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Post by Admin on Feb 25, 2024 5:26:37 GMT
In the past, researchers have sequenced DNA from Neanderthals and other extinct humans dating as far back as 430,000 years ago, but there is little genetic information from the period between about 47,000 and 40,000 years ago, and no Homo sapiens DNA from before that time period. According to a recent study in Nature, modern humans appeared in Europe at least 45,000 years ago while current evidence shows that Neanderthals disappeared relatively shortly before that, around 40,000 years ago. In the study, researchers presented genome-wide data from three individuals dated to between 45,930 and 42,580 years ago from a cave in Bulgaria called Bacho Kiro Cave, which may help researchers fill in gaps in evolution and migration. “Unlike two previously studied individuals of similar ages from Romania and Siberia who did not contribute detectably to later populations, these individuals are more closely related to present-day and ancient populations in East Asia and the Americas than to later west Eurasian populations,” the authors wrote. “This indicates that they belonged to a modern human migration into Europe that was not previously known from the genetic record, and provides evidence that there was at least some continuity between the earliest modern humans in Europe and later people in Eurasia.” The DNA extract from the cave in Bulgaria also had another secret to divulge: All three individuals had Neanderthal ancestors a few generations back in their family history, confirming that the first European modern humans mixed with Neanderthals and suggesting that such mixing could have been common. “The Bacho Kiro Cave genomes show that several distinct modern human populations existed during the early Upper Paleolithic in Eurasia,” the study noted. “Some of these populations … show no detectable affinities to later populations, whereas [other] groups … contributed to later populations with Asian ancestry as well as some western Eurasian humans.” This evidence suggests that mixing between Neanderthals and the first modern humans who arrived in Europe was perhaps more common than is often assumed. www.nature.com/articles/s41586-021-03335-3In a separate Nature study, also published in 2021, a group of researchers analyzed a genome generated from the skull of a female individual from Zlatý kůň in Czech Republic. The researchers found that the person belonged to a population that appears to have contributed genetically neither to later Europeans nor to Asians. The skull was found alongside other “skeletal elements” in 1950 inside a cave called Koněprusy, not far from the capital of present-day Czech, Prague. Zlatý kůň, the name researchers gave to the person the skull came from – who they refer to as a “she” – is also the name of a hill atop the cave. “Her genome carries ~3% Neanderthal ancestry, similar to those of other Upper Paleolithic hunter-gatherers,” the researchers wrote. “However, the lengths of the Neanderthal segments are longer than those observed in the currently oldest modern human genome of the ~45,000-year-old Ust’-Ishim individual from Siberia, suggesting that this individual from Zlatý kůň is one of the earliest Eurasian inhabitants following the expansion out of Africa.” DNA were extracted from about 15 mg of bone powder from the temporal bone. The mitochondrial genome was sequenced, with about 4% of the mtDNA stemming from human contamination. The reconstructed DNA, the researchers found, belong to rare haplogroup N and is branch length is similar to those of the current oldest sequenced modern human mtDNA genomes, including that from the Bacho Kiro cave in Bulgaria. While the Zlatý kůň individual fills an important gap in DNA evidence about early humans, it is also a bit of an outlier. The person shares more alleles with Asians than Europeans, which matches with evidence from other Upper Paleolithic and Mesolithic European hunter-gatherers when compared to present-day Europeans. “This suggests that Zlatý kůň falls basal to the split of the European and Asian populations,” the authors wrote. Of course, it’s important to realize there is still much left to learn: as the study notes, of the thousands of individuals who lived in this era, only two ancient Eurasian genomes have been produced from individuals like the one found in Zlatý kůň, appear to come before the split of Europeans and Asians. “Most of the Neanderthal ancestry in present-day and ancient humans probably originates from a common admixture event with a group of Neanderthals who were more closely related to European Neanderthals than to a Neanderthal from the Altai Mountains” of Mongolia, the authors noted. Neanderthal ancestry in Zlatý kůň, they added, shows the same relationship. www.ncbi.nlm.nih.gov/pmc/articles/PMC8175239/ |
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Post by Admin on Feb 25, 2024 5:31:06 GMT
