1
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Breton G, Barham L, Mudenda G, Soodyall H, Schlebusch CM, Jakobsson M. BaTwa populations from Zambia retain ancestry of past hunter-gatherer groups. Nat Commun 2024; 15:7307. [PMID: 39181874 PMCID: PMC11344834 DOI: 10.1038/s41467-024-50733-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: 03/16/2023] [Accepted: 07/19/2024] [Indexed: 08/27/2024] Open
Abstract
Sub-equatorial Africa is today inhabited predominantly by Bantu-speaking groups of Western African descent who brought agriculture to the Luangwa valley in eastern Zambia ~2000 years ago. Before their arrival the area was inhabited by hunter-gatherers, who in many cases were subsequently replaced, displaced or assimilated. In Zambia, we know little about the genetic affinities of these hunter-gatherers. We examine ancestry of two isolated communities in Zambia, known as BaTwa and possible descendants of recent hunter-gatherers. We genotype over two million genome-wide SNPs from two BaTwa populations (total of 80 individuals) and from three comparative farming populations to: (i) determine if the BaTwa carry genetic links to past hunter-gatherer-groups, and (ii) characterise the genetic affinities of past Zambian hunter-gatherer-groups. The BaTwa populations do harbour a hunter-gatherer-like genetic ancestry and Western African ancestry. The hunter-gatherer component is a unique local signature, intermediate between current-day Khoe-San ancestry from southern Africa and central African rainforest hunter-gatherer ancestry.
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Affiliation(s)
- Gwenna Breton
- Department of Organismal Biology, Human Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
- Department of Clinical Genetics and Genomics, Centre for Medical Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden.
| | - Lawrence Barham
- Department of Archaeology, Classics & Egyptology, University of Liverpool, Liverpool, UK
| | - George Mudenda
- Livingstone Museum, Livingstone, Zambia
- National Museums Board, Lusaka, Zambia
| | - Himla Soodyall
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa
- Academy of Science of South Africa, Pretoria, South Africa
| | - Carina M Schlebusch
- Department of Organismal Biology, Human Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa
- SciLifeLab, Uppsala, Sweden
| | - Mattias Jakobsson
- Department of Organismal Biology, Human Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
- Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa.
- SciLifeLab, Uppsala, Sweden.
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2
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Taylor DJ, Eizenga JM, Li Q, Das A, Jenike KM, Kenny EE, Miga KH, Monlong J, McCoy RC, Paten B, Schatz MC. Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References. Annu Rev Genomics Hum Genet 2024; 25:77-104. [PMID: 38663087 PMCID: PMC11451085 DOI: 10.1146/annurev-genom-021623-081639] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
The Human Genome Project was an enormous accomplishment, providing a foundation for countless explorations into the genetics and genomics of the human species. Yet for many years, the human genome reference sequence remained incomplete and lacked representation of human genetic diversity. Recently, two major advances have emerged to address these shortcomings: complete gap-free human genome sequences, such as the one developed by the Telomere-to-Telomere Consortium, and high-quality pangenomes, such as the one developed by the Human Pangenome Reference Consortium. Facilitated by advances in long-read DNA sequencing and genome assembly algorithms, complete human genome sequences resolve regions that have been historically difficult to sequence, including centromeres, telomeres, and segmental duplications. In parallel, pangenomes capture the extensive genetic diversity across populations worldwide. Together, these advances usher in a new era of genomics research, enhancing the accuracy of genomic analysis, paving the path for precision medicine, and contributing to deeper insights into human biology.
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Affiliation(s)
- Dylan J Taylor
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA; , ,
| | - Jordan M Eizenga
- Genomics Institute, University of California, Santa Cruz, California, USA; , ,
| | - Qiuhui Li
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA; ,
| | - Arun Das
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA; ,
| | - Katharine M Jenike
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA;
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA;
| | - Karen H Miga
- Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA
- Genomics Institute, University of California, Santa Cruz, California, USA; , ,
| | - Jean Monlong
- Institut de Recherche en Santé Digestive, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France;
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA; , ,
| | - Benedict Paten
- Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA
- Genomics Institute, University of California, Santa Cruz, California, USA; , ,
| | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA; ,
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA; , ,
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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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Marsh JI, Johri P. Biases in ARG-Based Inference of Historical Population Size in Populations Experiencing Selection. Mol Biol Evol 2024; 41:msae118. [PMID: 38874402 PMCID: PMC11245712 DOI: 10.1093/molbev/msae118] [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: 04/15/2024] [Revised: 06/05/2024] [Accepted: 06/11/2024] [Indexed: 06/15/2024] Open
Abstract
Inferring the demographic history of populations provides fundamental insights into species dynamics and is essential for developing a null model to accurately study selective processes. However, background selection and selective sweeps can produce genomic signatures at linked sites that mimic or mask signals associated with historical population size change. While the theoretical biases introduced by the linked effects of selection have been well established, it is unclear whether ancestral recombination graph (ARG)-based approaches to demographic inference in typical empirical analyses are susceptible to misinference due to these effects. To address this, we developed highly realistic forward simulations of human and Drosophila melanogaster populations, including empirically estimated variability of gene density, mutation rates, recombination rates, purifying, and positive selection, across different historical demographic scenarios, to broadly assess the impact of selection on demographic inference using a genealogy-based approach. Our results indicate that the linked effects of selection minimally impact demographic inference for human populations, although it could cause misinference in populations with similar genome architecture and population parameters experiencing more frequent recurrent sweeps. We found that accurate demographic inference of D. melanogaster populations by ARG-based methods is compromised by the presence of pervasive background selection alone, leading to spurious inferences of recent population expansion, which may be further worsened by recurrent sweeps, depending on the proportion and strength of beneficial mutations. Caution and additional testing with species-specific simulations are needed when inferring population history with non-human populations using ARG-based approaches to avoid misinference due to the linked effects of selection.
