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Pereira AG, Antonelli A, Silvestro D, Faurby S. Two Major Extinction Events in the Evolutionary History of Turtles: One Caused by an Asteroid, the Other by Hominins. Am Nat 2024; 203:644-654. [PMID: 38781523 DOI: 10.1086/729604] [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] [Indexed: 05/25/2024]
Abstract
AbstractWe live in a time of accelerated biological extinctions that has the potential to mirror past mass extinction events. However, the rarity of mass extinctions and the restructuring of diversity they cause complicate direct comparisons between the current extinction crisis and earlier events. Among animals, turtles (Testudinata) are one of few groups that have both a rich fossil record and sufficiently stable ecological and functional roles to enable meaningful comparisons between the end-Cretaceous mass extinction (∼66 Ma) and the ongoing wave of extinctions. Here we analyze the fossil record of the entire turtle clade and identify two peaks in extinction rates over their evolutionary history. The first coincides with the Cretaceous-Paleogene transition, reflecting patterns previously reported for other taxa. The second major extinction event started in the Pliocene and continues until now. This peak is detectable only for terrestrial turtles and started much earlier in Africa and Eurasia than elsewhere. On the basis of the timing, geography, and functional group of this extinction event, we postulate a link to co-occurring hominins rather than climate change as the cause. These results lend further support to the view that negative biodiversity impacts were already incurred by our ancestors and related lineages and demonstrate the severity of this continued impact through human activities.
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Aragoncillo-del Río J, Alcolea-González JJ, Luque L, Castillo-Jiménez S, Jiménez-Gisbert G, López-Sáez JA, Maíllo-Fernández JM, Ruiz-Alonso M, Triguero I, Yravedra J, Alcaraz-Castaño M. Human occupations of upland and cold environments in inland Spain during the Last Glacial Maximum and Heinrich Stadial 1: The new Magdalenian sequence of Charco Verde II. PLoS One 2023; 18:e0291516. [PMID: 37792682 PMCID: PMC10550185 DOI: 10.1371/journal.pone.0291516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 08/30/2023] [Indexed: 10/06/2023] Open
Abstract
The settlement of cold and arid environments by Pleistocene hunter-gatherers has been a heated topic in Paleolithic Archaeology and the Quaternary Sciences for years. In the Iberian Peninsula, a key area for studying human adaptations to such environments is composed by the large interior and upland regions of the northern and southern plateaus (Mesetas) and bordering areas. As, traditionally, these regions have been relatively under-investigated compared to the ecologically more favored coastal areas of the peninsula, our knowledge of the human settlement of the whole Iberian hinterland remains scarce for the Last Glacial. In this paper we present the discovery and first geoarcheological, paleoenvironmental and chronometric evidence obtained at Charco Verde II, a new site close to the southwestern foothills of the Iberian system range (Guadalajara province, Spain), bearing a sequence of Magdalenian human occupations starting at least at 20.8-21.4 ka cal BP during the Last Glacial Maximum, and covering Greenland Stadial 2 until ∼15.1-16.6 ka cal BP, including Heinrich stadial 1. As this site is located in an upland region which today faces one of the harshest climates in Iberia, such occupation sequence, occurred during some of the coldest and most arid phases of the Last Glacial, has relevant implications for our understanding of human-environment-climate interactions and population dynamics in Iberia and Western Europe. These findings support the hypothesis that the Iberian hinterland was not avoided by Upper Paleolithic hunter-gatherers due to ecological constraints, but it hosted a complex and relatively dense settlement at least in some areas, even during cold periods. This suggest, one more time, that the historical scarcity of Upper Paleolithic sites in inland Iberia is, to a significant extent, an artifact of research bias.
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Affiliation(s)
- Javier Aragoncillo-del Río
- Molina-Alto Tajo UNESCO Global Geopark, Molina de Aragón, Guadalajara, Spain
- Escuela Internacional de Doctorado de la UNED (EIDUNED), Madrid, Spain
| | | | - Luis Luque
- Area of Prehistory (Department of History and Philosophy), University of Alcalá, Alcalá de Henares, Spain
| | - Samuel Castillo-Jiménez
- Area of Prehistory (Department of History and Philosophy), University of Alcalá, Alcalá de Henares, Spain
| | - Guillermo Jiménez-Gisbert
- Area of Prehistory (Department of History and Philosophy), University of Alcalá, Alcalá de Henares, Spain
| | | | - José-Manuel Maíllo-Fernández
- Institute of Evolution in Africa (IDEA), University of Alcalá, Madrid, Spain
- Department of Prehistory and Archaeology, Universidad Nacional de Educación a Distancia (UNED), Madrid, Spain
| | - Mónica Ruiz-Alonso
- Environmental Archeology Research Group, Institute of History, CCHS CSIC, Madrid, Spain
| | - Ignacio Triguero
- Area of Prehistory (Department of History and Philosophy), University of Alcalá, Alcalá de Henares, Spain
| | - José Yravedra
- Department of Prehistory, Ancient History and Archaeology, Complutense University, Madrid, Spain
| | - Manuel Alcaraz-Castaño
- Area of Prehistory (Department of History and Philosophy), University of Alcalá, Alcalá de Henares, Spain
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3
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Bacon AM, Bourgon N, Dufour E, Demeter F, Zanolli C, Westaway KE, Joannes-Boyau R, Duringer P, Ponche JL, Morley MW, Suzzoni E, Frangeul S, Boesch Q, Antoine PO, Boualaphane S, Sichanthongtip P, Sihanam D, Huong NTM, Tuan NA, Fiorillo D, Tombret O, Patole-Edoumba E, Zachwieja A, Luangkhoth T, Souksavatdy V, Dunn TE, Shackelford L, Hublin JJ. Palaeoenvironments and hominin evolutionary dynamics in southeast Asia. Sci Rep 2023; 13:16165. [PMID: 37758744 PMCID: PMC10533506 DOI: 10.1038/s41598-023-43011-2] [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: 04/07/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Secure environmental contexts are crucial for hominin interpretation and comparison. The discovery of a Denisovan individual and associated fauna at Tam Ngu Hao 2 (Cobra) Cave, Laos, dating back to 164-131 ka, allows for environmental comparisons between this (sub)tropical site and the Palearctic Denisovan sites of Denisova Cave (Russia) and Baishiya Karst Cave (China). Denisovans from northern latitudes foraged in a mix of forested and open landscapes, including tundra and steppe. Using stable isotope values from the Cobra Cave assemblage, we demonstrate that, despite the presence of nearby canopy forests, the Denisovan individual from Cobra Cave primarily consumed plants and/or animals from open forests and savannah. Using faunal evidence and proxy indicators of climates, results herein highlight a local expansion of rainforest at ~ 130 ka, raising questions about how Denisovans responded to this local climate change. Comparing the diet and habitat of the archaic hominin from Cobra Cave with those of early Homo sapiens from Tam Pà Ling Cave (46-43 ka), Laos, it appears that only our species was able to exploit rainforest resources.
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Affiliation(s)
- Anne-Marie Bacon
- Université Paris Cité, CNRS, BABEL UMR 8045, 75012, Paris, France.
| | - Nicolas Bourgon
- IsoTROPIC Research Group, Max Planck Institute for Geoanthropology, 07745, Jena, Germany
- Max Planck Institute for Evolutionary Anthropology, Department of Human Evolution, 04103, Leipzig, Germany
| | - Elise Dufour
- UMR 7209 Archéozoologie, Archéobotanique, Sociétés, Pratiques, Environnements, MNHN, CNRS, Paris, France
| | - Fabrice Demeter
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Eco-anthropologie (EA), MNHN, CNRS, Université Paris Cité, Musée de l'Homme, 75016, Paris, France
| | - Clément Zanolli
- Univ. Bordeaux, CNRS, MCC, PACEA, UMR 5199, 33600, Pessac, France
| | - Kira E Westaway
- 'Traps' Luminescence Dating Facility, School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Renaud Joannes-Boyau
- Geoarchaeology and Archaeometry Research Group (GARG), Southern Cross University, Lismore, NSW, Australia
| | - Philippe Duringer
- Ecole et Observatoire des Sciences de la Terre, Institut de Physique du Globe de Strasbourg, UMR 7516 CNRS, Université de Strasbourg, Strasbourg, France
| | - Jean-Luc Ponche
- Laboratoire Image, Ville Environnement, UMR 7362 UdS CNRS, Université de Strasbourg, Strasbourg, France
| | - Mike W Morley
- Flinders Microarchaeology Laboratory, Archaeology, College of Humanities and Social Sciences, Flinders University, Sturt Road, Bedford Park, Adelaide, SA, 5042, Australia
| | - Eric Suzzoni
- Spitteurs Pan, Technical Cave Supervision and Exploration, La Chapelle en Vercors, France
| | - Sébastien Frangeul
- Spitteurs Pan, Technical Cave Supervision and Exploration, La Chapelle en Vercors, France
| | - Quentin Boesch
- Ecole et Observatoire des Sciences de la Terre, Institut de Physique du Globe de Strasbourg, UMR 7516 CNRS, Université de Strasbourg, Strasbourg, France
| | - Pierre-Olivier Antoine
- Institut des Sciences de l'Évolution de Montpellier, Univ Montpellier, CNRS, IRD, Montpellier, France
| | | | | | - Daovee Sihanam
- Ministry of Information, Culture and Tourism, Vientiane, Lao PDR
| | | | | | - Denis Fiorillo
- UMR 7209 Archéozoologie, Archéobotanique, Sociétés, Pratiques, Environnements, MNHN, CNRS, Paris, France
| | - Olivier Tombret
- UMR 7209 Archéozoologie, Archéobotanique, Sociétés, Pratiques, Environnements, MNHN, CNRS, Paris, France
| | - Elise Patole-Edoumba
- Muséum d'histoire naturelle de La Rochelle, UMRU 24140 Dynamiques, interactions, interculturalité asiatiques (UBM, LRUniv), La Rochelle, France
| | - Alexandra Zachwieja
- Department of Biomedical Sciences, University of Minnesota Medical School Duluth, Duluth, USA
| | | | | | - Tyler E Dunn
- Anatomical Sciences Education Center, Oregon Health & Sciences University, Portland, OR, USA
| | - Laura Shackelford
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jean-Jacques Hublin
- Max Planck Institute for Evolutionary Anthropology, Department of Human Evolution, 04103, Leipzig, Germany
- Chaire de Paléoanthropologie, CIRB (UMR 7241-U1050), Collège de France, Paris, France
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4
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Petersen BC. An economic model and evidence of the evolution of human intelligence in the Middle Pleistocene: Climate change and assortative mating. PLoS One 2023; 18:e0287964. [PMID: 37531351 PMCID: PMC10395973 DOI: 10.1371/journal.pone.0287964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 06/19/2023] [Indexed: 08/04/2023] Open
Abstract
A main objective of this paper is to provide the first model of how climate change, working through sexual selection, could have led to dramatic increases in hominin brain size, and presumably intelligence, in the Middle Pleistocene. The model is built using core elements from the field of family economics, including assortative mating and specialization and complementarities between mates. The main assumptions are that family public goods (e.g., conversation, shelter, fire) were particularly cognitively intensive to produce and became increasingly important for child survival during glacial phases. Intermediate climates (e.g., not the depths of severe glacial phases) create the largest gains from specialization, encouraging negative assortative mating. In contrast, severe glacial phases encourage positive assortative mating because of the rising importance of family public goods. One testable hypothesis is that absence of severe glacial phases should have led to stasis in brain size. Two other testable hypotheses are that severe glacial phases should have led to speciation events, as well as increases in brain size. The evidence shows that there was a million-year stasis in cranial size prior to the start of the severe glacial phases. This stasis is broken by a speciation event (Homo heidelbergensis), with the oldest fossil evidence dated near the close of the first severe glacial phase. In the next 300 kyr, there are two additional severe glacial phases, accompanied by considerable increases in cranial capacity. The last speciation event is Homo sapiens, with the earliest fossils dated near the end of the last of these two glacial phases.
