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Caron B, Del Manzo G, Villemant B, Bartolini A, Moreno E, Le Friant A, Bassinot F, Baudin F, Alves A. Marine records reveal multiple phases of Toba's last volcanic activity. Sci Rep 2023; 13:11575. [PMID: 37463958 DOI: 10.1038/s41598-023-37999-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 06/30/2023] [Indexed: 07/20/2023] Open
Abstract
The Indonesian Young Toba Tuff (YTT), classically dated around 74 ka BP, is considered as a short-lived explosive cataclysmic super-eruption. The huge amounts of ash and SO2 emitted are likely to have triggered a volcanic winter which accelerated the transition to the last glaciation, and may have induced a human genetic bottleneck. However, the global climatic impact of the YTT or its duration are hotly debated. The present work offers a new interpretation of the Toba volcanic complex eruptive history. Analysing the BAR94-25 marine core proximal to the Toba volcanic center and combining it with high-resolution tephrostratigraphy and δ18O stratigraphy, we show that the Toba complex produced a volcanic succession that consists of at least 17 distinct layers of tephra and cryptotephra. Textural and geochemical analyses show that the tephra layers can be divided in 3 main successive volcanic activity phases (VAP1 to VAP3) over a period of ~ 50 kyr. The main volcanic activity phase, VAP2, including the YTT, is likely composed of 6 eruptive events in an interval whose total duration is ~ 10 ka. Thus, we suggest that the eruptive model of the Toba volcano must be revised as the duration of the Toba volcanic activity was much longer than suggested by previous studies. The implications of re-estimating the emission rate and the dispersion of ashes and SO2 include global environmental reconstitutions, climate change modelling and possibly human migration and evolution.
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Affiliation(s)
- B Caron
- Institut des Sciences de la Terre de Paris, UMR 7193, Sorbonne Université, CNRS-INSU, 75252, Paris cedex 05, France.
| | - G Del Manzo
- Institut des Sciences de la Terre de Paris, UMR 7193, Sorbonne Université, CNRS-INSU, 75252, Paris cedex 05, France
- Université Paris Cité, Institut de Physique du Globe de Paris, CNRS, UMR 7154, 75005, Paris, France
| | - B Villemant
- Institut des Sciences de la Terre de Paris, UMR 7193, Sorbonne Université, CNRS-INSU, 75252, Paris cedex 05, France
| | - A Bartolini
- Centre de Recherche en Paléontologie-Paris, UMR 7207, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, 75005, Paris, France
| | - E Moreno
- Laboratoire d'Océanographie et du Climat: Expérimentations et Approches Numériques, UMR 7159 CNRS, IRD, Sorbonne Université/MNHN/IPSL, 75252, Paris cedex 05, France
| | - A Le Friant
- Université Paris Cité, Institut de Physique du Globe de Paris, CNRS, UMR 7154, 75005, Paris, France
| | - F Bassinot
- Laboratoire des Sciences du Climat et de l'Environnement LSCE/IPSL, UMR CEA-CNRS-UVSQ 8212, 91191, Gif-sur-Yvette, France
| | - F Baudin
- Institut des Sciences de la Terre de Paris, UMR 7193, Sorbonne Université, CNRS-INSU, 75252, Paris cedex 05, France
| | - A Alves
- Centre de Recherche en Paléontologie-Paris, UMR 7207, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, 75005, Paris, France
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2
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Yu X, Li H. Origin of ethnic groups, linguistic families, and civilizations in China viewed from the Y chromosome. Mol Genet Genomics 2021; 296:783-797. [PMID: 34037863 DOI: 10.1007/s00438-021-01794-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 04/22/2021] [Indexed: 12/20/2022]
Abstract
East Asia, geographically extending to the Pamir Plateau in the west, to the Himalayan Mountains in the southwest, to Lake Baikal in the north and to the South China Sea in the south, harbors a variety of people, cultures, and languages. To reconstruct the natural history of East Asians is a mission of multiple disciplines, including genetics, archaeology, linguistics, and ethnology. Geneticists confirm the recent African origin of modern East Asians. Anatomically modern humans arose in Africa and immigrated into East Asia via a southern route approximately 50,000 years ago. Following the end of the Last Glacial Maximum approximately 12,000 years ago, rice and millet were domesticated in the south and north of East Asia, respectively, which allowed human populations to expand and linguistic families and ethnic groups to develop. These Neolithic populations produced a strong relation between the present genetic structures and linguistic families. The expansion of the Hongshan people from northeastern China relocated most of the ethnic populations on a large scale approximately 5300 years ago. Most of the ethnic groups migrated to remote regions, producing genetic structure differences between the edge and center of East Asia. In central China, pronounced population admixture occurred and accelerated over time, which subsequently formed the Han Chinese population and eventually the Chinese civilization. Population migration between the north and the south throughout history has left a smooth gradient in north-south changes in genetic structure. Observation of the process of shaping the genetic structure of East Asians may help in understanding the global natural history of modern humans.