40,000-Year-Old Individual from Asia Provides Insight into Early Population Structure in Eurasia Highlights •By 40,000 years ago, ≥4 subpopulations of modern humans were established in Eurasia •The Tianyuan individual is more related to Asians than to past and present Europeans •He is not, however, equally similar to all early humans in Europe •His genetic similarity to some South Americans suggests early Asian population structure  Summary By at least 45,000 years before present, anatomically modern humans had spread across Eurasia [1, 2, 3], but it is not well known how diverse these early populations were and whether they contributed substantially to later people or represent early modern human expansions into Eurasia that left no surviving descendants today. Analyses of genome-wide data from several ancient individuals from Western Eurasia and Siberia have shown that some of these individuals have relationships to present-day Europeans [4, 5] while others did not contribute to present-day Eurasian populations [3, 6]. As contributions from Upper Paleolithic populations in Eastern Eurasia to present-day humans and their relationship to other early Eurasians is not clear, we generated genome-wide data from a 40,000-year-old individual from Tianyuan Cave, China, [1, 7] to study his relationship to ancient and present-day humans. We find that he is more related to present-day and ancient Asians than he is to Europeans, but he shares more alleles with a 35,000-year-old European individual than he shares with other ancient Europeans, indicating that the separation between early Europeans and early Asians was not a single population split. We also find that the Tianyuan individual shares more alleles with some Native American groups in South America than with Native Americans elsewhere, providing further support for population substructure in Asia [8] and suggesting that this persisted from 40,000 years ago until the colonization of the Americas. Our study of the Tianyuan individual highlights the complex migration and subdivision of early human populations in Eurasia. www.sciencedirect.com/science/article/pii/S0960982217311958 |
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Post by Admin on Feb 26, 2024 19:43:47 GMT
Results and Discussion
Due to the high fraction of microbial sequences in DNA libraries generated from the Tianyuan individual [7], we used hybridization to oligonucleotide probes [6, 9] to enrich for human DNA fragments carrying 3.7 million single-nucleotide polymorphisms (SNPs) (Tables S1A and S1B). We aligned captured sequences to the human reference genome hg19, and at the 2,228,374 sites covered by captured sequences, we obtained an average coverage of 2.98-fold (Tables S1B and S1C). We drew a random sequence for each site to represent the Tianyuan genome and merged this with published data from ancient (Table S1D) and present-day humans (Table S1E).
When sequencing ancient modern humans, it is important to account for contamination from present-day human DNA. We previously showed that DNA in these libraries has cytosine deamination patterns characteristic of ancient DNA and that human mtDNA contamination from these 15 libraries ranges from 0.2% to 1.5% [7]. To estimate nuclear contamination for the capture data, we used an approach [10] that takes advantage of the fact that the Tianyuan individual is male and thus carried one copy of the X chromosome. Assuming that polymorphic sites on the X chromosome are due to contamination rather than sequencing errors, we estimate nuclear contamination between 0.01% and 1.92% in the libraries used (Table S1A).
It has previously been shown using chromosome 21 that the Tianyuan individual shares more alleles with present-day Asians than with present-day Europeans [7]. We similarly find that the Tianyuan individual shares more alleles with present-day Eastern Eurasians, Oceanians, and Native Americans than with other present-day humans using the statistic [11] f3(Tianyuan, X; Mbuti), with the highest similarity to East and Southeast Asian populations (Figure 1A; Table S2A). However, present-day Europeans were found to carry a genetic component from a population that diverged from other non-Africans before they diverged from each other (a Basal Eurasian population [12]), such that analyses using only present-day Europeans may make the Tianyuan individual look more closely related to present-day Asians than he was. We therefore compared the Tianyuan individual to ancient Europeans who show no evidence of any Basal Eurasian ancestry [4] and are of an age similar to him (Kostenki14, GoyetQ116-1, and Vestonice16). The Tianyuan individual consistently shares more alleles with ancient and present-day East and Southeast Asians, as well as ancient and present-day Native Americans, than with either ancient or present-day Europeans (|Z| > 3; Figure 2A; Tables S2B–S2D). We also find that ancient and present-day East and Southeast Asians and Native Americans are all more closely related to each other than they are to the Tianyuan individual (Figures 2B and S1; Tables S2B–S2D). Taken together, our results indicate that the Tianyuan individual is related to an ancestral group that contributed to all more recent populations with Asian ancestry. Also, the Tianyuan individual’s age indicates that a genetic separation of Europe and Asia must have been earlier than 40,000 years ago. This is consistent with a split time of 40,000–80,000 years ago estimated for European and Asian populations based on mutation rates estimated from de novo mutations [13, 14, 15].