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Affiliation(s)
- Jacob I Marsh
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Parul Johri
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
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5
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Librado P, Tressières G, Chauvey L, Fages A, Khan N, Schiavinato S, Calvière-Tonasso L, Kusliy MA, Gaunitz C, Liu X, Wagner S, Der Sarkissian C, Seguin-Orlando A, Perdereau A, Aury JM, Southon J, Shapiro B, Bouchez O, Donnadieu C, Collin YRH, Gregersen KM, Jessen MD, Christensen K, Claudi-Hansen L, Pruvost M, Pucher E, Vulic H, Novak M, Rimpf A, Turk P, Reiter S, Brem G, Schwall C, Barrey É, Robert C, Degueurce C, Horwitz LK, Klassen L, Rasmussen U, Kveiborg J, Johannsen NN, Makowiecki D, Makarowicz P, Szeliga M, Ilchyshyn V, Rud V, Romaniszyn J, Mullin VE, Verdugo M, Bradley DG, Cardoso JL, Valente MJ, Telles Antunes M, Ameen C, Thomas R, Ludwig A, Marzullo M, Prato O, Bagnasco Gianni G, Tecchiati U, Granado J, Schlumbaum A, Deschler-Erb S, Mráz MS, Boulbes N, Gardeisen A, Mayer C, Döhle HJ, Vicze M, Kosintsev PA, Kyselý R, Peške L, O'Connor T, Ananyevskaya E, Shevnina I, Logvin A, Kovalev AA, Iderkhangai TO, Sablin MV, Dashkovskiy PK, Graphodatsky AS, Merts I, Merts V, Kasparov AK, Pitulko VV, Onar V, Öztan A, Arbuckle BS, McColl H, Renaud G, Khaskhanov R, Demidenko S, Kadieva A, Atabiev B, Sundqvist M, Lindgren G, López-Cachero FJ, Albizuri S, Trbojević Vukičević T, Rapan Papeša A, Burić M, Rajić Šikanjić P, Weinstock J, Asensio Vilaró D, Codina F, García Dalmau C, Morer de Llorens J, Pou J, de Prado G, Sanmartí J, Kallala N, Torres JR, Maraoui-Telmini B, Belarte Franco MC, Valenzuela-Lamas S, Zazzo A, Lepetz S, Duchesne S, Alexeev A, Bayarsaikhan J, Houle JL, Bayarkhuu N, Turbat T, Crubézy É, Shingiray I, Mashkour M, Berezina NY, Korobov DS, Belinskiy A, Kalmykov A, Demoule JP, Reinhold S, Hansen S, Wallner B, Roslyakova N, Kuznetsov PF, Tishkin AA, Wincker P, Kanne K, Outram A, Orlando L. Widespread horse-based mobility arose around 2200 BCE in Eurasia. Nature 2024; 631:819-825. [PMID: 38843826 PMCID: PMC11269178 DOI: 10.1038/s41586-024-07597-5] [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: 07/17/2023] [Accepted: 05/23/2024] [Indexed: 07/19/2024]
Abstract
Horses revolutionized human history with fast mobility1. However, the timeline between their domestication and their widespread integration as a means of transport remains contentious2-4. Here we assemble a collection of 475 ancient horse genomes to assess the period when these animals were first reshaped by human agency in Eurasia. We find that reproductive control of the modern domestic lineage emerged around 2200 BCE, through close-kin mating and shortened generation times. Reproductive control emerged following a severe domestication bottleneck starting no earlier than approximately 2700 BCE, and coincided with a sudden expansion across Eurasia that ultimately resulted in the replacement of nearly every local horse lineage. This expansion marked the rise of widespread horse-based mobility in human history, which refutes the commonly held narrative of large horse herds accompanying the massive migration of steppe peoples across Europe around 3000 BCE and earlier3,5. Finally, we detect significantly shortened generation times at Botai around 3500 BCE, a settlement from central Asia associated with corrals and a subsistence economy centred on horses6,7. This supports local horse husbandry before the rise of modern domestic bloodlines.
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Affiliation(s)
- Pablo Librado
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France.
- Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Spain.
| | - Gaetan Tressières
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Lorelei Chauvey
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Antoine Fages
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
- Zoological institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Naveed Khan
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
- Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan
| | - Stéphanie Schiavinato
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Laure Calvière-Tonasso
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Mariya A Kusliy
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Novosibirsk, Russia
| | - Charleen Gaunitz
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Xuexue Liu
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Stefanie Wagner
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
- INRAE Division Ecology and Biodiversity (ECODIV), Plant Genomic Resources Center (CNRGV), Castanet Tolosan Cedex, France
| | - Clio Der Sarkissian
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Andaine Seguin-Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Aude Perdereau
- Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France
| | - John Southon
- Department of Earth System Science, University of California, Irvine, CA, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | | | | | - Yvette Running Horse Collin
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
- Taku Skan Skan Wasakliyapi: Global Institute for Traditional Sciences, Rapid City, SD, USA
| | | | - Mads Dengsø Jessen
- Department for Prehistory Middle Ages and Renaissance, National Museum of Denmark, Copenhagen K, Denmark
| | | | | | - Mélanie Pruvost
- UMR 5199 De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA), CNRS, Université de Bordeaux, Pessac Cédex, France
| | | | | | - Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia
| | | | - Peter Turk
- Narodni muzej Slovenije, Ljubljana, Slovenia
| | - Simone Reiter
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Christoph Schwall
- Leibniz-Zentrum für Archäologie (LEIZA), Mainz, Germany
- Department of Prehistory & Western Asian/Northeast African Archaeology, Austrian Archaeological Institute (OeAI), Austrian Academy of Sciences (OeAW), Vienna, Austria
| | - Éric Barrey
- Université Paris-Saclay, AgroParisTech, INRAE GABI UMR1313, Jouy-en-Josas, France
| | - Céline Robert
- Université Paris-Saclay, AgroParisTech, INRAE GABI UMR1313, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, Maisons-Alfort, France
| | | | - Liora Kolska Horwitz
- National Natural History Collections, Edmond J. Safra Campus, Givat Ram, The Hebrew University, Jerusalem, Israel
| | | | - Uffe Rasmussen
- Department of Archaeology, Moesgaard Museum, Højbjerg, Denmark
| | - Jacob Kveiborg
- Department of Archaeological Science and Conservation, Moesgaard Museum, Højbjerg, Denmark
| | | | - Daniel Makowiecki
- Institute of Archaeology, Faculty of History, Nicolaus Copernicus University, Toruń, Poland
| | | | - Marcin Szeliga
- Institute of Archaeology, Maria Curie-Skłodowska University, Lublin, Poland
| | - Vasyl Ilchyshyn
- Kremenetsko-Pochaivskii Derzhavnyi Istoriko-arkhitekturnyi Zapovidnik, Kremenets, Ukraine
| | - Vitalii Rud
- Institute of Archaeology, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Jan Romaniszyn
- Faculty of Archaeology, Adam Mickiewicz University, Poznań, Poland
| | - Victoria E Mullin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Marta Verdugo
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - João L Cardoso
- ICArEHB, Campus de Gambelas, University of Algarve, Faro, Portugal