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Affiliation(s)
- Xueer Yu
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China.,Shanxi Academy of Advanced Research and Innovation, Fudan-Datong Institute of Chinese Origin, Datong, 037006, China
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China. .,Shanxi Academy of Advanced Research and Innovation, Fudan-Datong Institute of Chinese Origin, Datong, 037006, China.
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O'Connell KA, Oaks JR, Hamidy A, Shaney KJ, Kurniawan N, Smith EN, Fujita MK. Impacts of the Toba eruption and montane forest expansion on diversification in Sumatran parachuting frogs (Rhacophorus). Mol Ecol 2020; 29:2994-3009. [PMID: 32633832 DOI: 10.1111/mec.15541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 01/09/2023]
Abstract
Catastrophic events, such as volcanic eruptions, can have profound impacts on the demographic histories of resident taxa. Due to its presumed effect on biodiversity, the Pleistocene eruption of super-volcano Toba has received abundant attention. We test the effects of the Toba eruption on the diversification, genetic diversity, and demography of three co-distributed species of parachuting frogs (Genus Rhacophorus) on Sumatra. We generate target-capture data (~950 loci and ~440,000 bp) for three species of parachuting frogs and use these data paired with previously generated double digest restriction-site associated DNA (ddRADseq) data to estimate population structure and genetic diversity, to test for population size changes using demographic modelling, and to estimate the temporal clustering of size change events using a full-likelihood Bayesian method. We find that populations around Toba exhibit reduced genetic diversity compared with southern populations, and that northern populations exhibit a shift in effective population size around the time of the eruption (~80 kya). However, we infer a stronger signal of expansion in southern populations around ~400 kya, and at least two of the northern populations may have also expanded at this time. Taken together, these findings suggest that the Toba eruption precipitated population declines in northern populations, but that the demographic history of these three species was also strongly impacted by mid-Pleistocene forest expansion during glacial periods. We propose local rather than regional effects of the Toba eruption, and emphasize the dynamic nature of diversification on the Sunda Shelf.
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Affiliation(s)
- Kyle A O'Connell
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institute, Washington, DC, USA.,Division of Amphibians and Reptiles, Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institute, Washington, DC, USA.,Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA.,Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Jamie R Oaks
- Department of Biological Sciences and Museum of Natural History, Auburn University, Auburn, Alabama, USA
| | - Amir Hamidy
- Zoology Division, Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences. Gd, Bogor, West Java, Indonesia
| | - Kyle J Shaney
- Institute of Ecology, National Autonomous University of Mexico, Mexico City, Mexico
| | - Nia Kurniawan
- Department of Biology, Universitas Brawijaya, Malang, East Java, Indonesia
| | - Eric N Smith
- Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA
| | - Matthew K Fujita
- Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA
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Budd DA, Troll VR, Deegan FM, Jolis EM, Smith VC, Whitehouse MJ, Harris C, Freda C, Hilton DR, Halldórsson SA, Bindeman IN. Magma reservoir dynamics at Toba caldera, Indonesia, recorded by oxygen isotope zoning in quartz. Sci Rep 2017; 7:40624. [PMID: 28120860 PMCID: PMC5264179 DOI: 10.1038/srep40624] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 12/08/2016] [Indexed: 11/11/2022] Open
Abstract
Quartz is a common phase in high-silica igneous rocks and is resistant to post-eruptive alteration, thus offering a reliable record of magmatic processes in silicic magma systems. Here we employ the 75 ka Toba super-eruption as a case study to show that quartz can resolve late-stage temporal changes in magmatic δ18O values. Overall, Toba quartz crystals exhibit comparatively high δ18O values, up to 10.2‰, due to magma residence within, and assimilation of, local granite basement. However, some 40% of the analysed quartz crystals display a decrease in δ18O values in outermost growth zones compared to their cores, with values as low as 6.7‰ (maximum ∆core−rim = 1.8‰). These lower values are consistent with the limited zircon record available for Toba, and the crystallisation history of Toba quartz traces an influx of a low-δ18O component into the magma reservoir just prior to eruption. Here we argue that this late-stage low-δ18O component is derived from hydrothermally-altered roof material. Our study demonstrates that quartz isotope stratigraphy can resolve magmatic events that may remain undetected by whole-rock or zircon isotope studies, and that assimilation of altered roof material may represent a viable eruption trigger in large Toba-style magmatic systems.
