Mitochondrial haplogroup M discovered in prehistoric North Americans

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Abstract

We analyzed two mid-Holocene (∼5000 years before present) individuals from North America that belong to mitochondrial DNA (mtDNA) haplogroup M, a common type found in East Asia, but one that has never before been reported in ancient or living indigenous populations in the Americas. This study provides evidence that the founding migrants of the Americas exhibited greater genetic diversity than previously recognized, prompting us to reconsider the widely accepted five-founder model that posits that the Americas were colonized by only five founding mtDNA lineages. Additional genetic studies of prehistoric remains in the Americas are likely to reveal important insights into the early population history of Native Americans. However, the usefulness of this information will be tempered by the ability of researchers to distinguish novel founding lineages from contamination and, as such, we recommend strategies to successfully accomplish this goal.

Introduction

Extensive geographic surveys of contemporary Native American genetic diversity have been completed in the past decade (Bortolini et al., 2003, Malhi et al., 2002, Merriwether et al., 1995b, Tarazona-Santos et al., 2001, Zegura et al., 2004). These studies all suggest that the Americas were founded by a small number of migrants from East Asia. In addition, global genetic surveys suggest that Native American populations exhibit greater amounts of inter-population genetic differentiation relative to populations in other continental regions (Rosenberg et al., 2002). This large amount of inter-population genetic differentiation combined with the paucity of sampling in many regions in the Americas, makes it likely that significant undocumented genetic structure still exists in the Americas. In this study we demonstrate the existence of this undocumented genetic structure with the discovery of two individuals from China Lake, British Columbia (Fig. 1) that exhibit a mitochondrial DNA (mtDNA) haplogroup never before reported in any prehistoric or living indigenous population in the Americas. Both were found in the same burial, dated to 4950 ± 170 14C years before present (ybp), and were believed to be related due to similar morphological characteristics (Cybulski personal communication). Both individuals belong to haplogroup M, which is widely distributed throughout Asia (Kivisild et al., 2002). These individuals account for two of three samples dating to approximately 5000 ybp studied from the Northern Plateau region in Northwestern North America that were compared to 3658 sequences from Native Americans widely distributed throughout the Americas. The third sample dating to 4975 ± 40 14C ybp from Big Bar Lake, British Columbia (Fig. 1), exhibits a haplogroup A haplotype that is shared with contemporary indigenous individuals. The discovery of a new mitochondrial haplogroup in the Americas conflicts with the presumed five-founder model, which implies that all Native American mtDNA derives from only five lineages, the founding haplotypes of haplogroups A, B, C, D, and X (Eshleman et al., 2003). Our discovery demonstrates that a more genetically diverse group of migrants colonized the Americas than previously thought and supports the hypothesis that significant undocumented genetic diversity likely still remains in the Americas. While the documentation of additional founding lineages will provide a finer resolution understanding of the peopling process of the Americas, additional discoveries are contingent upon being able to distinguish authentic founding lineages from contamination in the genetic analysis of prehistoric remains. Here, we describe a strategy to help distinguish authentic results from contamination in prehistoric remains.

Section snippets

Contamination control

Because aDNA occurs in low copy number and is highly degraded (Lindahl, 1993, Pääbo, 1990), its extraction and analysis is highly susceptible to contamination originating from modern sources. First, the surfaces of archaeological specimens can become inadvertently contaminated by anyone who has handled the material. To control for this potential source of contamination, the portions of the bone and teeth used for DNA extraction were decontaminated with highly concentrated bleach. Contaminating

Results

The DNA sequences generated from PCR product exhibited a “clean” signal with no indication of double peaks due to contamination, DNA damage, or heteroplasmy. None of the DNA sequences generated in this study match those of individual researchers working in the ancient DNA laboratories. DNA sequences from multiple amplicons from multiple extractions performed in two independent laboratories from the two China Lake individuals exhibit the exact same mutations. Therefore it is unlikely that the

Discussion

Genetic studies of living populations have profoundly shaped the view of the peopling of the Americas. The present consensus from mtDNA, Y chromosome, and autosomal studies is that the Americas were first settled by a small number of migrants (Hey, 2005) likely from a single source population (Kolman et al., 1996, Merriwether et al., 1995a, Zegura et al., 2004). Many of these studies have contended that the Americas were colonized by a single haplotype from each of the accepted five founding

Acknowledgments

We are indebted to the members of the Canoe Creek, Soda Creek, and Dog Creek Bands who allowed the DNA testing of their ancestors. We would also like to thank Toomas Kivisild for consultation on what genetic markers to screen and Graciela Cabana for valuable comments on this manuscript.

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