- Universidade Aberta, Lisbon, Portugal
| | - Maria J Valente
- Faculdade de Ciências Humanas e Sociais, Centro de Estudos de Arqueologia, Artes e Ciências do Património, Universidade do Algarve, Faro, Portugal
| | - Miguel Telles Antunes
- Centre for Research on Science and Geological Engineering, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Carly Ameen
- Department of Archaeology and History, University of Exeter, Exeter, UK
| | - Richard Thomas
- School of Archaeology and Ancient History, University of Leicester, Leicester, UK
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany
- Albrecht Daniel Thaer-Institute, Faculty of Life Sciences, Humboldt University Berlin, Berlin, Germany
| | - Matilde Marzullo
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan, Italy
| | - Ornella Prato
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan, Italy
| | | | - Umberto Tecchiati
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan, Italy
| | - José Granado
- Department of Environmental Sciences, Integrative Prehistory and Archaeological Science, Basel University, Basel, Switzerland
| | - Angela Schlumbaum
- Department of Environmental Sciences, Integrative Prehistory and Archaeological Science, Basel University, Basel, Switzerland
| | - Sabine Deschler-Erb
- Department of Environmental Sciences, Integrative Prehistory and Archaeological Science, Basel University, Basel, Switzerland
| | - Monika Schernig Mráz
- Department of Environmental Sciences, Integrative Prehistory and Archaeological Science, Basel University, Basel, Switzerland
| | - Nicolas Boulbes
- Institut de Paléontologie Humaine, Fondation Albert Ier, Paris/UMR 7194 HNHP, MNHN-CNRS-UPVD/EPCC Centre Européen de Recherche Préhistorique, Tautavel, France
| | - Armelle Gardeisen
- Archéologie des Sociétés Méditeranéennes, Archimède IA-ANR-11-LABX-0032-01, CNRS UMR 5140, Université Paul Valéry, Montpellier, France
| | - Christian Mayer
- Department for Digitalization and Knowledge Transfer, Federal Monuments Authority Austria, Vienna, Austria
| | - Hans-Jürgen Döhle
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt - Landesmuseum für Vorgeschichte, Halle (Saale), Germany
| | - Magdolna Vicze
- National Institute of Archaeology, Hungarian National Museum, Budapest, Hungary
| | - Pavel A Kosintsev
- Paleoecology Laboratory, Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russia
- Department of History of the Institute of Humanities, Ural Federal University, Ekaterinburg, Russia
| | - René Kyselý
- Department of Natural Sciences and Archaeometry, Institute of Archaeology of the Czech Academy of Sciences, Prague, Czechia
| | | | | | - Elina Ananyevskaya
- Department of Archaeology, History Faculty, Vilnius University, Vilnius, Lithuania
| | - Irina Shevnina
- Laboratory for Archaeological Research, Akhmet Baitursynuly Kostanay Regional University, Kostanay, Kazakhstan
| | - Andrey Logvin
- Laboratory for Archaeological Research, Akhmet Baitursynuly Kostanay Regional University, Kostanay, Kazakhstan
| | - Alexey A Kovalev
- Department of Archaeological Heritage Preservation, Institute of Archaeology of the Russian Academy of Sciences, Moscow, Russia
| | - Tumur-Ochir Iderkhangai
- Department of Innovation and Technology, Ulaanbaatar Science and Technology Park, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Mikhail V Sablin
- Zoological Institute, Russian Academy of Sciences, St Petersburg, Russia
| | - Petr K Dashkovskiy
- Department of Russian Regional Studies, National and State-confessional Relations, Altai State University, Barnaul, Russia
| | - Alexander S Graphodatsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Novosibirsk, Russia
| | - Ilia Merts
- Toraighyrov University, Joint Research Center for Archeological Studies, Pavlodar, Kazakhstan
- Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | - Viktor Merts
- Toraighyrov University, Joint Research Center for Archeological Studies, Pavlodar, Kazakhstan
| | - Aleksei K Kasparov
- Institute of the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | - Vladimir V Pitulko
- Institute of the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, St Petersburg, Russia
| | - Vedat Onar
- Osteoarchaeology Practice and Research Center and Department of Anatomy, Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, Istanbul, Türkiye
| | - Aliye Öztan
- Archaeology Department, Ankara University, Ankara, Türkiye
| | - Benjamin S Arbuckle
- Department of Anthropology, Alumni Building, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Gabriel Renaud
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark (DTU), Copenhagen, Denmark
| | - Ruslan Khaskhanov
- Kh. Ibragimov Complex Institute of the Russian Academy of Sciences (CI RAS), Grozny, Russia
| | - Sergey Demidenko
- Institute of Archaeology, Russian Academy of Sciences, Moscow, Russia
| | - Anna Kadieva
- Department of Archaeological Monuments, State Historical Museum, Moscow, Russian Federation
| | | | | | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Center for Animal Breeding and Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - F Javier López-Cachero
- Institut d'Arqueologia de la Universitat de Barcelona (IAUB), Seminari d'Estudis i Recerques Prehistoriques (SERP-UB), Universitat de Barcelona (UB), Barcelona, Spain
| | - Silvia Albizuri
- Institut d'Arqueologia de la Universitat de Barcelona (IAUB), Seminari d'Estudis i Recerques Prehistoriques (SERP-UB), Universitat de Barcelona (UB), Barcelona, Spain
| | - Tajana Trbojević Vukičević
- Department of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | | | - Marcel Burić
- Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia
| | | | - Jaco Weinstock
- Faculty of Arts and Humanities (Archaeology), University of Southampton, Southampton, UK
| | - David Asensio Vilaró
- Secció de Prehistòria i Arqueologia, IAUB Institut d'Arqueologia de la Universitat de Barcelona, Barcelona, Spain
| | - Ferran Codina
- C/Major, 20, Norfeu, Arqueologia Art i Patrimoni S.C., La Tallada d'Empordà, Spain
| | | | | | - Josep Pou
- Ajuntament de Calafell, Calafell (Tarragona), Spain
| | - Gabriel de Prado
- Museu d'Arqueologia de Catalunya (MAC-Ullastret), Ullastret, Spain
| | - Joan Sanmartí
- IEC-Institut d'Estudis Catalans (Union Académique Internationale), Barcelona, Spain
- Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Nabil Kallala
- Ecole Tunisienne d'Histoire et d'Anthropologie, Tunis, Tunisia
- University of Tunis, Institut National du Patrimoine, Tunis, Tunisia
| | | | | | - Maria-Carme Belarte Franco
- IEC-Institut d'Estudis Catalans (Union Académique Internationale), Barcelona, Spain
- ICREA, Catalan Institution for Research and Advanced Studies, Barcelona, Spain
- ICAC (Catalan Institute of Classical Archaeology), Tarragona, Spain
| | - Silvia Valenzuela-Lamas
- Archaeology of Social Dynamics (ASD), Institució Milà i Fontanals, Consejo Superior de Investigaciones Científicas (IMF-CSIC), Barcelona, Spain
- UNIARQ - Unidade de Arqueologia, Universidade de Lisboa, Alameda da Universidade, Lisboa, Portugal
| | - Antoine Zazzo
- Centre National de Recherche Scientifique, Muséum national d'Histoire naturelle, Archéozoologie, Archéobotanique (AASPE), CP 56, Paris, France
| | - Sébastien Lepetz
- Centre National de Recherche Scientifique, Muséum national d'Histoire naturelle, Archéozoologie, Archéobotanique (AASPE), CP 56, Paris, France
