Anthropological dating methods
We show that this method provides age estimates that are highly correlated to radiocarbon dates, thus documenting the promise of this approach.
By studying the linear relationship between the dates of Neanderthal admixture and the radiocarbon dates, we obtain, to our knowledge, the first direct estimate of the historical generation interval of 26–30 y.
In addition, comparison with HC divergence relies on branch-shortening estimates that are small relative to the total divergence of millions of years, so that even very low error rates in allele detection can bias estimates.
These issues lead to substantial uncertainty in estimated age of the ancient samples, making this approach impractical for dating specimens that are tens of thousands of years old, a time period that encompasses the vast majority of ancient human samples sequenced to date.
Extensions of this methodology that use older shared events may be applicable for dating beyond the radiocarbon frontier.
Ancient DNA analyses have transformed research into human evolutionary history, making it possible to directly observe genetic variation patterns that existed in the past, instead of having to infer them retrospectively (1).
In addition, contamination of a sample by modern carbon, introduced during burial or by handling afterwards, can make a sample seem younger than it actually is (2).
The problem is particularly acute for samples that antedate 30,000 y ago because they retain very little original C.
Specifically, the authors compared the divergence between the Denisova and extant humans and calibrated the branch shortening relative to human–chimpanzee (HC) divergence time.
The idea of our method is to estimate the date of Neanderthal gene flow separately for the extant and ancient genomes.
Because the ancient sample is closer in time to the shared Neanderthal admixture event, we expect that the inferred dates of Neanderthal admixture will be more recent in ancient genomes (by an amount that is directly determined by the sample’s age) compared with the dates in the extant genomes. An assumption in our approach is that the Neanderthal admixture into the ancestors of modern humans occurred approximately at the same time and that the same interbreeding events contributed to the ancestry of all of the non-African samples being compared.
The use of ape divergence time for calibration, however, relies on estimates of mutation rate that are uncertain (7).
In particular, recent pedigree studies have yielded a yearly mutation rate that is approximately twofold lower than the one obtained from phylogenetic methods (7).
Previous studies have documented that most non-Africans derive 1–4% ancestry from Neanderthals from an admixture event that occurred ∼37,000–86,000 y before present (y BP) (9, 10), with some analyses proposing a second event (around the same time) into the ancestors of East Asians (11, 12).