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Matsumura H, Friess M, Kouchi M, Tanijiri T, Stringer C, Garcia G, Hanihara T, Moiseyev V, Suzuki D. Bioclimatic and masticatory influences on human cranial diversity verified by analysis of 3D morphometric homologous models. Sci Rep 2024; 14:26663. [PMID: 39496664 PMCID: PMC11535542 DOI: 10.1038/s41598-024-76715-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Accepted: 10/16/2024] [Indexed: 11/06/2024] Open
Abstract
This study analyzes the effects of bioclimate and masticatory factors on the regional variability of human cranial forms across 150 ethnic groups worldwide. Morphometric variables were generated using principal component analysis applied to 3D homologous models. Relationships between cranial form and bioclimate (temperature and precipitation) and masticatory factors (infratemporal space) were tested considering sampling bias due to past population movements during the late Pleistocene and/or early- to mid-Holocene. Cranial size correlated with thermal conditions, consistent with Bergmann's rule. The length/breadth proportion of the neurocranium aligned with Allen's rule for thermal adaptation, while no relationship with masticatory stress was found. Facial form responded to either climate or masticatory conditions, although the primary factor was unclear due to the high correlation between stresses. However, masticatory stress was identified as an equally significant factor behind facial flatness in cold regions, else than the effect of Allen's rule. High narrowness of nasal and orbital openings correlated significantly with cold temperatures and cranial size, suggesting not only functional but also allometric effect. This study demonstrated the complexity of environmental influences on cranial form diversity, nonetheless suggested reduction of selective pressure on cranial form caused by natural environmental stress due to the development of civilization.
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Affiliation(s)
- Hirofumi Matsumura
- School of Health Sciences, Sapporo Medical University, Sapporo, 060-8556, Japan.
| | - Martin Friess
- Département Homme et Environnement, Musée de l'Homme, Paris, 75116, France
| | - Makiko Kouchi
- National Institute of Advanced Industrial Science and Technology, Tokyo, 135-0064, Japan
| | | | - Chris Stringer
- Department of Earth Sciences, The Natural History Museum, London, SW7 5BD, UK
| | - Gisselle Garcia
- Department of Anthropology, American Museum of Natural History, New York, NY, 10024, USA
| | | | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography, Russian Federation, St Petersburg, 199034, Russia
| | - Daisuke Suzuki
- Department of Health Sciences, Hokkaido Chitose College of Rehabilitation, Chitose, 066-0055, Japan
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2
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Sekhavati Y, Strait D. Estimating ancestral ranges and biogeographical processes in early hominins. J Hum Evol 2024; 191:103547. [PMID: 38781711 DOI: 10.1016/j.jhevol.2024.103547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 05/05/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024]
Abstract
Historical biogeography provides crucial insights into understanding the evolutionary history of hominins. We applied maximum-likelihood and biogeographical stochastic mapping to infer the ancestral ranges of hominins and estimate the frequency of biogeographical events. These events were inferred using two time-calibrated phylogenetic trees that differ in the position of Australopithecus sediba. Results suggest that regardless of which phylogeny was selected, Northcentral Africa was the preferred ancestral region for the ancestor of the Homo-Pan clade, as well as the ancestor of Sahelanthropus and later hominins. The northern and middle part of eastern Africa was the preferred ancestral region for several clades originating at subsequent deep nodes of the trees (∼5-4 Ma). The choice of tree topology had one important effect on results: whether hominin ancestors appearing after ∼4 Ma were widespread or endemic. These different patterns highlight the biogeographic significance of the phylogenetic relationships of A. sediba. Overall, the results showed that dispersal, local extinction, and sympatry played vital roles in creating the hominin distribution, whereas vicariance and jump dispersal were not as common. The results suggested symmetry in the directionality of dispersals. Distance probably influenced how rapidly taxa colonized a new region, and dispersals often followed the closest path. These findings are potentially impacted by the imperfection of the fossil record, suggesting that the results should be interpreted cautiously.
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Affiliation(s)
- Yeganeh Sekhavati
- Department of Anthropology, Washington University in St. Louis, St. Louis, MO 63130, USA.
| | - David Strait
- Department of Anthropology, Washington University in St. Louis, St. Louis, MO 63130, USA; Palaeo-Research Institute, University of Johannesburg, Cnr Kingsway and University Road Auckland Park, PO Box 524, Auckland Park 2006, South Africa
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3
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Foley RA, Mirazón Lahr M. Ghosts of extinct apes: genomic insights into African hominid evolution. Trends Ecol Evol 2024; 39:456-466. [PMID: 38302324 DOI: 10.1016/j.tree.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 12/13/2023] [Accepted: 12/22/2023] [Indexed: 02/03/2024]
Abstract
We are accustomed to regular announcements of new hominin fossils. There are now some 6000 hominin fossils, and up to 31 species. However, where are the announcements of African ape fossils? The answer is that there are almost none. Our knowledge of African ape evolution is based entirely on genomic analyses, which show that extant diversity is very young. This contrasts with the extensive and deep diversity of hominins known from fossils. Does this difference point to low and late diversification of ape lineages, or high rates of extinction? The comparative evolutionary dynamics of African hominids are central to interpreting living ape adaptations, as well as understanding the patterns of hominin evolution and the nature of the last common ancestor.
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Affiliation(s)
- Robert A Foley
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, The Henry Wellcome Building, Fitzwilliam Street, Cambridge, CB2 1QH, UK.
| | - Marta Mirazón Lahr
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, The Henry Wellcome Building, Fitzwilliam Street, Cambridge, CB2 1QH, UK
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4
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Padilla-Iglesias C, Derkx I. Hunter-gatherer genetics research: Importance and avenues. EVOLUTIONARY HUMAN SCIENCES 2024; 6:e15. [PMID: 38516374 PMCID: PMC10955370 DOI: 10.1017/ehs.2024.7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 01/17/2024] [Accepted: 02/02/2024] [Indexed: 03/23/2024] Open
Abstract
Major developments in the field of genetics in the past few decades have revolutionised notions of what it means to be human. Although currently only a few populations around the world practise a hunting and gathering lifestyle, this mode of subsistence has characterised members of our species since its very origins and allowed us to migrate across the planet. Therefore, the geographical distribution of hunter-gatherer populations, dependence on local ecosystems and connections to past populations and neighbouring groups have provided unique insights into our evolutionary origins. However, given the vulnerable status of hunter-gatherers worldwide, the development of the field of anthropological genetics requires that we reevaluate how we conduct research with these communities. Here, we review how the inclusion of hunter-gatherer populations in genetics studies has advanced our understanding of human origins, ancient population migrations and interactions as well as phenotypic adaptations and adaptability to different environments, and the important scientific and medical applications of these advancements. At the same time, we highlight the necessity to address yet unresolved questions and identify areas in which the field may benefit from improvements.
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Affiliation(s)
| | - Inez Derkx
- Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
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Peyrégne S, Slon V, Kelso J. More than a decade of genetic research on the Denisovans. Nat Rev Genet 2024; 25:83-103. [PMID: 37723347 DOI: 10.1038/s41576-023-00643-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2023] [Indexed: 09/20/2023]
Abstract
Denisovans, a group of now extinct humans who lived in Eastern Eurasia in the Middle and Late Pleistocene, were first identified from DNA sequences just over a decade ago. Only ten fragmentary remains from two sites have been attributed to Denisovans based entirely on molecular information. Nevertheless, there has been great interest in using genetic data to understand Denisovans and their place in human history. From the reconstruction of a single high-quality genome, it has been possible to infer their population history, including events of admixture with other human groups. Additionally, the identification of Denisovan DNA in the genomes of present-day individuals has provided insights into the timing and routes of dispersal of ancient modern humans into Asia and Oceania, as well as the contributions of archaic DNA to the physiology of present-day people. In this Review, we synthesize more than a decade of research on Denisovans, reconcile controversies and summarize insights into their population history and phenotype. We also highlight how our growing knowledge about Denisovans has provided insights into our own evolutionary history.
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Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Viviane Slon
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anatomy and Anthropology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, Tel Aviv, Israel
| | - Janet Kelso
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
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6
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Rybin EP, Belousova NE, Derevianko AP, Douka K, Higham T. The Initial Upper Paleolithic of the Altai: New radiocarbon determinations for the Kara-Bom site. J Hum Evol 2023; 185:103453. [PMID: 37931353 DOI: 10.1016/j.jhevol.2023.103453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 11/08/2023]
Abstract
The Initial Upper Paleolithic (IUP) is one of the most important phases in the recent period of the evolution of humans. During a narrow period in the first half of Marine Isotope Stage 3 laminar industries, accompanied by developed symbolism and specific blade technology, emerged over a vast area, replacing different variants of the Middle Paleolithic. In western Eurasia, the earliest appearance of IUP technology is seen at the Boker Tachtit site, dated ca. 50 ka cal BP. The earliest evidence of IUP industries in the Balkans and Central Europe, linked to the spread of Homo sapiens, has been dated to around 48 ka cal BP. A key area of IUP dispersals are the mountains and piedmont of southern Siberia and eastern Central Asia. One of the reference assemblages here is Kara-Bom, an open-air site in the Siberian Altai. Three major settlement phases are distinguished in the sediment sequence. In this paper, we present the results of new radiocarbon determinations and Bayesian models. We find that the latest phase of the IUP, Upper Paleolithic 1 ('UP1') is bracketed between 43 and 35 ka cal BP (at 95.4% probability). The earliest IUP phase, 'UP2', begins to accumulate from ca. 49 ka cal BP and ends by ca. 45 ka cal BP. The Middle Paleolithic 'MP2' assemblages all fall prior to 50 ka cal BP. We can detect a spatial distribution of dates from the geographic core of the IUP beyond the Altai where it appears around 47-45 ka cal BP. The current distribution of dates suggests a west-east dispersal of the IUP technocomplex along the mountain belts of Central Asia and South Siberia.
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Affiliation(s)
- Evgeny P Rybin
- Institute of Archaeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences (IAET SB RAS): 17, Acad. Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Natalia E Belousova
- Institute of Archaeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences (IAET SB RAS): 17, Acad. Lavrentiev Avenue, Novosibirsk 630090, Russia.
| | - Anatoly P Derevianko
- Institute of Archaeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences (IAET SB RAS): 17, Acad. Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Katerina Douka
- Department of Evolutionary Anthropology, Faculty of Life Sciences, Djerassiplatz 1, University of Vienna, Vienna 1030, Austria; Human Evolution and Archaeological Sciences (HEAS), University of Vienna 1030 Vienna, Austria
| | - Tom Higham
- Department of Evolutionary Anthropology, Faculty of Life Sciences, Djerassiplatz 1, University of Vienna, Vienna 1030, Austria; Human Evolution and Archaeological Sciences (HEAS), University of Vienna 1030 Vienna, Austria.