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Affiliation(s)
- Bruce C Petersen
- Department of Economics, Washington University, St. Louis, Missouri, United States of America
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5
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Chen Z, Reynolds RH, Pardiñas AF, Gagliano Taliun SA, van Rheenen W, Lin K, Shatunov A, Gustavsson EK, Fogh I, Jones AR, Robberecht W, Corcia P, Chiò A, Shaw PJ, Morrison KE, Veldink JH, van den Berg LH, Shaw CE, Powell JF, Silani V, Hardy JA, Houlden H, Owen MJ, Turner MR, Ryten M, Al-Chalabi A. The contribution of Neanderthal introgression and natural selection to neurodegenerative diseases. Neurobiol Dis 2023; 180:106082. [PMID: 36925053 DOI: 10.1016/j.nbd.2023.106082] [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: 10/15/2022] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
Humans are thought to be more susceptible to neurodegeneration than equivalently-aged primates. It is not known whether this vulnerability is specific to anatomically-modern humans or shared with other hominids. The contribution of introgressed Neanderthal DNA to neurodegenerative disorders remains uncertain. It is also unclear how common variants associated with neurodegenerative disease risk are maintained by natural selection in the population despite their deleterious effects. In this study, we aimed to quantify the genome-wide contribution of Neanderthal introgression and positive selection to the heritability of complex neurodegenerative disorders to address these questions. We used stratified-linkage disequilibrium score regression to investigate the relationship between five SNP-based signatures of natural selection, reflecting different timepoints of evolution, and genome-wide associated variants of the three most prevalent neurodegenerative disorders: Alzheimer's disease, amyotrophic lateral sclerosis and Parkinson's disease. We found no evidence for enrichment of positively-selected SNPs in the heritability of Alzheimer's disease, amyotrophic lateral sclerosis and Parkinson's disease, suggesting that common deleterious disease variants are unlikely to be maintained by positive selection. There was no enrichment of Neanderthal introgression in the SNP-heritability of these disorders, suggesting that Neanderthal admixture is unlikely to have contributed to disease risk. These findings provide insight into the origins of neurodegenerative disorders within the evolution of Homo sapiens and addresses a long-standing debate, showing that Neanderthal admixture is unlikely to have contributed to common genetic risk of neurodegeneration in anatomically-modern humans.
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Affiliation(s)
- Zhongbo Chen
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London (UCL), London, UK; Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, UCL, London, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL, London, UK.
| | - Regina H Reynolds
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, UCL, London, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL, London, UK
| | - Antonio F Pardiñas
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Sarah A Gagliano Taliun
- Department of Medicine & Department of Neurosciences, Université de Montréal, Montréal, Québec, Canada; Montréal Heart Institute, Montréal, Québec, Canada
| | - Wouter van Rheenen
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, the Netherlands
| | - Kuang Lin
- Nuffield Department of Population Health, Oxford University, Oxford, UK
| | - Aleksey Shatunov
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Emil K Gustavsson
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, UCL, London, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL, London, UK
| | - Isabella Fogh
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Ashley R Jones
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Wim Robberecht
- Department of Neurology, University Hospital Leuven, Leuven, Belgium; Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease, Leuven, Belgium; Vesalius Research Center, Laboratory of Neurobiology, Leuven, Belgium
| | - Philippe Corcia
- ALS Center, Department of Neurology, CHRU Bretonneau, Tours, France
| | - Adriano Chiò
- Rita Levi Montalcini Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy; Azienda Ospedaliera Universitaria Città della Salute e della Scienza, Torino, Italy
| | - Pamela J Shaw
- Academic Neurology Unit, Department of Neuroscience, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, UK
| | - Karen E Morrison
- School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Jan H Veldink
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, the Netherlands
| | - Leonard H van den Berg
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, the Netherlands
| | - Christopher E Shaw
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - John F Powell
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Vincenzo Silani
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milano, Italy; Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, 20122 Milano, Italy
| | - John A Hardy
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London (UCL), London, UK; Reta Lila Weston Institute, Queen Square Institute of Neurology, UCL, London, UK; UK Dementia Research Institute, Queen Square Institute of Neurology, UCL, London, UK; NIHR University College London Hospitals Biomedical Research Centre, London, UK; Institute for Advanced Study, The Hong Kong University of Science and Technology, Hong Kong, SAR, China
| | - Henry Houlden
- Department of Neuromuscular Disease, Queen Square Institute of Neurology, UCL, London, UK
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Martin R Turner
- Nuffield Department of Clinical Neurosciences, Oxford University, Oxford, UK
| | - Mina Ryten
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, UCL, London, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL, London, UK
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
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6
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Gu L, Xia C, Yang S, Yang G. The adaptive evolution of cancer driver genes. BMC Genomics 2023; 24:215. [PMID: 37098512 PMCID: PMC10131384 DOI: 10.1186/s12864-023-09301-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 04/08/2023] [Indexed: 04/27/2023] Open
Abstract
BACKGROUND Cancer is a life-threatening disease in humans; yet, cancer genes are frequently reported to be under positive selection. This suggests an evolutionary-genetic paradox in which cancer evolves as a secondary product of selection in human beings. However, systematic investigation of the evolution of cancer driver genes is sparse. RESULTS Using comparative genomics analysis, population genetics analysis and computational molecular evolutionary analysis, the evolution of 568 cancer driver genes of 66 cancer types were evaluated at two levels, selection on the early evolution of humans (long timescale selection in the human lineage during primate evolution, i.e., millions of years), and recent selection in modern human populations (~ 100,000 years). Results showed that eight cancer genes covering 11 cancer types were under positive selection in the human lineage (long timescale selection). And 35 cancer genes covering 47 cancer types were under positive selection in modern human populations (recent selection). Moreover, SNPs associated with thyroid cancer in three thyroid cancer driver genes (CUX1, HERC2 and RGPD3) were under positive selection in East Asian and European populations, consistent with the high incidence of thyroid cancer in these populations. CONCLUSIONS These findings suggest that cancer can be evolved, in part, as a by-product of adaptive changes in humans. Different SNPs at the same locus can be under different selection pressures in different populations, and thus should be under consideration during precision medicine, especially for targeted medicine in specific populations.
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Affiliation(s)
- Langyu Gu
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510275, China.
| | - Canwei Xia
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Shiyu Yang
- The Affiliated Brain Hospital, Guangzhou Medical University, Guangzhou, 510180, Guangdong, China
| | - Guofen Yang
- Department of Gynecology, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510060, Guangdong, China.
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7
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Ghasidian E, Kafash A, Kehl M, Yousefi M, Heydari-Guran S. Modelling Neanderthals' dispersal routes from Caucasus towards east. PLoS One 2023; 18:e0281978. [PMID: 36821540 PMCID: PMC9949648 DOI: 10.1371/journal.pone.0281978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 02/05/2023] [Indexed: 02/24/2023] Open
Abstract
The study of the cultural materials associated with the Neanderthal physical remains from the sites in the Caucasus, Central Asia and Siberian Altai and adjacent areas documents two distinct techno-complexes of Micoquian and Mousterian. These findings potentially outline two dispersal routes for the Neanderthals out of Europe. Using data on topography and Palaeoclimate, we generated computer-based least-cost-path modelling for the Neanderthal dispersal routes from Caucasus towards the east. In this regard, two dispersal routes have been identified: A northern route from Greater Caucasus associated with Micoquian techno-complex towards Siberian Altai and a southern route from Lesser Caucasus associated with Mousterian towards Siberian Altai via the Southern Caspian Corridor. Based on archaeological, bio- and physio-geographical data, our model hypothesises that during climatic deterioration phases (e.g. MIS 4) the connection between Greater and Lesser Caucasus was limited. This issue perhaps resulted in the separate development and spread of two cultural groups of Micoquian and Mousterian with an input from two different population sources of Neanderthal influxes: eastern and southern Europe refugia for these two northern and southern dispersal routes respectively. Of these two, we focus on the southern dispersal route, for it comprises a 'rapid dispersal route' towards east. The significant location of the Southern Caspian corridor between high mountains of Alborz and the Caspian Sea, provided a special biogeographical zone and a refugium. This exceptional physio-geographic condition brings forward the Southern Caspian corridor as a potential place of admixture of different hominin species including Neanderthals and homo sapiens.
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Affiliation(s)
- Elham Ghasidian
- Neanderthal Museum, Mettmann, Germany
- DiyarMehr Institute for Palaeolithic Research, Kermanshah, Iran
- Institute for Prehistoric Archaeology, University of Cologne, Koln, Germany
- Institute of Geography, University of Cologne, Cologne, Germany
| | - Anooshe Kafash
- Department of Environmental Science, Faculty of Natural Resources, University of Tehran, Tehran, Iran
| | - Martin Kehl
- Institute for Prehistoric Archaeology, University of Cologne, Koln, Germany
- Institute of Geography, University of Cologne, Cologne, Germany
| | - Masoud Yousefi
- Department of Environmental Science, Faculty of Natural Resources, University of Tehran, Tehran, Iran
| | - Saman Heydari-Guran
- Neanderthal Museum, Mettmann, Germany
- DiyarMehr Institute for Palaeolithic Research, Kermanshah, Iran
- Institute for Prehistoric Archaeology, University of Cologne, Koln, Germany
- Institute of Geography, University of Cologne, Cologne, Germany
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8
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Gerschwitz‐Eidt MA, Dillenberger MS, Kadereit JW. Phylogeny of Saxifraga section Saxifraga subsection Arachnoideae (Saxifragaceae) and the origin of low elevation shade-dwelling species. Ecol Evol 2023; 13:e9728. [PMID: 36636428 PMCID: PMC9829489 DOI: 10.1002/ece3.9728] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 12/23/2022] [Indexed: 01/11/2023] Open
Abstract
Saxifraga section Saxifraga subsection Arachnoideae is a lineage of 12 species distributed mainly in the European Alps. It is unusual in terms of ecological diversification by containing both high elevation species from exposed alpine habitats and low elevation species from shady habitats such as overhanging rocks and cave entrances. Our aims are to explore which of these habitat types is ancestral, and to identify the possible drivers of this remarkable ecological diversification. Using a Hybseq DNA-sequencing approach and a complete species sample we reconstructed and dated the phylogeny of subsection Arachnoideae. Using Landolt indicator values, this phylogenetic tree was used for the reconstruction of the evolution of temperature, light and soil pH requirements in this lineage. Diversification of subsection Arachnoideae started in the late Pliocene and continued through the Pleistocene. Both diversification among and within clades was largely allopatric, and species from shady habitats with low light requirements are distributed in well-known refugia. We hypothesize that low light requirements evolved when species persisting in cold-stage refugia were forced into marginal habitats by more competitive warm-stage vegetation. While we do not claim that such competition resulted in speciation, it very likely resulted in adaptive evolution.
