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Post by Admin on Oct 24, 2023 21:38:23 GMT
 Fig. 3. Influence of latitude and time on the level of Neanderthal ancestry. (A) Ancestry level in Europe and (B) ancestry level in Asia. The analysis considers the full dataset of ancient and modern DNA samples (Full Eurasia, n = 2625). The y axis corresponds to the range where both regions (Asia and Europe) have the most data. Similar gradients of spatial introgression are observed when replacing latitude and longitude by the topographic distance from a putative source of the OOA expansion in East Africa (text S2), as well as when computing the F4 ratio from a dataset presumably less affected by background selection (text S3). However, our analysis does not support the hypothesis that a slightly higher level of NE ancestry in East Asia than in western Europe today could be explained by the greater distance to the source of the MH expansion in Asia than in Europe (19). This hypothesis was made from modern DNA data only, while our results also considered ancient DNA samples. Using paleogenomic data, we show the reverse pattern for samples older than 20,000 years BP, with more NE ancestry observed in Europe than in Asia (Fig. 3). The current pattern of NE ancestry being higher in Asia than in Europe must thus have developed at a later stage. Temporal variation in Neanderthal ancestry Our results suggest that the longitudinal gradient slope has remained similar over the past 40,000 years (table S1), whereas the latitudinal gradient of NE ancestry has significantly changed over time (F = 4.4, P = 0.03). The latitudinal pattern is more prominent during the early period in Europe and becomes less visible ~30,000 years BP, together with an overall reduction in NE ancestry (Fig. 3). While this implies that the level of NE ancestry in Eurasia may not have been uniformly distributed across space as is observed today, this expectation needs to be confirmed with more paleogenomes because the interaction between latitude and time is no longer significant when considering the average of all candidate models (based on a cumulative weighted AIC of 90%, Swi3 0.90; table S2) instead of the best model only. The variation in NE ancestry across time is now debated. It has been proposed that ancient European genomes showed more NE ancestry compared to present-day Europeans (4), but this result was questioned because of a methodological bias in the ancestry estimation procedure (42). Nevertheless, it has been estimated that NE ancestry could have been as high as 10% at the time of admixture before decreasing rapidly to the current rate of ~2% (43). Here, we show that the temporal reduction in NE ancestry is linked to latitude. The southern samples in Europe show an almost constant NE ancestry through time, while the northern samples experienced a reduction between approximately 40,000 and 20,000 years BP. The latitudinal gradient could have undergone important changes, possibly due to population expansions and contractions experienced by MHs during the Last Glacial Maximum (LGM) or other more limited ice ages. Our results show that this gradient becomes less evident in modern data (Fig. 3). Because the longitudinal pattern has been less affected during the past 40,000 years, it may represent a relict signature of the OOA range expansion that occurred during MH evolution between ~60,000 and 45,000 years BP. Natural selection has been invoked to explain the reduction in NE ancestry over time (15, 44), but different historical processes could have also played an important role. This includes population expansions and contractions (45, 46), as well as interactions between genetically differentiated populations with different levels of NE ancestry (16, 17). In Europe, a prominent genetic transition occurred during the spread of early Neolithic farmers, when they partially replaced Paleolithic/Mesolithic hunter-gatherers [i.e., the so-called Neolithic transition (33, 34, 35)]. At least along the Danube route from Anatolia to Central Europe, paleogenetic analyses have revealed that the first stage of the Neolithic transition occurred through the migration of FAs, followed by admixture with local HGs in a second stage, e.g., (32, 33, 35, 47). This transition began in the Fertile Crescent ~11,000 years BP (48), and its consequences on the distribution of NE ancestry have been weakly explored thus far (16). |
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Post by Admin on Oct 25, 2023 21:19:43 GMT
Less Neanderthal ancestry in early farmers than hunter-gatherers in Europe We thus explored more specifically the variation in the level of NE ancestry across time and population groups (HGs, FAs, and OTs, n = 2534 in total). The OT group includes all ancient samples that are neither FAs nor HGs, including, for example, the Bronze Age and more recent periods. Samples from the MD group were excluded from this analysis because they do not allow us to explore temporal variation in NE ancestry (all modern data are associated with the same date). We included population groups, continental area (either Europe or Asia), time, and their interactions as fixed variables, also correcting for spatial autocorrelation in the dataset. This model is called “Ancient Eurasia” because it only considers ancient samples, and its best LMM is presented in table S1. We observed an influence of time on the differences between Europe and