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7
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Matsumura H, Tanijiri T, Kouchi M, Hanihara T, Friess M, Moiseyev V, Stringer C, Miyahara K. Global patterns of the cranial form of modern human populations described by analysis of a 3D surface homologous model. Sci Rep 2022; 12:13826. [PMID: 35970916 PMCID: PMC9378707 DOI: 10.1038/s41598-022-15883-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 06/30/2022] [Indexed: 11/09/2022] Open
Abstract
This study assessed the regional diversity of the human cranial form by using geometric homologous models based on scanned data from 148 ethnic groups worldwide. This method adopted a template-fitting technique for a nonrigid transformation via the iterative closest point algorithm to generate the homologous meshes. Through the application of principal component analysis to 342 sampled homologous models, the largest variation was detected in overall size, and small South Asian crania were clearly verified. The next greatest diversity was found in the length/breadth proportion of the neurocranium, which showed the contrast between the elongated crania of Africans and the globular crania of Northeast Asians. Notably, this component was slightly correlated with the facial profile. Well-known facial features, such as the forward projection of the cheek among Northeast Asians and compaction of the European maxilla, were reconfirmed. These facial variations were highly correlated with the calvarial outline, particularly the degree of frontal and occipital inclines. An allometric pattern was detected in facial proportions in relation to overall cranial size; in larger crania, the facial profiles tend to be longer and narrower, as demonstrated among many American natives and Northeast Asians. Although our study did not include data on environmental variables that are likely to affect cranial morphology, such as climate or dietary conditions, the large datasets of homologous cranial models will be usefully available for seeking various attributions to phenotypic skeletal characteristics.
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Affiliation(s)
- Hirofumi Matsumura
- School of Health Sciences, Sapporo Medical University, Sapporo, 060-8556, Japan.
| | | | - Makiko Kouchi
- National Institute of Advanced Industrial Science and Technology, Tokyo, 135-0064, Japan
| | | | - Martin Friess
- Département Homme et Environnement, Musée de l'Homme, 75116, Paris, France
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, St Petersburg, 199034, Russia
| | - Chris Stringer
- Department of Earth Sciences, The Natural History Museum, London, SW7 5BD, UK
| | - Kengo Miyahara
- Kyoto City Archeological Research Institute, Kyoto, 602-8435, Japan
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8
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Bukhari W, Khalilidehkordi E, Mason DF, Barnett MH, Taylor BV, Fabis-Pedrini M, Kermode AG, Subramanian S, Waters P, Broadley SA. NMOSD and MS prevalence in the Indigenous populations of Australia and New Zealand. J Neurol 2022; 269:836-845. [PMID: 34213614 DOI: 10.1007/s00415-021-10665-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/06/2021] [Accepted: 06/14/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND We studied the prevalence of neuromyelitis optica spectrum disorder (NMOSD) and multiple sclerosis (MS) in Indigenous populations of Australia and New Zealand with the aim of assessing potential differences. METHODS Cases of possible NMOSD and MS were collected from Australia and New Zealand. Clinical details, MR imaging, and serologic results were used to apply 2015 IPND diagnostic criteria for NMOSD and 2010 McDonald criteria for MS. Frequencies of self-determined ethnic ancestry were calculated for confirmed NMOSD, suspected NMOSD, and MS. Prevalence rates for NMOSD and MS according to ancestry were compared. RESULTS There were 75 cases with NMOSD, 89 with suspected NMSOD, and 101 with MS. NMOSD cases were more likely to have Asian, Indigenous, or Other ancestry compared to suspected NMOSD or MS. There were no differences in the clinical phenotype of NMOSD seen in Indigenous compared to European ancestry populations. Per 100,000, the prevalence estimate for NMOSD in people with Māori ancestry was 1.50 (95% CI 0.52-2.49) which was similar to those with Asian ancestry 1.57 (95% CI 1.15-1.98). NMOSD prevalence in Australian Aboriginal and Torres Strait Islander populations was 0.38 (95% CI 0.00-0.80) per 100,000. CONCLUSION The prevalence of NMOSD in the Māori population is similar to South East Asian countries, reflecting their historical origins. The prevalence of MS in this group is intermediate between those with South East Asian and European ancestry living in New Zealand. Both NMOSD and particularly MS appear to be uncommon in the Indigenous populations of Australia.
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Affiliation(s)
- Wajih Bukhari
- Menzies Health Institute Queensland, School of Medicine, Griffith University, Gold Coast Campus, Brisbane, QLD, 4222, Australia
| | - Elham Khalilidehkordi
- Menzies Health Institute Queensland, School of Medicine, Griffith University, Gold Coast Campus, Brisbane, QLD, 4222, Australia
- Department of Neurology, Gold Coast University Hospital, Southport, QLD, 4215, Australia
| | - Deborah F Mason
- New Zealand Brain Research Institute, Christchurch, 8011, New Zealand
- Department of Medicine, University of Otago, Christchurch, 8011, New Zealand
- Department of Neurology, Canterbury District Health Board, Christchurch, 8041, New Zealand
| | - Michael H Barnett
- Brain and Mind Centre, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Bruce V Taylor
- Menzies Institute for Medical Research, University of Tasmania,, Hobart, TAS, 7000, Australia
- Department of Neurology, Royal Hobart Hospital, Hobart, TAS, 7000, Australia
| | | | - Allan G Kermode
- Peron Institute, University of Western Australia, Nedlands, WA, 6009, Australia
- Institute of Immunology and Infectious Diseases, Murdoch University, Perth, WA, 6150, Australia
| | - Sankar Subramanian
- GeneCology Research Centre, University of Sunshine Coast, Sippy Downs, QLD, 4556, Australia
| | - Patrick Waters
- Nuffield Department of Clinical Neurosciences, John Radcliffe Infirmary, University of Oxford, Oxford, OX3 9DU, UK
| | - Simon A Broadley
- Menzies Health Institute Queensland, School of Medicine, Griffith University, Gold Coast Campus, Brisbane, QLD, 4222, Australia.
- Department of Neurology, Gold Coast University Hospital, Southport, QLD, 4215, Australia.
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9
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Gellis J, Foley R. A novel system for classifying tooth root phenotypes. PLoS One 2021; 16:e0251953. [PMID: 34739489 PMCID: PMC8570528 DOI: 10.1371/journal.pone.0251953] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/16/2021] [Indexed: 11/19/2022] Open
Abstract
Human root and canal number and morphology are highly variable, and internal root canal form and count does not necessarily co-vary directly with external morphology. While several typologies and classifications have been developed to address individual components of teeth, there is a need for a comprehensive system, that captures internal and external root features across all teeth. Using CT scans, the external and internal root morphologies of a global sample of humans are analysed (n = 945). From this analysis a method of classification that captures external and internal root morphology in a way that is intuitive, reproducible, and defines the human phenotypic set is developed. Results provide a robust definition of modern human tooth root phenotypic diversity. The method is modular in nature, allowing for incorporation of past and future classification systems. Additionally, it provides a basis for analysing hominin root morphology in evolutionary, ecological, genetic, and developmental contexts.
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Affiliation(s)
- Jason Gellis
- Department of Archaeology, The Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge, England
| | - Robert Foley
- Department of Archaeology, The Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge, England
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10
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Matsumura H, Xie G, Nguyen LC, Hanihara T, Li Z, Nguyen KTK, Ho XT, Nguyen TN, Huang SC, Hung HC. Female craniometrics support the 'two-layer model' of human dispersal in Eastern Eurasia. Sci Rep 2021; 11:20830. [PMID: 34675295 PMCID: PMC8531373 DOI: 10.1038/s41598-021-00295-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/07/2021] [Indexed: 11/24/2022] Open
Abstract
This study reports a cranio-morphometric analysis of female human remains from seven archaeological sites in China, Vietnam and Taiwan that date between 16,000 and 5300 BP. The aim of the analysis is to test the “two-layer” model of human dispersal in eastern Eurasia, using previously unanalysed female remains to balance the large sample of previously-analysed males. The resulting craniometric data indicate that the examined specimens all belong to the “first layer” of dispersal, and share a common ancestor with recent Australian and Papuan populations, and the ancient Jomon people of Japan. The analysed specimens pre-date the expansion of agricultural populations of East/Northeast Asian origin—that is, the “second layer” of human dispersal proposed by the model. As a result of this study, the two-layer model, which has hitherto rested on evidence only from male skeletons, is now strongly supported by female-derived data. Further comparisons reveal that the people of the first layer were closer in terms of their facial morphology to modern Africans and Sri Lankan Veddah than to modern Asians and Europeans, suggesting that the Late Pleistocene through Middle Holocene hunter-gatherers examined in this study were direct descendants of the anatomically modern humans who first migrated out of Africa through southern Eurasia.
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Affiliation(s)
- Hirofumi Matsumura
- School of Health Science, Sapporo Medical University, Sapporo, Hokkaido, Japan.
| | - Guangmao Xie
- Guangxi Institute of Cultural Relic Protection and Archaeology, Nanning, Guangxi, China. .,College of History, Culture and Tourism, Guangxi Normal University, Guilin, Guangxi, China.
| | - Lan Cuong Nguyen
- Institute of Archaeology, Vietnam Academy of Social Science, Hanoi, Vietnam
| | - Tsunehiko Hanihara
- Department of Anatomy, School of Medicine, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Zhen Li
- Guangxi Institute of Cultural Relic Protection and Archaeology, Nanning, Guangxi, China
| | - Khanh Trung Kien Nguyen
- Southern Institute of Social Sciences, Vietnam Academy of Social Science, Ho Chi Minh City, Vietnam
| | - Xuan Tinh Ho
- Department of Culture, Sports and Tourism of Quang Nam, Tam Kỳ, Quang Nam, Vietnam
| | | | - Shih-Chiang Huang
- Department of Anthropology, National Taiwan University, Taipei, Taiwan, ROC
| | - Hsiao-Chun Hung
- Department of Archaeology and Natural History, Australian National University, Canberra, Australia.