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Affiliation(s)
- Michael A. Gerschwitz‐Eidt
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg‐UniversitätMainzGermany
| | - Markus S. Dillenberger
- Institut für Biologie, AG Systematische Botanik und Pflanzengeographie, Freie Universität BerlinBerlinGermany
| | - Joachim W. Kadereit
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg‐UniversitätMainzGermany,Present address:
Systematik, Biodiversität und Evolution der PflanzenLudwig‐Maximilians‐Universität MünchenMunichGermany
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9
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Meneganzin A, Pievani T, Manzi G. Pan-Africanism vs. single-origin of Homo sapiens: Putting the debate in the light of evolutionary biology. Evol Anthropol 2022; 31:199-212. [PMID: 35848454 PMCID: PMC9540121 DOI: 10.1002/evan.21955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 02/23/2022] [Accepted: 06/14/2022] [Indexed: 12/03/2022]
Abstract
The scenario of Homo sapiens origin/s within Africa has become increasingly complex, with a pan-African perspective currently challenging the long-established single-origin hypothesis. In this paper, we review the lines of evidence employed in support of each model, highlighting inferential limitations and possible terminological misunderstandings. We argue that the metapopulation scenario envisaged by pan-African proponents well describes a mosaic diversification among late Middle Pleistocene groups. However, this does not rule out a major contribution that emerged from a single population where crucial derived features-notably, a globular braincase-appeared as the result of a punctuated, cladogenetic event. Thus, we suggest that a synthesis is possible and propose a scenario that, in our view, better reconciles with consolidated expectations in evolutionary theory. These indicate cladogenesis in allopatry as an ordinary pattern for the origin of a new species, particularly during phases of marked climatic and environmental instability.
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Affiliation(s)
| | | | - Giorgio Manzi
- Department of Environmental BiologySapienza University of RomeRomeItaly
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10
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Population interconnectivity over the past 120,000 years explains distribution and diversity of Central African hunter-gatherers. Proc Natl Acad Sci U S A 2022; 119:e2113936119. [PMID: 35580185 PMCID: PMC9173804 DOI: 10.1073/pnas.2113936119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We combined ethnographic, archaeological, genetic, and paleoclimatic data to model the dynamics of Central African hunter-gatherer populations over the past 120,000 years. We show, against common assumptions, that their distribution and density are explained by changing environments rather than by a displacement following recent farming expansions, and that they have maintained large population sizes and genetic diversity, despite fluctuations in niche availability. Our results provide insights into the evolution of genetic and cultural diversity in Homo sapiens. The evolutionary history of African hunter-gatherers holds key insights into modern human diversity. Here, we combine ethnographic and genetic data on Central African hunter-gatherers (CAHG) to show that their current distribution and density are explained by ecology rather than by a displacement to marginal habitats due to recent farming expansions, as commonly assumed. We also estimate the range of hunter-gatherer presence across Central Africa over the past 120,000 years using paleoclimatic reconstructions, which were statistically validated by our newly compiled dataset of dated archaeological sites. Finally, we show that genomic estimates of divergence times between CAHG groups match our ecological estimates of periods favoring population splits, and that recoveries of connectivity would have facilitated subsequent gene flow. Our results reveal that CAHG stem from a deep history of partially connected populations. This form of sociality allowed the coexistence of relatively large effective population sizes and local differentiation, with important implications for the evolution of genetic and cultural diversity in Homo sapiens.
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11
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Scerri EML, Roberts P, Yoshi Maezumi S, Malhi Y. Tropical forests in the deep human past. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200500. [PMID: 35249383 PMCID: PMC8899628 DOI: 10.1098/rstb.2020.0500] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Since Darwin, studies of human evolution have tended to give primacy to open 'savannah' environments as the ecological cradle of our lineage, with dense tropical forests cast as hostile, unfavourable frontiers. These perceptions continue to shape both the geographical context of fieldwork as well as dominant narratives concerning hominin evolution. This paradigm persists despite new, ground-breaking research highlighting the role of tropical forests in the human story. For example, novel research in Africa's rainforests has uncovered archaeological sites dating back into the Pleistocene; genetic studies have revealed very deep human roots in Central and West Africa and in the tropics of Asia and the Pacific; an unprecedented number of coexistent hominin species have now been documented, including Homo erectus, the 'Hobbit' (Homo floresiensis), Homo luzonensis, Denisovans, and Homo sapiens. Some of the earliest members of our own species to reach South Asia, Southeast Asia, Oceania and the tropical Americas have shown an unexpected rapidity in their adaptation to even some of the more 'extreme' tropical settings. This includes the early human manipulation of species and even habitats. This volume builds on these currently disparate threads and, for the first time, draws together a group of interdisciplinary, agenda-setting papers that firmly places a broader spectrum of tropical environments at the heart of the deep human past. This article is part of the theme issue 'Tropical forests in the deep human past'.
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Affiliation(s)
- Eleanor M L Scerri
- Pan-African Evolution Research Group, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745, Jena, Germany.,Department of Classics and Archaeology, University of Malta, Msida, Malta.,Department of Prehistoric Archaeology, University of Cologne, 50931 Cologne, Germany
| | - Patrick Roberts
- Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745, Jena, Germany.,School of Social Sciences, University of Queensland, Brisbane, Australia
| | - S Yoshi Maezumi
- Department of Ecosystem and Landscape Dynamics, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Yadvinder Malhi
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, South Parks Road, Oxford OX1 3QY, UK
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12
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Blinkhorn J, Timbrell L, Grove M, Scerri EML. Evaluating refugia in recent human evolution in Africa. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200485. [PMID: 35249393 PMCID: PMC8899617 DOI: 10.1098/rstb.2020.0485] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 01/21/2022] [Indexed: 11/12/2022] Open
Abstract
Homo sapiens have adapted to an incredible diversity of habitats around the globe. This capacity to adapt to different landscapes is clearly expressed within Africa, with Late Pleistocene Homo sapiens populations occupying savannahs, woodlands, coastlines and mountainous terrain. As the only area of the world where Homo sapiens have clearly persisted through multiple glacial-interglacial cycles, Africa is the only continent where classic refugia models can be formulated and tested to examine and describe changing patterns of past distributions and human phylogeographies. The potential role of refugia has frequently been acknowledged in the Late Pleistocene palaeoanthropological literature, yet explicit identification of potential refugia has been limited by the patchy nature of palaeoenvironmental and archaeological records, and the low temporal resolution of climate or ecological models. Here, we apply potential climatic thresholds on human habitation, rooted in ethnographic studies, in combination with high-resolution model datasets for precipitation and biome distributions to identify persistent refugia spanning the Late Pleistocene (130-10 ka). We present two alternate models suggesting that between 27% and 66% of Africa may have provided refugia to Late Pleistocene human populations, and examine variability in precipitation, biome and ecotone distributions within these refugial zones. This article is part of the theme issue 'Tropical forests in the deep human past'.
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Affiliation(s)
- James Blinkhorn
- Pan-African Evolution Research Group, Max Planck Institute for the Science of Human History, Jena, Germany
- Centre for Quaternary Research, Department of Geography, Royal Holloway, University of London, Egham, UK
| | - Lucy Timbrell
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
| | - Matt Grove
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
| | - Eleanor M. L. Scerri
- Pan-African Evolution Research Group, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Classics and Archaeology, University of Malta, Msida, Malta
- Institute of Prehistoric Archaeology, University of Cologne, Cologne, Germany
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13
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Zhang P, Zhang X, Zhang X, Gao X, Huerta-Sanchez E, Zwyns N. Denisovans and Homo sapiens on the Tibetan Plateau: dispersals and adaptations. Trends Ecol Evol 2022; 37:257-267. [PMID: 34863581 PMCID: PMC9140327 DOI: 10.1016/j.tree.2021.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/31/2021] [Accepted: 11/01/2021] [Indexed: 10/19/2022]
Abstract
Recent archaeological discoveries suggest that both archaic Denisovans and Homo sapiens occupied the Tibetan Plateau earlier than expected. Genetic studies show that a pulse of Denisovan introgression was involved in the adaptation of Tibetan populations to high-altitude hypoxia. These findings challenge the traditional view that the plateau was one of the last places on earth colonized by H. sapiens and warrant a reappraisal of the population history of this highland. Here, we integrate archaeological and genomic evidence relevant to human dispersal, settlement, and adaptation in the region. We propose two testable models to address the peopling of the plateau in the broader context of H. sapiens dispersal and their encounters with Denisovans in Asia.
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Affiliation(s)
- Peiqi Zhang
- Department of Anthropology, University of California, Davis, CA 95616, USA.
| | - Xinjun Zhang
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Xiaoling Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; CAS Center for Excellence in Life and Paleoenvironment, Beijing 10044, China
| | - Xing Gao
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; CAS Center for Excellence in Life and Paleoenvironment, Beijing 10044, China
| | - Emilia Huerta-Sanchez
- Department of Ecology and Evolutionary Biology and Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
| | - Nicolas Zwyns
- Department of Anthropology, University of California, Davis, CA 95616, USA; Department of Human Evolution, Max Planck Insititute for Evolutionary Anthropology, Leipzig 04103, Germany
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14
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Branco C, Kanellou M, González-Martín A, Arenas M. Consequences of the Last Glacial Period on the Genetic Diversity of Southeast Asians. Genes (Basel) 2022; 13:genes13020384. [PMID: 35205429 PMCID: PMC8871837 DOI: 10.3390/genes13020384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/12/2022] [Accepted: 02/15/2022] [Indexed: 11/17/2022] Open
Abstract
The last glacial period (LGP) promoted a loss of genetic diversity in Paleolithic populations of modern humans from diverse regions of the world by range contractions and habitat fragmentation. However, this period also provided some currently submersed lands, such as the Sunda shelf in Southeast Asia (SEA), that could have favored the expansion of our species. Concerning the latter, still little is known about the influence of the lowering sea level on the genetic diversity of current SEA populations. Here, we applied approximate Bayesian computation, based on extensive spatially explicit computer simulations, to evaluate the fitting of mtDNA data from diverse SEA populations with alternative evolutionary scenarios that consider and ignore the LGP and migration through long-distance dispersal (LDD). We found that both the LGP and migration through LDD should be taken into consideration to explain the currently observed genetic diversity in these populations and supported a rapid expansion of first populations throughout SEA. We also found that temporarily available lands caused by the low sea level of the LGP provided additional resources and migration corridors that favored genetic diversity. We conclude that migration through LDD and temporarily available lands during the LGP should be considered to properly understand and model the first expansions of modern humans.
