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Post by Admin on Dec 16, 2017 19:09:42 GMT
If you live outside of Africa, up to 4 percent of your early family tree might be made up of Neanderthal cousins. Residents of Pacific islands like Fiji have 5 percent Denisovan heritage on average. Denisovans are a hominin species discovered only nine years ago in research published in Nature. The authors of the new report argue that the key to unwrapping the human origin story is investigation beyond pure archaeology. “What we are seeing in the behavioral record is that the spread of so-called modern human behaviors did not occur in a simple time-transgressive process from west to east,” another of the report's authors, anthropologist Christopher Bae, writes. “Ecological variation needs to be considered in concert with behavioral variation between the different hominin populations." Katerina Douka, a researcher in archaeological science, and another of the report's authors, adds: "There have been an increasing number of multidisciplinary research programs launched in Asia over the past few decades. The information that is being reported is helping to fill in the gaps in the evolutionary records." The peopling of Asia In recent years, there has been increasing focus on the paleoanthropology of Asia, particularly the migration patterns of early modern humans as they spread out of Africa. Bae et al. review the current state of the Late Pleistocene Asian human evolutionary record from archaeology, hominin paleontology, geochronology, genetics, and paleoclimatology. They evaluate single versus multiple dispersal models and southern versus the northern dispersal routes across the Asian continent. They also review behavioral and environmental variability and how these may have affected modern human dispersals and interactions with indigenous populations. Structured Abstract BACKGROUND The earliest fossils of Homo sapiens are located in Africa and dated to the late Middle Pleistocene. At some point later, modern humans dispersed into Asia and reached the far-away locales of Europe, Australia, and eventually the Americas. Given that Neandertals, Denisovans, mid-Pleistocene Homo, and H. floresiensis were present in Asia before the appearance of modern humans, the timing and nature of the spread of modern humans across Eurasia continue to be subjects of intense debate. For instance, did modern humans replace the indigenous populations when moving into new regions? Alternatively, did population contact and interbreeding occur regularly? In terms of behavior, did technological innovations and symbolism facilitate dispersals of modern humans? For example, it is often assumed that only modern humans were capable of using watercraft and navigating to distant locations such as Australia and the Japanese archipelago—destinations that would not have been visible to the naked eye from the departure points, even during glacial stages when sea levels would have been much lower. Moreover, what role did major climatic fluctuations and environmental events (e.g., the Toba volcanic super-eruption) play in the dispersal of modern humans across Asia? Did extirpations of groups occur regularly, and did extinctions of populations take place? Questions such as these are paramount in understanding hominin evolution and Late Pleistocene Asian paleoanthropology. ADVANCES An increasing number of multidisciplinary field and laboratory projects focused on archaeological sites and fossil localities from different areas of Asia are producing important findings, allowing researchers to address key evolutionary questions that have long perplexed the field. For instance, technological advances have increased our ability to successfully collect ancient DNA from hominin fossils, providing proof that interbreeding occurred on a somewhat regular basis. New finds of H. sapiens fossils, with increasingly secure dating associations, are emerging in different areas of Asia, some seemingly from the first half of the Late Pleistocene. Cultural variability discerned from archaeological studies indicates that modern human behaviors did not simply spread across Asia in a time-transgressive pattern. This regional variation, which is particularly distinct in Southeast Asia, could be related at least in part to environmental and ecological variation (e.g., Palearctic versus Oriental biogeographic zones). OUTLOOK Recent findings from archaeology, hominin paleontology, geochronology, and genetics indicate that the strict “out of Africa” model, which posits that there was only a single dispersal into Eurasia at ~60,000 years ago, is in need of revision. In particular, a multiple-dispersal model, perhaps beginning at the advent of the Late Pleistocene, needs to be examined more closely. An increasingly robust record from Late Pleistocene Asian paleoanthropology is helping to build and establish new views about the origin and dispersal of modern humans.
