Revising mtDNA haplotypes of the ancient Hungarian conquerors with next generation sequencing.

Endre Neparáczki,György Pálfi,Zoltán Maróti,Tibor Kalmár,Erika Molnár,István Raskó,Klaudia Kocsy,István Nagy,Tibor Török,Péter Bihari,Gábor Endre Tóth

doi:10.1371/journal.pone.0174886

Abstract

As part of the effort to create a high resolution representative sequence database of the medieval Hungarian conquerors we have resequenced the entire mtDNA genome of 24 published ancient samples with Next Generation Sequencing, whose haplotypes had been previously determined with traditional PCR based methods. We show that PCR based methods are prone to erroneous haplotype or haplogroup determination due to ambiguous sequence reads, and many of the resequenced samples had been classified inaccurately. The SNaPshot method applied with published ancient DNA authenticity criteria is the most straightforward and cheapest PCR based approach for testing a large number of coding region SNP-s, which greatly facilitates correct haplogroup determination.

Highlights

Comparing ancient DNA sequences extracted from well dated archaeological remains from different periods and locations provide crucial information about past human population history
As multicopy mitochondrial DNA (mtDNA) is best preserved in archaeological remains than low copy nuclear DNA, most ancient sequences are derived from mitochondria [30]
HVR polymorphisms have a limited reliability for haplogroup determination, in addition several informative coding region SNP-s (CR-SNP) were selected to unambiguously define haplogroups [31]

Summary

Introduction

Comparing ancient DNA (aDNA) sequences extracted from well dated archaeological remains from different periods and locations provide crucial information about past human population history (reviewed in [1]). Nowadays Generation Sequencing technology (NGS) provides a growing number of high quality aDNA sequence data, but until recently the majority of aDNA studies have been restricted to short fragments from the hypervariable region-1 (HVR-I) of the mitochondrial DNA (mtDNA) genome, using PCR based methods. In spite of the applied authenticity criteria [6], many of the published databases may contain unreliable sequences, which distort statistical analyses. This problem is especially relevant for many of the ancient populations, from which only PCR based HVR data are available

Methods

Results

Conclusion