A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing

Abstract

Summary A complete mitochondrial (mt) genome sequence was reconstructed from a 38,000-year-old Neandertal individual using 8,341 mtDNA sequences identified among 4.8 Gb of DNA generated from ~0.3 grams of bone. Analysis of the assembled sequence unequivocally establishes that the Neandertal mtDNA falls outside the variation of extant human mtDNAs and allows an estimate of the divergence date between the two mtDNA lineages of 660,000±140,000 years. Of the 13 proteins encoded in the mtDNA, subunit 2 of cytochrome c oxidase of the mitochondrial electron transport chain has experienced the largest number of amino acid substitutions in human ancestors since the separation from Neandertals. There is evidence that purifying selection in the Neandertal mtDNA was reduced compared to other primate lineages suggesting that the effective population size of Neandertals was small.

A female Viking warrior confirmed by genomics

“…The bone extract contained 0.54% endogenous human DNA and the tooth extract contained 3.88%. The obtained DNA sequences showed all the characteristics of authentic and ancient DNA (Briggs et al, 2007) (Supporting Information Figure S4.1a,b), with mitochondrial contamination estimated to 0.42% (Green et al, 2008). …”

“…Molecular sex assignment was estimated based on the ratio of sequences aligning to the two sex chromosomes, X and Y (Skoglund, Storå, Götherström, & Jakobsson, 2013) (Figure 3, S4). Levels of contamination were estimated based on the analyses of contradictory positions in mitochondrial sequences (Green et al, 2008). The consensus mitochondrial DNA (mtDNA) sequences were called using samtools package (Li et al 2009) while the initial haplogroup assignment was in HAPLOFIND tool (Vianello et al, 2013).…”

High-throughput sequencing of complete human mtDNA genomes from the Caucasus and West Asia: high diversity and demographic inferences

“…Sequence reads that passed these filters were sorted according to unique sequence tags. Consensus mtDNA sequences were assembled using the software MIA 22 by mapping reads to the revised Cambridge reference sequence (rCRS). 23 A multiple alignment of the consensus sequences was carried out using the software MAFFT v6.708b.…”

Mammoth genomics

“…The next draft nuclear genome of an extinct species likely to become available is that of our closest relative, the Neanderthal, following on from publication of a complete Neanderthal mitochondrial genome sequence 10 . For some time yet, much work in genomics will consist of fully annotating and completing genome sequences, as indeed most published sequences of extant vertebrates, let alone that of the extinct mammoth, remain drafts.…”

“…microquasars 10 -whether catalogued or not -are responsible for the feature around 620 GeV. And let's not forget that a completely new type of astrophysical object could also produce the detected electron excess; after all, pulsars were discovered only in 1967, and until 1992 we were blissfully unaware of microquasars.…”