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Post by Admin on Feb 5, 2018 18:41:01 GMT
The peopling of Asia In recent years, there has been increasing focus on the paleoanthropology of Asia, particularly the migration patterns of early modern humans as they spread out of Africa. Bae et al. review the current state of the Late Pleistocene Asian human evolutionary record from archaeology, hominin paleontology, geochronology, genetics, and paleoclimatology. They evaluate single versus multiple dispersal models and southern versus the northern dispersal routes across the Asian continent. They also review behavioral and environmental variability and how these may have affected modern human dispersals and interactions with indigenous populations. Science, this issue p. eaai9067 Structured Abstract BACKGROUND The earliest fossils of Homo sapiens are located in Africa and dated to the late Middle Pleistocene. At some point later, modern humans dispersed into Asia and reached the far-away locales of Europe, Australia, and eventually the Americas. Given that Neandertals, Denisovans, mid-Pleistocene Homo, and H. floresiensis were present in Asia before the appearance of modern humans, the timing and nature of the spread of modern humans across Eurasia continue to be subjects of intense debate. For instance, did modern humans replace the indigenous populations when moving into new regions? Alternatively, did population contact and interbreeding occur regularly? In terms of behavior, did technological innovations and symbolism facilitate dispersals of modern humans? For example, it is often assumed that only modern humans were capable of using watercraft and navigating to distant locations such as Australia and the Japanese archipelago—destinations that would not have been visible to the naked eye from the departure points, even during glacial stages when sea levels would have been much lower. Moreover, what role did major climatic fluctuations and environmental events (e.g., the Toba volcanic super-eruption) play in the dispersal of modern humans across Asia? Did extirpations of groups occur regularly, and did extinctions of populations take place? Questions such as these are paramount in understanding hominin evolution and Late Pleistocene Asian paleoanthropology. ADVANCES An increasing number of multidisciplinary field and laboratory projects focused on archaeological sites and fossil localities from different areas of Asia are producing important findings, allowing researchers to address key evolutionary questions that have long perplexed the field. For instance, technological advances have increased our ability to successfully collect ancient DNA from hominin fossils, providing proof that interbreeding occurred on a somewhat regular basis. New finds of H. sapiens fossils, with increasingly secure dating associations, are emerging in different areas of Asia, some seemingly from the first half of the Late Pleistocene. Cultural variability discerned from archaeological studies indicates that modern human behaviors did not simply spread across Asia in a time-transgressive pattern. This regional variation, which is particularly distinct in Southeast Asia, could be related at least in part to environmental and ecological variation (e.g., Palearctic versus Oriental biogeographic zones). OUTLOOK Recent findings from archaeology, hominin paleontology, geochronology, and genetics indicate that the strict “out of Africa” model, which posits that there was only a single dispersal into Eurasia at ~60,000 years ago, is in need of revision. In particular, a multiple-dispersal model, perhaps beginning at the advent of the Late Pleistocene, needs to be examined more closely. An increasingly robust record from Late Pleistocene Asian paleoanthropology is helping to build and establish new views about the origin and dispersal of modern humans. Abstract The traditional “out of Africa” model, which posits a dispersal of modern Homo sapiens across Eurasia as a single wave at ~60,000 years ago and the subsequent replacement of all indigenous populations, is in need of revision. Recent discoveries from archaeology, hominin paleontology, geochronology, genetics, and paleoenvironmental studies have contributed to a better understanding of the Late Pleistocene record in Asia. Important findings highlighted here include growing evidence for multiple dispersals predating 60,000 years ago in regions such as southern and eastern Asia. Modern humans moving into Asia met Neandertals, Denisovans, mid-Pleistocene Homo, and possibly H. floresiensis, with some degree of interbreeding occurring. These early human dispersals, which left at least some genetic traces in modern populations, indicate that later replacements were not wholesale. Science 08 Dec 2017: Vol. 358, Issue 6368, eaai9067
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Post by Admin on Jul 13, 2018 18:38:14 GMT
This long excursion—once thought only to have been attempted late in the journey of humankind—has been getting pushed further and further back in time thanks to advancing archaeological research. Findings published in Nature have extended the start of our worldwide trekking back to beyond 2.1 million years ago. Previously, we knew that people were wandering around eastern Europe by 1.85 million years ago, as their bones and tools were discovered at a cave site called Dmanisi in Georgia. Presented in the new paper, evidence for this earlier—and further—human movement comes in the form of flaked stone tools found in sediments at Shangchen, in the southern Chinese Loess Plateau. An onslaught of recent findings from Asia has prompted some researchers to suggest that humans came “Out of Asia.” However, while it appears that people were in this region very early, humanity remains an African invention. Our earliest ancestors arose in Africa some 6 million years ago, although the earliest remains of those belonging to our branch of the family tree—that of Homo—only date back to 2.8 million years ago. A single jawbone found in Ethiopia pushed back the origins of our genus some 400,000 years.
