Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes

Abstract

Analysis of Neandertal DNA holds great potential for investigating the population history of this group of hominins, but progress has been limited due to the rarity of samples and damaged state of the DNA. We present a method of targeted ancient DNA sequence retrieval that greatly reduces sample destruction and sequencing demands and use this method to reconstruct the complete mitochondrial DNA (mtDNA) genomes of five Neandertals from across their geographic range. We find that mtDNA genetic diversity in Neandertals that lived 38,000 to 70,000 years ago was approximately one-third of that in contemporary modern humans. Together with analyses of mtDNA protein evolution, these data suggest that the long-term effective population size of Neandertals was smaller than that of modern humans and extant great apes.

Almost 20 years of Neanderthal palaeogenetics: adaptation, admixture, diversity, demography and extinction

“…possible for the first time to retrieve complete mitochondrial genomes, first by shotgun sequencing of a sample from Vindija cave [13] and later with targeted hybridization-capture enrichment methods [14]. The whole mtDNA genome allowed a more precise estimate of the divergence time between modern human and Neanderthal mtDNA lineages, which was reported to be 660 000 years considering all sites of the mtDNA [13] or close to 400 000 years considering only third codon sites of the mtDNA [15].…”

Complete mtDNA genomes of Filipino ethnolinguistic groups: a melting pot of recent and ancient lineages in the Asia-Pacific region

“…17 DNA libraries were sequenced on an Illumina GA IIx machine (Illumina Inc., San Diego, CA, USA) with post processing using Illumina software followed by the Improved Base Identification System. 18 Sequencing reads were mapped to the revised Cambridge Reference Sequence of the human mitochondrial genome (GenBank: NC012920.1) 19 using the program MIA, 20 implemented in an MPI-EVA sequence assembly-analyses pipeline for detecting mtDNA heteroplasmy 21 and low-level mutations 22 (Table 3) also does not support a discrete FEN vs FEnN grouping. The 54 haplogroups have a patchy distribution across the different FE groups ( Figure 1, Table 2).…”

Computational challenges in the analysis of ancient DNA

“…Furthermore, because ancient DNA molecules are often fragmented to very short pieces [15], ancient DNA sequencing is not limited in practice by the short read length of current sequencers. The mean ancient DNA fragment length has varied between 60 and 150 bp in most recent large-scale sequencing studies [9-11,13,16-18], but can vary greatly from sample to sample.…”