1
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Guran SH, Yousefi M, Kafash A, Ghasidian E. Reconstructing contact and a potential interbreeding geographical zone between Neanderthals and anatomically modern humans. Sci Rep 2024; 14:20475. [PMID: 39227643 PMCID: PMC11372063 DOI: 10.1038/s41598-024-70206-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 08/13/2024] [Indexed: 09/05/2024] Open
Abstract
While the interbreeding of Homo neanderthalensis (hereafter Neanderthal) and Anatomically modern human (AMH) has been proven, owing to the shortage of fossils and absence of appropriate DNA, the timing and geography of their interbreeding are not clearly known. In this study, we applied ecological niche modelling (maximum entropy approach) and GIS to reconstruct the palaeodistribution of Neanderthals and AMHs in Southwest Asia and Southeast Europe and identify their contact and potential interbreeding zone during marine isotope stage 5 (MIS 5), when the second wave of interbreeding occurred. We used climatic variables characterizing the environmental conditions of MIS 5 ca. 120 to 80 kyr (averaged value) along with the topography and coordinates of Neanderthal and modern human archaeological sites to characterize the palaeodistribution of each species. Overlapping the models revealed that the Zagros Mountains were a contact and potential interbreeding zone for the two human species. We believe that the Zagros Mountains acted as a corridor connecting the Palearctic/Afrotropical realms, facilitating northwards dispersal of AMHs and southwards dispersal of Neanderthals during MIS 5. Our analyses are comparable with archaeological and genetic evidence collected during recent decades.
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Affiliation(s)
- Saman H Guran
- Institute for Prehistoric Archaeology, University of Cologne, Cologne, Germany.
- DiyarMehr Institute for Palaeolithic Research, Kermanshah, Iran.
| | - Masoud Yousefi
- Stiftung Neanderthal Museum, Mettmann, Germany
- Department of Biology, Hakim Sabzevari University, Sabzevar, Iran
| | - Anooshe Kafash
- School of Culture and Society, Department of Archaeology and Heritage Studies, Aarhus University, Aarhus, Denmark
| | - Elham Ghasidian
- DiyarMehr Institute for Palaeolithic Research, Kermanshah, Iran
- Stiftung Neanderthal Museum, Mettmann, Germany
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2
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Langdon QK, Groh JS, Aguillon SM, Powell DL, Gunn T, Payne C, Baczenas JJ, Donny A, Dodge TO, Du K, Schartl M, Ríos-Cárdenas O, Gutiérrez-Rodríguez C, Morris M, Schumer M. Swordtail fish hybrids reveal that genome evolution is surprisingly predictable after initial hybridization. PLoS Biol 2024; 22:e3002742. [PMID: 39186811 DOI: 10.1371/journal.pbio.3002742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 09/06/2024] [Accepted: 07/09/2024] [Indexed: 08/28/2024] Open
Abstract
Over the past 2 decades, biologists have come to appreciate that hybridization, or genetic exchange between distinct lineages, is remarkably common-not just in particular lineages but in taxonomic groups across the tree of life. As a result, the genomes of many modern species harbor regions inherited from related species. This observation has raised fundamental questions about the degree to which the genomic outcomes of hybridization are repeatable and the degree to which natural selection drives such repeatability. However, a lack of appropriate systems to answer these questions has limited empirical progress in this area. Here, we leverage independently formed hybrid populations between the swordtail fish Xiphophorus birchmanni and X. cortezi to address this fundamental question. We find that local ancestry in one hybrid population is remarkably predictive of local ancestry in another, demographically independent hybrid population. Applying newly developed methods, we can attribute much of this repeatability to strong selection in the earliest generations after initial hybridization. We complement these analyses with time-series data that demonstrates that ancestry at regions under selection has remained stable over the past approximately 40 generations of evolution. Finally, we compare our results to the well-studied X. birchmanni × X. malinche hybrid populations and conclude that deeper evolutionary divergence has resulted in stronger selection and higher repeatability in patterns of local ancestry in hybrids between X. birchmanni and X. cortezi.
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Affiliation(s)
- Quinn K Langdon
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, Mexico
| | - Jeffrey S Groh
- Center for Population Biology and Department of Evolution and Ecology, University of California, Davis, Davis, California, United States of America
| | - Stepfanie M Aguillon
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, Mexico
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, United States of America
| | - Daniel L Powell
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, Mexico
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Theresa Gunn
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, Mexico
| | - Cheyenne Payne
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, Mexico
| | - John J Baczenas
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Alex Donny
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, Mexico
| | - Tristram O Dodge
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, Mexico
| | - Kang Du
- Xiphophorus Genetic Stock Center, Texas State University San Marcos, San Marcos, United States of America
| | - Manfred Schartl
- Xiphophorus Genetic Stock Center, Texas State University San Marcos, San Marcos, United States of America
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany
| | - Oscar Ríos-Cárdenas
- Red de Biología Evolutiva, Instituto de Ecología, A.C., Xalapa, Veracruz, Mexico
| | | | - Molly Morris
- Department of Biological Sciences, Ohio University, Athens, Ohio, United States of America
| | - Molly Schumer
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, Mexico
- Freeman Hrabowski Fellow, Howard Hughes Medical Institute, Stanford, California, United States of America
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3
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Li L, Comi TJ, Bierman RF, Akey JM. Recurrent gene flow between Neanderthals and modern humans over the past 200,000 years. Science 2024; 385:eadi1768. [PMID: 38991054 DOI: 10.1126/science.adi1768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 05/14/2024] [Indexed: 07/13/2024]
Abstract
Although it is well known that the ancestors of modern humans and Neanderthals admixed, the effects of gene flow on the Neanderthal genome are not well understood. We develop methods to estimate the amount of human-introgressed sequences in Neanderthals and apply it to whole-genome sequence data from 2000 modern humans and three Neanderthals. We estimate that Neanderthals have 2.5 to 3.7% human ancestry, and we leverage human-introgressed sequences in Neanderthals to revise estimates of Neanderthal ancestry in modern humans, show that Neanderthal population sizes were significantly smaller than previously estimated, and identify two distinct waves of modern human gene flow into Neanderthals. Our data provide insights into the genetic legacy of recurrent gene flow between modern humans and Neanderthals.
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Affiliation(s)
- Liming Li
- Department of Medical Genetics and Developmental Biology, School of Medicine, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing 210009, China
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
| | - Troy J Comi
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
| | - Rob F Bierman
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
| | - Joshua M Akey
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
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4
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Du S, Chen J, Li J, Qian W, Wu S, Peng Q, Liu Y, Pan T, Li Y, Hadi SS, Tan J, Yuan Z, Wang J, Tang K, Wang Z, Wen Y, Dong X, Zhou W, Ruiz-Linares A, Shi Y, Jin L, Liu F, Zhang M, Wang S. A multi-ancestry GWAS meta-analysis of facial features and its application in predicting archaic human features. J Genet Genomics 2024:S1673-8527(24)00181-4. [PMID: 39002897 DOI: 10.1016/j.jgg.2024.07.005] [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: 07/04/2024] [Revised: 07/06/2024] [Accepted: 07/06/2024] [Indexed: 07/15/2024]
Abstract
Facial morphology, a complex trait influenced by genetics, holds great significance in evolutionary research. However, due to limited fossil evidence, the facial characteristics of Neanderthals and Denisovans have remained largely unknown. In this study, we conducted a large-scale multi-ethnic meta-analysis of the genome-wide association study (GWAS), including 9674 East Asians and 10,115 Europeans, quantitatively assessing 78 facial traits using 3D facial images. We identified 71 genomic loci associated with facial features, including 21 novel loci. We developed a facial polygenic score (FPS) that enables the prediction of facial features based on genetic information. Interestingly, the distribution of FPSs among populations from diverse continental groups exhibited relevant correlations with observed facial features. Furthermore, we applied the FPS to predict the facial traits of seven Neanderthals and one Denisovan using ancient DNA and aligned predictions with the fossil records. Our results suggested that Neanderthals and Denisovans likely shared similar facial features, such as a wider but shorter nose and a wider endocanthion distance. The decreased mouth width was characterized specifically in Denisovans. The integration of genomic data and facial trait analysis provides valuable insights into the evolutionary history and adaptive changes in human facial morphology.
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Affiliation(s)
- Siyuan Du
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Jieyi Chen
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China; Center for Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Jiarui Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Wei Qian
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Sijie Wu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Qianqian Peng
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Yu Liu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Ting Pan
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yi Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Sibte Syed Hadi
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh 11452, Kingdom of Saudi Arabia
| | - Jingze Tan
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ziyu Yuan
- Fudan-Taizhou Institute of Health Sciences, Taizhou, Jiangsu 225326, China
| | - Jiucun Wang
- Fudan-Taizhou Institute of Health Sciences, Taizhou, Jiangsu 225326, China; Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai 200120, China; Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai 200438, China
| | - Kun Tang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Zhuo Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yanqin Wen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Xinran Dong
- Center for Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Wenhao Zhou
- Center for Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai 201102, China; Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong 510623, China
| | - Andrés Ruiz-Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China; Aix-Marseille Université, CNRS, EFS, ADES, Marseille 13005, France; Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Li Jin
- Fudan-Taizhou Institute of Health Sciences, Taizhou, Jiangsu 225326, China; Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai 200120, China; Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai 200438, China
| | - Fan Liu
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh 11452, Kingdom of Saudi Arabia; Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, 3015 CN Rotterdam, the Netherlands
| | - Manfei Zhang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, China; Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai 200120, China.
| | - Sijia Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
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5
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Aneli S, Ceccatelli Berti C, Gilea AI, Birolo G, Mutti G, Pavesi A, Baruffini E, Goffrini P, Capelli C. Functional characterization of archaic-specific variants in mitonuclear genes: insights from comparative analysis in S. cerevisiae. Hum Mol Genet 2024; 33:1152-1163. [PMID: 38558123 DOI: 10.1093/hmg/ddae057] [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: 01/17/2024] [Revised: 02/29/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024] Open
Abstract
Neanderthal and Denisovan hybridisation with modern humans has generated a non-random genomic distribution of introgressed regions, the result of drift and selection dynamics. Cross-species genomic incompatibility and more efficient removal of slightly deleterious archaic variants have been proposed as selection-based processes involved in the post-hybridisation purge of archaic introgressed regions. Both scenarios require the presence of functionally different alleles across Homo species onto which selection operated differently according to which populations hosted them, but only a few of these variants have been pinpointed so far. In order to identify functionally divergent archaic variants removed in humans, we focused on mitonuclear genes, which are underrepresented in the genomic landscape of archaic humans. We searched for non-synonymous, fixed, archaic-derived variants present in mitonuclear genes, rare or absent in human populations. We then compared the functional impact of archaic and human variants in the model organism Saccharomyces cerevisiae. Notably, a variant within the mitochondrial tyrosyl-tRNA synthetase 2 (YARS2) gene exhibited a significant decrease in respiratory activity and a substantial reduction of Cox2 levels, a proxy for mitochondrial protein biosynthesis, coupled with the accumulation of the YARS2 protein precursor and a lower amount of mature enzyme. Our work suggests that this variant is associated with mitochondrial functionality impairment, thus contributing to the purging of archaic introgression in YARS2. While different molecular mechanisms may have impacted other mitonuclear genes, our approach can be extended to the functional screening of mitonuclear genetic variants present across species and populations.
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Affiliation(s)
- Serena Aneli
- Department of Public Health Sciences and Pediatrics, University of Turin, C.so Galileo Galilei 22, Turin 10126, Italy
| | - Camilla Ceccatelli Berti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Alexandru Ionut Gilea
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Giovanni Birolo
- Department of Medical Sciences, University of Turin, Via Santena 5, Turin 10126, Italy
| | - Giacomo Mutti
- Barcelona Supercomputing Centre (BSC-CNS), Department of Life Sciences, Plaça Eusebi Güell, 1-3, Barcelona 08034, Spain
- Institute for Research in Biomedicine (IRB Barcelona), Department of Mechanisms of Disease, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Angelo Pavesi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Enrico Baruffini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Paola Goffrini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Cristian Capelli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
- Department of Biology, University of Oxford, 11a Mansfield Rd, Oxford OX1 3SZ, United Kingdom
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6
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Brázda V, Šislerová L, Cucchiarini A, Mergny JL. G-quadruplex propensity in H. neanderthalensis, H. sapiens and Denisovans mitochondrial genomes. NAR Genom Bioinform 2024; 6:lqae060. [PMID: 38817800 PMCID: PMC11137754 DOI: 10.1093/nargab/lqae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 04/18/2024] [Accepted: 05/17/2024] [Indexed: 06/01/2024] Open
Abstract
Current methods of processing archaeological samples combined with advances in sequencing methods lead to disclosure of a large part of H. neanderthalensis and Denisovans genetic information. It is hardly surprising that the genome variability between modern humans, Denisovans and H. neanderthalensis is relatively limited. Genomic studies may provide insight on the metabolism of extinct human species or lineages. Detailed analysis of G-quadruplex sequences in H. neanderthalensis and Denisovans mitochondrial DNA showed us interesting features. Relatively similar patterns in mitochondrial DNA are found compared to modern humans, with one notable exception for H. neanderthalensis. An interesting difference between H. neanderthalensis and H. sapiens corresponds to a motif found in the D-loop region of mtDNA, which is responsible for mitochondrial DNA replication. This area is directly responsible for the number of mitochondria and consequently for the efficient energy metabolism of cell. H. neanderthalensis harbor a long uninterrupted run of guanines in this region, which may cause problems for replication, in contrast with H. sapiens, for which this run is generally shorter and interrupted. One may propose that the predominant H. sapiens motif provided a selective advantage for modern humans regarding mtDNA replication and function.