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Post by Admin on Sept 12, 2018 18:16:17 GMT
Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this variation can provide insights into evolutionary processes that shape both human adaptation and variation in disease susceptibility1. Although the Hapmap Project2 and the 1000 Genomes Project3 have greatly enhanced our understanding of genetic variation globally, the characterization of African populations remains limited. Other efforts examining African genetic diversity have been limited by variant density and sample sizes in individual populations4, or have focused on isolated groups, such as hunter gatherers (HG)5,6, limiting relevance to more widespread populations across Africa. The African Genome Variation Project (AGVP) is an international collaboration that expands on these efforts by systematically assessing genetic diversity among 1,481 individuals from 18 ethno-linguistic groups from sub-Saharan Africa (SSA) (Fig. 1 and Supplementary Methods Tables 1 and 2) with the HumanOmni2.5M genotyping array and whole-genome sequences (WGS) from 320 individuals (Supplementary Methods Table 2). Importantly, the AGVP has evolved to help develop local resources for public health and genomic research, including strengthening research capacity, training, and collaboration across the region. We envisage that data from this project will provide a global resource for researchers, as well as facilitate genetic studies in Africa7. Figure 1: Populations studied in the AGVP. a, 18 African populations studied in the AGVP including 2 populations from the 1000 Genomes Project. (The term ‘Ethiopia’ encompasses the Oromo, Amhara and Somali ethno-linguistic groups.) b, c, ADMIXTURE analysis of these 18 populations alone (n = 1,481) (b) and in a global context (n = 3,904) (c). Each colour represents a different ancestral cluster, with clusters 2–6 represented along the y-axis in b and clusters 2–18 represented in c. K = 6 and K = 18 were the most likely clusters on ADMIXTURE analysis. ADMIXTURE analysis suggests substructure between North, East, West and South Africa. Studying these populations in the context of Eurasian and African HG populations suggest extensive Eurasian and HG admixture across Africa. On examining ∼2.2 million variants, we found modest differentiation among SSA populations (mean pairwise FST 0.019) (Supplementary Methods and Supplementary Table 1). Differentiation among the Niger-Congo language groups—the predominant linguistic grouping across Africa was noted to be modest (mean pairwise FST 0.009) (Supplementary Table 1), providing evidence for the ‘Bantu expansion’—a recent population expansion and movement throughout SSA originating in West Africa around 3,000 to 5,000 years ago8. We identified 29.8 million single-nucleotide polymorphisms (SNPs) from Ethiopian, Zulu and Bagandan WGS (Extended Data Fig. 1 and Supplementary Methods). A substantial proportion of unshared (11%–23%) and novel (16%–24%) variants were observed, with the highest proportion among Ethiopian populations (Extended Data Fig. 1). The high proportion of unshared variation among populations recapitulates the need for large-scale sequencing across Africa, including among genetically divergent populations. We used principal component analysis to explore relationships among AGVP populations (Extended Data Figs 2, 3, 4, 5, Supplementary Figs 1 and 2). PC1 appeared to represent a cline extending from West and East African populations towards Ethiopian populations, possibly suggesting Eurasian gene flow, while PC2 separated West African and South/East African populations (Extended Data Fig. 2). Inclusion of the 1000 Genomes Project, North African and Khoe-San (Khoisan) populations in principal component analysis (Extended Data Figs 3, 4, 5, and Supplementary Figs 1 and 2) suggested possible HG ancestry among southern Niger-Congo groups—highlighted by clustering towards the Khoe-San, in addition to confirming a cline towards Eurasian populations. ‘Unsupervised’ (that is, without including known information on individual ancestry) ADMIXTURE9 (https://www.genetics.ucla.edu/software/admixture/) analysis including the 1000 Genomes Project and Human Origins data sets (Fig. 1), also supported evidence for substantial Eurasian and HG ancestry in SSA (Fig. 1 and Extended Data Fig. 6).
