Nuclear DNA from two early Neandertals reveals 80,000 years of genetic continuity in Europe

Abstract

Little is known about the population history of Neandertals over the hundreds of thousands of years of their existence. We retrieved nuclear genomic sequences from two Neandertals, one from Hohlenstein-Stadel Cave in Germany and the other from Scladina Cave in Belgium, who lived around 120,000 years ago. Despite the deeply divergent mitochondrial lineage present in the former individual, both Neandertals are genetically closer to later Neandertals from Europe than to a roughly contemporaneous individual from Siberia. That the Hohlenstein-Stadel and Scladina individuals lived around the time of their most recent common ancestor with later Neandertals suggests that all later Neandertals trace at least part of their ancestry back to these early European Neandertals.

A high-coverage Neandertal genome from Chagyrskaya Cave

“…Chagyrskaya 8 is thus related to Neandertal populations that moved east sometime between 120 and 80 thousand years ago (8,31). Interestingly, the artifacts found in Chagyrskaya Cave show similarities to artifact assemblages in Central and Eastern Europe (10) (SI1), suggesting that Neandertal populations coming from western Eurasia to Siberia may have been brought their material culture with them (10,32).…”

AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination

“…The observed and expected frequencies of the distance between pairs of C-to-T substitutions are compared among sequences that exhibit two internal C-to-T substitutions (excluding the first and last 5 bases). The colours correspond to sequence data from different archaic humans (>500,000 sequences each; Les Cottés Z4-1514, Spy 94a, Vindija 87, Mezmaiskaya 2, Goyet Q56-1 from [55]; Scladina I-4A and Hohlenstein-Stadel from [23]; Denisova 2 from [56]; Mezmaiskaya 1 from [57]). The present-day human DNA control dataset is represented in black [9].…”

“…For each dataset, we then compared the contamination rate estimates from AuthentiCT to the estimates from contDeam [17] and from the conditional substitution analysis ([22], as computed in [23]) ( Figure 3 ). While the latter approach underestimates the contamination proportion (average bias: - 6.73%; Root Mean Square Error (RMSE): 0.0741; based on 100,000 sequences), contDeam overestimates it (average bias: 2.36-1.19%; RMSE: 0.0396-0.0320; based on 10,000 and 100,000 sequences, respectively).…”

“…To further validate the method, we next applied AuthentiCT to published sequences from archaic human specimens [22, 23, 55, 57] without introducing sequences from present-day DNA. We compared our results with a previous approach (Peyregne et al 2019) that relies solely on the divergence to a present-day African genome (HGDP00456, [45]).…”

“…In contrast, local genealogies along the nuclear genome may differ from the overall population relationship (incomplete lineage sorting), making the identification of diagnostic positions difficult. By leveraging differences in allele frequencies between populations, it is possible to estimate the proportion of present-day human DNA contamination among nuclear sequences from archaic hominins [21-23]. However, this approach remains challenging for the analysis of early modern humans because of the lack of knowledge about rare sequence variants in the sample of interest that are unlikely to be shared with the present-day human contaminant.…”