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Post by Admin on Feb 28, 2024 2:37:43 GMT
 Figure 1. f3(Tianyuan, X; Mbuti) for All Sites Where X Is a Present-Day Human Population or an Ancient Individual The f3 statistic ranges from 0.04 to 0.25. A higher value (red) indicates higher shared genetic drift between the Tianyuan individual and the (A) present-day population or (B) ancient individual. The intersection of the dotted lines indicates where the Tianyuan Cave is located. See also Table S2A.  Figure 2. Comparisons Relating the Tianyuan Individual to Ancient and Present-Day Eurasians and Native Americans (A) D(Tianyuan, X; Y, Mbuti) and D(Y, X; Tianyuan, Mbuti), where Y is the East and Southeast Asian Han or Ami or the Native American Mixe or Surui and X is the ancient West Eurasian individual Kostenki14, GoyetQ116-1, or Vestonice16. (B) Maximum-likelihood tree showing East and Southeast Asians, Native Americans, and ancient Eurasians, with bootstrap support of 100% unless indicated otherwise. The scale bar shows the average standard error (SE) of the entries in the covariance matrix. (C) D(GoyetQ116-1, Vestonice16; Y, Mbuti), where Y is the Tianyuan individual, an East and Southeast Asian population, or a Native American population. For (A) and (C), thick bars are within 1 SE of the estimate, thin bars are within 1.96 SE of the estimate (95% confidence interval), and the dashed vertical line indicates D = 0. See also Figures S1 and S2 and Tables S2 and S3. When combined with data from other early Upper Paleolithic individuals from Eurasia [3, 4, 5, 6], our results show that several distinct populations existed in Eurasia before 35 kya. One population, represented by the 37,000-year-old Kostenki14, contributed genetic ancestry to present-day Europeans; a second population represented by the Tianyuan individual contributed to present-day East and Southeast Asians; and one or more additional populations represented by the 45,000-year-old Ust’-Ishim and the 40,000-year-old Oase1 individuals did not contribute detectably to any present-day populations. Including the inferred Basal Eurasian population contributing to present-day Europeans and ancient Near East individuals [12, 16], a minimum of four populations must therefore have coexisted in Eurasia before 35 kya. Among the Upper Paleolithic individuals from Western Eurasia analyzed here, a 35,000-year-old individual from Belgium, GoyetQ116-1 [4], shares more alleles with the Tianyuan individual than any other Western Eurasian individual does (f3(Tianyuan, GoyetQ116-1; Mbuti) = 0.23, Figure 1B and Table S2A; D(GoyetQ116-1, Vestonice16; Tianyuan, Mbuti) > 0, Figures 2C and S2A and Tables S3A and S3B). Furthermore, admixture between the populations to which GoyetQ116-1 and the Tianyuan individual belong improves the fit of a tree relating these populations to one another (Figure S1). The excess of alleles shared by the Tianyuan individual with GoyetQ116-1 compared to other ancient Europeans persists when we restrict the analysis to deaminated sequence fragments and when we exclude potentially deaminated bases (Figure S2Aii and S2Aiii; Table S3B), suggesting that DNA contamination from present-day humans and nucleotide misincorporation induced by cytosine deamination do not explain this allele sharing. We also find no evidence that the similarities between the Tianyuan individual and GoyetQ116-1 are due to sequencing error, data processing artifacts, or reference bias (Table S3G). Notably, ancient European individuals related to GoyetQ116-1, such as the 19,000-year-old El Miron individual from Spain [4], do not share more alleles with the Tianyuan individual than other ancient European individuals do (Figure S2B). Present-day East and Southeast Asian populations do not share significantly more alleles with GoyetQ116-1 than they do with other ancient Western Eurasians (Figures 2C and S2A). GoyetQ116-1 carries a mitochondrial genome belonging to haplogroup M, and M-derived haplogroups can be found in present-day East Eurasian, Oceanian, and Native American populations but are almost completely absent in European populations [17, 18]. These results suggest that despite the geographical distance between them, the Tianyuan individual and GoyetQ116-1 may share ancestry from a population