| | - Sylvie Duchesne
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Anatoly Alexeev
- Institute for Humanities Research and Indigenous Studies of the North (IHRISN), Yakutsk, Russia
| | - Jamsranjav Bayarsaikhan
- Max Planck Institute of Geoanthropology, Jena, Germany
- Institute of Archaeology, Mongolian Academy of Science, Ulaanbaatar, Mongolia
| | - Jean-Luc Houle
- Department of Folk Studies and Anthropology, Western Kentucky University, Bowling Green, KY, USA
| | - Noost Bayarkhuu
- Archaeological Research Center and Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Tsagaan Turbat
- Archaeological Research Center and Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Éric Crubézy
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | | | - Marjan Mashkour
- Centre National de Recherche Scientifique, Muséum national d'Histoire naturelle, Archéozoologie, Archéobotanique (AASPE), CP 56, Paris, France
- Central Laboratory, Bioarchaeology Laboratory, Archaeozoology section, University of Tehran, Tehran, Iran
| | - Natalia Ya Berezina
- Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitriy S Korobov
- Institute of Archaeology, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Jean-Paul Demoule
- UMR du CNRS 8215 Trajectoires, Institut d'Art et Archéologie, Paris, France
| | - Sabine Reinhold
- Eurasia Department of the German Archaeological Institute, Berlin, Germany
| | - Svend Hansen
- Eurasia Department of the German Archaeological Institute, Berlin, Germany
| | - Barbara Wallner
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Natalia Roslyakova
- Department of Russian History and Archaeology, Samara State University of Social Sciences and Education, Samara, Russia
| | - Pavel F Kuznetsov
- Department of Russian History and Archaeology, Samara State University of Social Sciences and Education, Samara, Russia
| | - Alexey A Tishkin
- Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France
| | - Katherine Kanne
- Department of Archaeology and History, University of Exeter, Exeter, UK
- School of Archaeology, University College Dublin, Dublin, Ireland
| | - Alan Outram
- Department of Archaeology and History, University of Exeter, Exeter, UK
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France.
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6
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Khatib CM, Klein-Petersen AW, Rønnstad ATM, Egeberg A, Christensen MO, Silverberg JI, Thomsen SF, Irvine AD, Thyssen JP. Increased loss-of-function filaggrin gene mutation prevalence in atopic dermatitis patients across northern latitudes indicates genetic fitness: A systematic review and meta-analysis. Exp Dermatol 2024; 33:e15130. [PMID: 38989976 DOI: 10.1111/exd.15130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 05/23/2024] [Accepted: 06/24/2024] [Indexed: 07/12/2024]
Abstract
Loss-of-function (LoF) mutations in the filaggrin gene (FLG) constitute the strongest genetic risk for atopic dermatitis (AD). A latitude-dependent difference in the prevalence of LoF FLG mutations was systematically evaluated. A systematic review and meta-analysis were performed to estimate the prevalence of LoF FLG mutations in AD patients and the general population by geography and ethnicity. Risk of bias was assessed by Newcastle-Ottawa Scale and Jadad score. StatsDirect, version 3 software was used to calculate all outcomes. PubMed and EMBASE were searched until 9th December 2021. Studies were included if they contained data on the prevalence of LoF FLG mutations in AD patients or from the general population or associations between AD and LoF FLG mutations and were authored in English. Overall, 248 studies and 229 310 AD patients and individuals of the general population were included in the quantitative analysis. The prevalence of LoF FLG mutations was 19.1% (95% CI, 17.3-21.0) in AD patients and 5.8% (95% CI, 5.3-6.2) in the general population. There was a significant positive association between AD and LoF FLG mutations in all latitudes in the Northern hemisphere, but not in all ethnicities. The prevalence of LoF FLG mutations became gradually more prevalent in populations residing farther north of the Equator but was negligible in Middle Easterners and absent in most African populations. FLG LoF mutations are common and tend to increase with northern latitude, suggesting potential clinical implications for future AD management. The existence of possible genetic fitness from FLG LoF mutations remains unknown.
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Affiliation(s)
- Casper Milde Khatib
- Department of Dermatology, Bispebjerg Hospital, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Alexander Egeberg
- Department of Dermatology, Bispebjerg Hospital, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Simon Francis Thomsen
- Department of Dermatology, Bispebjerg Hospital, University of Copenhagen, Copenhagen, Denmark
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7
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Lim SS, Ramos PS, Williams EM. The Explication of Race in Rheumatology Disparities. Arthritis Care Res (Hoboken) 2024. [PMID: 38923855 DOI: 10.1002/acr.25388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 05/14/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024]
Affiliation(s)
- S Sam Lim
- Emory University School of Medicine, Emory University and Grady Health System, Atlanta, Georgia
| | - Paula S Ramos
- Medical University of South Carolina, Charleston, and University of Rochester, Rochester, New York
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8
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Saltré F, Chadœuf J, Higham T, Ochocki M, Block S, Bunney E, Llamas B, Bradshaw CJA. Environmental conditions associated with initial northern expansion of anatomically modern humans. Nat Commun 2024; 15:4364. [PMID: 38777837 PMCID: PMC11111671 DOI: 10.1038/s41467-024-48762-8] [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: 04/28/2022] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
The ability of our ancestors to switch food sources and to migrate to more favourable environments enabled the rapid global expansion of anatomically modern humans beyond Africa as early as 120,000 years ago. Whether this versatility was largely the result of environmentally determined processes or was instead dominated by cultural drivers, social structures, and interactions among different groups, is unclear. We develop a statistical approach that combines both archaeological and genetic data to infer the more-likely initial expansion routes in northern Eurasia and the Americas. We then quantify the main differences in past environmental conditions between the more-likely routes and other potential (less-likely) routes of expansion. We establish that, even though cultural drivers remain plausible at finer scales, the emergent migration corridors were predominantly constrained by a combination of regional environmental conditions, including the presence of a forest-grassland ecotone, changes in temperature and precipitation, and proximity to rivers.
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Affiliation(s)
- Frédérik Saltré
- Global Ecology | Partuyarta Ngadluku Wardli Kuu, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA, 5001, Australia.