Asia (F = 9.22, P < 0.01) and population groups (F = 9.41, P < 0.01), with an overall higher NE ancestry level for HGs than for FAs, particularly visible in Europe (Fig. 4). At approximately 10,000 years BP, when the first FA appeared in the Near East, the difference between FAs and HGs was significant in Europe [HG: 0.024 ± 0.001 (estimated mean ± SE), FA: 0.019 ± 0.001, t ratio = −6.14, P < 0.001], as well as in Asia (HG: 0.022 ± 0.001, FA: 0.018 ± 0.001, t ratio = −6.14, P < 0.001). Approximately 6000 years BP, when farming was well established but some HG populations persisted, the difference in NE ancestry was still significant between the HG (0.023 ± 0.001) and FA (0.020 ± 0.0002) populations in Europe (t ratio = −4.21, P < 0.001), as well as between the HG and OT (0.020 ± 0.0003) populations (t ratio = 3.51, P = 0.001), but not between the FA and OT populations (t ratio = −0.41, P = 0.91). A similar situation was observed in Asia at this time (FAs versus HGs, t ratio = −4.26, P < 0.001; HGs versus OTs, t ratio = 3.51, P = 0.001; FAs versus OTs, t ratio = −0.41, P = 0.91). Overall, this means that earlier FAs carried less NE ancestry than the former HGs of the same area. This difference vanished over time, since the level of NE ancestry in FAs increased during the cohabitation period with HGs in both geographic regions (Fig. 4). Admixture between late HGs and FAs could possibly explain part of the decrease in NE ancestry in HG over time, but it is probably not the only factor since this decrease appears to have started before the appearance of farming ~10,000 years BP (Fig. 4). However, this result should be interpreted with caution since the ancient samples are scarce and even absent between 30,000 and 20,000 years BP. Further data and studies could help shed light on this specific point. While Asian FAs reached an average level similar to that of HGs, European FAs did not reach such a high level (Fig. 4). Thus, FAs could have acted as a population that diluted NE ancestry in western Eurasia (text S4), as previously suggested (16, 17).  Fig. 4. Temporal variation in the level of Neanderthal ancestry in different cultural populations. HG, hunter-gatherers; FA, Neolithic farmers; OT, other ancient samples. (A) Ancestry level in Europe and (B) ancestry level in Asia. The solid and dotted lines represent the estimated values and 95% confidence intervals, respectively. The colored dots represent the distribution of ancient DNA samples used in the best Ancient Eurasia analysis (n = 2534). Multiple episodes of range expansion of populations where levels of NE ancestry differed could provide an explanation for the spatiotemporal change in NE ancestry. Our results support our former hypothesis that past human range expansions (i.e., HGs then FAs) contributed to the creation of spatial gradients of NE ancestry, with the level increasing from their source in southwest Asia (Figs. 2 and 3). During the OOA, HGs accumulated NE introgression as they expanded, in accordance with the range expansion hypothesis (19). The second range expansion into western Eurasia, that of early FAs, is critical to explain the overall dilution of NE ancestry in this area. The earliest FAs derived from HG populations in Anatolia and the Levant, with a lower level of NE ancestry than HG populations in the rest of Europe, as expected from their geographic proximity to the source of the OOA expansion (see text S4). The later expansion of the steppe pastoralists does not seem to have had as much influence as there is not a significant difference between the FA and OT population groups, but this would require a more detailed examination, as our OT group includes populations from different cultural periods. |
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Post by Admin on Jun 10, 2024 19:00:14 GMT
Neandertal ancestry through time: Insights from genomes of ancient and present-day humans Abstract Gene flow from Neandertals has shaped the landscape of genetic and phenotypic variation in modern humans. We identify the location and size of introgressed Neandertal ancestry segments in more than 300 genomes spanning the last 50,000 years. We study how Neandertal ancestry is shared among individuals to infer the time and duration of the Neandertal gene flow. We find the correlation of Neandertal segment locations across individuals and their divergence to sequenced Neandertals, both support a model of single major Neandertal gene flow. Our catalog of introgressed segments through time confirms that most natural selection–positive and negative–on Neandertal ancestry variants occurred immediately after the gene flow, and provides new insights into how the contact with Neandertals shaped human origins and adaptation. www.biorxiv.org/content/10.1101/2024.05.13.593955v1.full |
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Post by Admin on Jun 14, 2024 19:30:10 GMT