that did not contribute ancestry to the other Upper Paleolithic Eurasians analyzed to date. Other younger connections between Eastern and Western Eurasia have also been found. Lipson and Reich [19] find that the 24,000-year-old Mal’ta1 [20] and 16,500-year-old AfontovaGora3 [4] from western Siberia and several 7,000- to 14,000-year-old Western Eurasian individuals show evidence of gene flow from a population related to the East and Southeast Asian Ami. We observe that the Eastern European hunter-gatherer Karelia [9], like the ancient Siberians and Western Eurasians, also show evidence of Asian gene flow. We also find that the pattern occurs for more East and Southeast Asian populations than just the Ami (Figures S2C and S2D; Tables S3C–S3F). Previous demographic inference studies [21, 22, 23] have inferred non-zero levels of migration between the ancestors of present-day European and Asian populations. Using the Tianyuan individual, we directly show that the separation of populations ancestral to more recent Europeans and Asians was a complex process that may have involved a sub-structured ancestral population and gene flow subsequent to geographic separation of populations. Present-day Asian individuals carry ancestry from both Neanderthals and Denisovans [24, 25, 26, 27]. We find that the Tianyuan individual carried about as much Neanderthal DNA as other Upper Paleolithic Eurasians (∼4%–5%), which is more than that in present-day Eurasians (∼1%–2%; Figures S3A and S3B; Table S4C) and is consistent with the hypothesis that purifying selection acting since introgression has reduced the amount of Neanderthal DNA in present-day genomes [4]. We do not detect Denisovan ancestry at the levels observed in Oceanian populations [26] in the genome of the Tianyuan individual (Tables S4A and S4B). However, due to insufficient power to detect low levels of Denisovan admixture, we cannot exclude that the Tianyuan individual carries DNA derived from Denisovans at levels similar to present-day mainland Asians [28] (Figure S3C). We also do not detect admixture from other putative archaic groups (Figures S3D–S3G), despite morphological suggestions of admixture from an archaic population [29]. Most Asian and Native American populations share similar numbers of alleles with the Tianyuan individual (Tables S2Bv and S2Dviii). However, three South American populations—the Surui and Karitiana in Brazil (“Amazonians”) and the Chane in northern Argentina and southern Bolivia—share more alleles with the Tianyuan individual than other Native American populations do (Figure 3A; Tables S2E, S2H, and S2J). The two Amazonian populations were recently shown to share more alleles with the present-day Papuan and Andamanese Onge than with other Native Americans [8, 30, 31] (Figures 3B and 3C), suggesting that at least two populations contributed ancestry to Native Americans in Central and South America. A 12,000-year-old individual from North America (Anzick-1 [32]) does not share more alleles with the Tianyuan individual (or with Oceanians or the Andamanese [8]) than with other Native Americans (Figures 3A–3C; Tables S2Dviii and S2J). The Surui and Chane show the highest levels of allele sharing with the Tianyuan individual (D(Surui/Chane, Mixe, Tianyuan, Mbuti) = 0.02, Z > 3; Table S2J), which is higher than, or similar to, levels of allele sharing with the Papuan or Onge (Table S2J). Using an analysis robust to uncertainty of the exact population history [9], we find that the Amazonians can be described as a mixture of other Native American populations and 9%–15% of an ancestral population related to the Tianyuan individual, the Papuan, or the Onge (SE 4%–10%; Table S2G). Although the SE is high, we note that the Amazonians are consistently modeled as a mixture of other Native Americans and the Tianyuan individual, the Papuan, or the Onge. The mixture proportion estimates are also similar across all analyses, indicating that the relationship between the Tianyuan individual and the Amazonians is similar to that reported between the Papuan and the Amazonians and Onge and the Amazonians. |
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Post by Admin on Mar 4, 2024 20:15:04 GMT