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Affiliation(s)
- Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
- Brno University of Technology, Faculty of Chemistry, Purkyňova 118, 612 00 Brno, Czech Republic
| | - Lucie Šislerová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
- Brno University of Technology, Faculty of Chemistry, Purkyňova 118, 612 00 Brno, Czech Republic
| | - Anne Cucchiarini
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
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7
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Stankey CT, Bourges C, Haag LM, Turner-Stokes T, Piedade AP, Palmer-Jones C, Papa I, Silva Dos Santos M, Zhang Q, Cameron AJ, Legrini A, Zhang T, Wood CS, New FN, Randzavola LO, Speidel L, Brown AC, Hall A, Saffioti F, Parkes EC, Edwards W, Direskeneli H, Grayson PC, Jiang L, Merkel PA, Saruhan-Direskeneli G, Sawalha AH, Tombetti E, Quaglia A, Thorburn D, Knight JC, Rochford AP, Murray CD, Divakar P, Green M, Nye E, MacRae JI, Jamieson NB, Skoglund P, Cader MZ, Wallace C, Thomas DC, Lee JC. A disease-associated gene desert directs macrophage inflammation through ETS2. Nature 2024; 630:447-456. [PMID: 38839969 PMCID: PMC11168933 DOI: 10.1038/s41586-024-07501-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 05/01/2024] [Indexed: 06/07/2024]
Abstract
Increasing rates of autoimmune and inflammatory disease present a burgeoning threat to human health1. This is compounded by the limited efficacy of available treatments1 and high failure rates during drug development2, highlighting an urgent need to better understand disease mechanisms. Here we show how functional genomics could address this challenge. By investigating an intergenic haplotype on chr21q22-which has been independently linked to inflammatory bowel disease, ankylosing spondylitis, primary sclerosing cholangitis and Takayasu's arteritis3-6-we identify that the causal gene, ETS2, is a central regulator of human inflammatory macrophages and delineate the shared disease mechanism that amplifies ETS2 expression. Genes regulated by ETS2 were prominently expressed in diseased tissues and more enriched for inflammatory bowel disease GWAS hits than most previously described pathways. Overexpressing ETS2 in resting macrophages reproduced the inflammatory state observed in chr21q22-associated diseases, with upregulation of multiple drug targets, including TNF and IL-23. Using a database of cellular signatures7, we identified drugs that might modulate this pathway and validated the potent anti-inflammatory activity of one class of small molecules in vitro and ex vivo. Together, this illustrates the power of functional genomics, applied directly in primary human cells, to identify immune-mediated disease mechanisms and potential therapeutic opportunities.
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Affiliation(s)
- C T Stankey
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London, UK
- Department of Immunology and Inflammation, Imperial College London, London, UK
- Washington University School of Medicine, St Louis, MO, USA
| | - C Bourges
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London, UK
| | - L M Haag
- Division of Gastroenterology, Infectious Diseases and Rheumatology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - T Turner-Stokes
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London, UK
- Department of Immunology and Inflammation, Imperial College London, London, UK
| | - A P Piedade
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London, UK
| | - C Palmer-Jones
- Department of Gastroenterology, Royal Free Hospital, London, UK
- Institute for Liver and Digestive Health, Division of Medicine, University College London, London, UK
| | - I Papa
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London, UK
| | | | - Q Zhang
- Genomics of Inflammation and Immunity Group, Human Genetics Programme, Wellcome Sanger Institute, Hinxton, UK
| | - A J Cameron
- Wolfson Wohl Cancer Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - A Legrini
- Wolfson Wohl Cancer Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - T Zhang
- Wolfson Wohl Cancer Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - C S Wood
- Wolfson Wohl Cancer Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - F N New
- NanoString Technologies, Seattle, WA, USA
| | - L O Randzavola
- Department of Immunology and Inflammation, Imperial College London, London, UK
| | - L Speidel
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
- Genetics Institute, University College London, London, UK
| | - A C Brown
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - A Hall
- The Sheila Sherlock Liver Centre, Royal Free Hospital, London, UK
- Department of Cellular Pathology, Royal Free Hospital, London, UK
| | - F Saffioti
- Institute for Liver and Digestive Health, Division of Medicine, University College London, London, UK
- The Sheila Sherlock Liver Centre, Royal Free Hospital, London, UK
| | - E C Parkes
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London, UK
| | - W Edwards
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - H Direskeneli
- Department of Internal Medicine, Division of Rheumatology, Marmara University, Istanbul, Turkey
| | - P C Grayson
- Systemic Autoimmunity Branch, NIAMS, National Institutes of Health, Bethesda, MD, USA
| | - L Jiang
- Department of Rheumatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - P A Merkel
- Division of Rheumatology, Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Epidemiology, Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - G Saruhan-Direskeneli
- Department of Physiology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - A H Sawalha
- Division of Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Lupus Center of Excellence, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - E Tombetti
- Department of Biomedical and Clinical Sciences, Milan University, Milan, Italy
- Internal Medicine and Rheumatology, ASST FBF-Sacco, Milan, Italy
| | - A Quaglia
- Department of Cellular Pathology, Royal Free Hospital, London, UK
- UCL Cancer Institute, London, UK
| | - D Thorburn
- Institute for Liver and Digestive Health, Division of Medicine, University College London, London, UK
- The Sheila Sherlock Liver Centre, Royal Free Hospital, London, UK
| | - J C Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
| | - A P Rochford
- Department of Gastroenterology, Royal Free Hospital, London, UK
- Institute for Liver and Digestive Health, Division of Medicine, University College London, London, UK
| | - C D Murray
- Department of Gastroenterology, Royal Free Hospital, London, UK
- Institute for Liver and Digestive Health, Division of Medicine, University College London, London, UK
| | - P Divakar
- NanoString Technologies, Seattle, WA, USA
| | - M Green
- Experimental Histopathology STP, The Francis Crick Institute, London, UK
| | - E Nye
- Experimental Histopathology STP, The Francis Crick Institute, London, UK
| | - J I MacRae
- Metabolomics STP, The Francis Crick Institute, London, UK
| | - N B Jamieson
- Wolfson Wohl Cancer Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - P Skoglund
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
| | - M Z Cader
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - C Wallace
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- MRC Biostatistics Unit, Cambridge Institute of Public Health, Cambridge, UK
| | - D C Thomas
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - J C Lee
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London, UK.
- Department of Gastroenterology, Royal Free Hospital, London, UK.
- Institute for Liver and Digestive Health, Division of Medicine, University College London, London, UK.
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8
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Foley RA, Mirazón Lahr M. Ghosts of extinct apes: genomic insights into African hominid evolution. Trends Ecol Evol 2024; 39:456-466. [PMID: 38302324 DOI: 10.1016/j.tree.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 12/13/2023] [Accepted: 12/22/2023] [Indexed: 02/03/2024]
Abstract
We are accustomed to regular announcements of new hominin fossils. There are now some 6000 hominin fossils, and up to 31 species. However, where are the announcements of African ape fossils? The answer is that there are almost none. Our knowledge of African ape evolution is based entirely on genomic analyses, which show that extant diversity is very young. This contrasts with the extensive and deep diversity of hominins known from fossils. Does this difference point to low and late diversification of ape lineages, or high rates of extinction? The comparative evolutionary dynamics of African hominids are central to interpreting living ape adaptations, as well as understanding the patterns of hominin evolution and the nature of the last common ancestor.
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Affiliation(s)
- Robert A Foley
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, The Henry Wellcome Building, Fitzwilliam Street, Cambridge, CB2 1QH, UK.
| | - Marta Mirazón Lahr
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, The Henry Wellcome Building, Fitzwilliam Street, Cambridge, CB2 1QH, UK
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9
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Yaworsky PM, Nielsen ES, Nielsen TK. The Neanderthal niche space of Western Eurasia 145 ka to 30 ka ago. Sci Rep 2024; 14:7788. [PMID: 38565571 PMCID: PMC10987600 DOI: 10.1038/s41598-024-57490-4] [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: 12/13/2023] [Accepted: 03/19/2024] [Indexed: 04/04/2024] Open
Abstract
Neanderthals occupied Western Eurasia between 350 ka and 40 ka ago, during the climatically volatile Pleistocene. A key issue is to what extent Neanderthal populations expanded into areas of Western Eurasia and what conditions facilitated such range expansions. The range extent of Neanderthals is generally based on the distribution of Neanderthal material, but the land-altering nature of glacial periods has erased much of the already sparse material evidence of Neanderthals, particularly in the northern latitudes. To overcome this obstacle species distribution models can estimate past distributions of Neanderthals, however, most implementations are generally constrained spatially and temporally and may be artificially truncating the Neanderthal niche space. Using dated contexts from Neanderthal sites from across Western Eurasia, millennial-scale paleoclimate reconstructions, and a spatiotemporal species distribution model, we infer the fundamental climatic niche space of Neanderthals and estimate the extent of Neanderthal occupation. We find that (a.) despite the long timeframe, Neanderthals occupy a relatively narrow fundamental climatic niche space, (b.) the estimated projected potential Neanderthal niche space suggests a larger geographic range than the material record suggests, and (c.) that there was a general decline in the size of the projected potential Neanderthal niche from 145 ka ago onward, possibly contributing to their extinction.
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Affiliation(s)
- Peter M Yaworsky
- Department of Archeology and Heritage Studies, School of Culture and Society, Aarhus University, Moesgård Allé 20, Building 4216, 8270, Højbjerg, Denmark.
- Center for Ecological Dynamics in a Novel Biosphere, Department of Biology, Aarhus University, Ny Munkegade 114-116, 8000, Aarhus C, Denmark.
| | - Emil S Nielsen
- Department of Archeology and Heritage Studies, School of Culture and Society, Aarhus University, Moesgård Allé 20, Building 4216, 8270, Højbjerg, Denmark
- Center for Ecological Dynamics in a Novel Biosphere, Department of Biology, Aarhus University, Ny Munkegade 114-116, 8000, Aarhus C, Denmark
| | - Trine K Nielsen
- Department of Archeology and Heritage Studies, School of Culture and Society, Aarhus University, Moesgård Allé 20, Building 4216, 8270, Højbjerg, Denmark
- Center for Ecological Dynamics in a Novel Biosphere, Department of Biology, Aarhus University, Ny Munkegade 114-116, 8000, Aarhus C, Denmark
- Moesgaard Museum, Moesgård Allé 15, 8270, Højbjerg, Denmark
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10
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Zeberg H, Jakobsson M, Pääbo S. The genetic changes that shaped Neandertals, Denisovans, and modern humans. Cell 2024; 187:1047-1058. [PMID: 38367615 DOI: 10.1016/j.cell.2023.12.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/20/2023] [Accepted: 12/20/2023] [Indexed: 02/19/2024]
Abstract
Modern human ancestors diverged from the ancestors of Neandertals and Denisovans about 600,000 years ago. Until about 40,000 years ago, these three groups existed in parallel, occasionally met, and exchanged genes. A critical question is why modern humans, and not the other two groups, survived, became numerous, and developed complex cultures. Here, we discuss genetic differences among the groups and some of their functional consequences. As more present-day genome sequences become available from diverse groups, we predict that very few, if any, differences will distinguish all modern humans from all Neandertals and Denisovans. We propose that the genetic basis of what constitutes a modern human is best thought of as a combination of genetic features, where perhaps none of them is present in each and every present-day individual.
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Affiliation(s)
- Hugo Zeberg
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Physiology and Pharmacology, Karolinska Institutet, 17165 Stockholm, Sweden.
| | - Mattias Jakobsson
- Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Okinawa Institute of Science and Technology, Onnason 904-0495, Okinawa, Japan.
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11
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Mallick S, Micco A, Mah M, Ringbauer H, Lazaridis I, Olalde I, Patterson N, Reich D. The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes. Sci Data 2024; 11:182. [PMID: 38341426 PMCID: PMC10858950 DOI: 10.1038/s41597-024-03031-7] [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: 08/10/2023] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
More than two hundred papers have reported genome-wide data from ancient humans. While the raw data for the vast majority are fully publicly available testifying to the commitment of the paleogenomics community to open data, formats for both raw data and meta-data differ. There is thus a need for uniform curation and a centralized, version-controlled compendium that researchers can download, analyze, and reference. Since 2019, we have been maintaining the Allen Ancient DNA Resource (AADR), which aims to provide an up-to-date, curated version of the world's published ancient human DNA data, represented at more than a million single nucleotide polymorphisms (SNPs) at which almost all ancient individuals have been assayed. The AADR has gone through six public releases at the time of writing and review of this manuscript, and crossed the threshold of >10,000 individuals with published genome-wide ancient DNA data at the end of 2022. This note is intended as a citable descriptor of the AADR.
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Affiliation(s)
- Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Harald Ringbauer
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- BIOMICs Research Group, University of the Basque Country, 01006, Vitoria-Gasteiz, Spain
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
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12
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Lei H, Li J, Zhao B, Kou SH, Xiao F, Chen T, Wang SM. Evolutionary origin of germline pathogenic variants in human DNA mismatch repair genes. Hum Genomics 2024; 18:5. [PMID: 38287404 PMCID: PMC10823654 DOI: 10.1186/s40246-024-00573-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 01/17/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND Mismatch repair (MMR) system is evolutionarily conserved for genome stability maintenance. Germline pathogenic variants (PVs) in MMR genes that lead to MMR functional deficiency are associated with high cancer risk. Knowing the evolutionary origin of germline PVs in human MMR genes will facilitate understanding the biological base of MMR deficiency in cancer. However, systematic knowledge is lacking to address the issue. In this study, we performed a comprehensive analysis to know the evolutionary origin of human MMR PVs. METHODS We retrieved MMR gene variants from the ClinVar database. The genomes of 100 vertebrates were collected from the UCSC genome browser and ancient human sequencing data were obtained through comprehensive data mining. Cross-species conservation analysis was performed based on the phylogenetic relationship among 100 vertebrates. Rescaled ancient sequencing data were used to perform variant calling for archeological analysis. RESULTS Using the phylogenetic approach, we traced the 3369 MMR PVs identified in modern humans in 99 non-human vertebrate genomes but found no evidence for cross-species conservation as the source for human MMR PVs. Using the archeological approach, we searched the human MMR PVs in over 5000 ancient human genomes dated from 45,045 to 100 years before present and identified a group of MMR PVs shared between modern and ancient humans mostly within 10,000 years with similar quantitative patterns. CONCLUSION Our study reveals that MMR PVs in modern humans were arisen within the recent human evolutionary history.
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Affiliation(s)
- Huijun Lei
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310018, Zhejiang, China
- Department of Cancer Prevention, Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, China
| | - Jiaheng Li
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Bojin Zhao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Si Hoi Kou
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Fengxia Xiao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Tianhui Chen
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310018, Zhejiang, China.
- Department of Cancer Prevention, Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, China.
| | - San Ming Wang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China.