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia.
| | - Joël Chadœuf
- UR 1052, French National Institute for Agricultural Research (INRA), Montfavet, France
| | - Thomas Higham
- Department of Evolutionary Biology, University of Vienna, University Biology Building, Carl Djerassi Platz 1, A-1030, Wien, Austria
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3TG, UK
| | - Monty Ochocki
- Department of Evolutionary Biology, University of Vienna, University Biology Building, Carl Djerassi Platz 1, A-1030, Wien, Austria
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3TG, UK
| | - Sebastián Block
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544-1003, USA
| | - Ellyse Bunney
- Commonwealth Scientific and Industrial Research Organisation, Urrbrae, SA, 5064, Australia
| | - Bastien Llamas
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- Australian Centre for Ancient DNA, School of Biological Sciences, The Environment Institute, University of Adelaide, Adelaide, SA, 5005, Australia
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
- Indigenous Genomics, Telethon Kids Institute, Adelaide, SA, 5000, Australia
| | - Corey J A Bradshaw
- Global Ecology | Partuyarta Ngadluku Wardli Kuu, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA, 5001, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
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9
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Randolph HE, Aracena KA, Lin YL, Mu Z, Barreiro LB. Shaping immunity: The influence of natural selection on population immune diversity. Immunol Rev 2024; 323:227-240. [PMID: 38577999 DOI: 10.1111/imr.13329] [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] [Indexed: 04/06/2024]
Abstract
Humans exhibit considerable variability in their immune responses to the same immune challenges. Such variation is widespread and affects individual and population-level susceptibility to infectious diseases and immune disorders. Although the factors influencing immune response diversity are partially understood, what mechanisms lead to the wide range of immune traits in healthy individuals remain largely unexplained. Here, we discuss the role that natural selection has played in driving phenotypic differences in immune responses across populations and present-day susceptibility to immune-related disorders. Further, we touch on future directions in the field of immunogenomics, highlighting the value of expanding this work to human populations globally, the utility of modeling the immune response as a dynamic process, and the importance of considering the potential polygenic nature of natural selection. Identifying loci acted upon by evolution may further pinpoint variants critically involved in disease etiology, and designing studies to capture these effects will enrich our understanding of the genetic contributions to immunity and immune dysregulation.
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Affiliation(s)
- Haley E Randolph
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, Illinois, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | | | - Yen-Lung Lin
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Zepeng Mu
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, Illinois, USA
| | - Luis B Barreiro
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, Illinois, USA
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA
- Committee on Immunology, University of Chicago, Chicago, Illinois, USA
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10
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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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11
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Salles T, Joannes-Boyau R, Moffat I, Husson L, Lorcery M. Physiography, foraging mobility, and the first peopling of Sahul. Nat Commun 2024; 15:3430. [PMID: 38653772 DOI: 10.1038/s41467-024-47662-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 04/09/2024] [Indexed: 04/25/2024] Open
Abstract
The route and speed of migration into Sahul by Homo sapiens remain a major research question in archaeology. Here, we introduce an approach which models the impact of the physical environment on human mobility by combining time-evolving landscapes with Lévy walk foraging patterns, this latter accounting for a combination of short-distance steps and occasional longer moves that hunter-gatherers likely utilised for efficient exploration of new environments. Our results suggest a wave of dispersal radiating across Sahul following riverine corridors and coastlines. Estimated migration speeds, based on archaeological sites and predicted travelled distances, fall within previously reported range from Sahul and other regions. From our mechanistic movement simulations, we then analyse the likelihood of archaeological sites and highlight areas in Australia that hold archaeological potential. Our approach complements existing methods and provides interesting perspectives on the Pleistocene archaeology of Sahul that could be applied to other regions around the world.
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Affiliation(s)
- Tristan Salles
- School of Geosciences, The University of Sydney, Sydney, NSW, Australia.
| | - Renaud Joannes-Boyau
- Geoarchaeology and Archaeometry Research Group, Southern Cross University, Lismore, NSW, Australia
| | - Ian Moffat
- Geoarchaeology and Archaeometry Research Group, Southern Cross University, Lismore, NSW, Australia
- Archaeology, College of Humanities, Arts and Social Sciences, Flinders University, Adelaide, SA, Australia
| | - Laurent Husson
- ISTerre, CNRS, Université Grenoble-Alpes, Grenoble, France
| | - Manon Lorcery
- School of Geosciences, The University of Sydney, Sydney, NSW, Australia
- ISTerre, CNRS, Université Grenoble-Alpes, Grenoble, France
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12
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Liu X, Zhang K, Kaya NA, Jia Z, Wu D, Chen T, Liu Z, Zhu S, Hillmer AM, Wuestefeld T, Liu J, Chan YS, Hu Z, Ma L, Jiang L, Zhai W. Tumor phylogeography reveals block-shaped spatial heterogeneity and the mode of evolution in Hepatocellular Carcinoma. Nat Commun 2024; 15:3169. [PMID: 38609353 PMCID: PMC11015015 DOI: 10.1038/s41467-024-47541-9] [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: 08/04/2022] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Solid tumors are complex ecosystems with heterogeneous 3D structures, but the spatial intra-tumor heterogeneity (sITH) at the macroscopic (i.e., whole tumor) level is under-explored. Using a phylogeographic approach, we sequence genomes and transcriptomes from 235 spatially informed sectors across 13 hepatocellular carcinomas (HCC), generating one of the largest datasets for studying sITH. We find that tumor heterogeneity in HCC segregates into spatially variegated blocks with large genotypic and phenotypic differences. By dissecting the transcriptomic heterogeneity, we discover that 30% of patients had a "spatially competing distribution" (SCD), where different spatial blocks have distinct transcriptomic subtypes co-existing within a tumor, capturing the critical transition period in disease progression. Interestingly, the tumor regions with more advanced transcriptomic subtypes (e.g., higher cell cycle) often take clonal dominance with a wider geographic range, rejecting neutral evolution for SCD patients. Extending the statistical tests for detecting natural selection to many non-SCD patients reveal varying levels of selective signal across different tumors, implying that many evolutionary forces including natural selection and geographic isolation can influence the overall pattern of sITH. Taken together, tumor phylogeography unravels a dynamic landscape of sITH, pinpointing important evolutionary and clinical consequences of spatial heterogeneity in cancer.