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11
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Liu Y, Wang T, Wu X, Fan X, Wang W, Xie G, Li Z, Yang Q, Cao P, Yang R, Liu F, Dai Q, Feng X, Ping W, Miao B, Wu Y, Liu Y, Fu Q. Maternal genetic history of southern East Asians over the past 12,000 years. J Genet Genomics 2021; 48:899-907. [PMID: 34419425 DOI: 10.1016/j.jgg.2021.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/04/2021] [Accepted: 06/05/2021] [Indexed: 12/13/2022]
Abstract
Southern East Asia, including Guangxi and Fujian provinces in China, is home to diverse ethnic groups, languages, and cultures. Previous studies suggest a high complexity regarding population dynamics and the history of southern East Asians. However, large-scale genetic studies on ancient populations in this region are hindered by limited sample preservation. Here, using highly efficient DNA capture techniques, we obtain 48 complete mitochondrial genomes of individuals from Guangxi and Fujian in China and reconstruct their maternal genetic history over the past 12,000 years. We find a strong connection between southern East Asians dating to ~12,000-6000 years ago and present-day Southeast Asians. In addition, stronger genetic affinities to northern East Asians are observed in historical southern East Asians than Neolithic southern East Asians, suggesting increased interactions between northern and southern East Asians over time. Overall, we reveal dynamic connections between ancient southern East Asians and populations located in surrounding regions, as well as a shift in maternal genetic structure within the populations over time.
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Affiliation(s)
- Yalin Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Sino-Danish Center, University of the Chinese Academy of Sciences, Beijing 100049, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Tianyi Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; University of the Chinese Academy of Sciences, Beijing 100049, China; Northwest University, Xi'an 710069, China
| | - Xichao Wu
- Fujian Longyan Museum, Longyan 364000, China
| | - Xuechun Fan
- International Research Center for Austronesian Archaeology, Pingtan 350000, China; Fujian Museum, Fuzhou 350001, China
| | - Wei Wang
- Institute of Cultural Heritage, Shandong University, Qingdao 266237, China
| | - Guangmao Xie
- Guangxi Institute of Cultural Relic Protection and Archaeology, Nanning 530022, China; College of History, Culture and Tourism, Guangxi Normal University, Guilin 541001, China
| | - Zhen Li
- Guangxi Institute of Cultural Relic Protection and Archaeology, Nanning 530022, China
| | - Qingping Yang
- Guangxi Institute of Cultural Relic Protection and Archaeology, Nanning 530022, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Ruowei Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Wanjing Ping
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Bo Miao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Northwest University, Xi'an 710069, China
| | - Yun Wu
- Yunnan Institute of Cultural Relics and Archaeology, Kunming 650118, China; Archaeological Institute for Yangtze Civilization, Wuhan University, Wuhan 430072, China
| | - Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China.
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; University of the Chinese Academy of Sciences, Beijing 100049, China.
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12
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Rowold DJ, Chennakrishnaiah S, Gayden T, Luis JR, Alfonso-Sanchez MA, Bukhari A, Garcia-Bertrand R, Herrera RJ. The Y-chromosome of the Soliga, an ancient forest-dwelling tribe of South India. Gene 2021; 763S:100026. [PMID: 32550553 PMCID: PMC7286085 DOI: 10.1016/j.gene.2019.100026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 12/03/2019] [Accepted: 12/17/2019] [Indexed: 11/05/2022]
Abstract
A previous autosomal STR study provided evidence of a connection between the ancient Soliga tribe at the southern tip of the Indian subcontinent and Australian aboriginal populations, possibly reflecting an eastbound coastal migration circa (15 Kya). The Soliga are considered to be among India's earliest inhabitants. In this investigation, we focus on the Y chromosomal characteristics shared between the Soliga population and other Indian tribes as well as western Eurasia and Sub-Saharan Africa groups. Some noteworthy findings of this present analysis include the following: The three most frequent haplogroups detected in the Soliga population are F*, H1 and J2. F*, the oldest (43 to 63 Kya), has a significant frequency bias in favor of Indian tribes versus castes. This observation coupled with the fact that Y-STR haplotypes shared with sub-Saharan African populations are found only in F* males of the Soliga, Irula and Kurumba may indicate a unique genetic connection between these Indian tribes and sub-Saharan Africans. In addition, our study suggests that haplogroup H is confined mostly to South Asia and immediate neighbors and the H1 network may indicate minimal sharing of Y-STR haplotypes among South Asian collections, tribal and otherwise. Also, J2, brought into India by Neolithic farmers, is present at a significantly higher frequency in caste versus tribal communities. This last observation may reflect the marginalization of Indian tribes to isolated regions not ideal for agriculture. Hg F*, H1 and J2 of the Soliga population chronicle the demographic history of the Indian tribal communities. Frequency bias for F* in Indian tribes may be a result of genetic drift due isolation and low population growth. Sharing of Y-STR haplotypes among tribal populations may be indicative of a common source population.
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Affiliation(s)
- Diane J Rowold
- Foundation for Applied Molecular Science (FfAME), Gainesville, FL 32601, USA; Department of Pediatrics, Nicklaus Children's Hospital, Miami, FL, USA
| | | | - Tenzin Gayden
- Department of Human Genetics, McGill University, Montreal, Canada
| | | | - Miguel A Alfonso-Sanchez
- Departamento de Genética y Antropología Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Bilbao, Spain
| | - Areej Bukhari
- Departamento de Genética y Antropología Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Bilbao, Spain
| | | | - Rene J Herrera
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, USA
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13
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Ferreira JC, Alshamali F, Montinaro F, Cavadas B, Torroni A, Pereira L, Raveane A, Fernandes V. Projecting Ancient Ancestry in Modern-Day Arabians and Iranians: A Key Role of the Past Exposed Arabo-Persian Gulf on Human Migrations. Genome Biol Evol 2021; 13:6364187. [PMID: 34480555 PMCID: PMC8435661 DOI: 10.1093/gbe/evab194] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
The Arabian Peninsula is strategic for investigations centered on the early structuring of modern humans in the wake of the out-of-Africa migration. Despite its poor climatic conditions for the recovery of ancient human DNA evidence, the availability of both genomic data from neighboring ancient specimens and informative statistical tools allow modeling the ancestry of local modern populations. We applied this approach to a data set of 741,000 variants screened in 291 Arabians and 78 Iranians, and obtained insightful evidence. The west-east axis was a strong forcer of population structure in the Peninsula, and, more importantly, there were clear continuums throughout time linking western Arabia with the Levant, and eastern Arabia with Iran and the Caucasus. Eastern Arabians also displayed the highest levels of the basal Eurasian lineage of all tested modern-day populations, a signal that was maintained even after correcting for a possible bias due to a recent sub-Saharan African input in their genomes. Not surprisingly, eastern Arabians were also the ones with highest similarity with Iberomaurusians, who were, so far, the best proxy for the basal Eurasians amongst the known ancient specimens. The basal Eurasian lineage is the signature of ancient non-Africans who diverged from the common European-eastern Asian pool before 50,000 years ago, prior to the later interbred with Neanderthals. Our results appear to indicate that the exposed basin of the Arabo-Persian Gulf was the possible home of basal Eurasians, a scenario to be further investigated by searching ancient Arabian human specimens.
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Affiliation(s)
- Joana C Ferreira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal.,ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
| | - Farida Alshamali
- Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai, United Arab Emirates
| | - Francesco Montinaro
- Department of Biology-Genetics, University of Bari, Italy.,Estonian Biocentre, Institute of Genomics, University of Tartu, Estonia
| | - Bruno Cavadas
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal
| | - Antonio Torroni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Italy
| | - Luisa Pereira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal
| | - Alessandro Raveane
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Italy.,Laboratory of Haematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Veronica Fernandes
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal
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14
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Heydari-Guran S, Benazzi S, Talamo S, Ghasidian E, Hariri N, Oxilia G, Asiabani S, Azizi F, Naderi R, Safaierad R, Hublin JJ, Foley RA, Lahr MM. The discovery of an in situ Neanderthal remain in the Bawa Yawan Rockshelter, West-Central Zagros Mountains, Kermanshah. PLoS One 2021; 16:e0253708. [PMID: 34437543 PMCID: PMC8389444 DOI: 10.1371/journal.pone.0253708] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 06/11/2021] [Indexed: 11/19/2022] Open
Abstract
Neanderthal extinction has been a matter of debate for many years. New discoveries, better chronologies and genomic evidence have done much to clarify some of the issues. This evidence suggests that Neanderthals became extinct around 40,000–37,000 years before present (BP), after a period of coexistence with Homo sapiens of several millennia, involving biological and cultural interactions between the two groups. However, the bulk of this evidence relates to Western Eurasia, and recent work in Central Asia and Siberia has shown that there is considerable local variation. Southwestern Asia, despite having a number of significant Neanderthal remains, has not played a major part in the debate over extinction. Here we report a Neanderthal deciduous canine from the site of Bawa Yawan in the West-Central Zagros Mountains of Iran. The tooth is associated with Zagros Mousterian lithics, and its context is preliminary dated to between ~43,600 and ~41,500 years ago.