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13
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Abrams G, Devièse T, Pirson S, De Groote I, Flas D, Jungels C, Jadin I, Cattelain P, Bonjean D, Mathys A, Semal P, Higham T, Di Modica K. Investigating the co-occurrence of Neanderthals and modern humans in Belgium through direct radiocarbon dating of bone implements. J Hum Evol 2024; 186:103471. [PMID: 38043357 DOI: 10.1016/j.jhevol.2023.103471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 11/13/2023] [Accepted: 11/18/2023] [Indexed: 12/05/2023]
Affiliation(s)
- Grégory Abrams
- Department of Archaeology, Ghent University, B-9000, Gent, Belgium; Scientific Department, Espace Muséal d'Andenne, B-5300, Andenne, Belgium; Faculty of Archaeology, Archaeological Sciences, Bio-Archaeology, Leiden University, 2333 CC, Leiden, the Netherlands.
| | - Thibaut Devièse
- Centre Européen de Recherche et d'Enseignement des Géosciences de l'Environnement, Aix-Marseille Université, CNRS, IRD, INRAE, BP80-13545, Aix-en-Provence, cedex 4, France.
| | - Stéphane Pirson
- Direction scientifique et technique, Agence wallonne du Patrimoine, B-5100, Namur, Belgium
| | - Isabelle De Groote
- Department of Archaeology, Ghent University, B-9000, Gent, Belgium; School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, L3 3AF, UK
| | - Damien Flas
- Laboratoire Méditerranéen de Préhistoire Europe Afrique, Aix-Marseille University, CNRS, 13097, Aix-en-Provence, cedex 2, France; Department of Prehistory, University of Liège, B-4000, Liège, Belgium
| | - Cécile Jungels
- Scientific Department, Préhistomuseum, B-4400, Flémalle, Belgium; Les Chercheurs de la Wallonie, B-4400, Flémalle, Belgium
| | - Ivan Jadin
- Operational Direction Earth and History of Life, Quaternary Environments & Humans, Anthropology & Prehistory, Royal Belgium Institute of Natural Sciences, B-1000, Brussels, Belgium
| | - Pierre Cattelain
- Department of Prehistory, University of Liège, B-4000, Liège, Belgium; Cedarc-Musée du Malgré-Tout, B-5670, Belgium; Centre de Recherches en Archéologie et Patrimoine, Université Libre de Bruxelles, B-1150, Brussels, Belgium
| | - Dominique Bonjean
- Scientific Department, Espace Muséal d'Andenne, B-5300, Andenne, Belgium
| | - Aurore Mathys
- Biological Collection and Data Management, Royal Museum for Central Africa, B-3080, Tervuren, Belgium; Scientific Heritage Service, Royal Belgian Institute of Natural Sciences, B-1000, Brussels, Belgium; Art, Archaeology and Heritage Unit, University of Liège, B-4000, Liège, Belgium
| | - Patrick Semal
- Scientific Heritage Service, Royal Belgian Institute of Natural Sciences, B-1000, Brussels, Belgium
| | - Thomas Higham
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, A-1030, Vienna, Austria
| | - Kévin Di Modica
- Scientific Department, Espace Muséal d'Andenne, B-5300, Andenne, Belgium
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14
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Langdon QK, Groh JS, Aguillon SM, Powell DL, Gunn T, Payne C, Baczenas JJ, Donny A, Dodge TO, Du K, Schartl M, Ríos-Cárdenas O, Gutierrez-Rodríguez C, Morris M, Schumer M. Genome evolution is surprisingly predictable after initial hybridization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.21.572897. [PMID: 38187753 PMCID: PMC10769416 DOI: 10.1101/2023.12.21.572897] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Over the past two decades, evolutionary biologists have come to appreciate that hybridization, or genetic exchange between distinct lineages, is remarkably common - not just in particular lineages but in taxonomic groups across the tree of life. As a result, the genomes of many modern species harbor regions inherited from related species. This observation has raised fundamental questions about the degree to which the genomic outcomes of hybridization are repeatable and the degree to which natural selection drives such repeatability. However, a lack of appropriate systems to answer these questions has limited empirical progress in this area. Here, we leverage independently formed hybrid populations between the swordtail fish Xiphophorus birchmanni and X. cortezi to address this fundamental question. We find that local ancestry in one hybrid population is remarkably predictive of local ancestry in another, demographically independent hybrid population. Applying newly developed methods, we can attribute much of this repeatability to strong selection in the earliest generations after initial hybridization. We complement these analyses with time-series data that demonstrates that ancestry at regions under selection has remained stable over the past ~40 generations of evolution. Finally, we compare our results to the well-studied X. birchmanni×X. malinche hybrid populations and conclude that deeper evolutionary divergence has resulted in stronger selection and higher repeatability in patterns of local ancestry in hybrids between X. birchmanni and X. cortezi.
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Affiliation(s)
- Quinn K. Langdon
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California
| | - Jeffrey S. Groh
- Center for Population Biology and Department of Evolution and Ecology, University of California, Davis
| | - Stepfanie M. Aguillon
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles
| | - Daniel L. Powell
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | - Theresa Gunn
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | - Cheyenne Payne
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | | | - Alex Donny
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | - Tristram O. Dodge
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | - Kang Du
- Xiphophorus Genetic Stock Center, Texas State University San Marcos
| | - Manfred Schartl
- Xiphophorus Genetic Stock Center, Texas State University San Marcos
- Developmental Biochemistry, Biocenter, University of Würzburg
| | | | | | | | - Molly Schumer
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
- Freeman Hrabowski Fellow, Howard Hughes Medical Institute
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15
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Lien A, Legori LP, Kraft L, Sackett PW, Renaud G. Benchmarking software tools for trimming adapters and merging next-generation sequencing data for ancient DNA. FRONTIERS IN BIOINFORMATICS 2023; 3:1260486. [PMID: 38131007 PMCID: PMC10733496 DOI: 10.3389/fbinf.2023.1260486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Ancient DNA is highly degraded, resulting in very short sequences. Reads generated with modern high-throughput sequencing machines are generally longer than ancient DNA molecules, therefore the reads often contain some portion of the sequencing adaptors. It is crucial to remove those adaptors, as they can interfere with downstream analysis. Furthermore, overlapping portions when DNA has been read forward and backward (paired-end) can be merged to correct sequencing errors and improve read quality. Several tools have been developed for adapter trimming and read merging, however, no one has attempted to evaluate their accuracy and evaluate their potential impact on downstream analyses. Through the simulation of sequencing data, seven commonly used tools were analyzed in their ability to reconstruct ancient DNA sequences through read merging. The analyzed tools exhibit notable differences in their abilities to correct sequence errors and identify the correct read overlap, but the most substantial difference is observed in their ability to calculate quality scores for merged bases. Selecting the most appropriate tool for a given project depends on several factors, although some tools such as fastp have some shortcomings, whereas others like leeHom outperform the other tools in most aspects. While the choice of tool did not result in a measurable difference when analyzing population genetics using principal component analysis, it is important to note that downstream analyses that are sensitive to wrongly merged reads or that rely on quality scores can be significantly impacted by the choice of tool.
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Affiliation(s)
- Annette Lien
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Louis Kraft
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Peter Wad Sackett
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Gabriel Renaud
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
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16
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Childebayeva A, Zavala EI. Review: Computational analysis of human skeletal remains in ancient DNA and forensic genetics. iScience 2023; 26:108066. [PMID: 37927550 PMCID: PMC10622734 DOI: 10.1016/j.isci.2023.108066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023] Open
Abstract
Degraded DNA is used to answer questions in the fields of ancient DNA (aDNA) and forensic genetics. While aDNA studies typically center around human evolution and past history, and forensic genetics is often more concerned with identifying a specific individual, scientists in both fields face similar challenges. The overlap in source material has prompted periodic discussions and studies on the advantages of collaboration between fields toward mutually beneficial methodological advancements. However, most have been centered around wet laboratory methods (sampling, DNA extraction, library preparation, etc.). In this review, we focus on the computational side of the analytical workflow. We discuss limitations and considerations to consider when working with degraded DNA. We hope this review provides a framework to researchers new to computational workflows for how to think about analyzing highly degraded DNA and prompts an increase of collaboration between the forensic genetics and aDNA fields.
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Affiliation(s)
- Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anthropology, University of Kansas, Lawrence, KS, USA
| | - Elena I. Zavala
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Biology, University of Oregon, Eugene, OR, USA
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17
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Kou SH, Li J, Tam B, Lei H, Zhao B, Xiao F, Wang S. TP53 germline pathogenic variants in modern humans were likely originated during recent human history. NAR Cancer 2023; 5:zcad025. [PMID: 37304756 PMCID: PMC10251638 DOI: 10.1093/narcan/zcad025] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/05/2023] [Accepted: 05/16/2023] [Indexed: 06/13/2023] Open
Abstract
TP53 is crucial for maintaining genome stability and preventing oncogenesis. Germline pathogenic variation in TP53 damages its function, causing genome instability and increased cancer risk. Despite extensive study in TP53, the evolutionary origin of the human TP53 germline pathogenic variants remains largely unclear. In this study, we applied phylogenetic and archaeological approaches to identify the evolutionary origin of TP53 germline pathogenic variants in modern humans. In the phylogenic analysis, we searched 406 human TP53 germline pathogenic variants in 99 vertebrates distributed in eight clades of Primate, Euarchontoglires, Laurasiatheria, Afrotheria, Mammal, Aves, Sarcopterygii and Fish, but we observed no direct evidence for the cross-species conservation as the origin; in the archaeological analysis, we searched the variants in 5031 ancient human genomes dated between 45045 and 100 years before present, and identified 45 pathogenic variants in 62 ancient humans dated mostly within the last 8000 years; we also identified 6 pathogenic variants in 3 Neanderthals dated 44000 to 38515 years before present and 1 Denisovan dated 158 550 years before present. Our study reveals that TP53 germline pathogenic variants in modern humans were likely originated in recent human history and partially inherited from the extinct Neanderthals and Denisovans.
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Affiliation(s)
- Si Hoi Kou
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Jiaheng Li
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Benjamin Tam
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Huijun Lei
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Bojin Zhao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Fengxia Xiao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - San Ming Wang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
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Gicqueau A, Schuh A, Henrion J, Viola B, Partiot C, Guillon M, Golovanova L, Doronichev V, Gunz P, Hublin JJ, Maureille B. Anatomically modern human in the Châtelperronian hominin collection from the Grotte du Renne (Arcy-sur-Cure, Northeast France). Sci Rep 2023; 13:12682. [PMID: 37542146 PMCID: PMC10403518 DOI: 10.1038/s41598-023-39767-2] [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: 03/08/2023] [Accepted: 07/31/2023] [Indexed: 08/06/2023] Open
Abstract
Around 42,000 years ago, anatomically modern humans appeared in Western Europe to the detriment of indigenous Neanderthal groups. It is during this period that new techno-cultural complexes appear, such as the Châtelperronian that extends from northern Spain to the Paris Basin. The Grotte du Renne (Arcy-sur-Cure) is a key site for discussing the biological identity of its makers. This deposit has yielded several Neanderthal human remains in its Châtelperronian levels. However, the last inventory of the paleoanthropological collection attributed to this techno-complex allowed the identification of an ilium belonging to a neonate (AR-63) whose morphology required a thorough analysis to assess its taxonomic attribution. Using geometric morphometrics, we quantified its morphology and compared it to that of 2 Neanderthals and 32 recent individuals deceased during the perinatal period to explore their morphological variation. Our results indicate a morphological distinction between the ilia of Neanderthals and anatomically modern neonates. Although AR-63 is slightly outside recent variability, it clearly differs from the Neanderthals. We propose that this is due to its belonging to an early modern human lineage whose morphology differs slightly from present-day humans. We also explore different hypotheses about the presence of this anatomically modern neonate ilium among Neanderthal remains.
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Affiliation(s)
- Arthur Gicqueau
- Univ. de Toulouse Jean Jaurès, CNRS, Ministère de La Culture, TRACES, UMR5608 CNRS, F-31058, Toulouse, France.
- Univ. Bordeaux, CNRS, Ministère de la Culture, PACEA, UMR5199, F-33600, Pessac, France.
- Department of Human Evolution, Max Planck Institute for Evolutionnary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany.
| | - Alexandra Schuh
- Univ. Bordeaux, CNRS, Ministère de la Culture, PACEA, UMR5199, F-33600, Pessac, France
- Department of Human Origins, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Juliette Henrion
- Univ. Bordeaux, CNRS, Ministère de la Culture, PACEA, UMR5199, F-33600, Pessac, France
| | - Bence Viola
- Department of Anthropology, University of Toronto, Toronto, Canada
| | - Caroline Partiot
- Austrian Archaeological Institute (OeAI) at the Austrian Academy of Sciences (OeAW), Franz Klein-Gasse 1, 1190, Wien/Vienna, Austria
- Museum national d'histoire naturelle, Eco-Anthropologie, UMR7206, F-Paris, France
| | - Mark Guillon
- Univ. Bordeaux, CNRS, Ministère de la Culture, PACEA, UMR5199, F-33600, Pessac, France
- Inrap, Boulevard de Verdun, F-76120, Le Grand Quevilly, France
| | | | | | - Philipp Gunz
- Department of Human Origins, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Jean-Jacques Hublin
- Department of Human Evolution, Max Planck Institute for Evolutionnary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
- Chaire Internationale de Paléoanthropologie, Collège de France, F-75231, Paris, France
| | - Bruno Maureille
- Univ. Bordeaux, CNRS, Ministère de la Culture, PACEA, UMR5199, F-33600, Pessac, France.
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19
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Essel E, Zavala EI, Schulz-Kornas E, Kozlikin MB, Fewlass H, Vernot B, Shunkov MV, Derevianko AP, Douka K, Barnes I, Soulier MC, Schmidt A, Szymanski M, Tsanova T, Sirakov N, Endarova E, McPherron SP, Hublin JJ, Kelso J, Pääbo S, Hajdinjak M, Soressi M, Meyer M. Ancient human DNA recovered from a Palaeolithic pendant. Nature 2023:10.1038/s41586-023-06035-2. [PMID: 37138083 DOI: 10.1038/s41586-023-06035-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/30/2023] [Indexed: 05/05/2023]
Abstract
Artefacts made from stones, bones and teeth are fundamental to our understanding of human subsistence strategies, behaviour and culture in the Pleistocene. Although these resources are plentiful, it is impossible to associate artefacts to specific human individuals1 who can be morphologically or genetically characterized, unless they are found within burials, which are rare in this time period. Thus, our ability to discern the societal roles of Pleistocene individuals based on their biological sex or genetic ancestry is limited2-5. Here we report the development of a non-destructive method for the gradual release of DNA trapped in ancient bone and tooth artefacts. Application of the method to an Upper Palaeolithic deer tooth pendant from Denisova Cave, Russia, resulted in the recovery of ancient human and deer mitochondrial genomes, which allowed us to estimate the age of the pendant at approximately 19,000-25,000 years. Nuclear DNA analysis identifies the presumed maker or wearer of the pendant as a female individual with strong genetic affinities to a group of Ancient North Eurasian individuals who lived around the same time but were previously found only further east in Siberia. Our work redefines how cultural and genetic records can be linked in prehistoric archaeology.
