Abstract
The issue of errors in genetic data sets is of growing concern, particularly in population genetics where whole genome mtDNA sequence data is coming under increased scrutiny. Multiplexed PCR reactions, combined with SNP typing, are currently under-exploited in this context, but have the potential to genotype whole populations rapidly and accurately, significantly reducing the amount of errors appearing in published data sets. To show the sensitivity of this technique for screening mtDNA genomic sequence data, 20 historic samples of the enigmatic Andaman Islanders and 12 modern samples from three Indian tribal populations (Chenchu, Lambadi and Lodha) were genotyped for 20 coding region sites after provisional haplogroup assignment with control region sequences. The genotype data from the historic samples significantly revise the topologies for the Andaman M31 and M32 mtDNA lineages by rectifying conflicts in published data sets. The new Indian data extend the distribution of the M31a lineage to South Asia, challenging previous interpretations of mtDNA phylogeography. This genetic connection between the ancestors of the Andamanese and South Asian tribal groups ∼30 kya has important implications for the debate concerning migration routes and settlement patterns of humans leaving Africa during the late Pleistocene, and indicates the need for more detailed genotyping strategies. The methodology serves as a low-cost, high-throughput model for the production and authentication of data from modern or ancient DNA, and demonstrates the value of museum collections as important records of human genetic diversity.
Highlights
The rapidly increasing number of characterised human single nucleotide polymorphisms (SNPs) available on public databases represents a powerful resource with which to improve our understanding of population history, disease susceptibility and forensic studies[1]
Some authors argue against whole genome sequencing as a routine approach[11], there is general agreement that mtDNA population genetics requires coding region information to both increase resolution and identify homoplasy common in control region data
The final cross-validated results of the single base extension (SBE) amplifications are presented in Table 1, and show that all target SNPs were determined for each sample, demonstrating the robustness of the multiplex methodology
Summary
The rapidly increasing number of characterised human single nucleotide polymorphisms (SNPs) available on public databases represents a powerful resource with which to improve our understanding of population history, disease susceptibility and forensic studies[1]. The potential for contamination or mix-ups between samples increases rapidly with the number of steps or genotyping reactions required, and the approach requires a large amount of resources (time, reagents, template DNA).
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