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Post by Admin on Sept 15, 2018 19:07:50 GMT
To assess the effect of gene flow on population differentiation in SSA, we masked Eurasian ancestry across the genome (Supplementary Methods and Supplementary Note 6). This markedly reduced population differentiation, as measured by a decline in mean pairwise FST from 0.021 to 0.015 (Supplementary Note 6), suggests that Eurasian ancestry has a substantial impact on differentiation among SSA populations. We speculate that residual differentiation between Ethiopian and other SSA populations after masking Eurasian ancestry (pairwise FST = 0.027) may be a remnant of East African diversity pre-dating the Bantu expansion10. Figure 2: Dating and proportion of Eurasian and HG admixture among African populations. Population admixture in SSA Formal tests for admixture (the three population test or f3 statistic)11, confirmed widespread Eurasian and HG admixture in SSA (Supplementary Tables 2 and 3). Quantification of admixture (Supplementary Table 4, Supplementary Methods and Supplementary Notes 3 and 4) indicated substantial Eurasian ancestry in many African populations (ranging from 0% to 50%), with the greatest proportion in East Africa (Fig. 2 and Supplementary Table 4). Similarly, HG admixture ranged from 0% to 23%, being greatest among Zulu and Sotho (Fig. 2 and Supplementary Table 5). We found evidence for historically complex and regionally distinct admixture with multiple HG and Eurasian populations across SSA (Fig. 2 and Supplementary Note 5). Specifically, ancient Eurasian admixture was observed in central West African populations (Yoruba; ∼7,500–10,500 years ago), old admixture among Ethiopian populations (∼2,400–3,200 years ago) consistent with previous reports10,12, and more recent complex admixture in some East African populations (∼150–1,500 years ago) (Fig. 2, Extended Data Fig. 7 and Supplementary Note 5). Our finding of ancient Eurasian admixture corroborates findings of non-zero Neanderthal ancestry in Yoruba, which is likely to have been introduced through Eurasian admixture and back migration, possibly facilitated by greening of the Sahara desert during this period13,14. We also find evidence for complex and regionally distinct HG admixture across SSA (Fig. 2, Extended Data Figs 7 and Supplementary Note 5), with ancient gene flow (∼9,000 years ago) among Igbo and more recent admixture in East and South Africa (multiple events ranging from 100 years ago to 3,000 years ago), broadly consistent with historical movements reflecting the Bantu expansion. An exploration of the likeliest sources of admixture in our data suggested that HG admixture in Igbo was most closely represented by modern day Khoe-San populations rather than by rainforest HG populations (Supplementary Note 5). Given limited archaeological and linguistic evidence for the presence of Khoe-San populations in West Africa, this extant HG admixture might represent ancient populations, consistent with the presence of mass HG graves from the early Holocene period comprising skeletons with distinct morphological features15, and with evidence of HG rock art dating to this period in the western Sahara16,17. In East Africa, our analyses suggested that Mbuti rainforest HG populations most closely represented ancient HG mixing populations (Supplementary Note 5), with admixture dating to ∼3,000 years ago, suggesting that HG ancestry here is likely to be older than previously reported18. The primary source of HG admixture in Zulu and Sotho populations was from Khoe-San populations (Fig. 2 and Supplementary Note 5), consistent with linguistic assimilation of click consonants among these populations.
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