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Affiliation(s)
- Elena Essel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Elena I Zavala
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Biology, San Francisco State University, San Francisco, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Ellen Schulz-Kornas
- Department of Cariology, Endodontology and Periodontology, University of Leipzig, Leipzig, Germany
| | - Maxim B Kozlikin
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Helen Fewlass
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benjamin Vernot
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Michael V Shunkov
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Anatoly P Derevianko
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Katerina Douka
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS) Research Network, University of Vienna, Vienna, Austria
| | - Ian Barnes
- Earth Sciences Department, Natural History Museum, London, UK
| | - Marie-Cécile Soulier
- Maison de la Recherche, Université de Toulouse-Jean Jaurès, CNRS UMR 5608 TRACES, Toulouse, France
| | - Anna Schmidt
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Merlin Szymanski
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tsenka Tsanova
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Chemistry "Giacomo Ciamician", Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Nikolay Sirakov
- National Institute of Archaeology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | | | | | - Jean-Jacques Hublin
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Chaire de Paléoanthropologie, Collège de France, Paris, France
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mateja Hajdinjak
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Marie Soressi
- Faculty of Archaeology, Leiden University, Leiden, The Netherlands.
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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20
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Grine FE, Mongle CS, Kollmer W, Romanos G, du Plessis A, Maureille B, Braga J. Hypercementosis in Late Pleistocene Homo sapiens fossils from Klasies River Main Site, South Africa. Arch Oral Biol 2023; 149:105664. [PMID: 36889227 DOI: 10.1016/j.archoralbio.2023.105664] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 02/23/2023] [Accepted: 02/26/2023] [Indexed: 03/06/2023]
Abstract
OBJECTIVE To examine early Homo sapiens fossils from the Late Pleistocene site of Klasies River Main Site, South Africa for evidence of hypercementosis. The specimens represent seven adult individuals dated to between 119,000 and 58,000 years ago. These observations are contextualized in relation to the incidences of hypercementosis among recent human populations and fossil human samples and the potential etiologies of hypercementosis. DESIGN The fossils were investigated utilizing micro-CT and nano-CT scanning to visualize and measure cementum apposition on permanent incisor, premolar and molar roots. Cementum thickness was measured at mid-root level, and the volume of the cementum sleeve was calculated for the two fossil specimens that display marked hypercementosis. RESULTS Two of the fossils display no evidence of cementum hypertrophy. Three exhibit moderate cementum thickening, barely attaining the quantitative threshold for hypercementosis. Two evince marked hypercementosis. One of the Klasies specimens with marked hypercementosis is judged to be an older individual with periapical abscessing. The second specimen is a younger adult, and seemingly similar in age to other Klasies fossils that exhibit only minimal cementum apposition. However, this second specimen exhibits dento-alveolar ankylosis of the premolar and molars. CONCLUSIONS These two fossils from Klasies River Main Site provide the earliest manifestation of hypercementosis in Homo sapiens.
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Affiliation(s)
- Frederick E Grine
- Department of Anthropology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Anatomical Sciences, Stony Brook University, Stony Brook, NY 11794, USA.
| | - Carrie S Mongle
- Department of Anthropology, Stony Brook University, Stony Brook, NY 11794, USA; Turkana Basin Institute, Stony Brook University, Stony Brook, NY 11794, USA
| | - William Kollmer
- Department of Anthropology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Periodontology, Stony Brook University School of Dental Medicine, Stony Brook, NY 11794, USA
| | - Georgios Romanos
- Department of Periodontology, Stony Brook University School of Dental Medicine, Stony Brook, NY 11794, USA
| | - Anton du Plessis
- Department of Physics, Stellenbosch University, Stellenbosch 7602, South Africa; Object Research Systems, 460 Saint-Catherine St. W, Montreal, Quebec H3B 1A7, Canada
| | - Bruno Maureille
- Université de Bordeaux, CNRS, Ministère de la Culture, PACEA, UMR5199, F-33600 Pessac, France
| | - José Braga
- Center for Anthrobiology & Genomics Institute of Toulouse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 37 allées Jules Guesde, Toulouse 31000, France
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21
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Zupanič Pajnič I, Geršak ŽM, Leskovar T, Črešnar M. Kinship analysis of 5th- to 6th-century skeletons of Romanized indigenous people from the Bled-Pristava archaeological site. Forensic Sci Int Genet 2023; 65:102886. [PMID: 37137206 DOI: 10.1016/j.fsigen.2023.102886] [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: 12/15/2022] [Revised: 03/31/2023] [Accepted: 04/27/2023] [Indexed: 05/05/2023]
Abstract
The familial relationship between skeletons buried together in a shared grave is important for understanding the burial practices of past human populations. Four skeletons were excavated from the Late Antiquity part of the Bled-Pristava burial site in Slovenia, dated to the 5th to 6th century. They were anthropologically characterized as two adults (a middle-aged man and a young woman) and two non-adults (of unknown sex). Based on stratigraphy, the skeletons were considered to be buried simultaneously in one grave. Our aim was to determine whether the skeletons were related. Petrous bones and teeth were used for genetic analysis. Specific precautions were followed to prevent contamination of ancient DNA with contemporary DNA, and an elimination database was established. Bone powder was obtained using a MillMix tissue homogenizer. Prior to extracting the DNA using Biorobot EZ1, 0.5 g of powder was decalcified. The PowerQuant System was used for quantification, various autosomal kits for autosomal short tandem repeat (STR) typing, and the PowerPlex Y23 kit for Y-STR typing. All analyses were performed in duplicate. Up to 28 ng DNA/g of powder was extracted from the samples analyzed. Almost full autosomal STR profiles obtained from all four skeletons and almost full Y-STR haplotypes obtained from two male skeletons were compared, and the possibility of a familial relationship was evaluated. No amplification was obtained in the negative controls, and no match was found in the elimination database. Autosomal STR statistical calculations confirmed that the adult male was the father of two non-adult individuals and one young adult individual from the grave. The relationship between the males (father and son) was additionally confirmed by an identical Y-STR haplotype that belonged to the E1b1b haplogroup, and a combined likelihood ratio for autosomal and Y-STRs was calculated. Kinship analysis confirmed with high confidence (kinship probability greater than 99.9% was calculated for all three children) that all four skeletons belonged to the same family (a father, two daughters, and a son). Through genetic analysis, the burial of members of the same family in a shared grave was confirmed as a burial practice of the population living in the Bled area in Late Antiquity.
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Affiliation(s)
- Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia.
| | - Živa Miriam Geršak
- Institute of Radiology, University Medical Centre Ljubljana, Zaloška 7, Ljubljana, Slovenia
| | - Tamara Leskovar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
| | - Matija Črešnar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
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22
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Pathogenic Variants Associated with Rare Monogenic Diseases Established in Ancient Neanderthal and Denisovan Genome-Wide Data. Genes (Basel) 2023; 14:genes14030727. [PMID: 36980999 PMCID: PMC10048696 DOI: 10.3390/genes14030727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
Ancient anatomically modern humans (AMHs) encountered other archaic human species, most notably Neanderthals and Denisovans, when they left Africa and spread across Europe and Asia ~60,000 years ago. They interbred with them, and modern human genomes retain DNA inherited from these interbreeding events. High quality (high coverage) ancient human genomes have recently been sequenced allowing for a direct estimation of individual heterozygosity, which has shown that genetic diversity in these archaic human groups was very low, indicating low population sizes. In this study, we analyze ten ancient human genome-wide data, including four sequenced with high-coverage. We screened these ancient genome-wide data for pathogenic mutations associated with monogenic diseases, and established unusual aggregation of pathogenic mutations in individual subjects, including quadruple homozygous cases of pathogenic variants in the PAH gene associated with the condition phenylketonuria in a ~120,000 years old Neanderthal. Such aggregation of pathogenic mutations is extremely rare in contemporary populations, and their existence in ancient humans could be explained by less significant clinical manifestations coupled with small community sizes, leading to higher inbreeding levels. Our results suggest that pathogenic variants associated with rare diseases might be the result of introgression from other archaic human species, and archaic admixture thus could have influenced disease risk in modern humans.
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23
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Evolutionary Origin of Germline Pathogenic MUTYH Variations in Modern Humans. Biomolecules 2023; 13:biom13030429. [PMID: 36979362 PMCID: PMC10046817 DOI: 10.3390/biom13030429] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/30/2022] [Accepted: 01/04/2023] [Indexed: 03/02/2023] Open
Abstract
MUTYH plays an essential role in preventing oxidation-caused DNA damage. Pathogenic germline variations in MUTYH damage its function, causing intestinal polyposis and colorectal cancer. Determination of the evolutionary origin of the variation is essential to understanding the etiological relationship between MUTYH variation and cancer development. In this study, we analyzed the origins of pathogenic germline variants in human MUTYH. Using a phylogenic approach, we searched pathogenic MUTYH variants in modern humans in the MUTYH of 99 vertebrates across eight clades. We did not find pathogenic variants shared between modern humans and the non-human vertebrates following the evolutionary tree, ruling out the possibility of cross-species conservation as the origin of human pathogenic variants in MUTYH. We then searched the variants in the MUTYH of 5031 ancient humans and extinct Neanderthals and Denisovans. We identified 24 pathogenic variants in 42 ancient humans dated between 30,570 and 480 years before present (BP), and three pathogenic variants in Neanderthals dated between 65,000 and 38,310 years BP. Data from our study revealed that human pathogenic MUTYH variants mostly arose in recent human history and were partially inherited from Neanderthals.
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24
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Talamo S, Kromer B, Richards MP, Wacker L. Back to the future: The advantage of studying key events in human evolution using a new high resolution radiocarbon method. PLoS One 2023; 18:e0280598. [PMID: 36791053 PMCID: PMC9931112 DOI: 10.1371/journal.pone.0280598] [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: 09/21/2022] [Accepted: 01/03/2023] [Indexed: 02/16/2023] Open
Abstract
Radiocarbon dating is the most widely applied dating method in archaeology, especially in human evolution studies, where it is used to determine the chronology of key events, such as the replacement of Neanderthals by modern humans in Europe. However, the method does not always provide precise and accurate enough ages to understand the important processes of human evolution. Here we review the newest method developments in radiocarbon dating ('Radiocarbon 3.0'), which can lead us to much better chronologies and understanding of the major events in recent human evolution. As an example, we apply these new methods to discuss the dating of the important Palaeolithic site of Bacho Kiro (Bulgaria).
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Affiliation(s)
- Sahra Talamo
- Department of Chemistry G. Ciamician, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- * E-mail:
| | - Bernd Kromer
- Institute for Environmental Physics, University of Heidelberg, Heidelberg, Germany
| | | | - Lukas Wacker
- Laboratory for Ion Beam Physics, ETH Zurich, Zurich, Switzerland
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25
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Doronicheva EV, Golovanova LV, Doronichev VB, Kurbanov RN. Archaeological evidence for two culture diverse Neanderthal populations in the North Caucasus and contacts between them. PLoS One 2023; 18:e0284093. [PMID: 37053172 PMCID: PMC10101426 DOI: 10.1371/journal.pone.0284093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 03/23/2023] [Indexed: 04/14/2023] Open
Abstract
Neanderthals were widespread during the Middle Palaeolithic (MP) across Europe and Asia, including the Caucasus Mountains. Occupying the border between eastern Europe and West Asia, the Caucasus is important region regarding the Neanderthal occupation of Eurasia. On current radiometric estimates, the MP is represented in the Caucasus between about 260-210 ka and about 40 ka. Archaeological record indicates that several culture diverse MP hominin populations inhabited the Caucasus, but the region complex population history during this period remains poorly understood. In this paper, we identify for the first time the archaeological evidence indicating contacts between two culture diverse MP Neanderthal populations in the North Caucasus and discuss the nature of these contacts. Basing on the lithic assemblages that we excavated at Mezmaiskaya cave in the north-western Caucasus (Kuban River basin) and Saradj-Chuko grotto in the north-central Caucasus (Terek River basin), dating from MIS 5 to MIS 3, and comparative data from other MP sites in the Caucasus, we identify two large cultural regions that existed during the late MP in the North Caucasus. The distinctive toolkits and stone knapping technologies indicate that the MP assemblages from Mezmaiskaya cave and other sites in the west of North Caucasus represent a Caucasian variant of the Eastern Micoquian industry that was wide spread in central and eastern Europe, while the assemblages from Saradj-Chuko Grotto and other sites in the east of North Caucasus closely resemble the Zagros Mousterian industry that was wide spread in the Armenian Highlands, Lesser Caucasus and Zagros Mountains. The archaeological evidence implies that two culture diverse populations of Neanderthals settled the North Caucasus during the Late Pleistocene from two various source regions: from the Armenian Highlands and Lesser Caucasus along the Caspian Sea coast, and from Russian plain along the Sea of Azov coast.
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Affiliation(s)
- Ekaterina V Doronicheva
- Autonomous Nonprofit Organization in the Field of Humanitarian and Scientific Research «Laboratory of Prehistory», St. Petersburg, Russia
| | - Liubov V Golovanova
- Autonomous Nonprofit Organization in the Field of Humanitarian and Scientific Research «Laboratory of Prehistory», St. Petersburg, Russia
| | - Vladimir B Doronichev
- Autonomous Nonprofit Organization in the Field of Humanitarian and Scientific Research «Laboratory of Prehistory», St. Petersburg, Russia
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Sirocko F, Albert J, Britzius S, Dreher F, Martínez-García A, Dosseto A, Burger J, Terberger T, Haug G. Thresholds for the presence of glacial megafauna in central Europe during the last 60,000 years. Sci Rep 2022; 12:20055. [PMID: 36414639 PMCID: PMC9681729 DOI: 10.1038/s41598-022-22464-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/14/2022] [Indexed: 11/23/2022] Open
Abstract
Lake sediment records from Holzmaar and the infilled maar of Auel (Eifel, Germany) are used to reconstruct landscape changes and megafauna abundances. Our data document a forested landscape from 60,000 to 48,000 yr b2k and a stepwise vegetation change towards a glacial desert after 26,000 yr b2k. The Eifel landscape was continuously inhabited from 48,000 to 9000 yr b2k by large mammals, documented by the presence of spores of coprophilous fungi from Sordaria and Sporormiella fungi that grow on fecal remains of the megafauna. Megafauna reached higher numbers during cold stadial climates but was present also during the warmer interstadials. Highest abundance was at 56,500/48,500/38,500/33,000/27,000/21,000/16,200/14,000 yr b2k, i.e. under different climate regimes. Some of these dates were associated with clear human presence, which indicates that megafauna was not overkilled by humans. In contrast, human presence could quite likely have been stimulated by the abundant food supply. Megafauna presence decreased significantly when tree abundance increased during interstadials. The Megafauna disappeared finally at 11,400 yr b2k with the development of the early Holocene forest cover, which appears to be the most important threshold for megafauna presence.
