Mitochondrial Haplogrouping and Short Tandem Repeat Analyses in Anthropological Research using Next-Generation Sequencing Technologies

Abstract

The field of anthropological genetics aims to reveal, characterize, and understand the biological diversity of modern and ancient human populations. This goal is achieved by analyzing different regions of the autosomes, sex chromosomes, and mitochondrial genome. The last decade has introduced a new wave of technologies known as next-generation sequencing (NGS) technologies with high throughput and increased data output. NGS has been employed in the medical and forensic fields but is slow to take hold in anthropological genetics. This work demonstrates the utility of NGS to answer anthropological questions and genetically characterize populations. The accuracy of mitochondrial haplogrouping using smaller ranges of the mitogenome was assessed. When using less than the full mitogenome, haplogrouping was accurate for 95% of samples. Using only the control region, 50% of samples were precisely haplogrouped and 82% of Native American haplogroups were distinguishable from Asian haplogroups. Examining autosomal and Y-chromosome STRs, nine loci exhibited increased sequence-based allelic diversity. Five loci (D2S441, D7S820, vWA, DYS392, DYS635) demonstrated statistical differences in the frequency distributions of length-based and sequence-based alleles for Native American and Asian samples; two of these loci (vWA and DYS635) demonstrated higher significance levels when using sequence-based alleles. One locus (D2S1338) demonstrated statistical differences in the sequence-based alleles alone. This indicates the D2S1338, vWA, and DYS635 loci are populationally informative using sequence-based alleles obtained by NGS. These are some of the fundamental areas in which anthropological genetics can advance using next-generation sequencing technologies.