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Affiliation(s)
- David A Budd
- Department of Earth Sciences, CEMPEG, Uppsala University, Sweden
| | - Valentin R Troll
- Department of Earth Sciences, CEMPEG, Uppsala University, Sweden.,Istituto Nazionale di Geofisica e Vulcanologia, Rome, Italy
| | - Frances M Deegan
- Department of Earth Sciences, CEMPEG, Uppsala University, Sweden.,Department of Geosciences, Swedish Museum of Natural History, Stockholm, Sweden
| | - Ester M Jolis
- Department of Earth Sciences, CEMPEG, Uppsala University, Sweden
| | - Victoria C Smith
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, UK
| | - Martin J Whitehouse
- Department of Geosciences, Swedish Museum of Natural History, Stockholm, Sweden
| | - Chris Harris
- Department of Geological Sciences, University of Cape Town, South Africa
| | - Carmela Freda
- Istituto Nazionale di Geofisica e Vulcanologia, Rome, Italy
| | - David R Hilton
- Scripps Institution of Oceanography, University of California, San Diego, USA
| | - Sæmundur A Halldórsson
- Scripps Institution of Oceanography, University of California, San Diego, USA.,Institute of Earth Sciences, University of Iceland, Reykjavik, Iceland
| | - Ilya N Bindeman
- Department of Geological Sciences, University of Oregon, Oregon, USA
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5
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Visconti G. Anthropocene: another academic invention? RENDICONTI LINCEI-SCIENZE FISICHE E NATURALI 2014. [DOI: 10.1007/s12210-014-0317-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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6
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Wilting A, Christiansen P, Kitchener AC, Kemp YJM, Ambu L, Fickel J. Geographical variation in and evolutionary history of the Sunda clouded leopard (Neofelis diardi) (Mammalia: Carnivora: Felidae) with the description of a new subspecies from Borneo. Mol Phylogenet Evol 2010; 58:317-28. [PMID: 21074625 DOI: 10.1016/j.ympev.2010.11.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 10/19/2010] [Accepted: 11/03/2010] [Indexed: 12/01/2022]
Abstract
Recent morphological and molecular studies led to the recognition of two extant species of clouded leopards; Neofelis nebulosa from mainland southeast Asia and Neofelis diardi from the Sunda Islands of Borneo and Sumatra, including the Batu Islands. In addition to these new species-level distinctions, preliminary molecular data suggested a genetic substructure that separates Bornean and Sumatran clouded leopards, indicating the possibility of two subspecies of N. diardi. This suggestion was based on an analysis of only three Sumatran and seven Bornean individuals. Accordingly, in this study we re-evaluated this proposed subspecies differentiation using additional molecular (mainly historical) samples of eight Bornean and 13 Sumatran clouded leopards; a craniometric analysis of 28 specimens; and examination of pelage morphology of 20 museum specimens and of photographs of 12 wild camera-trapped animals. Molecular (mtDNA and microsatellite loci), craniomandibular and dental analyses strongly support the differentiation of Bornean and Sumatran clouded leopards, but pelage characteristics fail to separate them completely, most probably owing to small sample sizes, but it may also reflect habitat similarities between the two islands and their recent divergence. However, some provisional discriminating pelage characters are presented that need further testing. According to our estimates both populations diverged from each other during the Middle to Late Pleistocene (between 400 and 120 kyr). We present a discussion on the evolutionary history of Neofelis diardi sspp. on the Sunda Shelf, a revised taxonomy for the Sunda clouded leopard, N. diardi, and formally describe the Bornean subspecies, Neofelis diardi borneensis, including the designation of a holotype (BM.3.4.9.2 from Baram, Sarawak) in accordance with the rules of the International Code of Zoological Nomenclature.