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Affiliation(s)
- Xiaodong Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Ke Zhang
- Department of General Surgery, Beijing Ditan Hospital, Capital Medical University, No. 8, Jingshun East Street, Chaoyang District, Beijing, P.R. China
| | - Neslihan A Kaya
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Zhe Jia
- Department of General Surgery, Beijing Ditan Hospital, Capital Medical University, No. 8, Jingshun East Street, Chaoyang District, Beijing, P.R. China
| | - Dafei Wu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Tingting Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Zhiyuan Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Sinan Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Centre for Quantitative Medicine, Program in Health Services and Systems Research, Duke-NUS Medical School, Singapore, Singapore
| | - Axel M Hillmer
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Torsten Wuestefeld
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jin Liu
- Centre for Quantitative Medicine, Program in Health Services and Systems Research, Duke-NUS Medical School, Singapore, Singapore
| | - Yun Shen Chan
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Zheng Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Liang Ma
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Li Jiang
- Department of General Surgery, Beijing Ditan Hospital, Capital Medical University, No. 8, Jingshun East Street, Chaoyang District, Beijing, P.R. China.
| | - Weiwei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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13
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Reynolds AZ, Niedbalski SD. Sex-biased gene regulation varies across human populations as a result of adaptive evolution. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024; 183:e24888. [PMID: 38100225 PMCID: PMC11279473 DOI: 10.1002/ajpa.24888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 11/14/2023] [Accepted: 11/28/2023] [Indexed: 03/03/2024]
Abstract
OBJECTIVES Studies of human sexual dimorphism and gender disparities in health focus on ostensibly universal molecular sex differences, such as sex chromosomes and circulating hormone levels, while ignoring the extraordinary diversity in biology, behavior, and culture acquired by different human populations over their unique evolutionary histories. MATERIALS AND METHODS Using RNA-Seq data and whole genome sequences from 1000G and HGDP, we investigate variation in sex-biased gene expression across 11 human populations and test whether population-level variation in sex-biased expression may have resulted from adaptive evolution in regions containing sex-specific regulatory variants. RESULTS We find that sex-biased gene expression in humans is highly variable, mostly population-specific, and demonstrates between population reversals. Expression quantitative trait locus mapping reveals sex-specific regulatory regions with evidence of recent positive natural selection, suggesting that variation in sex-biased expression may have evolved as an adaptive response to ancestral environments experienced by human populations. DISCUSSION These results indicate that sex-biased gene expression is more flexible than previously thought and is not generally shared among human populations. Instead, molecular phenotypes associated with sex depend on complex interactions between population-specific molecular evolution and physiological responses to contemporary socioecologies.
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Affiliation(s)
- Adam Z. Reynolds
- Department of Anthropology, University of New Mexico, Albuquerque, NM
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14
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Tomlinson S, Lomolino MV, Anderson A, Austin JJ, Brown SC, Haythorne S, Perry GLW, Wilmshurst JM, Wood JR, Fordham DA. Reconstructing colonization dynamics to establish how human activities transformed island biodiversity. Sci Rep 2024; 14:5261. [PMID: 38438419 PMCID: PMC10912269 DOI: 10.1038/s41598-024-55180-9] [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: 12/12/2023] [Accepted: 02/21/2024] [Indexed: 03/06/2024] Open
Abstract
Drivers and dynamics of initial human migrations across individual islands and archipelagos are poorly understood, hampering assessments of subsequent modification of island biodiversity. We developed and tested a new statistical-simulation approach for reconstructing the pattern and pace of human migration across islands at high spatiotemporal resolutions. Using Polynesian colonisation of New Zealand as an example, we show that process-explicit models, informed by archaeological records and spatiotemporal reconstructions of past climates and environments, can provide new and important insights into the patterns and mechanisms of arrival and establishment of people on islands. We find that colonisation of New Zealand required there to have been a single founding population of approximately 500 people, arriving between 1233 and 1257 AD, settling multiple areas, and expanding rapidly over both North and South Islands. These verified spatiotemporal reconstructions of colonisation dynamics provide new opportunities to explore more extensively the potential ecological impacts of human colonisation on New Zealand's native biota and ecosystems.
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Affiliation(s)
- Sean Tomlinson
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia.
| | - Mark V Lomolino
- College of Environmental Science and Forestry, State University of New York, Syracuse, NY, 13210, USA
| | - Atholl Anderson
- School of Culture, History and Language, Australian National University, Canberra, ACT, 0200, Australia
- Ngai Tahu Research Centre, University of Canterbury, Christchurch, 8140, New Zealand
| | - Jeremy J Austin
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Stuart C Brown
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
- Globe Institute, University of Copenhagen, Copenhagen, 1353, Denmark
| | - Sean Haythorne
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
- Centre of Excellence for Biosecurity Risk Analysis, University of Melbourne, Parkville, VIC, 3010, Australia
| | - George L W Perry
- School of Environment, University of Auckland, Auckland, 1142, New Zealand
| | - Janet M Wilmshurst
- Ecosystems & Conservation, Manaaki Whenua Landcare Research, Lincoln, 7640, New Zealand
| | - Jamie R Wood
- The Environment Institute, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Damien A Fordham
- The Environment Institute, University of Adelaide, Adelaide, SA, 5005, Australia.
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Copenhagen, 1353, Denmark.
- Center for Mountain Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, 1353, Denmark.
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15
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Chen Y, Yu XY, Xu SJ, Shi XQ, Zhang XX, Sun C. An indel introduced by Neanderthal introgression, rs3835124:ATTTATT > ATT, might contribute to prostate cancer risk by regulating PDK1 expression. Ann Hum Genet 2024; 88:126-137. [PMID: 37846608 DOI: 10.1111/ahg.12533] [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: 02/28/2023] [Revised: 07/25/2023] [Accepted: 08/04/2023] [Indexed: 10/18/2023]
Abstract
INTRODUCTION Prostate cancer is one of the most common cancer types in males and rs12621278:A > G has been suggested to be associated with this disease by previous genome-wide association studies. One thousand genomes project data analysis indicated that rs12621278:A > G is within two long-core haplotypes. However, the origin, causal variant(s), and molecular function of these haplotypes were remaining unclear. MATERIALS AND METHODS Population genetics analysis and functional genomics work was performed for this locus. RESULTS Phylogeny analysis verified that the rare haplotype is derived from Neanderthal introgression. Genome annotation suggested that three genetic variants in the core haplotypes, rs116108611:G > A, rs139972066:AAAAAAAA > AAAAAAAAA, and rs3835124:ATTTATT > ATT, are located in functional regions. Luciferase assay indicated that rs139972066:AAAAAAAA > AAAAAAAAA and rs116108611:G > A are not able to alter ITGA6 (integrin alpha 6) and ITGA6 antisense RNA 1 expression, respectively. In contrast, rs3835124:ATTTATT > ATT can significantly influence PDK1 (pyruvate dehydrogenase kinase 1) expression, which was verified by expression quantitative trait locus analysis. This genetic variant can alter transcription factor cut like homeobox 1 interaction efficiency. The introgressed haplotype was observed to be subject to positive selection in East Asian populations. The molecular function of the haplotype suggested that Neanderthal should be with lower PDK1 expression and further different energy homeostasis from modern human. CONCLUSION This study provided new insight into the contribution of Neanderthal introgression to human phenotypes.