The sequencing of the Neandertal (1–4) and Denisovan (5, 6) genomes has revealed extensive gene flow between the ancestors of modern humans and archaic hominins. As a result, most non-Africans harbor 1–2% of Neandertal ancestry, with East Asians exhibiting ~20% more Neandertal ancestry compared to West Eurasians (6). This gene flow has been inferred to have occurred between 41,000–54,000 years ago, but it remains debated if there were secondary interactions between Neandertals and early modern humans (e.g., Oase, Bacho Kiro and Ust’-Ishim) or in the ancestors of East Asians or potential dilution in ancestors of West Eurasians from a group without Neandertal ancestry (7–11). Moreover, previous studies have identified that the distribution of Neandertal ancestry is not uniform across the genome: some regions are significantly depleted of Neanderthal ancestry (referred as “archaic deserts”), while other regions contain variants at unusually high frequency possibly because they harbor beneficial mutations (“candidates of adaptive introgression”) (12–17). The evolutionary forces––e.g., genetic drift or natural selection–– that have shaped these patterns are not fully understood. Most of the previous studies have focused on present-day individuals, where separating the effects of past demography and selection is challenging (18). Here, we generate a catalog of Neandertal ancestry in 59 ancient (sampled between 45,000–2,200 years before present (yBP)) and 275 diverse present-day modern humans, providing a systematic analysis of Neandertal ancestry through time and space. We recover the origin and trajectory of variants inherited from Neandertals, which allows us to refine the estimates of when the gene flow occurred (7, 9, 19) and directly observe how selection has shaped the patterns of ancestry across the genome (18, 20). Together, these analyses help characterize the population history and legacy of Neandertal gene flow in modern humans. www.ncbi.nlm.nih.gov/pmc/articles/PMC11118355/ |
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Post by Admin on Jun 25, 2024 17:04:37 GMT
Identifying the location of Neandertal ancestry in modern humans We use genomic data from 59 ancient modern human individuals ranging between 45,000–2,200 yBP, including 33 individuals that are older than 10,000 years. We also include the genomes from 275 diverse present-day individuals from worldwide populations that are part of the Simons Genome Diversity Project (SGDP) (Materials and Methods Section 1). Our data set contains a combination of whole-genome sequences and variants enriched for target positions using two different SNP capture arrays; the “1240k” (containing ~1.2 million sites segregating in modern humans) and the archaic admixture array (containing ~1.7 million Neandertal ancestry informative sites (8)) (table S1, Materials and Methods Section 2). We cluster individuals into 14 population groups that are stratified by geographic location and time using the data on the 1240k array (Fig. 1A, fig. S10, table S8, Materials and Methods Section 4.1).  Fig. 1: Calling of Neandertal ancestry in ancient and present-day individuals world wide (A) Sample overview of the population clusters through time. ancient East Asians (ancientEAS), ancient North Eurasians (ANE), ancient North Siberians (ANS), early out of Africa (EarlyOoA), East Asians (EAS), post-Last Glacial Maximum West Eurasian Hunter-Gatherers (postLGM-WEurHG), pre-Last Glacial Maximum West Eurasian Hunter-Gatherers (preLGM-WEurHG), South Asians (SA), Southwest Asians (SWA), West Eurasians (WEur). Bars represent the span from oldest to youngest individual; n is the number of individuals. (B) Sample location and age of individuals. Triangles: present-day individuals, dots: ancient individuals (C) Workflow overview for admixfrog. High quality genomes are used as representatives for the unobserved ancestries (blue, red and green) of a given target genome. The genotypes of all SNPs in a small bin are latent states that are coestimated from aligned sequencing reads. (D) Inferred ancestry segments across the autosomes in three ancient modern human individuals. Red segments represent Neandertal ancestry. (E) Ancestry covariance for the same individuals calculated on the genotype likelihoods from admixfrog. The dotted line indicates the inferred decay of coancestry. To infer Neandertal ancestry segments in a single target modern human genome, we use admixfrog, a hidden Markov model-based approach (21). For each diploid individual at each window (0.005cM), admixfrog estimates a combination of two ancestries from three possibilities: i) Neandertal (using the three high-coverage Neandertal genomes as reference (2–4)), ii) Denisovan (using the high-coverage Altai Denisovan genome (6)), or iii) modern human (using a panel of individuals of sub-Saharan African-related ancestry who have minimal Neandertal ancestry (22)). admixfrog coestimates genotype likelihoods and contamination, and is thus well-suited for ancient DNA (Fig. 1C Materials and Methods Section 3.1). We performed extensive simulations to test the performance of admixfrog, and find that the method works reliably for shotgun genomes and the archaic admixture array, for samples with a coverage of at least 0.2x, but it has lower power for 1240k capture array that has few archaic informative markers (fig S2–8, table S1 and S3, Materials and Methods Section 3.1 – 3.3). Moreover, since we have access to only one Denisovan genome that is highly diverged from the introgressing Denisovan into most human populations (23), our ability to reliably detect Denisovan ancestry is limited (fig. S9, table S6). Thus, we focused on Neandertal ancestry only. Using 58 ancient and 231 present-day non-African individuals (Fig. 1B), we generated a comprehensive catalog of Neandertal ancestry segments that we use to infer the source, timing and function of Neandertal ancestry in modern humans (Fig. 1D,,EE). |
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