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Affiliation(s)
- Frank Sirocko
- grid.5802.f0000 0001 1941 7111Institute for Geoscience, Johannes Gutenberg-University, Mainz, Germany
| | - Johannes Albert
- grid.5802.f0000 0001 1941 7111Institute for Geoscience, Johannes Gutenberg-University, Mainz, Germany
| | - Sarah Britzius
- grid.5802.f0000 0001 1941 7111Institute for Geoscience, Johannes Gutenberg-University, Mainz, Germany ,grid.419509.00000 0004 0491 8257Max Planck Institute for Chemistry, Mainz, Germany
| | - Frank Dreher
- grid.5802.f0000 0001 1941 7111Institute for Geoscience, Johannes Gutenberg-University, Mainz, Germany
| | | | - Anthony Dosseto
- grid.1007.60000 0004 0486 528XWollongong Isotope Geochronology Laboratory, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW Australia
| | - Joachim Burger
- Institute of Organismic and Molecular Evolution (iomE), Palaeogenetics Group, Mainz, Germany
| | - Thomas Terberger
- grid.7450.60000 0001 2364 4210Göttingen, Seminar for Pre- and Protohistory, University of Göttingen, Göttingen, Germany
| | - Gerald Haug
- grid.419509.00000 0004 0491 8257Max Planck Institute for Chemistry, Mainz, Germany
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27
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Doronicheva EV, Golovanova LV, Kostina JV, Legkov SA, Poplevko GN, Revina EI, Rusakova OY, Doronichev VB. Functional characterization of Mousterian tools from the Caucasus using comprehensive use-wear and residue analysis. Sci Rep 2022; 12:17421. [PMID: 36261487 PMCID: PMC9581955 DOI: 10.1038/s41598-022-20612-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/15/2022] [Indexed: 01/12/2023] Open
Abstract
The authors discuss functional characterization of Mousterian tools on the basis of their use-wear and residue analysis of five lithic tools from Mezmaiskaya cave and Saradj-Chuko grotto in the North Caucasus. The results represent the first comprehensive use-wear and residue analysis carried out on Mousterian stone artefacts in the Caucasus. This study unequivocally confirms the use of bitumen for hafting stone tools in two different Middle Paleolithic cultural contexts defined in the Caucasus, Eastern Micoquian and Zagros Mousterian.
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Affiliation(s)
- E. V. Doronicheva
- ANO Laboratory of Prehistory, Liflyandskaya street 6M, St. Petersburg, Russia 190020
| | - L. V. Golovanova
- ANO Laboratory of Prehistory, Liflyandskaya street 6M, St. Petersburg, Russia 190020
| | - J. V. Kostina
- grid.4886.20000 0001 2192 9124A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninskiy prospekt 29-2, Moscow, Russia 119991
| | - S. A. Legkov
- grid.4886.20000 0001 2192 9124A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninskiy prospekt 29-2, Moscow, Russia 119991
| | - G. N. Poplevko
- grid.4886.20000 0001 2192 9124Laboratory for Experimental–Traceological Studies, Institute for the History of Material Culture, Russian Academy of Sciences, Dvortsovaya embankment 18, St. Petersburg, Russia 191186
| | - E. I. Revina
- Rostov Regional Museum of Local Lore, Bolshaya Sadovaya street 79, Rostov-on-Don, Russia 344006
| | - O. Y. Rusakova
- grid.4886.20000 0001 2192 9124A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninskiy prospekt 29-2, Moscow, Russia 119991
| | - V. B. Doronichev
- ANO Laboratory of Prehistory, Liflyandskaya street 6M, St. Petersburg, Russia 190020
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28
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Djakovic I, Key A, Soressi M. Optimal linear estimation models predict 1400-2900 years of overlap between Homo sapiens and Neandertals prior to their disappearance from France and northern Spain. Sci Rep 2022; 12:15000. [PMID: 36229473 PMCID: PMC9561710 DOI: 10.1038/s41598-022-19162-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 08/25/2022] [Indexed: 11/26/2022] Open
Abstract
Recent fossil discoveries suggest that Neandertals and Homo sapiens may have co-existed in Europe for as long as 5 to 6000 years. Yet, evidence for their contemporaneity at any regional scale remains highly elusive. In France and northern Spain, a region which features some of the latest directly-dated Neandertals in Europe, Protoaurignacian assemblages attributed to Homo sapiens appear to ‘replace’ Neandertal-associated Châtelperronian assemblages. Using the earliest and latest known occurrences as starting points, Bayesian modelling has provided indication that these occupations may in fact have been partly contemporaneous. The reality, however, is that we are unlikely to ever identify the ‘first’ or ‘last’ appearance of a species or cultural tradition in the archaeological and fossil record. Here, we use optimal linear estimation modelling to estimate the first appearance date of Homo sapiens and the extinction date of Neandertals in France and northern Spain by statistically inferring these ‘missing’ portions of the Protoaurignacian and Châtelperronian archaeological records. Additionally, we estimate the extinction date of Neandertals in this region using a dataset of directly-dated Neandertal fossil remains. Our total dataset consists of sixty-six modernly produced radiocarbon determinations which we recalibrated using the newest calibration curve (IntCal20) to produce updated age ranges. The results suggest that the onset of the Homo sapiens occupation of this region likely preceded the extinction of Neandertals and the Châtelperronian by up to 1400–2900 years. This reaffirms the Bayesian-derived duration of co-existence between these groups during the initial Upper Palaeolithic of this region using a novel independent method, and indicates that our understanding of the timing of these occupations may not be suffering from substantial gaps in the record. Whether or not this co-existence featured some form of direct interaction, however, remains to be resolved.
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Affiliation(s)
- Igor Djakovic
- Faculty of Archaeology, Leiden University, Leiden, The Netherlands.
| | - Alastair Key
- Department of Archaeology, University of Cambridge, Cambridge, CB2 3DZ, UK
| | - Marie Soressi
- Faculty of Archaeology, Leiden University, Leiden, The Netherlands
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Alagöz G, Molz B, Eising E, Schijven D, Francks C, Stein JL, Fisher SE. Using neuroimaging genomics to investigate the evolution of human brain structure. Proc Natl Acad Sci U S A 2022; 119:e2200638119. [PMID: 36161899 PMCID: PMC9546597 DOI: 10.1073/pnas.2200638119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 08/15/2022] [Indexed: 01/16/2023] Open
Abstract
Alterations in brain size and organization represent some of the most distinctive changes in the emergence of our species. Yet, there is limited understanding of how genetic factors contributed to altered neuroanatomy during human evolution. Here, we analyze neuroimaging and genetic data from up to 30,000 people in the UK Biobank and integrate with genomic annotations for different aspects of human evolution, including those based on ancient DNA and comparative genomics. We show that previously reported signals of recent polygenic selection for cortical anatomy are not replicable in a more ancestrally homogeneous sample. We then investigate relationships between evolutionary annotations and common genetic variants shaping cortical surface area and white-matter connectivity for each hemisphere. Our analyses identify single-nucleotide polymorphism heritability enrichment in human-gained regulatory elements that are active in early brain development, affecting surface areas of several parts of the cortex, including left-hemispheric speech-associated regions. We also detect heritability depletion in genomic regions with Neanderthal ancestry for connectivity of the uncinate fasciculus; this is a white-matter tract involved in memory, language, and socioemotional processing with relevance to neuropsychiatric disorders. Finally, we show that common genetic loci associated with left-hemispheric pars triangularis surface area overlap with a human-gained enhancer and affect regulation of ZIC4, a gene implicated in neurogenesis. This work demonstrates how genomic investigations of present-day neuroanatomical variation can help shed light on the complexities of our evolutionary past.
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Affiliation(s)
- Gökberk Alagöz
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6500 AH Nijmegen, The Netherlands
| | - Barbara Molz
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6500 AH Nijmegen, The Netherlands
| | - Else Eising
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6500 AH Nijmegen, The Netherlands
| | - Dick Schijven
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6500 AH Nijmegen, The Netherlands
| | - Clyde Francks
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6500 AH Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6500 HB Nijmegen, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Jason L. Stein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Simon E. Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6500 AH Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6500 HB Nijmegen, The Netherlands
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30
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Skov L, Peyrégne S, Popli D, Iasi LNM, Devièse T, Slon V, Zavala EI, Hajdinjak M, Sümer AP, Grote S, Bossoms Mesa A, López Herráez D, Nickel B, Nagel S, Richter J, Essel E, Gansauge M, Schmidt A, Korlević P, Comeskey D, Derevianko AP, Kharevich A, Markin SV, Talamo S, Douka K, Krajcarz MT, Roberts RG, Higham T, Viola B, Krivoshapkin AI, Kolobova KA, Kelso J, Meyer M, Pääbo S, Peter BM. Genetic insights into the social organization of Neanderthals. Nature 2022; 610:519-525. [PMID: 36261548 PMCID: PMC9581778 DOI: 10.1038/s41586-022-05283-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 08/26/2022] [Indexed: 11/22/2022]
Abstract
Genomic analyses of Neanderthals have previously provided insights into their population history and relationship to modern humans1-8, but the social organization of Neanderthal communities remains poorly understood. Here we present genetic data for 13 Neanderthals from two Middle Palaeolithic sites in the Altai Mountains of southern Siberia: 11 from Chagyrskaya Cave9,10 and 2 from Okladnikov Cave11-making this one of the largest genetic studies of a Neanderthal population to date. We used hybridization capture to obtain genome-wide nuclear data, as well as mitochondrial and Y-chromosome sequences. Some Chagyrskaya individuals were closely related, including a father-daughter pair and a pair of second-degree relatives, indicating that at least some of the individuals lived at the same time. Up to one-third of these individuals' genomes had long segments of homozygosity, suggesting that the Chagyrskaya Neanderthals were part of a small community. In addition, the Y-chromosome diversity is an order of magnitude lower than the mitochondrial diversity, a pattern that we found is best explained by female migration between communities. Thus, the genetic data presented here provide a detailed documentation of the social organization of an isolated Neanderthal community at the easternmost extent of their known range.
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Affiliation(s)
- Laurits Skov
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Stéphane Peyrégne
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Divyaratan Popli
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Leonardo N M Iasi
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Thibaut Devièse
- European Centre for Research and Education in Environmental Geosciences (CEREGE), Aix-Marseille University, CNRS, IRD, INRAE, Collège de France, Aix-en-Provence, France
| | - Viviane Slon
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anatomy and Anthropology Sackler, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Elena I Zavala
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mateja Hajdinjak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- The Francis Crick Institute, London, UK
| | - Arev P Sümer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Steffi Grote
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alba Bossoms Mesa
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - David López Herráez
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Birgit Nickel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sarah Nagel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Julia Richter
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Elena Essel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Marie Gansauge
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anna Schmidt
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Petra Korlević
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Wellcome Sanger Institute, Hinxton, UK
| | - Daniel Comeskey
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, UK
| | - Anatoly P Derevianko
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Aliona Kharevich
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergey V Markin
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Sahra Talamo
- Department of Chemistry G. Ciamician, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Katerina Douka
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Human Evolution and Archaeological Sciences Forschungsverbund, University of Vienna, Vienna, Austria
| | - Maciej T Krajcarz
- Institute of Geological Sciences, Polish Academy of Sciences, Warsaw, Poland
| | - Richard G Roberts
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia
- Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
| | - Thomas Higham
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences Forschungsverbund, University of Vienna, Vienna, Austria
| | - Bence Viola
- Department of Anthropology, University of Toronto, Toronto, Ontario, Canada
| | - Andrey I Krivoshapkin
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Kseniya A Kolobova
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benjamin M Peter
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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Reilly PF, Tjahjadi A, Miller SL, Akey JM, Tucci S. The contribution of Neanderthal introgression to modern human traits. Curr Biol 2022; 32:R970-R983. [PMID: 36167050 PMCID: PMC9741939 DOI: 10.1016/j.cub.2022.08.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Neanderthals, our closest extinct relatives, lived in western Eurasia from 400,000 years ago until they went extinct around 40,000 years ago. DNA retrieved from ancient specimens revealed that Neanderthals mated with modern human contemporaries. As a consequence, introgressed Neanderthal DNA survives scattered across the human genome such that 1-4% of the genome of present-day people outside Africa are inherited from Neanderthal ancestors. Patterns of Neanderthal introgressed genomic sequences suggest that Neanderthal alleles had distinct fates in the modern human genetic background. Some Neanderthal alleles facilitated human adaptation to new environments such as novel climate conditions, UV exposure levels and pathogens, while others had deleterious consequences. Here, we review the body of work on Neanderthal introgression over the past decade. We describe how evolutionary forces shaped the genomic landscape of Neanderthal introgression and highlight the impact of introgressed alleles on human biology and phenotypic variation.
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Affiliation(s)
| | - Audrey Tjahjadi
- Department of Anthropology, Yale University, New Haven, CT, USA
| | | | - Joshua M Akey
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
| | - Serena Tucci
- Department of Anthropology, Yale University, New Haven, CT, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
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Andreeva TV, Malyarchuk AB, Soshkina AD, Dudko NA, Plotnikova MY, Rogaev EI. Methodologies for Ancient DNA Extraction from Bones for Genomic Analysis: Approaches and Guidelines. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422090034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Churchill SE, Keys K, Ross AH. Midfacial Morphology and Neandertal-Modern Human Interbreeding. BIOLOGY 2022; 11:1163. [PMID: 36009790 PMCID: PMC9404802 DOI: 10.3390/biology11081163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/29/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
Ancient DNA from, Neandertal and modern human fossils, and comparative morphological analyses of them, reveal a complex history of interbreeding between these lineages and the introgression of Neandertal genes into modern human genomes. Despite substantial increases in our knowledge of these events, the timing and geographic location of hybridization events remain unclear. Six measures of facial size and shape, from regional samples of Neandertals and early modern humans, were used in a multivariate exploratory analysis to try to identify regions in which early modern human facial morphology was more similar to that of Neandertals, which might thus represent regions of greater introgression of Neandertal genes. The results of canonical variates analysis and hierarchical cluster analysis suggest important affinities in facial morphology between both Middle and Upper Paleolithic early modern humans of the Near East with Neandertals, highlighting the importance of this region for interbreeding between the two lineages.