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Affiliation(s)
- Ying Chen
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, P. R. China
| | - Xin-Yi Yu
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, P. R. China
| | - Shuang-Jia Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, P. R. China
| | - Xiao-Qian Shi
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, P. R. China
| | - Xin-Xin Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, P. R. China
| | - Chang Sun
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, P. R. China
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16
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Lebrasseur O, More KD, Orlando L. Equine herpesvirus 4 infected domestic horses associated with Sintashta spoke-wheeled chariots around 4,000 years ago. Virus Evol 2024; 10:vead087. [PMID: 38465241 PMCID: PMC10924538 DOI: 10.1093/ve/vead087] [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: 06/28/2023] [Revised: 11/27/2023] [Accepted: 01/11/2024] [Indexed: 03/12/2024] Open
Abstract
Equine viral outbreaks have disrupted the socio-economic life of past human societies up until the late 19th century and continue to be of major concern to the horse industry today. With a seroprevalence of 60-80 per cent, equine herpesvirus 4 (EHV-4) is the most common horse pathogen on the planet. Yet, its evolutionary history remains understudied. Here, we screen the sequenced data of 264 archaeological horse remains to detect the presence of EHV-4. We recover the first ancient EHV-4 genome with 4.2× average depth-of-coverage from a specimen excavated in the Southeastern Urals and dated to the Early Bronze Age period, approximately 3,900 years ago. The recovery of an EHV-4 virus outside the upper respiratory tract not only points to an animal particularly infected but also highlights the importance of post-cranial bones in pathogen characterisation. Bayesian phylogenetic reconstruction provides a minimal time estimate for EHV-4 diversification to around 4,000 years ago, a time when modern domestic horses spread across the Central Asian steppes together with spoke-wheeled Sintashta chariots, or earlier. The analyses also considerably revise the diversification time of the two EHV-4 subclades from the 16th century based solely on modern data to nearly a thousand years ago. Our study paves the way for a robust reconstruction of the history of non-human pathogens and their impact on animal health.
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Affiliation(s)
- Ophélie Lebrasseur
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS/Université Paul Sabatier, 37 Allées Jules Guesde, 31000, Toulouse, France
- Instituto Nacional de Antropología y Pensamiento Latinoamericano, 3 de Febrero 1370 (1426), Ciudad Autónoma de Buenos Aires, Argentina
| | - Kuldeep Dilip More
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS/Université Paul Sabatier, 37 Allées Jules Guesde, 31000, Toulouse, France
| | - Ludovic Orlando
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS/Université Paul Sabatier, 37 Allées Jules Guesde, 31000, Toulouse, France
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17
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Mirchandani CD, Shultz AJ, Thomas GWC, Smith SJ, Baylis M, Arnold B, Corbett-Detig R, Enbody E, Sackton TB. A Fast, Reproducible, High-throughput Variant Calling Workflow for Population Genomics. Mol Biol Evol 2024; 41:msad270. [PMID: 38069903 PMCID: PMC10764099 DOI: 10.1093/molbev/msad270] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/27/2023] [Accepted: 11/22/2023] [Indexed: 01/05/2024] Open
Abstract
The increasing availability of genomic resequencing data sets and high-quality reference genomes across the tree of life present exciting opportunities for comparative population genomic studies. However, substantial challenges prevent the simple reuse of data across different studies and species, arising from variability in variant calling pipelines, data quality, and the need for computationally intensive reanalysis. Here, we present snpArcher, a flexible and highly efficient workflow designed for the analysis of genomic resequencing data in nonmodel organisms. snpArcher provides a standardized variant calling pipeline and includes modules for variant quality control, data visualization, variant filtering, and other downstream analyses. Implemented in Snakemake, snpArcher is user-friendly, reproducible, and designed to be compatible with high-performance computing clusters and cloud environments. To demonstrate the flexibility of this pipeline, we applied snpArcher to 26 public resequencing data sets from nonmammalian vertebrates. These variant data sets are hosted publicly to enable future comparative population genomic analyses. With its extensibility and the availability of public data sets, snpArcher will contribute to a broader understanding of genetic variation across species by facilitating the rapid use and reuse of large genomic data sets.
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Affiliation(s)
- Cade D Mirchandani
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Allison J Shultz
- Ornithology Department, Natural History Museum of Los Angeles County, Los Angeles, CA 90007, USA
| | | | - Sara J Smith
- Informatics Group, Harvard University, Cambridge, MA, USA
- Biology, Mount Royal University, Calgary, AB T3E 6K6, Canada
| | - Mara Baylis
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Brian Arnold
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Center for Statistics and Machine Learning, Princeton University, Princeton, NJ, USA
| | - Russ Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Erik Enbody
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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18
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McClellan JM, Zoghbi AW, Buxbaum JD, Cappi C, Crowley JJ, Flint J, Grice DE, Gulsuner S, Iyegbe C, Jain S, Kuo PH, Lattig MC, Passos-Bueno MR, Purushottam M, Stein DJ, Sunshine AB, Susser ES, Walsh CA, Wootton O, King MC. An evolutionary perspective on complex neuropsychiatric disease. Neuron 2024; 112:7-24. [PMID: 38016473 PMCID: PMC10842497 DOI: 10.1016/j.neuron.2023.10.037] [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: 08/02/2022] [Revised: 08/09/2023] [Accepted: 10/26/2023] [Indexed: 11/30/2023]
Abstract
The forces of evolution-mutation, selection, migration, and genetic drift-shape the genetic architecture of human traits, including the genetic architecture of complex neuropsychiatric illnesses. Studying these illnesses in populations that are diverse in genetic ancestry, historical demography, and cultural history can reveal how evolutionary forces have guided adaptation over time and place. A fundamental truth of shared human biology is that an allele responsible for a disease in anyone, anywhere, reveals a gene critical to the normal biology underlying that condition in everyone, everywhere. Understanding the genetic causes of neuropsychiatric disease in the widest possible range of human populations thus yields the greatest possible range of insight into genes critical to human brain development. In this perspective, we explore some of the relationships between genes, adaptation, and history that can be illuminated by an evolutionary perspective on studies of complex neuropsychiatric disease in diverse populations.
