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Gibraltar Neanderthal; Forbes’ Quarry; paleogenetics; ancient DNA; library preparation
Abstract:
The remains of 2 Neanderthals were found in Gibraltar: the first at Forbes Quarry in 1848 and the second at Devil’s Tower in 1926. Since their discovery, present-day human DNA contamination has accumulated in the specimens. By developing a DNA library preparation method that reduces modern contamination before sequencing, we were able to isolate enough endogenous DNA from the specimens to determine their sex and to infer that the Forbes’ Quarry Neanderthal is more similar to 60,000- to 120,000-y-old Neanderthal specimens in Europe and western Asia than to younger Neanderthals. The laboratory protocols presented here improve access to ancient DNA from specimens that are highly contaminated with present-day human DNA.The Forbes’ Quarry and Devil’s Tower partial crania from Gibraltar are among the first Neanderthal remains ever found. Here, we show that small amounts of ancient DNA are preserved in the petrous bones of the 2 individuals despite unfavorable climatic conditions. However, the endogenous Neanderthal DNA is present among an overwhelming excess of recent human DNA. Using improved DNA library construction methods that enrich for DNA fragments carrying deaminated cytosine residues, we were able to sequence 70 and 0.4 megabase pairs (Mbp) nuclear DNA of the Forbes’ Quarry and Devil’s Tower specimens, respectively, as well as large parts of the mitochondrial genome of the Forbes’ Quarry individual. We confirm that the Forbes’ Quarry individual was a female and the Devil’s Tower individual a male. We also show that the Forbes’ Quarry individual is genetically more similar to the ˜120,000-y-old Neanderthals from Scladina Cave in Belgium (Scladina I-4A) and Hohlenstein-Stadel Cave in Germany, as well as to a ˜60,000- to 70,000-y-old Neanderthal from Russia (Mezmaiskaya 1), than to a ˜49,000-y-old Neanderthal from El Sidrón (El Sidrón 1253) in northern Spain and other younger Neanderthals from Europe and western Asia. This suggests that the Forbes’ Quarry fossil predates the latter Neanderthals. The preservation of archaic human DNA in the warm coastal climate of Gibraltar, close to the shores of Africa, raises hopes for the future recovery of archaic human DNA from regions in which climatic conditions are less than optimal for DNA preservation.