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Affiliation(s)
- Steven E. Churchill
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA;
- Centre for the Exploration of the Deep Human Journey, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Kamryn Keys
- Human Identification & Forensic Analysis Laboratory, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA;
| | - Ann H. Ross
- Human Identification & Forensic Analysis Laboratory, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA;
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Theofanopoulou C, Andirkó A, Boeckx C, Jarvis ED. Oxytocin and vasotocin receptor variation and the evolution of human prosociality. COMPREHENSIVE PSYCHONEUROENDOCRINOLOGY 2022; 11:100139. [PMID: 35757177 PMCID: PMC9227999 DOI: 10.1016/j.cpnec.2022.100139] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 11/04/2022] Open
Abstract
Modern human lifestyle strongly depends on complex social traits like empathy, tolerance and cooperation. These diverse facets of social cognition have been associated with variation in the oxytocin receptor (OTR) and its sister genes, the vasotocin/vasopressin receptors (VTR1A/AVPR1A and AVPR1B/VTR1B). Here, we compared the available genomic sequences of these receptors between modern humans, archaic humans, and 12 non-human primate species, and identified sites that show heterozygous variation in modern humans and archaic humans distinct from variation in other primates, and for which we could find association studies with clinical implications. On these sites, we performed a range of analyses (variant clustering, pathogenicity prediction, regulation, linkage disequilibrium frequency), and reviewed the literature on selection data in different modern-human populations. We found five sites with modern human specific variation, where the modern human allele is the major allele in the global population (OTR: rs1042778, rs237885, rs6770632; VTR1A: rs10877969; VTR1B: rs33985287). Among them, variation in the OTR-rs6770632 site was predicted to be the most functional. Two alleles (OTR: rs59190448 and rs237888) present only in modern humans and archaic humans were putatively under positive selection in modern humans, with rs237888 predicted to be a highly functional site. Three sites showed convergent evolution between modern humans and bonobos (OTR: rs2228485 and rs237897; VTR1A: rs1042615), with OTR-rs2228485 ranking highly in terms of functionality and reported to be under balancing selection in modern humans (Schaschl, 2015) [1]. Our findings have implications for understanding hominid prosociality, as well as the similarities between modern human and bonobo social behavior.
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Affiliation(s)
| | - Alejandro Andirkó
- Section of General Linguistics, Universitat de Barcelona, Spain
- Universitat de Barcelona Institute for Complex Systems, USA
| | - Cedric Boeckx
- Section of General Linguistics, Universitat de Barcelona, Spain
- Universitat de Barcelona Institute for Complex Systems, USA
- ICREA, Spain
| | - Erich D. Jarvis
- Laboratory of Neurogenetics of Language, Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
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35
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Andreeva TV, Manakhov AD, Gusev FE, Patrikeev AD, Golovanova LV, Doronichev VB, Shirobokov IG, Rogaev EI. Genomic analysis of a novel Neanderthal from Mezmaiskaya Cave provides insights into the genetic relationships of Middle Palaeolithic populations. Sci Rep 2022; 12:13016. [PMID: 35906446 PMCID: PMC9338269 DOI: 10.1038/s41598-022-16164-9] [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: 05/03/2022] [Accepted: 07/05/2022] [Indexed: 11/09/2022] Open
Abstract
The Mezmaiskaya cave is located on the North Caucasus near the border that divides Europe and Asia. Previously, fossil remains for two Neanderthals were reported from Mezmaiskaya Cave. A tooth from the third archaic hominin specimen (Mezmaiskaya 3) was retrieved from layer 3 in Mezmaiskaya Cave. We performed genome sequencing of Mezmaiskaya 3. Analysis of partial nuclear genome sequence revealed that it belongs to a Homo sapiens neanderthalensis female. Based on a high-coverage mitochondrial genome sequence, we demonstrated that the relationships of Mezmaiskaya 3 to Mezmaiskaya 1 and Stajnia S5000 individuals were closer than those to other Neanderthals. Our data demonstrate the close genetic connections between the early Middle Palaeolithic Neanderthals that were replaced by genetically distant later group in the same geographic areas. Based on mitochondrial DNA (mtDNA) data, we suggest that Mezmaiskaya 3 was the latest Neanderthal individual from the early Neanderthal’s branches. We proposed a hierarchical nomenclature for the mtDNA haplogroups of Neanderthals. In addition, we retrieved ancestral mtDNA mutations in presumably functional sites fixed in the Neanderthal clades, and also provided the first data showing mtDNA heteroplasmy in Neanderthal specimen.
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Affiliation(s)
- Tatiana V Andreeva
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia, 354340. .,Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia, 119333. .,Faculty of Biology, Centre for Genetics and Genetic Technologies, Lomonosov Moscow State University, Moscow, Russia, 119192.
| | - Andrey D Manakhov
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia, 354340.,Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia, 119333.,Faculty of Biology, Centre for Genetics and Genetic Technologies, Lomonosov Moscow State University, Moscow, Russia, 119192
| | - Fedor E Gusev
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia, 354340.,Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia, 119333.,Faculty of Biology, Centre for Genetics and Genetic Technologies, Lomonosov Moscow State University, Moscow, Russia, 119192
| | - Anton D Patrikeev
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia, 119333
| | | | | | - Ivan G Shirobokov
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, St. Petersburg, Russia, 199034
| | - Evgeny I Rogaev
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia, 354340. .,Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia, 119333. .,Faculty of Biology, Centre for Genetics and Genetic Technologies, Lomonosov Moscow State University, Moscow, Russia, 119192. .,Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, 01604, USA.
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Stenseth NC, Andersson L, Hoekstra HE. Gregor Johann Mendel and the development of modern evolutionary biology. Proc Natl Acad Sci U S A 2022; 119:e2201327119. [PMID: 35858454 PMCID: PMC9335310 DOI: 10.1073/pnas.2201327119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Nils Chr. Stenseth
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843
| | - Hopi E. Hoekstra
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Department of Molecular & Cellular Biology, Harvard University, Cambridge, MA 02138
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
- HHMI, Harvard University, Cambridge, MA 02138
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37
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Peyrégne S, Kelso J, Peter BM, Pääbo S. The evolutionary history of human spindle genes includes back-and-forth gene flow with Neandertals. eLife 2022; 11:e75464. [PMID: 35816093 PMCID: PMC9273211 DOI: 10.7554/elife.75464] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 06/14/2022] [Indexed: 12/13/2022] Open
Abstract
Proteins associated with the spindle apparatus, a cytoskeletal structure that ensures the proper segregation of chromosomes during cell division, experienced an unusual number of amino acid substitutions in modern humans after the split from the ancestors of Neandertals and Denisovans. Here, we analyze the history of these substitutions and show that some of the genes in which they occur may have been targets of positive selection. We also find that the two changes in the kinetochore scaffold 1 (KNL1) protein, previously believed to be specific to modern humans, were present in some Neandertals. We show that the KNL1 gene of these Neandertals shared a common ancestor with present-day Africans about 200,000 years ago due to gene flow from the ancestors (or relatives) of modern humans into Neandertals. Subsequently, some non-Africans inherited this modern human-like gene variant from Neandertals, but none inherited the ancestral gene variants. These results add to the growing evidence of early contacts between modern humans and archaic groups in Eurasia and illustrate the intricate relationships among these groups.
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Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary AnthropologyLeipzigGermany
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary AnthropologyLeipzigGermany
| | - Benjamin M Peter
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary AnthropologyLeipzigGermany
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary AnthropologyLeipzigGermany
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38
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Brand CM, Colbran LL, Capra JA. Predicting Archaic Hominin Phenotypes from Genomic Data. Annu Rev Genomics Hum Genet 2022; 23:591-612. [PMID: 35440148 DOI: 10.1146/annurev-genom-111521-121903] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ancient DNA provides a powerful window into the biology of extant and extinct species, including humans' closest relatives: Denisovans and Neanderthals. Here, we review what is known about archaic hominin phenotypes from genomic data and how those inferences have been made. We contend that understanding the influence of variants on lower-level molecular phenotypes-such as gene expression and protein function-is a promising approach to using ancient DNA to learn about archaic hominin traits. Molecular phenotypes have simpler genetic architectures than organism-level complex phenotypes, and this approach enables moving beyond association studies by proposing hypotheses about the effects of archaic variants that are testable in model systems. The major challenge to understanding archaic hominin phenotypes is broadening our ability to accurately map genotypes to phenotypes, but ongoing advances ensure that there will be much more to learn about archaic hominin phenotypes from their genomes. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Colin M Brand
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA; , .,Bakar Computational Health Sciences Institute, University of California, San Francisco, California, USA
| | - Laura L Colbran
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John A Capra
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA; , .,Bakar Computational Health Sciences Institute, University of California, San Francisco, California, USA
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Vallini L, Marciani G, Aneli S, Bortolini E, Benazzi S, Pievani T, Pagani L. Genetics and Material Culture Support Repeated Expansions into Paleolithic Eurasia from a Population Hub Out of Africa. Genome Biol Evol 2022; 14:evac045. [PMID: 35445261 PMCID: PMC9021735 DOI: 10.1093/gbe/evac045] [Citation(s) in RCA: 8] [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] [Accepted: 03/21/2022] [Indexed: 11/14/2022] Open
Abstract
The population dynamics that followed the Out of Africa (OoA) expansion and the whereabouts of the early migrants before the differentiation that ultimately led to the formation of Oceanian, West and East Eurasian macropopulations have long been debated. Shedding light on these events may, in turn, provide clues to better understand the cultural evolution in Eurasia between 50 and 35 ka. Here, we analyze Eurasian Paleolithic DNA evidence to provide a comprehensive population model and validate it in light of available material culture. Leveraging on our integrated approach we propose the existence of a Eurasian population Hub, where Homo sapiens lived between the OoA and the broader colonization of Eurasia, which was characterized by multiple events of expansion and local extinction. A major population wave out of Hub, of which Ust'Ishim, Bacho Kiro, and Tianyuan are unadmixed representatives, is broadly associated with Initial Upper Paleolithic lithics and populated West and East Eurasia before or around 45 ka, before getting largely extinct in Europe. In this light, we suggest a parsimonious placement of Oase1 as an individual related to Bacho Kiro who experienced additional Neanderthal introgression. Another expansion, started before 38 ka, is broadly associated with Upper Paleolithic industries and repopulated Europe with sporadic admixtures with the previous wave (GoyetQ116-1) and more systematic ones, whereas moving through Siberia (Yana, Mal'ta). Before these events, we also confirm Zlatý Kůň as the most basal human lineage sequenced to date OoA, potentially representing an earlier wave of expansion out of the Hub.
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Affiliation(s)
| | - Giulia Marciani
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
- Department of Physical Sciences, Earth and Environment, University of Siena, Italy
| | - Serena Aneli
- Department of Biology, University of Padova, Italy
- Department of Public Health Sciences and Pediatrics, University of Turin, Italy
| | - Eugenio Bortolini
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Stefano Benazzi
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Luca Pagani
- Department of Biology, University of Padova, Italy
- Institute of Genomics, University of Tartu, Estonia
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Wohns AW, Wong Y, Jeffery B, Akbari A, Mallick S, Pinhasi R, Patterson N, Reich D, Kelleher J, McVean G. A unified genealogy of modern and ancient genomes. Science 2022; 375:eabi8264. [PMID: 35201891 PMCID: PMC10027547 DOI: 10.1126/science.abi8264] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The sequencing of modern and ancient genomes from around the world has revolutionized our understanding of human history and evolution. However, the problem of how best to characterize ancestral relationships from the totality of human genomic variation remains unsolved. Here, we address this challenge with nonparametric methods that enable us to infer a unified genealogy of modern and ancient humans. This compact representation of multiple datasets explores the challenges of missing and erroneous data and uses ancient samples to constrain and date relationships. We demonstrate the power of the method to recover relationships between individuals and populations as well as to identify descendants of ancient samples. Finally, we introduce a simple nonparametric estimator of the geographical location of ancestors that recapitulates key events in human history.
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Affiliation(s)
- Anthony Wilder Wohns
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
| | - Yan Wong
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
| | - Ben Jeffery
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
| | - Ali Akbari
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA 02138, USA
- Department of Genetics, Harvard Medical School; Boston, MA 02115, USA
| | - Swapan Mallick
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute; Boston, MA 02115, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna; 1090 Vienna, Austria
| | - Nick Patterson
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA 02138, USA
- Howard Hughes Medical Institute; Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School; Boston, MA 02115, USA
| | - David Reich
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA 02138, USA
- Howard Hughes Medical Institute; Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School; Boston, MA 02115, USA
| | - Jerome Kelleher
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
- Corresponding author.
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Slimak L, Zanolli C, Higham T, Frouin M, Schwenninger JL, Arnold LJ, Demuro M, Douka K, Mercier N, Guérin G, Valladas H, Yvorra P, Giraud Y, Seguin-Orlando A, Orlando L, Lewis JE, Muth X, Camus H, Vandevelde S, Buckley M, Mallol C, Stringer C, Metz L. Modern human incursion into Neanderthal territories 54,000 years ago at Mandrin, France. SCIENCE ADVANCES 2022; 8:eabj9496. [PMID: 35138885 PMCID: PMC8827661 DOI: 10.1126/sciadv.abj9496] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Determining the extent of overlap between modern humans and other hominins in Eurasia, such as Neanderthals and Denisovans, is fundamental to understanding the nature of their interactions and what led to the disappearance of archaic hominins. Apart from a possible sporadic pulse recorded in Greece during the Middle Pleistocene, the first settlements of modern humans in Europe have been constrained to ~45,000 to 43,000 years ago. Here, we report hominin fossils from Grotte Mandrin in France that reveal the earliest known presence of modern humans in Europe between 56,800 and 51,700 years ago. This early modern human incursion in the Rhône Valley is associated with technologies unknown in any industry of that age outside Africa or the Levant. Mandrin documents the first alternating occupation of Neanderthals and modern humans, with a modern human fossil and associated Neronian lithic industry found stratigraphically between layers containing Neanderthal remains associated with Mousterian industries.
