Earliest modern human genomes constrain timing of Neanderthal admixture

Abstract

Modern humans arrived in Europe more than 45,000 years ago, overlapping at least 5,000 years with Neanderthals^1-4. Limited genomic data from these early modern humans have shown that at least two genetically distinct groups inhabited Europe, represented by Zlatý kůň, Czechia³ and Bacho Kiro, Bulgaria². Here we deepen our understanding of early modern humans by analysing one high-coverage genome and five low-coverage genomes from approximately 45,000-year-old remains from Ilsenhöhle in Ranis, Germany⁴, and a further high-coverage genome from Zlatý kůň. We show that distant familial relationships link the Ranis and Zlatý kůň individuals and that they were part of the same small, isolated population that represents the deepest known split from the Out-of-Africa lineage. Ranis genomes harbour Neanderthal segments that originate from a single admixture event shared with all non-Africans that we date to approximately 45,000-49,000 years ago. This implies that ancestors of all non-Africans sequenced so far resided in a common population at this time, and further suggests that modern human remains older than 50,000 years from outside Africa represent different non-African populations.

Fig. 1. Geographical distribution of modern human specimens older than 40 kyr that produced genome-wide data.

Specimens with new genome-wide data produced in this study are shaded in pink. Ages give 95.4% CIs on calibrated radiocarbon dates except for Zlatý kůň, for which we give the estimated age on the basis of Neanderthal segment lengths. The Ranis specimens within the dashed circle belong to the same individual. Credits: photographs of the Ranis specimens are adapted from ref. , Springer Nature Limited, under a Creative Commons licence, CC BY 4.0; the photograph of the Zlatý kůň skull is adapted from the Department of Anthropology, National History Museum of Prague (photographer: Marek Jantač); photographs of the Oase and Bacho Kiro specimens, © MPI-EVA/Rosen Spasov (from www.mpg.de/16663512/genomes-earliest-europeans), and of a 40-kyr-old modern human jawbone, © MPI for Evolutionary Anthropology/Svante Pääbo (from www.mpg.de/9278783/modern-humans-neandertals-interbreeding-europe); photograph of the Ust’-Ishim specimen is adapted from ref. , Springer Nature Limited, under a Creative Commons licence, CC BY 4.0; the photograph of the Tianyuan specimen is reproduced from www.science.org/content/article/last-ice-age-wiped-out-people-east-asia-well-europe (Shaoguang Zhang/Institute of Vertebrate Paleontology and Paleoanthropology). The base map was made with Natural Earth (www.naturalearthdata.com/).

Fig. 2. Genetic relatedness between pairs of individuals.

a, Biological kinship inferred from genomes of different specimens (prefix ‘RNI’ for Ranis and ‘ZKU’ for Zlatý kůň). The values within the squares indicate log-likelihood ratio between the two maximum likelihood models, for each pair. b, Heatmap representing the f₃-outgroup statistics results with a subset of early modern humans older than 40 kyr. c, Pairwise IBD sharing (greater than 12 cM) for comparisons between individuals Ranis12–Ranis13 and Ranis12–Zlatý kůň. d, Total IBD sharing in three different length categories plotted for the ten Ranis/Zlatý kůň pairs with the highest IBD sharing. Ranis6 and Ranis10 were excluded due to low coverage.

Fig. 3. Neanderthal ancestry.

a,b, Segments in Ranis13 (a) and segments in Zlatý kůň (b). Colours indicate the state of the called segment: grey for the homozygous African state (AFR), and dark orange and dark blue for homozygous Denisovan (DEN) and Neanderthal (NEA) states, respectively. The remaining three colours indicate heterozygous states as stated in the colour legend (AFRDEN for African/Denisovan, AFRNEA for African/Neanderthal and NEADEN for Neanderthal/Denisovan heterozygous states). c, Decay curves using the longest 100 Neanderthal segments in each genome. d, Estimates of generations between the Neanderthal introgression event and the life of the individual, on the basis of the length of the called segments (n = 100). Error bars represent the 95% CI obtained from the chi-squared distribution.

Fig. 4. Tree summarizing the main points of the study.

The scheme includes timing of the main Neanderthal introgression event and order of the population separations from the Out-of-Africa lineage.

Extended Data Fig. 1. Map of Ranis with the location of the specimens (named RNI0XX) included in this study.