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Affiliation(s)
- Andreas Wilting
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.
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Kawanishi K, Sunquist ME, Eizirik E, Lynam AJ, Ngoprasert D, Wan Shahruddin WN, Rayan DM, Sharma DSK, Steinmetz R. Near fixation of melanism in leopards of the Malay Peninsula. J Zool (1987) 2010. [DOI: 10.1111/j.1469-7998.2010.00731.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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8
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Storz JF, Beaumont MA, Alberts SC. Genetic evidence for long-term population decline in a savannah-dwelling primate: inferences from a hierarchical bayesian model. Mol Biol Evol 2002; 19:1981-90. [PMID: 12411607 DOI: 10.1093/oxfordjournals.molbev.a004022] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The purpose of this study was to test for evidence that savannah baboons (Papio cynocephalus) underwent a population expansion in concert with a hypothesized expansion of African human and chimpanzee populations during the late Pleistocene. The rationale is that any type of environmental event sufficient to cause simultaneous population expansions in African humans and chimpanzees would also be expected to affect other codistributed mammals. To test for genetic evidence of population expansion or contraction, we performed a coalescent analysis of multilocus microsatellite data using a hierarchical Bayesian model. Markov chain Monte Carlo (MCMC) simulations were used to estimate the posterior probability density of demographic and genealogical parameters. The model was designed to allow interlocus variation in mutational and demographic parameters, which made it possible to detect aberrant patterns of variation at individual loci that could result from heterogeneity in mutational dynamics or from the effects of selection at linked sites. Results of the MCMC simulations were consistent with zero variance in demographic parameters among loci, but there was evidence for a 10- to 20-fold difference in mutation rate between the most slowly and most rapidly evolving loci. Results of the model provided strong evidence that savannah baboons have undergone a long-term historical decline in population size. The mode of the highest posterior density for the joint distribution of current and ancestral population size indicated a roughly eightfold contraction over the past 1,000 to 250,000 years. These results indicate that savannah baboons apparently did not share a common demographic history with other codistributed primate species.
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Affiliation(s)
- Jay F Storz
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, 85721, USA.
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Abstract
This is a review of genetic evidence about the ancient demography of the ancestors of our species and about the genesis of worldwide human diversity. The issue of whether or not a population size bottleneck occurred among our ancestors is under debate among geneticists as well as among anthropologists. The bottleneck, if it occurred, would confirm the Garden of Eden (GOE) model of the origin of modern humans. The competing model, multiregional evolution (MRE), posits that the number of human ancestors has been large, occupying much of the temperate Old World for the last two million years. While several classes of genetic marker seem to contain a strong signal of demographic recovery from a small number of ancestors, other nuclear loci show no such signal. The pattern at these loci is compatible with the existence of widespread balancing selection in humans. The study of human diversity at (putatively) neutral genetic marker loci has been hampered since the beginning by ascertainment bias since they were discovered in Europeans. The high levels of polymorphism at microsatellite loci means that they are free of this bias. Microsatellites exhibit a clear almost linear diversity gradient away from Africa, so that New World populations are approximately 15% less diverse than African populations. This pattern is not compatible with a model of a single large population expansion and colonization of most of the Earth by our ancestors but suggests, instead, gradual loss of diversity in successive colonization bottlenecks as our species grew and spread.
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Affiliation(s)
- H Harpending
- Department of Anthropology, University of Utah, Salt Lake City, Utah 84112, USA
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10
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Hu G, Thilly WG. Multi-copy nuclear pseudogenes of mitochondrial DNA reveal recent acute genetic changes in the human genome. Curr Genet 1995; 28:410-4. [PMID: 8575012 DOI: 10.1007/bf00310808] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Four nuclear pseudogenes homologous to the 10031-10195-bp region of the human mitochondrial genome were detected by constant denaturant capillary electrophoresis. Among them, one pseudogene is present as at least five copies in each cell, in accordance with our previous observations of multi-copy mitochondrial DNA pseudogenes. The presence of multiple identical copies of pseudogenes suggests that the human genome underwent a series of genetic changes, including gene amplifications, very recently in evolutionary history, i.e., within the last 390000 years.
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Affiliation(s)
- G Hu
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge 02139, USA
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