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Affiliation(s)
- Ludovic Slimak
- CNRS, UMR 5608, TRACES, Université de Toulouse Jean Jaurès, 5 Allées Antonio Machado, 31058 Toulouse Cedex 9, France
- Corresponding author. (L.S.); (C.Z.)
| | - Clément Zanolli
- Université de Bordeaux, CNRS, MCC, PACEA, UMR 5199, 33600 Pessac, France
- Corresponding author. (L.S.); (C.Z.)
| | - Tom Higham
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK
- Department of Evolutionary Anthropology, University of Vienna, University Biology Building, Djerassiplatz 1, A-1030 Vienna, Austria
| | - Marine Frouin
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK
- Department of Geosciences, Stony Brook University, 255 Earth and Space Sciences Building, Stony Brook, NY 11794-2100, USA
- Turkana Basin Institute, Stony Brook University, Stony Brook, NY 11794-4364, USA
| | - Jean-Luc Schwenninger
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK
| | - Lee J. Arnold
- School of Physical Sciences, Environment Institute, Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, North Terrace Campus, Adelaide, SA 5005, Australia
| | - Martina Demuro
- School of Physical Sciences, Environment Institute, Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, North Terrace Campus, Adelaide, SA 5005, Australia
| | - Katerina Douka
- Department of Evolutionary Anthropology, University of Vienna, University Biology Building, Djerassiplatz 1, A-1030 Vienna, Austria
- Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische, Str. 10, 07745 Jena, Germany
| | - Norbert Mercier
- CNRS, UMR 5060, Institut de Recherche sur les Archéomatériaux and Centre de Recherche en Physique Appliquée à l’Archéologie (CRP2A), Maison de l’Archéologie, Université Bordeaux Montaigne, 33607 Pessac, France
| | - Gilles Guérin
- Laboratoire des Sciences du Climat et de l’Environnement, LSCE/IPSL, UMR 8212 CEA CNRS UVSQ, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Hélène Valladas
- Laboratoire des Sciences du Climat et de l’Environnement, LSCE/IPSL, UMR 8212 CEA CNRS UVSQ, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Pascale Yvorra
- Aix-Marseille Université, CNRS, Min. Culture, UMR 7269, LAMPEA, Maison Méditerranéenne des Sciences de l’Homme, BP 647, 5 rue du Château de l’Horloge, F-13094, Aix-en-Provence Cedex 2, France
| | - Yves Giraud
- Aix-Marseille Université, CNRS, Min. Culture, UMR 7269, LAMPEA, Maison Méditerranéenne des Sciences de l’Homme, BP 647, 5 rue du Château de l’Horloge, F-13094, Aix-en-Provence Cedex 2, France
| | | | - Ludovic Orlando
- CNRS, UMR 5288, CAGT, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Jason E. Lewis
- Turkana Basin Institute, Stony Brook University, Stony Brook, NY 11794-4364, USA
- Department of Anthropology, Stony Brook University, Stony Brook, NY 11794-4364, USA
| | | | - Hubert Camus
- PROTEE-EXPERT, 4 rue des Aspholdèles, 34750 Villeneuve-lès-Maguelone, France
| | - Ségolène Vandevelde
- Laboratoire des Sciences du Climat et de l’Environnement, LSCE/IPSL, UMR 8212 CEA CNRS UVSQ, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
- Université Paris 1–Panthéon-Sorbonne, Équipe Archéologies Environnementales, UMR 7041, ArScAn, Équipe Archéologies Environnementales, 21 allée de l’Université, 92023 Nanterre Cedex, France
| | - Mike Buckley
- Department of Earth and Environmental Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Carolina Mallol
- Archaeological Micromorphology and Biomarkers Laboratory (AMBI Lab), Instituto Universitario de Bio-Orgánica Antonio González, Departamento de Geografía e Historia, UDI Prehistoria, Arqueología e Historia Antigua, Facultad de Geografía e Historia, Universidad de La Laguna, Tenerife, Spain
| | - Chris Stringer
- Centre for Human Evolution Research (CHER), Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Laure Metz
- Aix-Marseille Université, CNRS, Min. Culture, UMR 7269, LAMPEA, Maison Méditerranéenne des Sciences de l’Homme, BP 647, 5 rue du Château de l’Horloge, F-13094, Aix-en-Provence Cedex 2, France
- College of Liberal Arts and Sciences, University of Connecticut, 215 Glenbrook Road, U-4098, Storrs, CT 06269-4098, USA
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Boschin F, Columbu A, Spagnolo V, Crezzini J, Bahain J, FalguèRes C, Benazzi S, Boscato P, Ronchitelli A, Moroni A, Martini I. Human occupation continuity in southern Italy towards the end of the Middle Palaeolithic: a palaeoenvironmental perspective from Apulia. JOURNAL OF QUATERNARY SCIENCE 2022; 37:204-216. [PMID: 35874299 PMCID: PMC9291488 DOI: 10.1002/jqs.3319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 01/07/2021] [Accepted: 04/09/2021] [Indexed: 06/15/2023]
Abstract
After the last interglacial [Marine Isotope Stage (MIS) 5e] Europe was affected by several harsh climatic oscillations. In this context southern Italy acted, like the rest of peninsular Mediterranean Europe, as a 'glacial refugium', allowing the survival of various species, and was involved in the spread of 'cold taxa' (e.g. woolly mammoth and woolly rhino) only during the coldest phases (MIS 4 and MIS 2). Both late Mousterian and early Upper Palaeolithic sites testify to a human occupation continuity in southern Italy and especially in Apulia in this time span. Here we present a focus on three key Apulian Palaeolithic sequences (Grotta di Santa Croce, Riparo L'Oscurusciuto and Grotta del Cavallo - layers F-E) jointly spanning from the late MIS 4 to the demise of Neanderthals around 43 ka. Novel chronological, sedimentological and zooarchaeological data are discussed for the first time in the light of the palaeoenvironmental information provided by recent analyses carried out on a speleothem from Pozzo Cucù cave (Bari) and the results of the magnetic susceptibility analysis from Riparo L'Oscurusciuto. This integrated reading allows a better understanding of the role played by the Apulian region as both a refugium for late Neaderthals and a suitable habitat for the early settling of modern humans.
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Affiliation(s)
- Francesco Boschin
- Dipartimento di Scienze Fisiche, della Terra, e dell'AmbienteUniversità Degli Studi di SienaSienaItaly
- Centro Studi sul QuaternarioSansepolcroArezzoItaly
| | - Andrea Columbu
- Dipartimento di Scienze Biologiche, Geologiche e AmbientaliUniversità di BolognaBolognaItaly
| | - Vincenzo Spagnolo
- Dipartimento di Scienze Fisiche, della Terra, e dell'AmbienteUniversità Degli Studi di SienaSienaItaly
- Centro Studi sul QuaternarioSansepolcroArezzoItaly
| | - Jacopo Crezzini
- Dipartimento di Scienze Fisiche, della Terra, e dell'AmbienteUniversità Degli Studi di SienaSienaItaly
- Centro Studi sul QuaternarioSansepolcroArezzoItaly
| | - Jean‐Jacques Bahain
- HNHP, UMR7194 ‘Histoire naturelle de l'Homme préhistorique’MNHN‐CNRS‐UPVD, Département Homme et Environnement du Muséum National d'Histoire Naturelle 1ParisFrance
| | - Christophe FalguèRes
- HNHP, UMR7194 ‘Histoire naturelle de l'Homme préhistorique’MNHN‐CNRS‐UPVD, Département Homme et Environnement du Muséum National d'Histoire Naturelle 1ParisFrance
| | - Stefano Benazzi
- Dipartimento di Beni CulturaliUniversità di BolognaRavennaItaly
| | - Paolo Boscato
- Dipartimento di Scienze Fisiche, della Terra, e dell'AmbienteUniversità Degli Studi di SienaSienaItaly
| | - Annamaria Ronchitelli
- Dipartimento di Scienze Fisiche, della Terra, e dell'AmbienteUniversità Degli Studi di SienaSienaItaly
| | - Adriana Moroni
- Dipartimento di Scienze Fisiche, della Terra, e dell'AmbienteUniversità Degli Studi di SienaSienaItaly
- Centro Studi sul QuaternarioSansepolcroArezzoItaly
| | - Ivan Martini
- Dipartimento di Scienze Fisiche, della Terra, e dell'AmbienteUniversità Degli Studi di SienaSienaItaly
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43
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Zavala EI, Thomas JT, Sturk-Andreaggi K, Daniels-Higginbotham J, Meyers KK, Barrit-Ross S, Aximu-Petri A, Richter J, Nickel B, Berg GE, McMahon TP, Meyer M, Marshall C. Ancient DNA Methods Improve Forensic DNA Profiling of Korean War and World War II Unknowns. Genes (Basel) 2022; 13:genes13010129. [PMID: 35052469 PMCID: PMC8774965 DOI: 10.3390/genes13010129] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 02/01/2023] Open
Abstract
The integration of massively parallel sequencing (MPS) technology into forensic casework has been of particular benefit to the identification of unknown military service members. However, highly degraded or chemically treated skeletal remains often fail to provide usable DNA profiles, even with sensitive mitochondrial (mt) DNA capture and MPS methods. In parallel, the ancient DNA field has developed workflows specifically for degraded DNA, resulting in the successful recovery of nuclear DNA and mtDNA from skeletal remains as well as sediment over 100,000 years old. In this study we use a set of disinterred skeletal remains from the Korean War and World War II to test if ancient DNA extraction and library preparation methods improve forensic DNA profiling. We identified an ancient DNA extraction protocol that resulted in the recovery of significantly more human mtDNA fragments than protocols previously used in casework. In addition, utilizing single-stranded rather than double-stranded library preparation resulted in increased attainment of reportable mtDNA profiles. This study emphasizes that the combination of ancient DNA extraction and library preparation methods evaluated here increases the success rate of DNA profiling, and likelihood of identifying historical remains.
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Affiliation(s)
- Elena I. Zavala
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany; (A.A.-P.); (J.R.); (B.N.); (M.M.)
- Correspondence: (E.I.Z.); (C.M.)
| | - Jacqueline Tyler Thomas
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA; (J.T.T.); (K.S.-A.); (J.D.-H.); (K.K.M.); (S.B.-R.); (T.P.M.)
- SNA International, Contractor Supporting the Armed Forces Medical Examiner System, Alexandria, VA 22314, USA
| | - Kimberly Sturk-Andreaggi
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA; (J.T.T.); (K.S.-A.); (J.D.-H.); (K.K.M.); (S.B.-R.); (T.P.M.)
- SNA International, Contractor Supporting the Armed Forces Medical Examiner System, Alexandria, VA 22314, USA
- Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 08 Uppsala, Sweden
| | - Jennifer Daniels-Higginbotham
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA; (J.T.T.); (K.S.-A.); (J.D.-H.); (K.K.M.); (S.B.-R.); (T.P.M.)
- SNA International, Contractor Supporting the Armed Forces Medical Examiner System, Alexandria, VA 22314, USA
| | - Kerriann K. Meyers
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA; (J.T.T.); (K.S.-A.); (J.D.-H.); (K.K.M.); (S.B.-R.); (T.P.M.)
- SNA International, Contractor Supporting the Armed Forces Medical Examiner System, Alexandria, VA 22314, USA
| | - Suzanne Barrit-Ross
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA; (J.T.T.); (K.S.-A.); (J.D.-H.); (K.K.M.); (S.B.-R.); (T.P.M.)
| | - Ayinuer Aximu-Petri
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany; (A.A.-P.); (J.R.); (B.N.); (M.M.)
| | - Julia Richter
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany; (A.A.-P.); (J.R.); (B.N.); (M.M.)
| | - Birgit Nickel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany; (A.A.-P.); (J.R.); (B.N.); (M.M.)
| | - Gregory E. Berg
- Defense Personnel Accounting Agency, Central Identification Laboratory, Hickam Air Force Base, Oahu, HI 96853, USA;
| | - Timothy P. McMahon
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA; (J.T.T.); (K.S.-A.); (J.D.-H.); (K.K.M.); (S.B.-R.); (T.P.M.)
- SNA International, Contractor Supporting the Armed Forces Medical Examiner System, Alexandria, VA 22314, USA
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany; (A.A.-P.); (J.R.); (B.N.); (M.M.)
| | - Charla Marshall
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA; (J.T.T.); (K.S.-A.); (J.D.-H.); (K.K.M.); (S.B.-R.); (T.P.M.)
- SNA International, Contractor Supporting the Armed Forces Medical Examiner System, Alexandria, VA 22314, USA
- Forensic Science Program, Pennsylvania State University, State College, PA 16802, USA
- Correspondence: (E.I.Z.); (C.M.)
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Microstratigraphic preservation of ancient faunal and hominin DNA in Pleistocene cave sediments. Proc Natl Acad Sci U S A 2022; 119:2113666118. [PMID: 34969841 PMCID: PMC8740756 DOI: 10.1073/pnas.2113666118] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2021] [Indexed: 01/26/2023] Open
Abstract
DNA preserved in sediments has emerged as an important source of information about past ecosystems, independent of the discovery of skeletal remains. However, little is known about the sources of sediment DNA, the factors affecting its long-term preservation, and the extent to which it may be translocated after deposition. Here, we show that impregnated blocks of intact sediment are excellent archives of DNA. DNA distribution is highly heterogeneous at the microscale in the cave sediment we studied, suggesting that postdepositional movement of DNA is unlikely to be a common phenomenon in cases where the stratigraphy is undisturbed. Combining micromorphological analysis with microstratigraphic retrieval of ancient DNA therefore allows genetic information to be associated with the detailed archaeological and ecological record preserved in sediments. Ancient DNA recovered from Pleistocene sediments represents a rich resource for the study of past hominin and environmental diversity. However, little is known about how DNA is preserved in sediments and the extent to which it may be translocated between archaeological strata. Here, we investigate DNA preservation in 47 blocks of resin-impregnated archaeological sediment collected over the last four decades for micromorphological analyses at 13 prehistoric sites in Europe, Asia, Africa, and North America and show that such blocks can preserve DNA of hominins and other mammals. Extensive microsampling of sediment blocks from Denisova Cave in the Altai Mountains reveals that the taxonomic composition of mammalian DNA differs drastically at the millimeter-scale and that DNA is concentrated in small particles, especially in fragments of bone and feces (coprolites), suggesting that these are substantial sources of DNA in sediments. Three microsamples taken in close proximity in one of the blocks yielded Neanderthal DNA from at least two male individuals closely related to Denisova 5, a Neanderthal toe bone previously recovered from the same layer. Our work indicates that DNA can remain stably localized in sediments over time and provides a means of linking genetic information to the archaeological and ecological records on a microstratigraphic scale.