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Affiliation(s)
- Catarina Branco
- Centro de Investigaciones Biomédicas (CINBIO), University of Vigo, 36310 Vigo, Spain; (C.B.); (M.K.)
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
| | - Marina Kanellou
- Centro de Investigaciones Biomédicas (CINBIO), University of Vigo, 36310 Vigo, Spain; (C.B.); (M.K.)
- School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Antonio González-Martín
- Department of Biodiversity, Ecology and Evolution, University Complutense of Madrid, 28040 Madrid, Spain;
| | - Miguel Arenas
- Centro de Investigaciones Biomédicas (CINBIO), University of Vigo, 36310 Vigo, Spain; (C.B.); (M.K.)
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
- Correspondence: ; Tel.: +34-986-130-047
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15
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Sultana RG. The labour market integration of migrants and refugees: career guidance and the newly arrived. INTERNATIONAL JOURNAL FOR EDUCATIONAL AND VOCATIONAL GUIDANCE 2022; 22:491-510. [PMID: 35194477 PMCID: PMC8853372 DOI: 10.1007/s10775-022-09529-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
This scoping paper sets out to consider various aspects of the phenomenon of people on the move, and to examine some of the ways in which career guidance has responded to the challenge of integrating the newly arrived. The paper is informed by a recognition of the dignity of individuals above any classificatory system that places persons in a hierarchy, with some having access to rights that others are denied. This stance requires career practitioners to confront the prevalent vocabulary, discourses and attitudes circulating in the mainstream in order to become aware of-and to overcome-personal prejudice, thus opening up possibilities for more socially just forms of service. A synthesis of relevant literature concerning the integration of migrants and refugees in the labour market is provided in order to signpost emancipatory forms of career guidance, ones that move beyond an emphasis on individual resilience to take seriously the impact of exclusionary social practices and structures. The paper concludes by highlighting a number of initiatives that suggest that career guidance is rising to the challenge of catering for a diverse group of newly arrived by mobilising theoretical frameworks that are fit for purpose, by developing bespoke training programmes for practitioners, and by sharing the lessons learnt from the field.
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Affiliation(s)
- Ronald G. Sultana
- Euro-Mediterranean Centre for Educational Research, University of Malta, Msida, MSD2080 Malta
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16
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Bretzke K, Preusser F, Jasim S, Miller C, Preston G, Raith K, Underdown SJ, Parton A, Parker AG. Multiple phases of human occupation in Southeast Arabia between 210,000 and 120,000 years ago. Sci Rep 2022; 12:1600. [PMID: 35102262 PMCID: PMC8803878 DOI: 10.1038/s41598-022-05617-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 01/13/2022] [Indexed: 11/21/2022] Open
Abstract
Changing climatic conditions are thought to be a major control of human presence in Arabia during the Paleolithic. Whilst the Pleistocene archaeological record shows that periods of increased monsoon rainfall attracted human occupation and led to increased population densities, the impact of arid conditions on human populations in Arabia remains largely speculative. Here, we present data from Jebel Faya in Southeast (SE) Arabia, which document four periods of human occupation between c. 210,000 and 120,000 years ago. The Jebel Faya record indicates that human occupation of SE Arabia was more regular and not exclusively linked to major humid periods. Our data show that brief phases of increased rainfall additionally enabled human settlement in the Faya region. These results imply that the mosaic environments in SE Arabia have likely formed a population refugia at the end of the Middle and the beginning of the Late Pleistocene.
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17
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Perception of Climate Change Effects over Time and the Contribution of Different Areas of Knowledge to Its Understanding and Mitigation. CLIMATE 2022. [DOI: 10.3390/cli10010007] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Climate change is a current subject that is attracting more and more attention, whether from academics or the public. This public attention is mainly due to the frequently published news in the media, reporting consequences caused by extreme weather events. On the other hand, scientists are looking into the origins of the phenomenon, seeking answers that will somehow help to mitigate the effects of climate change. This article presents a review of some of the different possible approaches taken on climate change, to demonstrate the need to build a multidisciplinary perspective of the problem. It is understood that only the integration of different perspectives, presented by different areas of knowledge, such as natural sciences, social and economic sciences and human sciences, will make it possible to build modeling and predictive scenarios, which realistically may represent the development of the earth system under the influence of climate change. In this way, with the support of all areas of knowledge, the creation of forecast models where all possible changes to the different variables of the earth system may be simulated will allow for the mitigation measures presented to be analyzed in advance and, thus, prioritized. This review shows that a multi and interdisciplinary approach, based on the knowledge acquired from different knowledge and science fields, presents itself as the way to solve this global and complex problem caused by climate change.
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18
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Tejero JM, Bar-Oz G, Bar-Yosef O, Meshveliani T, Jakeli N, Matskevich Z, Pinhasi R, Belfer-Cohen A. New insights into the Upper Palaeolithic of the Caucasus through the study of personal ornaments. Teeth and bones pendants from Satsurblia and Dzudzuana caves (Imereti, Georgia). PLoS One 2021; 16:e0258974. [PMID: 34748581 PMCID: PMC8575301 DOI: 10.1371/journal.pone.0258974] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 10/09/2021] [Indexed: 11/18/2022] Open
Abstract
The region of western Georgia (Imereti) in the Southern Caucasus has been a major geographic corridor for human migrations during the Middle and Upper Paleolithic. Data of recent research and excavations in this region display its importance as a possible route for the dispersal of anatomically modern humans (AMH) into northern Eurasia. Nevertheless, within the local research context, bone-working and personal ornaments have yet contributed but little to the Upper Palaeolithic (UP) regional sequence's characterization. Here we present an archaeozoological, technological and use-wear study of pendants from two local UP assemblages, originating in the Dzudzuana Cave and Satsurblia Cave. The ornaments were made mostly of perforated teeth, though some specimens were made on bone. Both the manufacturing marks made during preparation and use-wear traces indicate that they were personal ornaments, used as pendants or attached to garments. Detailed comparison between ornament assemblages from northern and southern Caucasus reveal that they are quite similar, supporting the observation of cultural bonds between the two regions, demonstrated previously through lithic techno-typological affinities. Furthermore, our study highlights the importance attributed to red deer (Cervus elaphus) by the UP societies of the Caucasus in sharing aesthetic values and/or a symbolic sphere.
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Affiliation(s)
- José-Miguel Tejero
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Seminari d’Estudis I Recerques Prehistòriques, Universitat de Barcelona, Barcelona, Spain
| | - Guy Bar-Oz
- Zinman Institute of Archaeology, University of Haifa, Haifa, Israel
| | - Ofer Bar-Yosef
- Department of Anthropology, Harvard University, Cambridge, MA, United States of America
| | | | | | | | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Anna Belfer-Cohen
- Institute of Archaeology, The Hebrew University of Jerusalem, Jerusalem, Israel
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19
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Holte SJ, Ohmann PR. Childhood in social learning models with changing environments: Implications for human evolution. Biosystems 2021; 210:104555. [PMID: 34601073 DOI: 10.1016/j.biosystems.2021.104555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/03/2021] [Accepted: 09/28/2021] [Indexed: 10/20/2022]
Abstract
Childhood is a time of learning, both individually and through social interactions. But the vulnerability inherent in childhood represents a fitness cost: individuals do not have progeny during childhood, and childhood is a net drain of familial or group resources. In this study we model childhood in resource acquisition scenarios where social learning through observation competes with learning through innovation across multiple generations in a variety of environments. In general, observing others allows useful knowledge to be gained more efficiently than self-exploration and may result in significantly greater resource acquisition. However, social learning needing a lengthy childhood to develop advanced cognitive ability may offset the net fitness advantage that might otherwise be gained. Through simulations we demonstrate that individuals with a substantial childhood burden acquire more lifetime resources by observing others than do individuals with negligible childhood costs using self-exploration, as long as the environment is fairly stable. This advantage decreases as the environment becomes less predictable, and reverses in rapidly changing environments where knowledge is unreliable. These results suggest that hominid evolution, with vastly growing cognitive abilities and a longer, more vulnerable childhood, may have been facilitated in similarly stable environments. On the other hand, hominid populations may have been particularly vulnerable to environmental instability. We apply this insight to the Out of Africa Homo sapiens migration roughly 50,000 years ago and show consistency with the serial founder model that best fits current archeological and genetic evidence. Our findings are important for models of social learning, especially those that describe the emergence and spread of Homo sapiens.
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Affiliation(s)
- Serena J Holte
- Department of Physics, University of Saint Thomas, St. Paul MN, 55105, USA
| | - Paul R Ohmann
- Department of Physics, University of Saint Thomas, St. Paul MN, 55105, USA.
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20
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Landscape genetics and the genetic legacy of Upper Paleolithic and Mesolithic hunter-gatherers in the modern Caucasus. Sci Rep 2021; 11:17985. [PMID: 34504229 PMCID: PMC8429691 DOI: 10.1038/s41598-021-97519-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 08/26/2021] [Indexed: 11/24/2022] Open
Abstract
This study clarifies the role of refugia and landscape permeability in the formation of the current genetic structure of peoples of the Caucasus. We report novel genome-wide data for modern individuals from the Caucasus, and analyze them together with available Paleolithic and Mesolithic individuals from Eurasia and Africa in order (1) to link the current and ancient genetic structures via landscape permeability, and (2) thus to identify movement paths between the ancient refugial populations and the Caucasus. The ancient genetic ancestry is best explained by landscape permeability implying that human movement is impeded by terrain ruggedness, swamps, glaciers and desert. Major refugial source populations for the modern Caucasus are those of the Caucasus, Anatolia, the Balkans and Siberia. In Rugged areas new genetic signatures take a long time to form, but once they do so, they remain for a long time. These areas act as time capsules harboring genetic signatures of ancient source populations and making it possible to help reconstruct human history based on patterns of variation today.
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21
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Aneli S, Caldon M, Saupe T, Montinaro F, Pagani L. Through 40,000 years of human presence in Southern Europe: the Italian case study. Hum Genet 2021; 140:1417-1431. [PMID: 34410492 PMCID: PMC8460580 DOI: 10.1007/s00439-021-02328-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 07/29/2021] [Indexed: 12/16/2022]
Abstract
The Italian Peninsula, a natural pier across the Mediterranean Sea, witnessed intricate population events since the very beginning of the human occupation in Europe. In the last few years, an increasing number of modern and ancient genomes from the area have been published by the international research community. This genomic perspective started unveiling the relevance of Italy to understand the post-Last Glacial Maximum (LGM) re-peopling of Europe, the earlier phase of the Neolithic westward migrations, and its linking role between Eastern and Western Mediterranean areas after the Iron Age. However, many open questions are still waiting for more data to be addressed in full. With this review, we summarize the current knowledge emerging from the available ancient Italian individuals and, by re-analysing them all at once, we try to shed light on the avenues future research in the area should cover. In particular, open questions concern (1) the fate of pre-Villabruna Europeans and to what extent their genomic components were absorbed by the post-LGM hunter-gatherers; (2) the role of Sicily and Sardinia before LGM; (3) to what degree the documented genetic structure within the Early Neolithic settlers can be described as two separate migrations; (4) what are the population events behind the marked presence of an Iranian Neolithic-like component in Bronze Age and Iron Age Italian and Southern European samples.