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Affiliation(s)
- Saman Heydari-Guran
- Stiftung Neanderthal Museum, Mettmann, Germany
- Department of Prehistoric Archaeology University of Cologne, Cologne, Germany
- DiyarMehr Centre for Palaeolithic Research, Kermanshah, Iran
- * E-mail:
| | - Stefano Benazzi
- Department of Cultural Heritage, University of Bologna, Bologna, Italy
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sahra Talamo
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Chemistry G. Ciamician, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Elham Ghasidian
- Stiftung Neanderthal Museum, Mettmann, Germany
- Department of Prehistoric Archaeology University of Cologne, Cologne, Germany
| | - Nemat Hariri
- Department of Prehistoric Archaeology University of Cologne, Cologne, Germany
- Department of Archaeology, University of Mohaghegh Ardabili University, Ardabil, Iran
| | - Gregorio Oxilia
- Department of Cultural Heritage, University of Bologna, Bologna, Italy
| | - Samran Asiabani
- DiyarMehr Centre for Palaeolithic Research, Kermanshah, Iran
- Department of Architecture, Faculty of Art and Architecture, Bu-Ali Sina University, Hamedan, Iran
| | - Faramarz Azizi
- DiyarMehr Centre for Palaeolithic Research, Kermanshah, Iran
| | - Rahmat Naderi
- DiyarMehr Centre for Palaeolithic Research, Kermanshah, Iran
| | - Reza Safaierad
- Department of Physical Geography, University of Tehran, Tehran, Iran
| | - Jean-Jacques Hublin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Collège de France, 11 Place Marcelin Berthelot, Paris, France
| | - Robert A. Foley
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, United Kingdom
| | - Marta M. Lahr
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, United Kingdom
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15
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Vizzari MT, Benazzo A, Barbujani G, Ghirotto S. A Revised Model of Anatomically Modern Human Expansions Out of Africa through a Machine Learning Approximate Bayesian Computation Approach. Genes (Basel) 2020; 11:E1510. [PMID: 33339234 PMCID: PMC7766041 DOI: 10.3390/genes11121510] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 01/25/2023] Open
Abstract
There is a wide consensus in considering Africa as the birthplace of anatomically modern humans (AMH), but the dispersal pattern and the main routes followed by our ancestors to colonize the world are still matters of debate. It is still an open question whether AMH left Africa through a single process, dispersing almost simultaneously over Asia and Europe, or in two main waves, first through the Arab Peninsula into southern Asia and Australo-Melanesia, and later through a northern route crossing the Levant. The development of new methodologies for inferring population history and the availability of worldwide high-coverage whole-genome sequences did not resolve this debate. In this work, we test the two main out-of-Africa hypotheses through an Approximate Bayesian Computation approach, based on the Random-Forest algorithm. We evaluated the ability of the method to discriminate between the alternative models of AMH out-of-Africa, using simulated data. Once assessed that the models are distinguishable, we compared simulated data with real genomic variation, from modern and archaic populations. This analysis showed that a model of multiple dispersals is four-fold as likely as the alternative single-dispersal model. According to our estimates, the two dispersal processes may be placed, respectively, around 74,000 and around 46,000 years ago.
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Affiliation(s)
| | | | | | - Silvia Ghirotto
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (M.T.V.); (A.B.); (G.B.)
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16
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Massilani D, Skov L, Hajdinjak M, Gunchinsuren B, Tseveendorj D, Yi S, Lee J, Nagel S, Nickel B, Devièse T, Higham T, Meyer M, Kelso J, Peter BM, Pääbo S. Denisovan ancestry and population history of early East Asians. Science 2020; 370:579-583. [DOI: 10.1126/science.abc1166] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/10/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Diyendo Massilani
- Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Laurits Skov
- Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Mateja Hajdinjak
- Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
- Francis Crick Institute, London NW1 1AT, UK
| | - Byambaa Gunchinsuren
- Institute of Archaeology, Mongolian Academy of Sciences, Ulaanbaatar 13343, Mongolia
| | | | - Seonbok Yi
- Department of Archaeology, Seoul National University, Gwanak-gu, Seoul 08826, Korea
| | - Jungeun Lee
- Department of Archaeology, Seoul National University, Gwanak-gu, Seoul 08826, Korea
| | - Sarah Nagel
- Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Birgit Nickel
- Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Thibaut Devièse
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Tom Higham
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Benjamin M. Peter
- Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
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17
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What have the revelations about Neanderthal DNA revealed about Homo sapiens? ANTHROPOLOGICAL REVIEW 2020. [DOI: 10.2478/anre-2020-0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genetic studies have presented increasing indications about the complexity of the interactions between Homo sapiens, Neanderthals and Denisovans, during Pleistocene. The results indicate potential replacement or admixture of the groups of hominins that lived in the same region at different times. Recently, the time of separation among these hominins in relation to the Last Common Ancestor – LCA has been reasonably well established. Events of mixing with emphasis on the Neanderthal gene flow into H. sapiens outside Africa, Denisovans into H. sapiens ancestors in Oceania and continental Asia, Neanderthals into Denisovans, as well as the origin of some phenotypic features in specific populations such as the color of the skin, eyes, hair and predisposition to develop certain kinds of diseases have also been found. The current information supports the existence of both replacement and interbreeding events, and indicates the need to revise the two main explanatory models, the Multiregional and the Out-of-Africa hypotheses, about the origin and evolution of H. sapiens and its co-relatives. There is definitely no longer the possibility of justifying only one model over the other. This paper aims to provide a brief review and update on the debate around this issue, considering the advances brought about by the recent genetic as well as morphological traits analyses.
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18
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Abstract
Updated analysis of
Plasmodium falciparum
malaria reveals markers of antimalarial resistance
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Affiliation(s)
- Carol Hopkins Sibley
- Department of Genome Sciences, University of Washington, Seattle, WA 98195-5065, USA
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19
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The Northern Route for Human dispersal in Central and Northeast Asia: New evidence from the site of Tolbor-16, Mongolia. Sci Rep 2019; 9:11759. [PMID: 31409814 PMCID: PMC6692324 DOI: 10.1038/s41598-019-47972-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/26/2019] [Indexed: 11/21/2022] Open
Abstract
The fossil record suggests that at least two major human dispersals occurred across the Eurasian steppe during the Late Pleistocene. Neanderthals and Modern Humans moved eastward into Central Asia, a region intermittently occupied by the enigmatic Denisovans. Genetic data indicates that the Denisovans interbred with Neanderthals near the Altai Mountains (South Siberia) but where and when they met H. sapiens is yet to be determined. Here we present archaeological evidence that document the timing and environmental context of a third long-distance population movement in Central Asia, during a temperate climatic event around 45,000 years ago. The early occurrence of the Initial Upper Palaeolithic, a techno-complex whose sudden appearance coincides with the first occurrence of H. sapiens in the Eurasian steppes, establishes an essential archaeological link between the Siberian Altai and Northwestern China . Such connection between regions provides empirical ground to discuss contacts between local and exogenous populations in Central and Northeast Asia during the Late Pleistocene.
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20
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Fernandes V, Brucato N, Ferreira JC, Pedro N, Cavadas B, Ricaut FX, Alshamali F, Pereira L. Genome-Wide Characterization of Arabian Peninsula Populations: Shedding Light on the History of a Fundamental Bridge between Continents. Mol Biol Evol 2019; 36:575-586. [PMID: 30649405 DOI: 10.1093/molbev/msz005] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The Arabian Peninsula (AP) was an important crossroad between Africa, Asia, and Europe, being the cradle of the structure defining these main human population groups, and a continuing path for their admixture. The screening of 741,000 variants in 420 Arabians and 80 Iranians allowed us to quantify the dominant sub-Saharan African admixture in the west of the peninsula, whereas South Asian and Levantine/European influence was stronger in the east, leading to a rift between western and eastern sides of the Peninsula. Dating of the admixture events indicated that Indian Ocean slave trade and Islamization periods were important moments in the genetic makeup of the region. The western-eastern axis was also observable in terms of positive selection of diversity conferring lactose tolerance, with the West AP developing local adaptation and the East AP acquiring the derived allele selected in European populations and existing in South Asia. African selected malaria resistance through the DARC gene was enriched in all Arabian genomes, especially in the western part. Clear European influences associated with skin and eye color were equally frequent across the Peninsula.
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Affiliation(s)
- Veronica Fernandes
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Nicolas Brucato
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France
| | - Joana C Ferreira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Nicole Pedro
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Bruno Cavadas
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - François-Xavier Ricaut
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France
| | - Farida Alshamali
- Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai, United Arab Emirates
| | - Luisa Pereira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.,Faculdade de Medicina da Universidade do Porto, Porto, Portugal
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21
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Upper Paleolithic cultural diversity in the Iranian Zagros Mountains and the expansion of modern humans into Eurasia. J Hum Evol 2019; 132:101-118. [DOI: 10.1016/j.jhevol.2019.04.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 04/09/2019] [Accepted: 04/09/2019] [Indexed: 01/27/2023]
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22
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Abstract
Hominin evolution is characterized by progressive regional differentiation, as well as migration waves, leading to anatomically modern humans that are assumed to have emerged in Africa and spread over the whole world. Why or whether Africa was the source region of modern humans and what caused their spread remains subject of ongoing debate. We present a spatially explicit, stochastic numerical model that includes ongoing mutations, demic diffusion, assortative mating and migration waves. Diffusion and assortative mating alone result in a structured population with relatively homogeneous regions bound by sharp clines. The addition of migration waves results in a power-law distribution of wave areas: for every large wave, many more small waves are expected to occur. This suggests that one or more out-of-Africa migrations would probably have been accompanied by numerous smaller migration waves across the world. The migration waves are considered "spontaneous", as the current model excludes environmental or other extrinsic factors. Large waves preferentially emanate from the central areas of large, compact inhabited areas. During the Pleistocene, Africa was the largest such area most of the time, making Africa the statistically most likely origin of anatomically modern humans, without a need to invoke additional environmental or ecological drivers.
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23
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Vyas DN, Mulligan CJ. Analyses of Neanderthal introgression suggest that Levantine and southern Arabian populations have a shared population history. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 169:227-239. [PMID: 30889271 DOI: 10.1002/ajpa.23818] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 01/11/2019] [Accepted: 02/21/2019] [Indexed: 01/31/2023]
Abstract
OBJECTIVES Modern humans are thought to have interbred with Neanderthals in the Near East soon after modern humans dispersed out of Africa. This introgression event likely took place in either the Levant or southern Arabia depending on the dispersal route out of Africa that was followed. In this study, we compare Neanderthal introgression in contemporary Levantine and southern Arabian populations to investigate Neanderthal introgression and to study Near Eastern population history. MATERIALS AND METHODS We analyzed genotyping data on >400,000 autosomal SNPs from seven Levantine and five southern Arabian populations and compared these data to those from populations from around the world including Neanderthal and Denisovan genomes. We used f4 and D statistics to estimate and compare levels of Neanderthal introgression between Levantine, southern Arabian, and comparative global populations. We also identified 1,581 putative Neanderthal-introgressed SNPs within our dataset and analyzed their allele frequencies as a means to compare introgression patterns in Levantine and southern Arabian genomes. RESULTS We find that Levantine and southern Arabian populations have similar levels of Neanderthal introgression to each other but lower levels than other non-Africans. Furthermore, we find that introgressed SNPs have very similar allele frequencies in the Levant and southern Arabia, which indicates that Neanderthal introgression is similarly distributed in Levantine and southern Arabian genomes. DISCUSSION We infer that the ancestors of contemporary Levantine and southern Arabian populations received Neanderthal introgression prior to separating from each other and that there has been extensive gene flow between these populations.