Green circles contain specimens from the same individual, Ranis12, and the dark orange areas are the squares they were excavated from. Genetic sexes of the individuals that the specimens belonged to are shown below their IDs. The blue area indicates the squares excavated in 2016–2022 while the rest of the grid was excavated in 1932–1938. Credit: background raster is adapted from ref. , Springer Nature Limited, under a Creative Commons licence, CC BY 4.0.

Extended Data Fig. 2. Number of identical by descent (IBD) segment sharing for the three pairs with the highest values among the Ranis and Zlatý kůň individuals, plotted against simulated relatives of various degrees.

Values on the x-axis stand for the sum of the shared IBD segments longer than 12 cM and values on the y-axis are the numbers of IBD segments longer than 12 cM. Biological relatives are simulated with Ped-sim. Units are reported in square brackets in the axis labels. For the Ranis and Zlatý kůň pairs, we subtracted the expected background IBD sharing for a homogeneous population of effective size 299.7 (estimated from ROH blocks, Supplementary Informations 7 & 8) before plotting it on top of simulated pairs. Ranis6 is not included due to low data quality.

Extended Data Fig. 3. Heatmap of pairwise comparisons of hunter-gatherers in f3-outgroup statistics.

An Mbuti genome is used as the outgroup.

Extended Data Fig. 4. Population relationships.

A. & B. F-statistics investigating the relationship between the Ranis and Zlatý kůň individuals and the other early modern humans using the 1240k array sites for Ranis as a group and the high-coverage genome of Zlatý kůň. Error bars correspond to three standard errors. C. Tree inferred by momi2, using high-coverage genomes. We use the following abbreviations: Yoruba (YRI), Han Chinese (CHB), Tuscani (TSI), Ust’-Ishim (UST), Ranis13 (RNI), Zlatý kůň (ZKU), and Vindija33.19 (NEA). IntrogNea represents the Neanderthal lineage that introgressed into the modern human population.

Extended Data Fig. 5. qpGraphs.

Analyses were conducted following the tree structure reported in Hajdinjak et al., and Posth et al.. A. Ranis13 and Zlatý kůň modeled as sister clades, B. Zlatý kůň representing an earlier split, and C. Ranis13 representing an earlier split from the Out-of-Africa lineage.

Extended Data Fig. 6. Inbreeding, population size and heterozygosity estimates.

A. Violin plots indicating the length distributions of the segments that are homozygous by descent (HBD, or ROH), using the African-American recombination map. The width of the violins is proportional to the number of HBD segments. B. Likelihood of IBD shared between Ranis13 and Zlatý kůň over a 2D grid of effective population size and the absolute value of time difference. The red star indicates the maximum likelihood estimate and the black dashed circle indicates the 95% confidence region. The colour bar indicates the log-likelihood values. C. Average heterozygosity (x10,000) in the autosomes of high-coverage ancient and present-day human genomes. Each point represents the heterozygosity estimate on a single autosome (n = 22). Archaics are in light orange and Africans are in dark orange, while non-Africans are in yellow. Other colours uniquely represent ancient modern humans. The lower and upper hinges in the boxplots in A and C correspond to the 25th and 75th percentiles. Upper and lower whiskers are at most 1.5 inter-quartile range away from the upper and lower hinges, respectively.

Extended Data Fig. 7. Molecular age estimates.

These ages were obtained (A.) based on branch shortening by missing mutation counts, with each point representing a chromosome and value on the top being the weighted mean value excluding the outliers (filled points) and (B.-D.) using the PSMC curves for three high-coverage early modern humans, in comparison to the genome of a present-day French individual. The lower and upper hinges in the boxplots in A correspond to the 25th and 75th percentiles. Upper and lower whiskers are at most 1.5 inter-quartile range away from the upper and lower hinges, respectively.

Extended Data Fig. 8. Sharing of the Neanderthal ancestry with present-day populations.

Correlations of the Neanderthal segments with the present-day SGDP populations for (A.) Ranis13 and (B.) Zlatý kůň. Each point represents a genome in the corresponding SGDP super-population. Correlation of the recombination breakpoints with HGDP and 1000 genomes populations for (C.) Ranis13 and (D.) Zlatý kůň. We use the following abbreviations: Americans (AMR), Central South Asians (CSA), East Asians (EAS), Europeans (EAS), Middle Easterners (MID), and Oceanians (OCE), and each point represents a genome from these populations. The lower and upper hinges in the boxplots in white correspond to the 25th and 75th percentiles. Upper and lower whiskers are at most 1.5 inter-quartile range away from the upper and lower hinges, respectively.