 Figure 3. Heatmap of D Statistics and Admixture Graph Model Comparing Native Americans to the Tianyuan Individual (A–C) Heatmaps of (A) D(X, Mixe; Tianyuan, Mbuti), (B) D(X, Mixe; Papuan, Mbuti), and (C) D(X, Mixe; Onge, Mbuti), where X are non-Mixe Native American populations. (D) Admixture graph model that fits allele frequency patterns (all empirical f statistics are within 3 SEs of expectation). Branch lengths are shown in units of Fst × 1,000. Admixture from a population related to the Altai Neanderthal into ancient individuals (shaded gray) was collapsed into a single node, as were the original nodes at the top of the graph (can be observed in Figure S4N). The orange lines indicate the edges leading to the Tianyuan individual and the East and Southeast Asian Ami after splitting from the edge leading to Kostenki14. The blue lines indicate the edges showing ancestral components related to the Tianyuan individual and the Papuan in the Native American Surui. See also Figure S4 and Table S2. We also studied a model relating the Tianyuan individual to other ancient individuals and present-day populations using a base model including the Altai Neanderthal, Denisovan, Ust’-Ishim, and Kostenki14 from Mallick et al. [33]. We added the Tianyuan individual, Mal’ta1, and the present-day Ami, Mixe, Surui, and Papuan. Because present-day European populations have recent ancestry from an unknown Basal Eurasian population, we use Kostenki14, which has recently been shown to have no Basal Eurasian ancestry [4] to represent Europeans. We caution that our model (Figure 3D) is unlikely to reflect the true population relationships, as we cannot model many demographic features, such as population structure or continuous migration [11]. Intriguingly, however, within this simple model, we find that all three South American populations can be modeled as sharing ancestry not only with other Native Americans, but also with populations related to the Tianyuan individual and the Papuan (Figure 3D; Table S2I). The fact that the Tianyuan individual, who lived in mainland Asia about 40,000 years ago, has affinities to some South American populations that is as strong as or stronger than that observed for the Papuan and Onge suggests that a population related to the Tianyuan individual, as well as to the present-day Papuan and Onge, was once widespread in eastern Asia. This group or another Asian population related to this group persisted at least until the colonization of the Americas and contributed to the genomes of some Native American populations. We show that the Tianyuan individual is more closely related to ancient and present-day East and Southeast Asians than to either ancient or present-day Europeans. To test whether he is from a population that is directly ancestral to any present-day East or Southeast Asians, we modified the test of direct ancestry described in Rasmussen et al. [32] to account for low-coverage sequence data, contamination, and sequencing error. We find that that the Tianyuan individual is not from a population that is directly ancestral to any group of present-day East or Southeast Asians (c > 0, c = 0 rejected with p < 0.00001 for every comparison in Table 1), but rather belonged to a population that diverged from the population that contributed to present-day East and Southeast Asians. This is consistent with his unique ties to the 35,000-year-old GoyetQ116-1 and to some South American populations, which are not observed in present-day East and Southeast Asians. Table 1. Maximum-Likelihood Test Determining whether the Tianyuan Individual Is Directly Ancestral to any Present-Day Population Population c k1 Han 0.1800 0.2809 Dai 0.1808 0.2812 Miao 0.1818 0.2814 Japanese 0.1819 0.2813 Ami 0.1822 0.2813 Burmese 0.1834 0.2817 Hezhen 0.1838 0.2817 Oroqen 0.1841 0.2821 Lahu 0.1864 0.2828 Igorot 0.1866 0.2830 Thai 0.1883 0.2833 Cambodian 0.1887 0.2834 Kusunda 0.1972 0.2859 Mayan 0.1973 0.2860 Papuan 0.1975 0.2855 Karitiana 0.1992 0.2866 Australian 0.2001 0.2867 Uygur 0.2143 0.2921 French 0.2420 0.3013 The Tianyuan individual is not from a population directly ancestral to any of the listed present-day populations (c ≠ 0, where c refers to the amount of private drift for the Tianyuan individual). See STAR Methods for a description of c and k1. See also Figure S3H. |
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