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Affiliation(s)
- Deven N Vyas
- Department of Anthropology, University of Florida, Gainesville, Florida.,Genetics Institute, University of Florida, Gainesville, Florida
| | - Connie J Mulligan
- Department of Anthropology, University of Florida, Gainesville, Florida.,Genetics Institute, University of Florida, Gainesville, Florida
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24
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Langgut D, Almogi-Labin A, Bar-Matthews M, Pickarski N, Weinstein-Evron M. Evidence for a humid interval at ∼56–44 ka in the Levant and its potential link to modern humans dispersal out of Africa. J Hum Evol 2018; 124:75-90. [DOI: 10.1016/j.jhevol.2018.08.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 08/06/2018] [Accepted: 08/07/2018] [Indexed: 12/13/2022]
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25
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Abstract
Anatomically modern humans (Homo sapiens, AMH) began spreading across Eurasia from Africa and adjacent Southwest Asia about 50,000-55,000 years ago (ca 50-55 ka). Some have argued that human genetic, fossil, and archaeological data indicate one or more prior dispersals, possibly as early as 120 ka. A recently reported age estimate of 65 ka for Madjedbebe, an archaeological site in northern Sahul (Pleistocene Australia-New Guinea), if correct, offers what might be the strongest support yet presented for a pre-55-ka African AMH exodus. We review evidence for AMH arrival on an arc spanning South China through Sahul and then evaluate data from Madjedbebe. We find that an age estimate of >50 ka for this site is unlikely to be valid. While AMH may have moved far beyond Africa well before 50-55 ka, data from the region of interest offered in support of this idea are not compelling.
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26
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Who were the Nataruk people? Mandibular morphology among late Pleistocene and early Holocene fisher-forager populations of West Turkana (Kenya). J Hum Evol 2018; 121:235-253. [PMID: 29857967 DOI: 10.1016/j.jhevol.2018.04.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 04/24/2018] [Accepted: 04/25/2018] [Indexed: 01/27/2023]
Abstract
Africa is the birthplace of the species Homo sapiens, and Africans today are genetically more diverse than other populations of the world. However, the processes that underpinned the evolution of African populations remain largely obscure. Only a handful of late Pleistocene African fossils (∼50-12 Ka) are known, while the more numerous sites with human fossils of early Holocene age are patchily distributed. In particular, late Pleistocene and early Holocene human diversity in Eastern Africa remains little studied, precluding any analysis of the potential factors that shaped human diversity in the region, and more broadly throughout the continent. These periods include the Last Glacial Maximum (LGM), a moment of extreme aridity in Africa that caused the fragmentation of population ranges and localised extinctions, as well as the 'African Humid Period', a moment of abrupt climate change and enhanced connectivity throughout Africa. East Africa, with its range of environments, may have acted as a refugium during the LGM, and may have played a critical biogeographic role during the heterogene`ous environmental recovery that followed. This environmental context raises a number of questions about the relationships among early Holocene African populations, and about the role played by East Africa in shaping late hunter-gatherer biological diversity. Here, we describe eight mandibles from Nataruk, an early Holocene site (∼10 Ka) in West Turkana, offering the opportunity of exploring population diversity in Africa at the height of the 'African Humid Period'. We use 3D geometric morphometric techniques to analyze the phenotypic variation of a large mandibular sample. Our results show that (i) the Nataruk mandibles are most similar to other African hunter-fisher-gatherer populations, especially to the fossils from Lothagam, another West Turkana locality, and to other early Holocene fossils from the Central Rift Valley (Kenya); and (ii) a phylogenetic connection may have existed between these Eastern African populations and some Nile Valley and Maghrebian groups, who lived at a time when a Green Sahara may have allowed substantial contact, and potential gene flow, across a vast expanse of Northern and Eastern Africa.
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Rabett RJ. The success of failed Homo sapiens dispersals out of Africa and into Asia. Nat Ecol Evol 2018; 2:212-219. [PMID: 29348642 DOI: 10.1038/s41559-017-0436-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 11/30/2017] [Indexed: 01/27/2023]
Abstract
The evidence for an early dispersal of Homo sapiens from Africa into the Levant during Marine Isotope Stage 5 (MIS-5) 126-74 ka (thousand years ago) was characterized for many years as an 'abortive' expansion: a precursor to a sustained dispersal from which all extant human populations can be traced. Recent archaeological and genetic data from both western and eastern parts of Eurasia and from Australia are starting to challenge that interpretation. This Perspective reviews the current evidence for a scenario where the MIS-5 dispersal encompassed a much greater geographic distribution and temporal duration. The implications of this for tracking and understanding early human dispersal in Southeast Asia specifically are considered, and the validity of measuring dispersal success only through genetic continuity into the present is examined.
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Affiliation(s)
- Ryan J Rabett
- Archaeology & Palaeoecology, School of Natural & Built Environment, Queen's University Belfast, Elmwood Avenue, Belfast, BT7 1NN, UK.
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Bae CJ, Douka K, Petraglia MD. On the origin of modern humans: Asian perspectives. Science 2017; 358:358/6368/eaai9067. [DOI: 10.1126/science.aai9067] [Citation(s) in RCA: 208] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Nakazawa Y. On the Pleistocene Population History in the Japanese Archipelago. CURRENT ANTHROPOLOGY 2017. [DOI: 10.1086/694447] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Blinkhorn J, Petraglia MD. Environments and Cultural Change in the Indian Subcontinent. CURRENT ANTHROPOLOGY 2017. [DOI: 10.1086/693462] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Reyes-Centeno H, Rathmann H, Hanihara T, Harvati K. Testing Modern Human Out-of-Africa Dispersal Models Using Dental Nonmetric Data. CURRENT ANTHROPOLOGY 2017. [DOI: 10.1086/694423] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Vyas DN, Al‐Meeri A, Mulligan CJ. Testing support for the northern and southern dispersal routes out of Africa: an analysis of Levantine and southern Arabian populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 164:736-749. [DOI: 10.1002/ajpa.23312] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 08/28/2017] [Accepted: 08/29/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Deven N. Vyas
- Department of AnthropologyUniversity of Florida, 1112 Turlington Hall, PO Box 117305Gainesville Florida 32611‐7305
- Genetics InstituteUniversity of Florida, Cancer & Genetics Research Complex, PO Box 103610Gainesville Florida 32610‐3610
| | - Ali Al‐Meeri
- Department of Clinical Biochemistry, Faculty of Medicine and Health SciencesUniversity of Sana'aSana'a Yemen
| | - Connie J. Mulligan
- Department of AnthropologyUniversity of Florida, 1112 Turlington Hall, PO Box 117305Gainesville Florida 32611‐7305
- Genetics InstituteUniversity of Florida, Cancer & Genetics Research Complex, PO Box 103610Gainesville Florida 32610‐3610
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Leonardi M, Barbujani G, Manica A. An earlier revolution: genetic and genomic analyses reveal pre-existing cultural differences leading to Neolithization. Sci Rep 2017; 7:3525. [PMID: 28615641 PMCID: PMC5471218 DOI: 10.1038/s41598-017-03717-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 05/02/2017] [Indexed: 01/28/2023] Open
Abstract
Archaeological evidence shows that, in the long run, Neolitization (the transition from foraging to food production) was associated with demographic growth. We used two methods (patterns of linkage disequilibrium from whole-genome SNPs and MSMC estimates on genomes) to reconstruct the demographic profiles for respectively 64 and 24 modern-day populations with contrasting lifestyles across the Old World (sub-Saharan Africa, south-eastern Asia, Siberia). Surprisingly, in all regions, food producers had larger effective population sizes (Ne) than foragers already 20 k years ago, well before the Neolithic revolution. As expected, this difference further increased ~12–10 k years ago, around or just before the onset of food production. Using paleoclimate reconstructions, we show that the early difference in Ne cannot be explained by food producers inhabiting more favorable regions. A number of mechanisms, including ancestral differences in census size, sedentism, exploitation of the natural resources, social stratification or connectivity between groups, might have led to the early differences in Ne detected in our analyses. Irrespective of the specific mechanisms involved, our results provide further evidence that long term cultural differences among populations of Palaeolithic hunter-gatherers are likely to have played an important role in the later Neolithization process.
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Affiliation(s)
- Michela Leonardi
- Department of Life Sciences and Biotechnology, University of Ferrara, Via Borsari 44, 44121, Ferrara, Italy. .,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oester Voldgade 5-7, DK-1350, Copenhagen, Denmark.
| | - Guido Barbujani
- Department of Life Sciences and Biotechnology, University of Ferrara, Via Borsari 44, 44121, Ferrara, Italy
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing street, CB2 3EJ, Cambridge, UK
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Inferring Human Demographic Histories of Non-African Populations from Patterns of Allele Sharing. Am J Hum Genet 2017; 100:766-772. [PMID: 28475859 DOI: 10.1016/j.ajhg.2017.04.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/31/2017] [Indexed: 11/22/2022] Open
Abstract
Recent human-genetics studies have come to different conclusions regarding how and when modern humans spread out of Africa and into the rest of the world. I present here a simple parsimony-based analysis that suggests that East Asians and Melanesians are sister groups, and I discuss what implications this has for recent claims made about the demographic histories of non-African populations.
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Malaspinas AS, Westaway MC, Muller C, Sousa VC, Lao O, Alves I, Bergström A, Athanasiadis G, Cheng JY, Crawford JE, Heupink TH, Macholdt E, Peischl S, Rasmussen S, Schiffels S, Subramanian S, Wright JL, Albrechtsen A, Barbieri C, Dupanloup I, Eriksson A, Margaryan A, Moltke I, Pugach I, Korneliussen TS, Levkivsky IP, Moreno-Mayar JV, Ni S, Racimo F, Sikora M, Xue Y, Aghakhanian FA, Brucato N, Brunak S, Campos PF, Clark W, Ellingvåg S, Fourmile G, Gerbault P, Injie D, Koki G, Leavesley M, Logan B, Lynch A, Matisoo-Smith EA, McAllister PJ, Mentzer AJ, Metspalu M, Migliano AB, Murgha L, Phipps ME, Pomat W, Reynolds D, Ricaut FX, Siba P, Thomas MG, Wales T, Wall C, Oppenheimer SJ, Tyler-Smith C, Durbin R, Dortch J, Manica A, Schierup MH, Foley RA, Mirazón Lahr M, Bowern C, Wall JD, Mailund T, Stoneking M, Nielsen R, Sandhu MS, Excoffier L, Lambert DM, Willerslev E. A genomic history of Aboriginal Australia. Nature 2016; 538:207-214. [PMID: 27654914 PMCID: PMC7617037 DOI: 10.1038/nature18299] [Citation(s) in RCA: 275] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 05/04/2016] [Indexed: 12/21/2022]
Abstract
The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama-Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25-40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ~10-32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama-Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51-72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.