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Affiliation(s)
- Serena Aneli
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy.
| | - Matteo Caldon
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy
| | - Tina Saupe
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia.,Department of Biology-Genetics, University of Bari, Via Edoardo Orabona 4, 70125, Bari, Italy
| | - Luca Pagani
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy.,Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
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22
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Chen N, Ren L, Du L, Hou J, Mullin VE, Wu D, Zhao X, Li C, Huang J, Qi X, Capodiferro MR, Achilli A, Lei C, Chen F, Su B, Dong G, Zhang X. Ancient genomes reveal tropical bovid species in the Tibetan Plateau contributed to the prevalence of hunting game until the late Neolithic. Proc Natl Acad Sci U S A 2020; 117:28150-28159. [PMID: 33077602 PMCID: PMC7668038 DOI: 10.1073/pnas.2011696117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Local wild bovids have been determined to be important prey on the northeastern Tibetan Plateau (NETP), where hunting game was a major subsistence strategy until the late Neolithic, when farming lifestyles dominated in the neighboring Loess Plateau. However, the species affiliation and population ecology of these prehistoric wild bovids in the prehistoric NETP remain unknown. Ancient DNA (aDNA) analysis is highly informative in decoding this puzzle. Here, we applied aDNA analysis to fragmented bovid and rhinoceros specimens dating ∼5,200 y B.P. from the Neolithic site of Shannashuzha located in the marginal area of the NETP. Utilizing both whole genomes and mitochondrial DNA, our results demonstrate that the range of the present-day tropical gaur (Bos gaurus) extended as far north as the margins of the NETP during the late Neolithic from ∼29°N to ∼34°N. Furthermore, comparative analysis with zooarchaeological and paleoclimatic evidence indicated that a high summer temperature in the late Neolithic might have facilitated the northward expansion of tropical animals (at least gaur and Sumatran-like rhinoceros) to the NETP. This enriched the diversity of wildlife, thus providing abundant hunting resources for humans and facilitating the exploration of the Tibetan Plateau as one of the last habitats for hunting game in East Asia.
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Affiliation(s)
- Ningbo Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), 650223 Kunming, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 712100 Yangling, China
| | - Lele Ren
- School of History and Culture, Lanzhou University, 730000 Lanzhou, China
| | - Linyao Du
- College of Earth and Environmental Sciences, Lanzhou University, 730000 Lanzhou, China
| | - Jiawen Hou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 712100 Yangling, China
| | - Victoria E Mullin
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, United Kingdom
| | - Duo Wu
- College of Earth and Environmental Sciences, Lanzhou University, 730000 Lanzhou, China
| | - Xueye Zhao
- Gansu Provincial Institute of Cultural Relics and Archaeology, 730000 Lanzhou, China
| | - Chunmei Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), 650223 Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China
| | - Jiahui Huang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), 650223 Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), 650223 Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China
| | | | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani," Università di Pavia, 27100 Pavia, Italy
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 712100 Yangling, China
| | - Fahu Chen
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, 100101 Beijing, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), 650223 Kunming, China;
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China
| | - Guanghui Dong
- College of Earth and Environmental Sciences, Lanzhou University, 730000 Lanzhou, China;
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, 100101 Beijing, China
| | - Xiaoming Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), 650223 Kunming, China;
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China
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23
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Boukhdoud L, Saliba C, Parker LD, Rotzel McInerney N, Ishak Mouawad G, Kharrat M, Kahale R, Chahine T, Maldonado JE, Bou Dagher-Kharrat M. First DNA sequence reference library for mammals and plants of the Eastern Mediterranean Region. Genome 2020; 64:39-49. [PMID: 33002384 DOI: 10.1139/gen-2019-0194] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The Mediterranean region is identified as one of the world's 36 biodiversity hotspots, with the Earth's most biologically rich yet threatened areas. Lebanon is a hub for Eastern Mediterranean Region (EMR) biodiversity with 9116 characterized plant and animal species (4486 fauna and 4630 flora). Using DNA barcoding as a tool has become crucial in the accurate identification of species in multiple contexts. It can also complement species morphological descriptions, which will add to our understanding of the biodiversity and richness of ecosystems and benefit conservation projects for endangered and endemic species. In this study, we create the first reference library of standard DNA markers for mammals and plants in the EMR, with a focus on endemic and endangered species. Plant leaves were collected from different nature reserves in Mount Lebanon, and mammal samples were obtained from taxidermized museum specimens or road kills. We generated the 12S rRNA sequences of 18 mammal species from 6 orders and 13 different families. We also obtained the trnL and rbcL barcode sequences of 52 plant species from 24 different families. Twenty-five plant species and two mammal species included in this study were sequenced for the first time using these markers.
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Affiliation(s)
- Liliane Boukhdoud
- Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Université Saint-Joseph, Campus Sciences et Technologies, Mar Roukos, Mkalles, BP: 1514 Riad el Solh, Beirut 1107 2050, Lebanon
| | - Carole Saliba
- Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Université Saint-Joseph, Campus Sciences et Technologies, Mar Roukos, Mkalles, BP: 1514 Riad el Solh, Beirut 1107 2050, Lebanon
| | - Lillian D Parker
- Smithsonian Conservation Biology Institute, Center for Conservation Genomics, National Zoological Park, 3001 Connecticut Ave. NW, Washington, DC 20008, USA.,George Mason University, Department of Biosciences, School of Systems Biology, 4400 University Dr., Fairfax, VA 22030, USA
| | - Nancy Rotzel McInerney
- Smithsonian Conservation Biology Institute, Center for Conservation Genomics, National Zoological Park, 3001 Connecticut Ave. NW, Washington, DC 20008, USA
| | - Ghiwa Ishak Mouawad
- Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Université Saint-Joseph, Campus Sciences et Technologies, Mar Roukos, Mkalles, BP: 1514 Riad el Solh, Beirut 1107 2050, Lebanon
| | - Mariane Kharrat
- Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Université Saint-Joseph, Campus Sciences et Technologies, Mar Roukos, Mkalles, BP: 1514 Riad el Solh, Beirut 1107 2050, Lebanon
| | - Rhea Kahale
- Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Université Saint-Joseph, Campus Sciences et Technologies, Mar Roukos, Mkalles, BP: 1514 Riad el Solh, Beirut 1107 2050, Lebanon
| | - Tony Chahine
- Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Université Saint-Joseph, Campus Sciences et Technologies, Mar Roukos, Mkalles, BP: 1514 Riad el Solh, Beirut 1107 2050, Lebanon
| | - Jesús E Maldonado
- Smithsonian Conservation Biology Institute, Center for Conservation Genomics, National Zoological Park, 3001 Connecticut Ave. NW, Washington, DC 20008, USA.,George Mason University, Department of Biosciences, School of Systems Biology, 4400 University Dr., Fairfax, VA 22030, USA
| | - Magda Bou Dagher-Kharrat
- Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Université Saint-Joseph, Campus Sciences et Technologies, Mar Roukos, Mkalles, BP: 1514 Riad el Solh, Beirut 1107 2050, Lebanon
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24
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New perspectives on Neanderthal dispersal and turnover from Stajnia Cave (Poland). Sci Rep 2020; 10:14778. [PMID: 32901061 PMCID: PMC7479612 DOI: 10.1038/s41598-020-71504-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/17/2020] [Indexed: 02/03/2023] Open
Abstract
The Micoquian is the broadest and longest enduring cultural facies of the Late Middle Palaeolithic that spread across the periglacial and boreal environments of Europe between Eastern France, Poland, and Northern Caucasus. Here, we present new data from the archaeological record of Stajnia Cave (Poland) and the paleogenetic analysis of a Neanderthal molar S5000, found in a Micoquian context. Our results demonstrate that the mtDNA genome of Stajnia S5000 dates to MIS 5a making the tooth the oldest Neanderthal specimen from Central-Eastern Europe. Furthermore, S5000 mtDNA has the fewest number of differences to mtDNA of Mezmaiskaya 1 Neanderthal from Northern Caucasus, and is more distant from almost contemporaneous Neanderthals of Scladina and Hohlenstein-Stadel. This observation and the technological affinity between Poland and the Northern Caucasus could be the result of increased mobility of Neanderthals that changed their subsistence strategy for coping with the new low biomass environments and the increased foraging radius of gregarious animals. The Prut and Dniester rivers were probably used as the main corridors of dispersal. The persistence of the Micoquian techno-complex in South-Eastern Europe infers that this axis of mobility was also used at the beginning of MIS 3 when a Neanderthal population turnover occurred in the Northern Caucasus.
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25
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Botta F, Dahl-Jensen D, Rahbek C, Svensson A, Nogués-Bravo D. Abrupt Change in Climate and Biotic Systems. Curr Biol 2020; 29:R1045-R1054. [PMID: 31593663 DOI: 10.1016/j.cub.2019.08.066] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Fifty years ago, Willi Dansgaard and colleagues discovered several abrupt climate change events in Greenland during the last glacial period. Since then, several ice cores retrieved from the Greenland ice sheet have verified the existence of 25 abrupt climate warming events now known as Dansgaard-Oeschger events. These events are characterized by a rapid 10-15°C warming over a few decades followed by a stable period of centuries or millennia before a gradual return to full glacial conditions. Similar warming events have been identified in other paleo-archives in the Northern hemisphere. These findings triggered wide interest in abrupt climate change and its impact on biological diversity, but ambiguous definitions have constrained our ability to assign biotic responses to the different types of climate change. Here, we provide a coherent definition for different types of climatic change, including 'abrupt climate change', and a summary of past abrupt climate-change events. We then review biotic responses to abrupt climate change, from the genetic to the ecosystem level, and show that abrupt climatic and ecological changes have been instrumental in shaping biodiversity. We also identify open questions, such as what causes species resilience after an abrupt change. However, identifying causal relationships between past climate change and biological responses remains difficult. We need to formalize and unify the definition of abrupt change across disciplines and further investigate past abrupt climate change periods to better anticipate and mitigate the impacts on biodiversity and society wrought by human-made climate change.
