Targeted investigation of the Neandertal genome by array-based sequence capture

Abstract

It is now possible to perform whole-genome shotgun sequencing as well as capture of specific genomic regions for extinct organisms. However, targeted resequencing of large parts of nuclear genomes has yet to be demonstrated for ancient DNA. Here we show that hybridization capture on microarrays can successfully recover more than a megabase of target regions from Neandertal DNA even in the presence of approximately 99.8% microbial DNA. Using this approach, we have sequenced approximately 14,000 protein-coding positions inferred to have changed on the human lineage since the last common ancestor shared with chimpanzees. By generating the sequence of one Neandertal and 50 present-day humans at these positions, we have identified 88 amino acid substitutions that have become fixed in humans since our divergence from the Neandertals.

Figure 1

(a) For the 9,525 substitutions where the Neandertal carries the derived human allele, the substitution has occurred prior the Neandertal-modern human split (blue part of the hominin lineage), whereas fixation could have happen any time later (grey part of the hominin lineage). (b) For the 88 substitutions where the Neandertal carries the ancestral, chimpanzee-like base, the fixation occurred after the Neandertal-modern human split (red part of the hominin lineage), whereas the substitution could have happened at any point along the hominin lineage (grey). (c) Percentage of the 13,841 positions captured. (d) Distribution of coverage for the positions that encode amino acid substitutions along the hominin lineage. The average coverage is 4.8-fold.

Figure 2

Evolutionary protein conservation at positions affected by the substitutions studied. For each bin of conservation GERP scores, the fractions of amino acid substitutions where the Neandertal carry the derived allele (blue) and the ancestral allele (red) are shown.