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Affiliation(s)
- Anna-Sapfo Malaspinas
- Centre for GeoGenetics, Natural History Museum of Denmark,
University of Copenhagen, Øster Voldgade 5–7, 1350, Copenhagen,
Denmark
- Institute of Ecology and Evolution, University of Bern,
Baltzerstrasse 6, CH-3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Michael C Westaway
- Environmental Futures Research Institute, Griffith University,
Nathan, Australia
| | - Craig Muller
- Centre for GeoGenetics, Natural History Museum of Denmark,
University of Copenhagen, Øster Voldgade 5–7, 1350, Copenhagen,
Denmark
| | - Vitor C Sousa
- Institute of Ecology and Evolution, University of Bern,
Baltzerstrasse 6, CH-3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Oscar Lao
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute
of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Isabel Alves
- Institute of Ecology and Evolution, University of Bern,
Baltzerstrasse 6, CH-3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Population and Conservation Genetics Group, Instituto Gulbenkian de
Ciência, Oeiras, Portugal
| | - Anders Bergström
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge, CB10 1SA, UK
| | | | - Jade Y Cheng
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus,
Denmark
- Department of Integrative Biology, University of California,
Berkeley, CA, USA
| | - Jacob E Crawford
- Department of Integrative Biology, University of California,
Berkeley, CA, USA
| | - Tim H Heupink
- Environmental Futures Research Institute, Griffith University,
Nathan, Australia
| | - Enrico Macholdt
- Department of Evolutionary Genetics, Max Planck Institute for
Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Stephan Peischl
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Interfaculty Bioinformatics Unit University of Bern, Baltzerstrasse
6, CH-3012 Bern, Switzerland
| | - Simon Rasmussen
- Center for Biological Sequence Analysis, Department of Systems
Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens
Lyngby, Denmark
| | - Stephan Schiffels
- Department for Archaeogenetics, Max Planck Institute for the
Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany
| | - Sankar Subramanian
- Environmental Futures Research Institute, Griffith University,
Nathan, Australia
| | - Joanne L Wright
- Environmental Futures Research Institute, Griffith University,
Nathan, Australia
| | - Anders Albrechtsen
- The Bioinformatics Centre, Department of Biology, University of
Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Chiara Barbieri
- Department of Evolutionary Genetics, Max Planck Institute for
Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
- Department of Linguistic and Cultural Evolution, Max Planck
Institute for the Science of Human History, Kahlaische Strasse 10, D-07745 Jena,
Germany
| | - Isabelle Dupanloup
- Institute of Ecology and Evolution, University of Bern,
Baltzerstrasse 6, CH-3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Anders Eriksson
- Dept of Zoology, University of Cambridge, Downing Street, CB2 3EJ,
UK
- Integrative Systems Biology Laboratory, Division of Biological and
Environmental Sciences & Engineering, King Abdullah University of Science and
Technology, 23955-6900 Thuwal, Kingdom of Saudi Arabia
| | - Ashot Margaryan
- Centre for GeoGenetics, Natural History Museum of Denmark,
University of Copenhagen, Øster Voldgade 5–7, 1350, Copenhagen,
Denmark
| | - Ida Moltke
- The Bioinformatics Centre, Department of Biology, University of
Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Irina Pugach
- Department of Evolutionary Genetics, Max Planck Institute for
Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Thorfinn S Korneliussen
- Centre for GeoGenetics, Natural History Museum of Denmark,
University of Copenhagen, Øster Voldgade 5–7, 1350, Copenhagen,
Denmark
| | - Ivan P Levkivsky
- Institute for theoretical physics, ETH Zürich,
Wolfgang-Pauli-Str. 27, 8093 Zürich, Switzerland
| | - J. Víctor Moreno-Mayar
- Centre for GeoGenetics, Natural History Museum of Denmark,
University of Copenhagen, Øster Voldgade 5–7, 1350, Copenhagen,
Denmark
| | - Shengyu Ni
- Department of Evolutionary Genetics, Max Planck Institute for
Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Fernando Racimo
- Department of Integrative Biology, University of California,
Berkeley, CA, USA
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum of Denmark,
University of Copenhagen, Øster Voldgade 5–7, 1350, Copenhagen,
Denmark
| | - Yali Xue
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge, CB10 1SA, UK
| | - Farhang A Aghakhanian
- Jeffrey Cheah School of Medicine & Health Sciences, Monash
University Malaysia, Jalan Lagoon Selatan, Sunway City, 46150 Selangor,
Malaysia
| | - Nicolas Brucato
- Evolutionary Medicine group, Laboratoire d’Anthropologie
Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la
Recherche Scientifique, Université de Toulouse 3, Toulouse, France
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, University of
Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Paula F Campos
- Centre for GeoGenetics, Natural History Museum of Denmark,
University of Copenhagen, Øster Voldgade 5–7, 1350, Copenhagen,
Denmark
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação
Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 289, 4050-123 Porto,
Portugal
| | - Warren Clark
- National Parks and Wildlife, Sturt Highway, Buronga, NSW 2739
Australia
| | | | | | - Pascale Gerbault
- UCL Research Department of Genetics, Evolution and Environment,
Darwin building, Gower Street, London WC1E 6BT, UK
| | - Darren Injie
- Centre for GeoGenetics, Natural History Museum of Denmark,
University of Copenhagen, Øster Voldgade 5–7, 1350, Copenhagen,
Denmark
| | - George Koki
- Papua New Guinea Institute of Medical Research, P.O. Box 60,
Goroka, Papua New Guinea
| | - Matthew Leavesley
- Archaeology, School of Humanities & Social Sciences,
University PO Box 320, University of Papua New Guinea & College of Arts,
Society & Education, James Cook University, Cairns, Australia
| | - Betty Logan
- Centre for GeoGenetics, Natural History Museum of Denmark,
University of Copenhagen, Øster Voldgade 5–7, 1350, Copenhagen,
Denmark
| | - Aubrey Lynch
- Centre for GeoGenetics, Natural History Museum of Denmark,
University of Copenhagen, Øster Voldgade 5–7, 1350, Copenhagen,
Denmark
| | | | | | - Alexander J Mentzer
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge, CB10 1SA, UK
| | | | - Andrea B Migliano
- UCL Department of Anthropology, 14 Taviton Street, London WC1H 0BW,
UK
| | - Les Murgha
- 86 Workshop Road, Yarrabah, QLD 4871 Australia
| | - Maude E Phipps
- Jeffrey Cheah School of Medicine & Health Sciences, Monash
University Malaysia, Jalan Lagoon Selatan, Sunway City, 46150 Selangor,
Malaysia
| | - William Pomat
- Papua New Guinea Institute of Medical Research, P.O. Box 60,
Goroka, Papua New Guinea
| | - Doc Reynolds
- Centre for GeoGenetics, Natural History Museum of Denmark,
University of Copenhagen, Øster Voldgade 5–7, 1350, Copenhagen,
Denmark
| | - Francois-Xavier Ricaut
- Evolutionary Medicine group, Laboratoire d’Anthropologie
Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la
Recherche Scientifique, Université de Toulouse 3, Toulouse, France
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, P.O. Box 60,
Goroka, Papua New Guinea
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment,
University College London, Gower Street, London WC1E 6BT
| | | | | | - Stephen J Oppenheimer
- School of Anthropology and Museum Ethnography, Oxford University,
Oxford, OX2 6PE, UK
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge, CB10 1SA, UK
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge, CB10 1SA, UK
| | - Joe Dortch
- Centre for Rock Art Research + Management, University of Western
Australia
| | - Andrea Manica
- Dept of Zoology, University of Cambridge, Downing Street, CB2 3EJ,
UK
| | - Mikkel H Schierup
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus,
Denmark
| | - Robert A Foley
- Centre for GeoGenetics, Natural History Museum of Denmark,
University of Copenhagen, Øster Voldgade 5–7, 1350, Copenhagen,
Denmark
- Leverhulme Centre for Human Evolutionary Studies, Department of
Archaeology and Anthropology, University of Cambridge, Fitzwilliam St, Cambridge CB2
1QH, UK
| | - Marta Mirazón Lahr
- Centre for GeoGenetics, Natural History Museum of Denmark,
University of Copenhagen, Øster Voldgade 5–7, 1350, Copenhagen,
Denmark
- Leverhulme Centre for Human Evolutionary Studies, Department of
Archaeology and Anthropology, University of Cambridge, Fitzwilliam St, Cambridge CB2
1QH, UK
| | - Claire Bowern
- Department of Linguistics, PO Box 208366 (370 Temple St), New
Haven, CT, 06520, USA
| | - Jeffrey D Wall
- Institute for Human Genetics, University of California, San
Francisco, CA, USA
| | - Thomas Mailund
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus,
Denmark
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for
Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Rasmus Nielsen
- Centre for GeoGenetics, Natural History Museum of Denmark,
University of Copenhagen, Øster Voldgade 5–7, 1350, Copenhagen,
Denmark
- Departments of Integrative Biology and Statistics, University of
California, Berkeley, CA, USA
| | - Manjinder S Sandhu
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge, CB10 1SA, UK
| | - Laurent Excoffier
- Institute of Ecology and Evolution, University of Bern,
Baltzerstrasse 6, CH-3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - David M Lambert
- Environmental Futures Research Institute, Griffith University,
Nathan, Australia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark,
University of Copenhagen, Øster Voldgade 5–7, 1350, Copenhagen,
Denmark
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge, CB10 1SA, UK
- Dept of Zoology, University of Cambridge, Downing Street, CB2 3EJ,
UK
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Mirazón Lahr M. The shaping of human diversity: filters, boundaries and transitions. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150241. [PMID: 27298471 PMCID: PMC4920297 DOI: 10.1098/rstb.2015.0241] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2016] [Indexed: 01/21/2023] Open
Abstract
The evolution of modern humans was a complex process, involving major changes in levels of diversity through time. The fossils and stone tools that record the spatial distribution of our species in the past form the backbone of our evolutionary history, and one that allows us to explore the different processes-cultural and biological-that acted to shape the evolution of different populations in the face of major climate change. Those processes created a complex palimpsest of similarities and differences, with outcomes that were at times accelerated by sharp demographic and geographical fluctuations. The result is that the population ancestral to all modern humans did not look or behave like people alive today. This has generated questions regarding the evolution of human universal characters, as well as the nature and timing of major evolutionary events in the history of Homo sapiens The paucity of African fossils remains a serious stumbling block for exploring some of these issues. However, fossil and archaeological discoveries increasingly clarify important aspects of our past, while breakthroughs from genomics and palaeogenomics have revealed aspects of the demography of Late Quaternary Eurasian hominin groups and their interactions, as well as those between foragers and farmers. This paper explores the nature and timing of key moments in the evolution of human diversity, moments in which population collapse followed by differential expansion of groups set the conditions for transitional periods. Five transitions are identified (i) at the origins of the species, 240-200 ka; (ii) at the time of the first major expansions, 130-100 ka; (iii) during a period of dispersals, 70-50 ka; (iv) across a phase of local/regional structuring of diversity, 45-25 ka; and (v) during a phase of significant extinction of hunter-gatherer diversity and expansion of particular groups, such as farmers and later societies (the Holocene Filter), 15-0 ka.This article is part of the themed issue 'Major transitions in human evolution'.