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Affiliation(s)
- Filippo Botta
- Center for Ice and Climate, Niels Bohr Institute, University of Copenhagen, Tagensvej 16, 2200, Copenhagen, Denmark; Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark.
| | - Dorthe Dahl-Jensen
- Center for Ice and Climate, Niels Bohr Institute, University of Copenhagen, Tagensvej 16, 2200, Copenhagen, Denmark
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark; Department of Life Sciences, Imperial College London, Ascot SL5 7PY, UK; Danish Institute for Advanced Study, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Anders Svensson
- Center for Ice and Climate, Niels Bohr Institute, University of Copenhagen, Tagensvej 16, 2200, Copenhagen, Denmark
| | - David Nogués-Bravo
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark.
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26
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Pargeter J, Khreisheh N, Shea JJ, Stout D. Knowledge vs. know-how? Dissecting the foundations of stone knapping skill. J Hum Evol 2020; 145:102807. [DOI: 10.1016/j.jhevol.2020.102807] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/02/2020] [Accepted: 04/02/2020] [Indexed: 10/24/2022]
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27
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Speleothem record attests to stable environmental conditions during Neanderthal-modern human turnover in southern Italy. Nat Ecol Evol 2020; 4:1188-1195. [PMID: 32632262 DOI: 10.1038/s41559-020-1243-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 06/09/2020] [Indexed: 11/09/2022]
Abstract
The causes of Neanderthal-modern human (MH) turnover are ambiguous. While potential biocultural interactions between the two groups are still little known, it is clear that Neanderthals in southern Europe disappeared about 42 thousand years ago (ka) after cohabitation for ~3,000 years with MH. Among a plethora of hypotheses on Neanderthal extinction, rapid climate changes during the Middle to Upper Palaeolithic transition (MUPT) are regarded as a primary factor. Here we show evidence for stable climatic and environmental conditions during the MUPT in a region (Apulia) where Neanderthals and MH coexisted. We base our findings on a rare glacial stalagmite deposited between ~106 and ~27 ka, providing the first continuous western Mediterranean speleothem palaeoclimate archive for this period. The uninterrupted growth of the stalagmite attests to the constant availability of rainfall and vegetated soils, while its δ13C-δ18O palaeoclimate proxies demonstrate that Apulia was not affected by dramatic climate oscillations during the MUPT. Our results imply that, because climate did not play a key role in the disappearance of Neanderthals in this area, Neanderthal-MH turnover must be approached from a perspective that takes into account climatic and environmental conditions favourable for both species.
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28
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Branco C, Ray N, Currat M, Arenas M. Influence of Paleolithic range contraction, admixture and long-distance dispersal on genetic gradients of modern humans in Asia. Mol Ecol 2020; 29:2150-2159. [PMID: 32436243 DOI: 10.1111/mec.15479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 12/29/2022]
Abstract
Cavalli-Sforza and coauthors originally explored the genetic variation of modern humans throughout the world and observed an overall east-west genetic gradient in Asia. However, the specific environmental and population genetics processes causing this gradient were not formally investigated and promoted discussion in recent studies. Here we studied the influence of diverse environmental and population genetics processes on Asian genetic gradients and identified which could have produced the observed gradient. To do so, we performed extensive spatially-explicit computer simulations of genetic data under the following scenarios: (a) variable levels of admixture between Paleolithic and Neolithic populations, (b) migration through long-distance dispersal (LDD), (c) Paleolithic range contraction induced by the last glacial maximum (LGM), and (d) Neolithic range expansions from one or two geographic origins (the Fertile Crescent and the Yangzi and Yellow River Basins). Next, we estimated genetic gradients from the simulated data and we found that they were sensible to the analysed processes, especially to the range contraction induced by LGM and to the number of Neolithic expansions. Some scenarios were compatible with the observed east-west genetic gradient, such as the Paleolithic expansion with a range contraction induced by the LGM or two Neolithic range expansions from both the east and the west. In general, LDD increased the variance of genetic gradients among simulations. We interpreted the obtained gradients as a consequence of both allele surfing caused by range expansions and isolation by distance along the vast east-west geographic axis of this continent.
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Affiliation(s)
- Catarina Branco
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.,Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain
| | - Nicolas Ray
- GeoHealth Group, Institute of Global Health, University of Geneva, Geneva, Switzerland.,Institute for Environmental Sciences, University of Geneva, Geneva, Switzerland
| | - Mathias Currat
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.,Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain
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29
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Potapova TA, Romashchenko AG, Yudin NS, Voevoda MI. Ethnicity-specific distribution of <em>TRPM8</em> gene variants in Eurasian populations: signs of selection. Vavilovskii Zhurnal Genet Selektsii 2020. [DOI: 10.18699/vj20.45-o] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- T. A. Potapova
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences
| | - A. G. Romashchenko
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences
| | - N. S. Yudin
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences; Novosibirsk State University
| | - M. I. Voevoda
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences;
Federal Research Center of Fundamental and Translational Medicine; Novosibirsk State University
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30
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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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31
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Ossendorf G, Groos AR, Bromm T, Tekelemariam MG, Glaser B, Lesur J, Schmidt J, Akçar N, Bekele T, Beldados A, Demissew S, Kahsay TH, Nash BP, Nauss T, Negash A, Nemomissa S, Veit H, Vogelsang R, Woldu Z, Zech W, Opgenoorth L, Miehe G. Middle Stone Age foragers resided in high elevations of the glaciated Bale Mountains, Ethiopia. Science 2020; 365:583-587. [PMID: 31395781 DOI: 10.1126/science.aaw8942] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 06/26/2019] [Indexed: 01/28/2023]
Abstract
Studies of early human settlement in alpine environments provide insights into human physiological, genetic, and cultural adaptation potentials. Although Late and even Middle Pleistocene human presence has been recently documented on the Tibetan Plateau, little is known regarding the nature and context of early persistent human settlement in high elevations. Here, we report the earliest evidence of a prehistoric high-altitude residential site. Located in Africa's largest alpine ecosystem, the repeated occupation of Fincha Habera rock shelter is dated to 47 to 31 thousand years ago. The available resources in cold and glaciated environments included the exploitation of an endemic rodent as a key food source, and this played a pivotal role in facilitating the occupation of this site by Late Pleistocene hunter-gatherers.
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Affiliation(s)
- Götz Ossendorf
- Institute of Prehistoric Archaeology, University of Cologne, Cologne, Germany.
| | | | - Tobias Bromm
- Department of Soil Biogeochemistry, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | | | - Bruno Glaser
- Department of Soil Biogeochemistry, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
| | - Joséphine Lesur
- MNHN/CNRS-UMR 7209 Archaeozoology, Archaeobotany Laboratory (AASPE), Paris, France
| | - Joachim Schmidt
- Institute of Biosciences, University of Rostock, Rostock, Germany
| | - Naki Akçar
- Institute of Geological Sciences, University of Bern, Bern, Switzerland
| | - Tamrat Bekele
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | - Alemseged Beldados
- Department of Archaeology and Heritage Management, Addis Ababa University, Addis Ababa, Ethiopia
| | - Sebsebe Demissew
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Barbara P Nash
- Department of Geology and Geophysics, University of Utah, Salt Lake City, UT, USA
| | - Thomas Nauss
- Faculty of Geography, Philipps University Marburg, Marburg, Germany
| | - Agazi Negash
- Paleoanthropology and Paleoenvironment Program, Addis Ababa University, Addis Ababa, Ethiopia
| | - Sileshi Nemomissa
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | - Heinz Veit
- Institute of Geography, University of Bern, Bern, Switzerland
| | - Ralf Vogelsang
- Institute of Prehistoric Archaeology, University of Cologne, Cologne, Germany
| | - Zerihun Woldu
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | - Wolfgang Zech
- Institute of Soil Science and Soil Geography, University of Bayreuth, Bayreuth, Germany
| | - Lars Opgenoorth
- Department of Ecology, Philipps University Marburg, Marburg, Germany.,Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Georg Miehe
- Faculty of Geography, Philipps University Marburg, Marburg, Germany
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32
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Non-Pessimistic Predictions of the Distributions and Suitability of Metasequoia glyptostroboides under Climate Change Using a Random Forest Model. FORESTS 2020. [DOI: 10.3390/f11010062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Metasequoia glyptostroboides Hu & W. C. Cheng, which is a remarkable rare relict plant, has gradually been reduced to its current narrow range due to climate change. Understanding the comprehensive distribution of M. glyptostroboides under climate change on a large spatio-temporal scale is of great significance for determining its forest adaptation. In this study, based on 394 occurrence data and 10 bioclimatic variables, the global potential distribution of M. glyptostroboides under eight different climate scenarios (i.e., the past three, the current one, and the next four) from the Quaternary glacial to the future was simulated by a random forest model built with the biomod2 package. The key bioclimatic variables affecting the distribution of M. glyptostroboides are BIO2 (mean diurnal range), BIO1 (annual mean temperature), BIO9 (mean temperature of driest quarter), BIO6 (min temperature of coldest month), and BIO18 (precipitation of warmest quarter). The result indicates that the temperature affects the potential distribution of M. glyptostroboides more than the precipitation. A visualization of the results revealed that the current relatively suitable habitats of M. glyptostroboides are mainly distributed in East Asia and Western Europe, with a total area of approximately 6.857 × 106 km2. With the intensification of global warming in the future, the potential distribution and the suitability of M. glyptostroboides have a relatively non-pessimistic trend. Whether under the mild (RCP4.5) and higher (RCP8.5) emission scenarios, the total area of suitable habitats will be wider than it is now by the 2070s, and the habitat suitability will increase to varying degrees within a wide spatial range. After speculating on the potential distribution of M. glyptostroboides in the past, the glacial refugia of M. glyptostroboides were inferred, and projections regarding the future conditions of these places are expected to be optimistic. In order to better protect the species, the locations of its priority protected areas and key protected areas, mainly in Western Europe and East Asia, were further identified. Our results will provide theoretical reference for the long-term management of M. glyptostroboides, and can be used as background information for the restoration of other endangered species in the future.
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33
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Fellag M, Loukil A, Saad J, Lepidi H, Bouzid F, Brégeon F, Drancourt M. Translocation of Mycobacterium tuberculosis after experimental ingestion. PLoS One 2019; 14:e0227005. [PMID: 31887178 PMCID: PMC6936814 DOI: 10.1371/journal.pone.0227005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 12/09/2019] [Indexed: 02/04/2023] Open
Abstract
Human tuberculosis is a life-threatening infection following the inhalation of Mycobacterium tuberculosis, while the closely related bacteria Mycobacterium bovis and Mycobacterium canettii are thought to be transmitted by ingestion. To explore whether M. tuberculosis could also infect individuals by ingestion, male BALBc mice were fed 2 x 106 CFUs of M. tuberculosis Beijing or phosphate-buffered saline as a negative control, over a 28-day experiment. While eight negative control mice remained disease-free, M. tuberculosis was identified in the lymph nodes and lungs of 8/14 mice and in the spleens of 4/14 mice by microscopy, PCR-based detection and culture. Whole-genome sequencing confirmed the identity of the inoculum and the tissue isolates. In these genetically identical mice, the dissemination of M. tuberculosis correlated with the results of the culture detection of four intestinal bacteria. These observations indicate that ingested M. tuberculosis mycobacteria can translocate, notably provoking lymphatic tuberculosis.
