HVS-I and/or HVS-II information available, we recognized the potential F2 types by matching and/or near-matching with the identified F2 types that have been tested for coding region information.…”

“…All of the individuals were confirmed to be unrelated before sampling and were given informed consent. To better understand the phylogeny of haplogroup F2, the previously reported data sets (Yao et al 2000(Yao et al , 2002a(Yao et al ,c, 2003Tsai et al 2001;Kivisild et al 2002;Oota et al 2002;Yao and Zhang 2002;Kong et al 2003a;Tajima et al 2003) were also included. As a result, a total of 3,090 mtDNAs from 57 populations across China were examined, and their detailed information was illustrated in Table 1.…”

“…The nucleotide change was originally detected in two mtDNAs (GD7809 and QD8147) when we systematically surveyed mtDNAs belonging to all the major haplogroups specific to East Asian by complete mtDNA sequencing (Kong et al 2003b). To substantiate whether the T12338C change is specific to haplogroup F2 and to learn more about the origin of haplogroup F2, we performed an extensive search for F2 in more than 3,000 Chinese mtDNAs in reported studies (Yao et al 2000(Yao et al , 2002a(Yao et al ,c, 2003Tsai et al 2001;Kivisild et al 2002;Oota et al 2002;Yao and Zhang 2002;Kong et al 2003a;Tajima et al 2003) and our unpublished data by motif-searching and/or (near-)matching methods (Yao et al 2002a. Our phylogeographic study revealed that the T12338C change was specific to haplogroup F2 and occurred in normal individuals across China, thus suggesting a polymorphic change rather than a pathogenic mutation.…”

Mosaics of ancient mitochondrial DNA: positive indicators of nonauthenticity

“…Such privileged conditions are, however, fairly unusual in ancient DNA projects: imagine that a Japanese archaeological team would (under hermetic conditions) freshly excavate some prehistoric bones and teeth from a burial site, say, in South America, and analyse the material in a laboratory in Japan, then, with the necessary precautions, some authentic results might be expected -provided that coding-region (and control-region) markers were employed which can clearly separate Asian from Native American mtDNA. 22 However, if a coffin from a church in Italy was opened and its dusty contents were analysed by a European team, then from the outset the results would be fraught with doubts about authenticity.…”