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Affiliation(s)
- Marta Mirazón Lahr
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, UK
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López S, van Dorp L, Hellenthal G. Human Dispersal Out of Africa: A Lasting Debate. Evol Bioinform Online 2016; 11:57-68. [PMID: 27127403 PMCID: PMC4844272 DOI: 10.4137/ebo.s33489] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 02/21/2016] [Accepted: 02/21/2016] [Indexed: 01/01/2023] Open
Abstract
Unraveling the first migrations of anatomically modern humans out of Africa has invoked great interest among researchers from a wide range of disciplines. Available fossil, archeological, and climatic data offer many hypotheses, and as such genetics, with the advent of genome-wide genotyping and sequencing techniques and an increase in the availability of ancient samples, offers another important tool for testing theories relating to our own history. In this review, we report the ongoing debates regarding how and when our ancestors left Africa, how many waves of dispersal there were and what geographical routes were taken. We explore the validity of each, using current genetic literature coupled with some of the key archeological findings.
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Affiliation(s)
- Saioa López
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Lucy van Dorp
- Department of Genetics, Evolution and Environment, University College London, London, UK
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, UK
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment, University College London, London, UK
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Abstract
East Africa is home to a rich array of stone-tool traditions that span human prehistory. It is unsurprising, therefore, that the region attracted pioneer prehistorians in the early twentieth century, including L. S. B. Leakey, E. J. Wayland and T. P. O'Brien, who created the first cultural framework for East African prehistory during the 1930s. Although aspects of this framework remain relevant today, others have become misunderstood relics of an old classification system that hinders current research. This is particularly evident in the classification of a Later Stone Age (LSA) culture - the Kenya (East African) Aurignacian, later known as Kenya (East African) Capsian. Although this cultural entity was redressed during the 1970s and 1980s and redefined as the Eburran industry, there is still mystique surrounding the current status of the Kenya Capsian, its original scope and definition, the relationship with the Eburran and its position within a modern understanding of the East African LSA. This is largely due to paradigmatic shifts in researcher attitudes, leading to the use of the Eburran as a false proxy. It is necessary now to completely remove the term Kenya Capsian as an indication of similarity among the different LSA technologies. However, there also needs to be less emphasis on the importance of the Eburran and recognition that it is just one example of a multitude of diverse localised LSA industries. This will open the way for future research into the LSA and facilitate our greater understanding of recent prehistory in East Africa.
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Affiliation(s)
- Alex Wilshaw
- Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge, Cambridgeshire UK
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40
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Tassi F, Ghirotto S, Mezzavilla M, Vilaça ST, De Santi L, Barbujani G. Early modern human dispersal from Africa: genomic evidence for multiple waves of migration. INVESTIGATIVE GENETICS 2015; 6:13. [PMID: 26550467 PMCID: PMC4636834 DOI: 10.1186/s13323-015-0030-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 10/27/2015] [Indexed: 12/22/2022]
Abstract
Background Anthropological and genetic data agree in indicating the African continent as the main place of origin for anatomically modern humans. However, it is unclear whether early modern humans left Africa through a single, major process, dispersing simultaneously over Asia and Europe, or in two main waves, first through the Arab Peninsula into southern Asia and Oceania, and later through a northern route crossing the Levant. Results Here, we show that accurate genomic estimates of the divergence times between European and African populations are more recent than those between Australo-Melanesia and Africa and incompatible with the effects of a single dispersal. This difference cannot possibly be accounted for by the effects of either hybridization with archaic human forms in Australo-Melanesia or back migration from Europe into Africa. Furthermore, in several populations of Asia we found evidence for relatively recent genetic admixture events, which could have obscured the signatures of the earliest processes. Conclusions We conclude that the hypothesis of a single major human dispersal from Africa appears hardly compatible with the observed historical and geographical patterns of genome diversity and that Australo-Melanesian populations seem still to retain a genomic signature of a more ancient divergence from Africa Electronic supplementary material The online version of this article (doi:10.1186/s13323-015-0030-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Francesca Tassi
- Department of Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy
| | - Silvia Ghirotto
- Department of Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy
| | - Massimo Mezzavilla
- Institute for Maternal and Child Health-IRCCS "BurloGarofolo", University of Trieste, Trieste, Italy
| | - Sibelle Torres Vilaça
- Department of Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy.,Present Address: Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Lisa De Santi
- Department of Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy
| | - Guido Barbujani
- Department of Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy
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Reyes-Centeno H, Hubbe M, Hanihara T, Stringer C, Harvati K. Testing modern human out-of-Africa dispersal models and implications for modern human origins. J Hum Evol 2015; 87:95-106. [DOI: 10.1016/j.jhevol.2015.06.008] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 03/02/2015] [Accepted: 06/14/2015] [Indexed: 11/26/2022]
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Triki-Fendri S, Sánchez-Diz P, Rey-González D, Alfadhli S, Ayadi I, Ben Marzoug R, Carracedo Á, Rebai A. Genetic structure of the Kuwaiti population revealed by paternal lineages. Am J Hum Biol 2015; 28:203-12. [PMID: 26293354 DOI: 10.1002/ajhb.22773] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/18/2015] [Accepted: 07/25/2015] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVE We analyzed the Y-chromosome haplogroup diversity in the Kuwaiti population to gain a more complete overview of its genetic landscape. METHOD A sample of 117 males from the Kuwaiti population was studied through the analysis of 22 Y-SNPs. The results were then interpreted in conjunction with those of other populations from the Middle East, South Asia, North and East Africa, and East Europe. RESULTS The analyzed markers allowed the discrimination of 19 different haplogroups with a diversity of 0.7713. J-M304 was the most frequent haplogroup in the Kuwaiti population (55.5%) followed by E-M96 (18%). They revealed a genetic homogeneity between the Kuwaiti population and those of the Middle East (FST = 6.1%, P-value < 0.0001), although a significant correlation between genetic and geographic distances was found (r = 0.41, P-value = 0.009). Moreover, the nonsignificant pairwise FST genetic distances between the Kuwait population on the one hand and the Arabs of Iran and those of Sudan on the other, corroborate the hypothesis of bidirectional gene flow between Arabia and both Iran and Sudan. CONCLUSION Overall, we have revealed that the Kuwaiti population has experienced significant gene flow from neighboring populations like Saudi Arabia, Iran, and East Africa. Therefore, we have confirmed that the population of Kuwait is genetically coextensive with those of the Middle East.
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Affiliation(s)
- Soumaya Triki-Fendri
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, BP1177 Route Sidi Mansour Km 6, Sfax, Tunisia
| | - Paula Sánchez-Diz
- Forensic Genetics Unit, Institute of Forensic Science, University of Santiago De Compostela, Santiago De Compostela, Galicia, Spain
| | - Danel Rey-González
- Forensic Genetics Unit, Institute of Forensic Science, University of Santiago De Compostela, Santiago De Compostela, Galicia, Spain
| | - Suad Alfadhli
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Kuwait University, Kuwait
| | - Imen Ayadi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, BP1177 Route Sidi Mansour Km 6, Sfax, Tunisia
| | - Riadh Ben Marzoug
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, BP1177 Route Sidi Mansour Km 6, Sfax, Tunisia
| | - Ángel Carracedo
- Forensic Genetics Unit, Institute of Forensic Science, University of Santiago De Compostela, Santiago De Compostela, Galicia, Spain.,Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Rebai
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, BP1177 Route Sidi Mansour Km 6, Sfax, Tunisia
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Evolution and dispersal of the genus Homo: A landscape approach. J Hum Evol 2015; 87:48-65. [PMID: 26235482 DOI: 10.1016/j.jhevol.2015.07.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 07/05/2015] [Accepted: 07/09/2015] [Indexed: 02/07/2023]
Abstract
The notion of the physical landscape as an arena of ecological interaction and human evolution is a powerful one, but its implementation at larger geographical and temporal scales is hampered by the challenges of reconstructing physical landscape settings in the geologically active regions where the earliest evidence is concentrated. We argue that the inherently dynamic nature of these unstable landscapes has made them important agents of biological change, creating complex topographies capable of selecting for, stimulating, obstructing or accelerating the latent and emerging properties of the human evolutionary trajectory. We use this approach, drawing on the concepts and methods of active tectonics, to develop a new perspective on the origins and dispersal of the Homo genus. We show how complex topography provides an easy evolutionary pathway to full terrestrialisation in the African context, and would have further equipped members of the genus Homo with a suite of adaptive characteristics that facilitated wide-ranging dispersal across ecological and climatic boundaries into Europe and Asia by following pathways of complex topography. We compare this hypothesis with alternative explanations for hominin dispersal, and evaluate it by mapping the distribution of topographic features at varying scales, and comparing the distribution of early Homo sites with the resulting maps and with other environmental variables.