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Affiliation(s)
- Mustapha Fellag
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Ahmed Loukil
- Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Jamal Saad
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Hubert Lepidi
- Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Fériel Bouzid
- Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Fabienne Brégeon
- Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Michel Drancourt
- Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- * E-mail:
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34
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Gokcumen O. Archaic hominin introgression into modern human genomes. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 171 Suppl 70:60-73. [PMID: 31702050 DOI: 10.1002/ajpa.23951] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/04/2019] [Accepted: 10/08/2019] [Indexed: 01/01/2023]
Abstract
Ancient genomes from multiple Neanderthal and the Denisovan individuals, along with DNA sequence data from diverse contemporary human populations strongly support the prevalence of gene flow among different hominins. Recent studies now provide evidence for multiple gene flow events that leave genetic signatures in extant and ancient human populations. These events include older gene flow from an unknown hominin in Africa predating out-of-Africa migrations, and in the last 50,000-100,000 years, multiple gene flow events from Neanderthals into ancestral Eurasian human populations, and at least three distinct introgression events from a lineage close to Denisovans into ancestors of extant Southeast Asian and Oceanic populations. Some of these introgression events may have happened as late as 20,000 years before present and reshaped the way in which we think about human evolution. In this review, I aim to answer anthropologically relevant questions with regard to recent research on ancient hominin introgression in the human lineage. How have genomic data from archaic hominins changed our view of human evolution? Is there any doubt about whether introgression from ancient hominins to the ancestors of present-day humans occurred? What is the current view of human evolutionary history from the genomics perspective? What is the impact of introgression on human phenotypes?
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Affiliation(s)
- Omer Gokcumen
- Department of Biological Sciences, North Campus, University at Buffalo, Buffalo, New York
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35
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Cultural bistability and connectedness in a subdivided population. Theor Popul Biol 2019; 129:103-117. [DOI: 10.1016/j.tpb.2019.03.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 02/06/2019] [Accepted: 03/19/2019] [Indexed: 02/05/2023]
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36
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Carter T, Contreras DA, Holcomb J, Mihailović DD, Karkanas P, Guérin G, Taffin N, Athanasoulis D, Lahaye C. Earliest occupation of the Central Aegean (Naxos), Greece: Implications for hominin and Homo sapiens' behavior and dispersals. SCIENCE ADVANCES 2019; 5:eaax0997. [PMID: 31663021 PMCID: PMC6795523 DOI: 10.1126/sciadv.aax0997] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 09/20/2019] [Indexed: 06/10/2023]
Abstract
We present evidence of Middle Pleistocene activity in the central Aegean Basin at the chert extraction and reduction complex of Stelida (Naxos, Greece). Luminescence dating places ~9000 artifacts in a stratigraphic sequence from ~13 to 200 thousand years ago (ka ago). These artifacts include Mousterian products, which arguably provide first evidence for Neanderthals in the region. This dated material attests to a much earlier history of regional exploration than previously believed, opening the possibility of alternative routes into Southeast Europe from Anatolia (and Africa) for (i) hominins, potentially during sea level lowstands (e.g., Marine Isotope Stage 8) permitting terrestrial crossings across the Aegean, and (ii) Homo sapiens of the Early Upper Paleolithic (Aurignacian), conceivably by sea.
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Affiliation(s)
- Tristan Carter
- Department of Anthropology and School of Geography and Earth Sciences, McMaster University, Hamilton L8S 4L9, Canada
| | - Daniel A. Contreras
- Department of Anthropology, University of Florida, Gainesville, FL 32611, USA
| | - Justin Holcomb
- Department of Anthropology, Boston University, Boston, MA 02215, USA
- Malcolm H. Wiener Laboratory of Archaeological Science, American School of Classical Studies at Athens, Athens 10676, Greece
| | | | - Panagiotis Karkanas
- Malcolm H. Wiener Laboratory of Archaeological Science, American School of Classical Studies at Athens, Athens 10676, Greece
| | - Guillaume Guérin
- IRAMAT-CRP2A, UMR 5060–CNRS/Université Bordeaux Montaigne, 33600 Pessac Cedex, France
| | - Ninon Taffin
- IRAMAT-CRP2A, UMR 5060–CNRS/Université Bordeaux Montaigne, 33600 Pessac Cedex, France
| | | | - Christelle Lahaye
- IRAMAT-CRP2A, UMR 5060–CNRS/Université Bordeaux Montaigne, 33600 Pessac Cedex, France
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Pargeter J, Khreisheh N, Stout D. Understanding stone tool-making skill acquisition: Experimental methods and evolutionary implications. J Hum Evol 2019; 133:146-166. [PMID: 31358178 DOI: 10.1016/j.jhevol.2019.05.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/22/2019] [Accepted: 05/22/2019] [Indexed: 02/08/2023]
Abstract
Despite its theoretical importance, the process of stone tool-making skill acquisition remains understudied and poorly understood. The challenges and costs of skill learning constitute an oft-neglected factor in the evaluation of alternative adaptive strategies and a potential source of bias in cultural transmission. Similarly, theory and data indicate that the most salient neural and cognitive demands of stone tool-making should occur during learning rather than expert performance. Unfortunately, the behavioral complexity and extensive learning requirements that make stone knapping skill acquisition an interesting object of study are the very features that make it so challenging to investigate experimentally. Here we present results from a multidisciplinary study of Late Acheulean handaxe-making skill acquisition involving twenty-six naïve participants and up to 90 hours training over several months, accompanied by a battery of psychometric, behavioral, and neuroimaging assessments. In this initial report, we derive a robust quantitative skill metric for the experimental handaxes using machine learning algorithms, reconstruct a group-level learning curve, and explore sources of individual variation in learning outcomes. Results identify particular cognitive targets of selection on the efficiency or reliability of tool-making skill acquisition, quantify learning costs, highlight the likely importance of social support, motivation, persistence, and self-control in knapping skill acquisition, and illustrate methods for reliably reconstructing ancient learning processes from archaeological evidence.
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Affiliation(s)
- Justin Pargeter
- Department of Anthropology, Emory University, Atlanta, GA, USA; Rock Art Research Institute, School of Geography, Archaeology and Environmental Studies, University of the Witwatersrand, Johannesburg, South Africa.
| | | | - Dietrich Stout
- Department of Anthropology, Emory University, Atlanta, GA, USA
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Habitat suitability and the genetic structure of human populations during the Last Glacial Maximum (LGM) in Western Europe. PLoS One 2019; 14:e0217996. [PMID: 31216315 PMCID: PMC6583941 DOI: 10.1371/journal.pone.0217996] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/22/2019] [Indexed: 11/19/2022] Open
Abstract
Human populations in Western Europe during the Last Glacial Maximum were geographically constrained to glacial refugia by the severity of the climate and ecological risk factors. In this research we use an agent-based model of human mobility and interaction, based on ethnographic and archaeological data, to explore the impact of ecological risk on human population structure via a reconstructed landscape of habitat suitability. The agent-based model allows us to evaluate the size and location of glacial refugia, the size of the populations occupying them and the degree of genetic relatedness between people occupying these areas. To do this, we model the probability of an agent foraging groups' survival as a function of habitat suitability. The model's simulated "genomes" (composed of regionally specific genetic markers) allow us to track long-term trends of inter-regional interaction and mobility. The results agree with previous archaeological studies situating a large glacial refugium spanning southern France and northeastern Spain, but we expand on those studies by demonstrating that higher rates of population growth in this central refugium led to continuous out-migration and therefore genetic homogeneity across Western Europe, with the possible exception of the Italian peninsula. These results concur with material culture data from known archaeological sites dating to the Last Glacial Maximum and make predictions for future ancient DNA studies.
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Demuro M, Arnold LJ, Aranburu A, Sala N, Arsuaga JL. New bracketing luminescence ages constrain the Sima de los Huesos hominin fossils (Atapuerca, Spain) to MIS 12. J Hum Evol 2019; 131:76-95. [DOI: 10.1016/j.jhevol.2018.12.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 12/05/2018] [Accepted: 12/05/2018] [Indexed: 01/01/2023]
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Allen PJ, Wiener JM, Gatzidis C, Stringer CB, Stewart JR. Investigating the Effect of the Environment on Prey Detection Ability in Humans. Sci Rep 2019; 9:7445. [PMID: 31092865 PMCID: PMC6520383 DOI: 10.1038/s41598-019-43797-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 04/24/2019] [Indexed: 11/09/2022] Open
Abstract
Visual search experiments used in the field of psychology may be applied to investigate the relationship between environments and prey detection rates that could influence hunting behaviours in ancient humans. Two lab-based experiments were designed to examine the effects of differing virtual environments, representing Marine Isotope Stage 3 (MIS3) in Europe, on participants’ ability to locate prey. The results show that prey detection performance is highly influenced by vegetation structure, both in terms of the biome type (wooded vs. grassland environments) and the density of the vegetation (trees in wooded and shrubs in grassland environments). However, the density of vegetation has a greater relative effect in grassland than in wooded biomes. Closer examination of the transition between biomes (relative percentages of trees vs. shrubs) at the same vegetative density shows a non-linear relationship between prey detection performance and the relative tree to shrub percentages. Changes in the distribution of biomes occurred throughout the Quaternary. The composition of those biomes will have likely affected hominin hunting behaviours because of their intermediary effects on prey detection performance. This may, therefore, have played a role in the turn-overs of hunter-gatherer hominin populations during MIS3 and at other times in the Quaternary.