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45
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Mughal MR, DeGiorgio M. Properties and unbiased estimation of F- and D-statistics in samples containing related and inbred individuals. Genetics 2022; 220:iyab090. [PMID: 34849832 PMCID: PMC8733448 DOI: 10.1093/genetics/iyab090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 05/26/2021] [Indexed: 11/14/2022] Open
Abstract
The Patterson F- and D-statistics are commonly used measures for quantifying population relationships and for testing hypotheses about demographic history. These statistics make use of allele frequency information across populations to infer different aspects of population history, such as population structure and introgression events. Inclusion of related or inbred individuals can bias such statistics, which may often lead to the filtering of such individuals. Here, we derive statistical properties of the F- and D-statistics, including their biases due to the inclusion of related or inbred individuals, their variances, and their corresponding mean squared errors. Moreover, for those statistics that are biased, we develop unbiased estimators and evaluate the variances of these new quantities. Comparisons of the new unbiased statistics to the originals demonstrates that our newly derived statistics often have lower error across a wide population parameter space. Furthermore, we apply these unbiased estimators using several global human populations with the inclusion of related individuals to highlight their application on an empirical dataset. Finally, we implement these unbiased estimators in open-source software package funbiased for easy application by the scientific community.
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Affiliation(s)
- Mehreen R Mughal
- Bioinformatics and Genomics at the Huck Institutes of the Life Sciences,
Pennsylvania State University, University Park, PA 16802, USA
| | - Michael DeGiorgio
- Department of Computer and Electrical Engineering and Computer Science, Florida
Atlantic University, Boca Raton, FL 33431, USA
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46
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Brown S, Massilani D, Kozlikin MB, Shunkov MV, Derevianko AP, Stoessel A, Jope-Street B, Meyer M, Kelso J, Pääbo S, Higham T, Douka K. The earliest Denisovans and their cultural adaptation. Nat Ecol Evol 2022; 6:28-35. [PMID: 34824388 PMCID: PMC7612221 DOI: 10.1038/s41559-021-01581-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 09/23/2021] [Indexed: 11/15/2022]
Abstract
Since the initial identification of the Denisovans a decade ago, only a handful of their physical remains have been discovered. Here we analysed ~3,800 non-diagnostic bone fragments using collagen peptide mass fingerprinting to locate new hominin remains from Denisova Cave (Siberia, Russia). We identified five new hominin bones, four of which contained sufficient DNA for mitochondrial analysis. Three carry mitochondrial DNA of the Denisovan type and one was found to carry mtDNA of the Neanderthal type. The former come from the same archaeological layer near the base of the cave's sequence and are the oldest securely dated evidence of Denisovans at 200 ka (thousand years ago) (205-192 ka at 68.2% or 217-187 ka at 95% probability). The stratigraphic context in which they were located contains a wealth of archaeological material in the form of lithics and faunal remains, allowing us to determine the material culture associated with these early hominins and explore their behavioural and environmental adaptations. The combination of bone collagen fingerprinting and genetic analyses has so far more-than-doubled the number of hominin bones at Denisova Cave and has expanded our understanding of Denisovan and Neanderthal interactions, as well as their archaeological signatures.
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Affiliation(s)
- Samantha Brown
- Max Planck Institute for the Science of Human History, Jena, Germany. .,Institute for Scientific Archaeology, University of Tübingen, Tübingen, Germany.
| | - Diyendo Massilani
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Maxim B. Kozlikin
- Institute of Archeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Michael V. Shunkov
- Institute of Archeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anatoly P. Derevianko
- Institute of Archeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexander Stoessel
- Max Planck Institute for the Science of Human History, Jena, Germany,Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany,Institute of Zoology and Evolutionary Research, Friedrich Schiller University Jena, Jena, Germany
| | - Blair Jope-Street
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Thomas Higham
- Oxford Radiocarbon Accelerator Unit, RLAHA, University of Oxford, Oxford, UK,Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Austria
| | - Katerina Douka
- Max Planck Institute for the Science of Human History, Jena, Germany. .,Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria.
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47
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Levi G, de Lombares C, Giuliani C, Iannuzzi V, Aouci R, Garagnani P, Franceschi C, Grimaud-Hervé D, Narboux-Nême N. DLX5/6 GABAergic Expression Affects Social Vocalization: Implications for Human Evolution. Mol Biol Evol 2021; 38:4748-4764. [PMID: 34132815 PMCID: PMC8557472 DOI: 10.1093/molbev/msab181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
DLX5 and DLX6 are two closely related transcription factors involved in brain development and in GABAergic differentiation. The DLX5/6 locus is regulated by FoxP2, a gene involved in language evolution and has been associated with neurodevelopmental disorders and mental retardation. Targeted inactivation of Dlx5/6 in mouse GABAergic neurons (Dlx5/6VgatCre mice) results in behavioral and metabolic phenotypes notably increasing lifespan by 33%. Here, we show that Dlx5/6VgatCre mice present a hyper-vocalization and hyper-socialization phenotype. While only 7% of control mice emitted more than 700 vocalizations/10 min, 30% and 56% of heterozygous or homozygous Dlx5/6VgatCre mice emitted more than 700 and up to 1,400 calls/10 min with a higher proportion of complex and modulated calls. Hyper-vocalizing animals were more sociable: the time spent in dynamic interactions with an unknown visitor was more than doubled compared to low-vocalizing individuals. The characters affected by Dlx5/6 in the mouse (sociability, vocalization, skull, and brain shape…) overlap those affected in the "domestication syndrome". We therefore explored the possibility that DLX5/6 played a role in human evolution and "self-domestication" comparing DLX5/6 genomic regions from Neanderthal and modern humans. We identified an introgressed Neanderthal haplotype (DLX5/6-N-Haplotype) present in 12.6% of European individuals that covers DLX5/6 coding and regulatory sequences. The DLX5/6-N-Haplotype includes the binding site for GTF2I, a gene associated with Williams-Beuren syndrome, a hyper-sociability and hyper-vocalization neurodevelopmental disorder. The DLX5/6-N-Haplotype is significantly underrepresented in semi-supercentenarians (>105 years of age), a well-established human model of healthy aging and longevity, suggesting their involvement in the coevolution of longevity, sociability, and speech.
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Affiliation(s)
- Giovanni Levi
- Physiologie Moléculaire et Adaptation, CNRS UMR7221, Département AVIV, Muséum National d'Histoire Naturelle, Paris, France
| | - Camille de Lombares
- Physiologie Moléculaire et Adaptation, CNRS UMR7221, Département AVIV, Muséum National d'Histoire Naturelle, Paris, France
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy
| | - Vincenzo Iannuzzi
- Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, Italy
| | - Rym Aouci
- Physiologie Moléculaire et Adaptation, CNRS UMR7221, Département AVIV, Muséum National d'Histoire Naturelle, Paris, France
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhniy Novgorod, Russia
| | - Dominique Grimaud-Hervé
- Histoire Naturelle de l’Homme Préhistorique, CNRS UMR 7194, Département H&E, Muséum National d'Histoire Naturelle, Paris, France
| | - Nicolas Narboux-Nême
- Physiologie Moléculaire et Adaptation, CNRS UMR7221, Département AVIV, Muséum National d'Histoire Naturelle, Paris, France
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48
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García-Olivares V, Muñoz-Barrera A, Lorenzo-Salazar JM, Zaragoza-Trello C, Rubio-Rodríguez LA, Díaz-de Usera A, Jáspez D, Iñigo-Campos A, González-Montelongo R, Flores C. A benchmarking of human mitochondrial DNA haplogroup classifiers from whole-genome and whole-exome sequence data. Sci Rep 2021; 11:20510. [PMID: 34654896 PMCID: PMC8519921 DOI: 10.1038/s41598-021-99895-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/28/2021] [Indexed: 12/18/2022] Open
Abstract
The mitochondrial genome (mtDNA) is of interest for a range of fields including evolutionary, forensic, and medical genetics. Human mitogenomes can be classified into evolutionary related haplogroups that provide ancestral information and pedigree relationships. Because of this and the advent of high-throughput sequencing (HTS) technology, there is a diversity of bioinformatic tools for haplogroup classification. We present a benchmarking of the 11 most salient tools for human mtDNA classification using empirical whole-genome (WGS) and whole-exome (WES) short-read sequencing data from 36 unrelated donors. We also assessed the best performing tool in third-generation long noisy read WGS data obtained with nanopore technology for a subset of the donors. We found that, for short-read WGS, most of the tools exhibit high accuracy for haplogroup classification irrespective of the input file used for the analysis. However, for short-read WES, Haplocheck and MixEmt were the most accurate tools. Based on the performance shown for WGS and WES, and the accompanying qualitative assessment, Haplocheck stands out as the most complete tool. For third-generation HTS data, we also showed that Haplocheck was able to accurately retrieve mtDNA haplogroups for all samples assessed, although only after following assembly-based approaches (either based on a referenced-based assembly or a hybrid de novo assembly). Taken together, our results provide guidance for researchers to select the most suitable tool to conduct the mtDNA analyses from HTS data.
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Affiliation(s)
- Víctor García-Olivares
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Adrián Muñoz-Barrera
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - José M Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | | | - Luis A Rubio-Rodríguez
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Ana Díaz-de Usera
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - David Jáspez
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Antonio Iñigo-Campos
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Rafaela González-Montelongo
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain.
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, Santa Cruz de Tenerife, Spain.
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
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49
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Serrano JG, Ordóñez AC, Fregel R. Paleogenomics of the prehistory of Europe: human migrations, domestication and disease. Ann Hum Biol 2021; 48:179-190. [PMID: 34459342 DOI: 10.1080/03014460.2021.1942205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
A substantial portion of ancient DNA research has been centred on understanding European populations' origin and evolution. A rchaeological evidence has already shown that the peopling of Europe involved an intricate pattern of demic and/or cultural diffusion since the Upper Palaeolithic, which became more evident during the Neolithic and Bronze Age periods. However, ancient DNA data has been crucial in determining if cultural changes occurred due to the movement of ideas or people. With the advent of next-generation sequencing and population-based paleogenomic research, ancient DNA studies have been directed not only at the study of continental human migrations, but also to the detailed analysis of particular archaeological sites, the processes of domestication, or the spread of disease during prehistoric times. With this vast paleogenomic effort added to a proper archaeological contextualisation of results, a deeper understanding of Europe's peopling is starting to emanate.
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Affiliation(s)
- Javier G Serrano
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Faculta de Ciencias, Universidad de La Laguna, La Laguna, Spain
| | - Alejandra C Ordóñez
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Faculta de Ciencias, Universidad de La Laguna, La Laguna, Spain.,Departamento Geografía e Historia, Facultad de Humanidades, Universidad de La Laguna, La Laguna, Spain
| | - Rosa Fregel
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Faculta de Ciencias, Universidad de La Laguna, La Laguna, Spain
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50
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Heydari-Guran S, Benazzi S, Talamo S, Ghasidian E, Hariri N, Oxilia G, Asiabani S, Azizi F, Naderi R, Safaierad R, Hublin JJ, Foley RA, Lahr MM. The discovery of an in situ Neanderthal remain in the Bawa Yawan Rockshelter, West-Central Zagros Mountains, Kermanshah. PLoS One 2021; 16:e0253708. [PMID: 34437543 PMCID: PMC8389444 DOI: 10.1371/journal.pone.0253708] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 06/11/2021] [Indexed: 11/19/2022] Open
Abstract
Neanderthal extinction has been a matter of debate for many years. New discoveries, better chronologies and genomic evidence have done much to clarify some of the issues. This evidence suggests that Neanderthals became extinct around 40,000–37,000 years before present (BP), after a period of coexistence with Homo sapiens of several millennia, involving biological and cultural interactions between the two groups. However, the bulk of this evidence relates to Western Eurasia, and recent work in Central Asia and Siberia has shown that there is considerable local variation. Southwestern Asia, despite having a number of significant Neanderthal remains, has not played a major part in the debate over extinction. Here we report a Neanderthal deciduous canine from the site of Bawa Yawan in the West-Central Zagros Mountains of Iran. The tooth is associated with Zagros Mousterian lithics, and its context is preliminary dated to between ~43,600 and ~41,500 years ago.
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Affiliation(s)
- Saman Heydari-Guran
- Stiftung Neanderthal Museum, Mettmann, Germany
- Department of Prehistoric Archaeology University of Cologne, Cologne, Germany
- DiyarMehr Centre for Palaeolithic Research, Kermanshah, Iran
- * E-mail:
| | - Stefano Benazzi
- Department of Cultural Heritage, University of Bologna, Bologna, Italy
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sahra Talamo
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Chemistry G. Ciamician, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Elham Ghasidian
- Stiftung Neanderthal Museum, Mettmann, Germany
- Department of Prehistoric Archaeology University of Cologne, Cologne, Germany
| | - Nemat Hariri
- Department of Prehistoric Archaeology University of Cologne, Cologne, Germany
- Department of Archaeology, University of Mohaghegh Ardabili University, Ardabil, Iran
| | - Gregorio Oxilia
- Department of Cultural Heritage, University of Bologna, Bologna, Italy
| | - Samran Asiabani
- DiyarMehr Centre for Palaeolithic Research, Kermanshah, Iran
- Department of Architecture, Faculty of Art and Architecture, Bu-Ali Sina University, Hamedan, Iran
| | - Faramarz Azizi
- DiyarMehr Centre for Palaeolithic Research, Kermanshah, Iran
| | - Rahmat Naderi
- DiyarMehr Centre for Palaeolithic Research, Kermanshah, Iran
| | - Reza Safaierad
- Department of Physical Geography, University of Tehran, Tehran, Iran
| | - Jean-Jacques Hublin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Collège de France, 11 Place Marcelin Berthelot, Paris, France
| | - Robert A. Foley
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, United Kingdom
| | - Marta M. Lahr
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, United Kingdom
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