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Pagani L, Schiffels S, Gurdasani D, Danecek P, Scally A, Chen Y, Xue Y, Haber M, Ekong R, Oljira T, Mekonnen E, Luiselli D, Bradman N, Bekele E, Zalloua P, Durbin R, Kivisild T, Tyler-Smith C. Tracing the route of modern humans out of Africa by using 225 human genome sequences from Ethiopians and Egyptians. Am J Hum Genet 2015; 96:986-91. [PMID: 26027499 PMCID: PMC4457944 DOI: 10.1016/j.ajhg.2015.04.019] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 04/29/2015] [Indexed: 12/25/2022] Open
Abstract
The predominantly African origin of all modern human populations is well established, but the route taken out of Africa is still unclear. Two alternative routes, via Egypt and Sinai or across the Bab el Mandeb strait into Arabia, have traditionally been proposed as feasible gateways in light of geographic, paleoclimatic, archaeological, and genetic evidence. Distinguishing among these alternatives has been difficult. We generated 225 whole-genome sequences (225 at 8× depth, of which 8 were increased to 30×; Illumina HiSeq 2000) from six modern Northeast African populations (100 Egyptians and five Ethiopian populations each represented by 25 individuals). West Eurasian components were masked out, and the remaining African haplotypes were compared with a panel of sub-Saharan African and non-African genomes. We showed that masked Northeast African haplotypes overall were more similar to non-African haplotypes and more frequently present outside Africa than were any sets of haplotypes derived from a West African population. Furthermore, the masked Egyptian haplotypes showed these properties more markedly than the masked Ethiopian haplotypes, pointing to Egypt as the more likely gateway in the exodus to the rest of the world. Using five Ethiopian and three Egyptian high-coverage masked genomes and the multiple sequentially Markovian coalescent (MSMC) approach, we estimated the genetic split times of Egyptians and Ethiopians from non-African populations at 55,000 and 65,000 years ago, respectively, whereas that of West Africans was estimated to be 75,000 years ago. Both the haplotype and MSMC analyses thus suggest a predominant northern route out of Africa via Egypt.
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Affiliation(s)
- Luca Pagani
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK; Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 1QH, UK; Department of Biological, Geological, and Environmental Sciences, University of Bologna, 40126 Bologna, Italy.
| | - Stephan Schiffels
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Deepti Gurdasani
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Petr Danecek
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Aylwyn Scally
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Yuan Chen
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Marc Haber
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK; The Lebanese American University, Chouran, Beirut 1102 2801, Lebanon
| | - Rosemary Ekong
- Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK
| | - Tamiru Oljira
- University of Addis Ababa and Center of Human Genetic Diversity, PO Box 1176, Ethiopia
| | - Ephrem Mekonnen
- University of Addis Ababa and Center of Human Genetic Diversity, PO Box 1176, Ethiopia
| | - Donata Luiselli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
| | - Neil Bradman
- Henry Stewart Group, 28/30 Little Russell Street, London WC1A 2HN, UK
| | - Endashaw Bekele
- University of Addis Ababa and Center of Human Genetic Diversity, PO Box 1176, Ethiopia
| | - Pierre Zalloua
- The Lebanese American University, Chouran, Beirut 1102 2801, Lebanon; Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Richard Durbin
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Toomas Kivisild
- Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
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Pugach I, Stoneking M. Genome-wide insights into the genetic history of human populations. INVESTIGATIVE GENETICS 2015; 6:6. [PMID: 25834724 PMCID: PMC4381409 DOI: 10.1186/s13323-015-0024-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 03/05/2015] [Indexed: 12/21/2022]
Abstract
Although mtDNA and the non-recombining Y chromosome (NRY) studies continue to provide valuable insights into the genetic history of human populations, recent technical, methodological and computational advances and the increasing availability of large-scale, genome-wide data from contemporary human populations around the world promise to reveal new aspects, resolve finer points, and provide a more detailed look at our past demographic history. Genome-wide data are particularly useful for inferring migrations, admixture, and fine structure, as well as for estimating population divergence and admixture times and fluctuations in effective population sizes. In this review, we highlight some of the stories that have emerged from the analyses of genome-wide SNP genotyping data concerning the human history of Southern Africa, India, Oceania, Island South East Asia, Europe and the Americas and comment on possible future study directions. We also discuss advantages and drawbacks of using SNP-arrays, with a particular focus on the ascertainment bias, and ways to circumvent it.
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Affiliation(s)
- Irina Pugach
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D04103 Leipzig, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D04103 Leipzig, Germany
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Guéritée J, House JR, Redortier B, Tipton MJ. The determinants of thermal comfort in cool water. Scand J Med Sci Sports 2014; 25:e459-71. [DOI: 10.1111/sms.12360] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2014] [Indexed: 01/15/2023]
Affiliation(s)
- J. Guéritée
- Department of Sport and Exercise Science; University of Portsmouth; Portsmouth UK
| | - J. R. House
- Department of Sport and Exercise Science; University of Portsmouth; Portsmouth UK
| | - B. Redortier
- Thermal comfort laboratory; Oxylane Research; Villeneuve d'Ascq France
| | - M. J. Tipton
- Department of Sport and Exercise Science; University of Portsmouth; Portsmouth UK
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Kopp GH, Roos C, Butynski TM, Wildman DE, Alagaili AN, Groeneveld LF, Zinner D. Out of Africa, but how and when? The case of hamadryas baboons (Papio hamadryas). J Hum Evol 2014; 76:154-64. [PMID: 25257698 DOI: 10.1016/j.jhevol.2014.08.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 08/07/2014] [Accepted: 08/07/2014] [Indexed: 11/30/2022]
Abstract
Many species of Arabian mammals are considered to be of Afrotropical origin and for most of them the Red Sea has constituted an obstacle for dispersal since the Miocene-Pliocene transition. There are two possible routes, the 'northern' and the 'southern', for terrestrial mammals (including humans) to move between Africa and Arabia. The 'northern route', crossing the Sinai Peninsula, is confirmed for several taxa by an extensive fossil record, especially from northern Egypt and the Levant, whereas the 'southern route', across the Bab-el-Mandab Strait, which links the Red Sea with the Gulf of Aden, is more controversial, although post-Pliocene terrestrial crossings of the Red Sea might have been possible during glacial maxima when sea levels were low. Hamadryas baboons (Papio hamadryas) are the only baboon taxon to disperse out of Africa and still inhabit Arabia. In this study, we investigate the origin of Arabian hamadryas baboons using mitochondrial sequence data from 294 samples collected in Arabia and Northeast Africa. Through the analysis of the geographic distribution of genetic diversity, the timing of population expansions, and divergence time estimates combined with palaeoecological data, we test: (i) if Arabian and African hamadryas baboons are genetically distinct; (ii) if Arabian baboons exhibit population substructure; and (iii) when, and via which route, baboons colonized Arabia. Our results suggest that hamadryas baboons colonized Arabia during the Late Pleistocene (130-12 kya [thousands of years ago]) and also moved back to Africa. We reject the hypothesis that hamadryas baboons were introduced to Arabia by humans, because the initial colonization considerably predates the earliest records of human seafaring in this region. Our results strongly suggest that the 'southern route' from Africa to Arabia could have been used by hamadryas baboons during the same time period as proposed for modern humans.
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Affiliation(s)
- Gisela H Kopp
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany.
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany.
| | - Thomas M Butynski
- King Khalid Wildlife Research Centre, Saudi Wildlife Authority, P.O. Box 61681, Riyadh 11575, Saudi Arabia; Conservation Programs, Zoological Society of London, Regent's Park, London NW1 4RY, United Kingdom.
| | - Derek E Wildman
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 540 E. Canfield Ave. 3240 Scott Hall, Detroit, MI 48220, USA.
| | - Abdulaziz N Alagaili
- KSU Mammals Research Chair, Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia; Saudi Wildlife Authority, P.O. Box 61681, Riyadh 11575, Saudi Arabia.
| | | | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany.
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Duggan AT, Stoneking M. Recent developments in the genetic history of East Asia and Oceania. Curr Opin Genet Dev 2014; 29:9-14. [PMID: 25170982 DOI: 10.1016/j.gde.2014.06.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 06/30/2014] [Indexed: 01/11/2023]
Abstract
Recent developments in our understanding of the genetic history of Asia and Oceania have been driven by technological advances. Specifically, our understanding of the past has been augmented by: genome sequences from ancient hominins and ancient modern humans; more comprehensive studies of existing populations (e.g., complete mtDNA genome sequences and genome-wide data) and the development of new statistics and analytical methods to interpret the abundance of new data. We review some of the new discoveries since we entered the age of archaic and modern genomics and how they have changed our understanding of the settlement and subsequent population dynamics in Asia and the Pacific.
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Affiliation(s)
- Ana T Duggan
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D04103 Leipzig, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D04103 Leipzig, Germany.
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Mokhtar SS, Marshall CR, Phipps ME, Thiruvahindrapuram B, Lionel AC, Scherer SW, Peng HB. Novel population specific autosomal copy number variation and its functional analysis amongst Negritos from Peninsular Malaysia. PLoS One 2014; 9:e100371. [PMID: 24956385 PMCID: PMC4067311 DOI: 10.1371/journal.pone.0100371] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 05/23/2014] [Indexed: 01/21/2023] Open
Abstract
Copy number variation (CNV) has been recognized as a major contributor to human genome diversity. It plays an important role in determining phenotypes and has been associated with a number of common and complex diseases. However CNV data from diverse populations is still limited. Here we report the first investigation of CNV in the indigenous populations from Peninsular Malaysia. We genotyped 34 Negrito genomes from Peninsular Malaysia using the Affymetrix SNP 6.0 microarray and identified 48 putative novel CNVs, consisting of 24 gains and 24 losses, of which 5 were identified in at least 2 unrelated samples. These CNVs appear unique to the Negrito population and were absent in the DGV, HapMap3 and Singapore Genome Variation Project (SGVP) datasets. Analysis of gene ontology revealed that genes within these CNVs were enriched in the immune system (GO:0002376), response to stimulus mechanisms (GO:0050896), the metabolic pathways (GO:0001852), as well as regulation of transcription (GO:0006355). Copy number gains in CNV regions (CNVRs) enriched with genes were significantly higher than the losses (P value <0.001). In view of the small population size, relative isolation and semi-nomadic lifestyles of this community, we speculate that these CNVs may be attributed to recent local adaptation of Negritos from Peninsular Malaysia.
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Affiliation(s)
- Siti Shuhada Mokhtar
- Institute of Medical Molecular Biotechnology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
| | - Christian R. Marshall
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Maude E. Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Sunway Campus, Selangor, Malaysia
| | | | - Anath C. Lionel
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Stephen W. Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Hoh Boon Peng
- Institute of Medical Molecular Biotechnology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
- * E-mail:
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