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Affiliation(s)
- Peter J Allen
- Department of Creative Technology, Faculty of Science and Technology, Bournemouth University, Talbot Campus, Fern Barrow, Poole, BH12 5BB, UK.
| | - Jan M Wiener
- Department of Psychology, Ageing and Dementia Research Centre, Bournemouth University, Talbot Campus, Fern Barrow, BH12 5BB, Poole, UK
| | - Christos Gatzidis
- Department of Creative Technology, Faculty of Science and Technology, Bournemouth University, Talbot Campus, Fern Barrow, Poole, BH12 5BB, UK
| | - Chris B Stringer
- CHER, Department of Earth Sciences, Natural History Museum, SW7 5BD, London, UK
| | - John R Stewart
- Department of Life and Environmental Science, Faculty of Science and Technology, Bournemouth University, Talbot Campus, Fern Barrow, BH12 5BB, Poole, UK
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41
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The evolutionary history of the human face. Nat Ecol Evol 2019; 3:726-736. [DOI: 10.1038/s41559-019-0865-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 03/07/2019] [Indexed: 12/24/2022]
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Villalba-Mouco V, van de Loosdrecht MS, Posth C, Mora R, Martínez-Moreno J, Rojo-Guerra M, Salazar-García DC, Royo-Guillén JI, Kunst M, Rougier H, Crevecoeur I, Arcusa-Magallón H, Tejedor-Rodríguez C, García-Martínez de Lagrán I, Garrido-Pena R, Alt KW, Jeong C, Schiffels S, Utrilla P, Krause J, Haak W. Survival of Late Pleistocene Hunter-Gatherer Ancestry in the Iberian Peninsula. Curr Biol 2019; 29:1169-1177.e7. [DOI: 10.1016/j.cub.2019.02.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 01/04/2019] [Accepted: 02/01/2019] [Indexed: 12/18/2022]
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High-throughput inference of pairwise coalescence times identifies signals of selection and enriched disease heritability. Nat Genet 2018; 50:1311-1317. [PMID: 30104759 PMCID: PMC6145075 DOI: 10.1038/s41588-018-0177-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 06/21/2018] [Indexed: 12/19/2022]
Abstract
Interest in reconstructing demographic histories has motivated the development of methods to estimate locus-specific pairwise coalescence times from whole-genome sequence data. Here we introduce a powerful new method, ASMC, that can estimate coalescence times using only SNP array data, and is orders of magnitude faster than previous approaches. We applied ASMC to detect recent positive selection in 113,851 phased British samples from the UK Biobank, and detected 12 genome-wide significant signals, including 6 novel loci. We also applied ASMC to sequencing data from 498 Dutch individuals to detect background selection at deeper time scales. We detected strong heritability enrichment in regions of high background selection in an analysis of 20 independent diseases and complex traits using stratified LD score regression, conditioned on a broad set of functional annotations (including other background selection annotations). These results underscore the widespread effects of background selection on the genetic architecture of complex traits.
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Did Our Species Evolve in Subdivided Populations across Africa, and Why Does It Matter? Trends Ecol Evol 2018; 33:582-594. [PMID: 30007846 PMCID: PMC6092560 DOI: 10.1016/j.tree.2018.05.005] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 05/15/2018] [Accepted: 05/17/2018] [Indexed: 01/27/2023]
Abstract
We challenge the view that our species, Homo sapiens, evolved within a single population and/or region of Africa. The chronology and physical diversity of Pleistocene human fossils suggest that morphologically varied populations pertaining to the H. sapiens clade lived throughout Africa. Similarly, the African archaeological record demonstrates the polycentric origin and persistence of regionally distinct Pleistocene material culture in a variety of paleoecological settings. Genetic studies also indicate that present-day population structure within Africa extends to deep times, paralleling a paleoenvironmental record of shifting and fractured habitable zones. We argue that these fields support an emerging view of a highly structured African prehistory that should be considered in human evolutionary inferences, prompting new interpretations, questions, and interdisciplinary research directions. The view that Homo sapiens evolved from a single region/population within Africa has been given primacy in studies of human evolution. However, developments across multiple fields show that relevant data are no longer consistent with this view. We argue instead that Homo sapiens evolved within a set of interlinked groups living across Africa, whose connectivity changed through time. Genetic models therefore need to incorporate a more complex view of ancient migration and divergence in Africa. We summarize this new framework emphasizing population structure, outline how this changes our understanding of human evolution, and identify new research directions.
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45
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A serial founder effect model of phonemic diversity based on phonemic loss in low-density populations. PLoS One 2018; 13:e0198346. [PMID: 29856877 PMCID: PMC5983421 DOI: 10.1371/journal.pone.0198346] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 05/17/2018] [Indexed: 11/19/2022] Open
Abstract
It has been observed that the number of phonemes in languages in use today tends to decrease with increasing distance from Africa. A previous formal model has recently reproduced the observed cline, but under two strong assumptions. Here we tackle the question of whether an alternative explanation for the worldwide phonemic cline is possible, by using alternative assumptions. The answer is affirmative. We show this by formalizing a proposal, following Atkinson, that this pattern may be due to a repeated bottleneck effect and phonemic loss. In our simulations, low-density populations lose phonemes during the Out-of-Africa dispersal of modern humans. Our results reproduce the observed global cline for the number of phonemes. In addition, we also detect a cline of phonemic diversity and reproduce it using our simulation model. We suggest how future work could determine whether the previous model or the new one (or even a combination of them) is valid. Simulations also show that the clines can still be present even 300 kyr after the Out-of-Africa dispersal, which is contrary to some previous claims which were not supported by numerical simulations.
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46
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Landová E, Bakhshaliyeva N, Janovcová M, Peléšková Š, Suleymanova M, Polák J, Guliev A, Frynta D. Association Between Fear and Beauty Evaluation of Snakes: Cross-Cultural Findings. Front Psychol 2018; 9:333. [PMID: 29615942 PMCID: PMC5865084 DOI: 10.3389/fpsyg.2018.00333] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 02/27/2018] [Indexed: 11/13/2022] Open
Abstract
According to the fear module theory, humans are evolutionarily predisposed to perceive snakes as prioritized stimuli and exhibit a fast emotional and behavioral response toward them. In Europe, highly dangerous snake species are distributed almost exclusively in the Mediterranean and Caspian areas. While the risk of a snakebite is relatively low in Central Europe, Azerbaijan, on the other hand, has a high occurrence of the deadly venomous Levant viper (Macrovipera lebetina). We hypothesize that co-habitation with this dangerous snake has shaped the way in which humans evaluate snake species resembling it. For that purpose, we asked respondents from the Czech Republic and Azerbaijan to rank photographs depicting 36 snake species according to perceived fear and beauty. The results revealed a high cross-cultural agreement in both evaluations (fear r2 = 0.683, p < 0.0001; beauty: r2 = 0.816, p < 0.0001). Snakes species eliciting higher fear tend to be also perceived as more beautiful, yet people are able to clearly distinguish between these two dimensions. Deadly venomous snakes representing a serious risk are perceived as highly fearful. This is especially true for the vipers and allies (pit vipers) possessing a characteristic body shape with a distinct triangular head and thick body, which was found as the most fear evoking by respondents from both countries. Although the attitude toward snakes is more negative among the respondents from Azerbaijan, their fear evaluation is similar to the Czechs. For instance, despite co-habitation with the Levant viper, it was not rated by the Azerbaijanis as more fearful than other dangerous snakes. In conclusion, agreement in the evaluation of snake fear and beauty is cross-culturally high and relative fear attributed to selected snake species is not directly explainable by the current environmental and cultural differences. This may provide some support for the evolutionary hypothesis of preparedness to fear snakes.
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Affiliation(s)
- Eva Landová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia.,Applied Neurosciences and Brain Imaging, National Institute of Mental Health, Klecany, Czechia
| | | | - Markéta Janovcová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia.,Applied Neurosciences and Brain Imaging, National Institute of Mental Health, Klecany, Czechia
| | - Šárka Peléšková
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia.,Applied Neurosciences and Brain Imaging, National Institute of Mental Health, Klecany, Czechia
| | - Mesma Suleymanova
- Natural Historical Museum Named After Gasanbey Zardabi, Baku, Azerbaijan
| | - Jakub Polák
- Applied Neurosciences and Brain Imaging, National Institute of Mental Health, Klecany, Czechia.,Department of Psychology, Faculty of Arts, Charles University, Prague, Czechia
| | - Akif Guliev
- Biology Faculty, Baku State University, Baku, Azerbaijan
| | - Daniel Frynta
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia.,Applied Neurosciences and Brain Imaging, National Institute of Mental Health, Klecany, Czechia
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Khan G, Zhang F, Gao Q, Fu P, Zhang Y, Chen S. Spiroides shrubs on Qinghai-Tibetan Plateau: Multilocus phylogeography and palaeodistributional reconstruction of Spiraea alpina and S. Mongolica (Rosaceae). Mol Phylogenet Evol 2018; 123:137-148. [PMID: 29462675 DOI: 10.1016/j.ympev.2018.02.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 01/31/2018] [Accepted: 02/10/2018] [Indexed: 11/28/2022]
Abstract
A common hypothesis for the rich biodiversity found in mountains is uplift-driven diversification. Using a multilocus approach, here we assessed the influence of Qinghai-Tibetan Plateau (QTP) uplift and fluctuating regional climate on genetic diversity of two sister spiroides shrubs, Spiraea alpina and S. mongolica. Combined with palaeodistributional reconstruction modelling, we investigated the current and past-predicted distribution of these species under different climatic episodes. The study demonstrated that continuous pulses of retreat and expansion during last glacial-interglacial episodes, combined with the uplifting of QTP shaped the current distribution of these species. All the populations showed high level of genetic diversity based on both cpDNA and SSR markers. The average gene diversity within populations based on cpDNA markers was 0.383 ± 0.052 for S. alpina and 0.477 ± 0.048 for S. mongolica. The observed and expected heterozygosities based on SSR for both Spiraea alpina and S. mongolicawere HE(0.72-0.90)/HO(0.35-0.78) and HE(0.77-0.92)/HO(0.47-0.77) respectively. Palaeodistributional reconstruction indicated species' preferences at southeastern edge of the plateau during last glacial maximum, at higher altitude areas of QTP and range expansion to central plateau during the interglacial episodes. Assignment tests in STRUCTURE, discriminant analysis of principal coordinates and Immigrants analysis in GENECLASS based on nuclear SSR markers did not support the hypothesis of gene flow between both the species. However, maximum likelihood approach based on cpDNA showed sharing of haplotypes between both species.
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Affiliation(s)
- Gulzar Khan
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China.
| | - Faqi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining 810008, China.
| | - Qingbo Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China.
| | - Pengcheng Fu
- School of Life Sciences, Luoyang Normal University, Luoyang 471022, China.
| | - Yu Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China.
| | - Shilong Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China.
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48
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Climatic shocks associate with innovation in science and technology. PLoS One 2018; 13:e0190122. [PMID: 29364910 PMCID: PMC5783359 DOI: 10.1371/journal.pone.0190122] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 12/08/2017] [Indexed: 01/26/2023] Open
Abstract
Human history is shaped by landmark discoveries in science and technology. However, across both time and space the rate of innovation is erratic: Periods of relative inertia alternate with bursts of creative science and rapid cascades of technological innovations. While the origins of the rise and fall in rates of discovery and innovation remain poorly understood, they may reflect adaptive responses to exogenously emerging threats and pressures. Here we examined this possibility by fitting annual rates of scientific discovery and technological innovation to climatic variability and its associated economic pressures and resource scarcity. In time-series data from Europe (1500–1900CE), we indeed found that rates of innovation are higher during prolonged periods of cold (versus warm) surface temperature and during the presence (versus absence) of volcanic dust veils. This negative temperature–innovation link was confirmed in annual time-series for France, Germany, and the United Kingdom (1901–1965CE). Combined, across almost 500 years and over 5,000 documented innovations and discoveries, a 0.5°C increase in temperature associates with a sizable 0.30–0.60 standard deviation decrease in innovation. Results were robust to controlling for fluctuations in population size. Furthermore, and consistent with economic theory and micro-level data on group innovation, path analyses revealed that the relation between harsher climatic conditions between 1500–1900CE and more innovation is mediated by climate-induced economic pressures and resource scarcity.
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49
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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: 5.8] [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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50
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