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Affiliation(s)
- Jon M McClellan
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Anthony W Zoghbi
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joseph D Buxbaum
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carolina Cappi
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - James J Crowley
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jonathan Flint
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Dorothy E Grice
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Suleyman Gulsuner
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Conrad Iyegbe
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sanjeev Jain
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bengaluru 560029, India
| | - Po-Hsiu Kuo
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei 100, Taiwan
| | | | | | - Meera Purushottam
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bengaluru 560029, India
| | - Dan J Stein
- SAMRC Unit on Risk and Resilience in Mental Disorders, Department of Psychiatry, University of Cape Town, Cape Town, South Africa
| | - Anna B Sunshine
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA; Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Ezra S Susser
- Department of Epidemiology, Mailman School of Public Health, and New York State Psychiatric Institute, Columbia University, New York, NY 10032, USA
| | - Christopher A Walsh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Olivia Wootton
- SAMRC Unit on Risk and Resilience in Mental Disorders, Department of Psychiatry, University of Cape Town, Cape Town, South Africa
| | - Mary-Claire King
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
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19
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Seeholzer GF, Brumfield RT. Speciation-by-Extinction. Syst Biol 2023; 72:1433-1442. [PMID: 37542735 DOI: 10.1093/sysbio/syad049] [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: 04/25/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/07/2023] Open
Abstract
Extinction is a dominant force shaping patterns of biodiversity through time; however its role as a catalyst of speciation through its interaction with intraspecific variation has been overlooked. Here, we synthesize ideas alluded to by Darwin and others into the model of "speciation-by-extinction" in which speciation results from the extinction of intermediate populations within a single geographically variable species. We explore the properties and distinguishing features of speciation-by-extinction with respect to other established speciation models. We demonstrate its plausibility by showing that the experimental extinction of populations within variable species can result in speciation. The prerequisites for speciation-by-extinction, geographically structured intraspecific variation and local extinction, are ubiquitous in nature. We propose that speciation-by-extinction may be a prevalent, but underappreciated, speciation mechanism.
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Affiliation(s)
- Glenn F Seeholzer
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
- Macaulay Library, Cornell Lab of Ornithology, Ithaca, NY, 14850, USA
| | - Robb T Brumfield
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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20
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Cooke R, Sayol F, Andermann T, Blackburn TM, Steinbauer MJ, Antonelli A, Faurby S. Undiscovered bird extinctions obscure the true magnitude of human-driven extinction waves. Nat Commun 2023; 14:8116. [PMID: 38114469 PMCID: PMC10730700 DOI: 10.1038/s41467-023-43445-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 11/09/2023] [Indexed: 12/21/2023] Open
Abstract
Birds are among the best-studied animal groups, but their prehistoric diversity is poorly known due to low fossilization potential. Hence, while many human-driven bird extinctions (i.e., extinctions caused directly by human activities such as hunting, as well as indirectly through human-associated impacts such as land use change, fire, and the introduction of invasive species) have been recorded, the true number is likely much larger. Here, by combining recorded extinctions with model estimates based on the completeness of the fossil record, we suggest that at least ~1300-1500 bird species (~12% of the total) have gone extinct since the Late Pleistocene, with 55% of these extinctions undiscovered (not yet discovered or left no trace). We estimate that the Pacific accounts for 61% of total bird extinctions. Bird extinction rate varied through time with an intense episode ~1300 CE, which likely represents the largest human-driven vertebrate extinction wave ever, and a rate 80 (60-95) times the background extinction rate. Thus, humans have already driven more than one in nine bird species to extinction, with likely severe, and potentially irreversible, ecological and evolutionary consequences.
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Affiliation(s)
- Rob Cooke
- UK Centre for Ecology & Hydrology, Maclean Building, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB, UK.
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden.
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30, Göteborg, Sweden.
| | - Ferran Sayol
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30, Göteborg, Sweden
- CREAF, E08193 Bellaterra (Cerdanyola del Vallès), Catalonia, Spain
| | - Tobias Andermann
- Department of Organismal Biology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Tim M Blackburn
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Manuel J Steinbauer
- Bayreuth Center of Ecology and Environmental Research (BayCEER) & Bayreuth Center of Sport Science (BaySpo), University of Bayreuth, 95447, Bayreuth, Germany
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30, Göteborg, Sweden
- Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AE, UK
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Søren Faurby
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30, Göteborg, Sweden
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21
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Tallman S, Sungo MDD, Saranga S, Beleza S. Whole genomes from Angola and Mozambique inform about the origins and dispersals of major African migrations. Nat Commun 2023; 14:7967. [PMID: 38042927 PMCID: PMC10693643 DOI: 10.1038/s41467-023-43717-x] [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: 03/10/2022] [Accepted: 11/17/2023] [Indexed: 12/04/2023] Open
Abstract
As the continent of origin for our species, Africa harbours the highest levels of diversity anywhere on Earth. However, many regions of Africa remain under-sampled genetically. Here we present 350 whole genomes from Angola and Mozambique belonging to ten Bantu ethnolinguistic groups, enabling the construction of a reference variation catalogue including 2.9 million novel SNPs. We investigate the emergence of Bantu speaker population structure, admixture involving migrations across sub-Saharan Africa and model the demographic histories of Angolan and Mozambican Bantu speakers. Our results bring together concordant views from genomics, archaeology, and linguistics to paint an updated view of the complexity of the Bantu Expansion. Moreover, we generate reference panels that better represents the diversity of African populations involved in the trans-Atlantic slave trade, improving imputation accuracy in African Americans and Brazilians. We anticipate that our collection of genomes will form the foundation for future African genomic healthcare initiatives.
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Affiliation(s)
- Sam Tallman
- University of Leicester, Department of Genetics & Genome Biology, University Road, Leicester, LE1 7RH, UK
- Genomics England, 1 Canada Square, London, E14 5AB, UK
| | | | - Sílvio Saranga
- Universidade Pedagógica, Avenida Eduardo Mondlane, CP 2107, Maputo, Mozambique
| | - Sandra Beleza
- University of Leicester, Department of Genetics & Genome Biology, University Road, Leicester, LE1 7RH, UK.
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22
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Fournier R, Tsangalidou Z, Reich D, Palamara PF. Haplotype-based inference of recent effective population size in modern and ancient DNA samples. Nat Commun 2023; 14:7945. [PMID: 38040695 PMCID: PMC10692198 DOI: 10.1038/s41467-023-43522-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 11/10/2023] [Indexed: 12/03/2023] Open
Abstract
Individuals sharing recent ancestors are likely to co-inherit large identical-by-descent (IBD) genomic regions. The distribution of these IBD segments in a population may be used to reconstruct past demographic events such as effective population size variation, but accurate IBD detection is difficult in ancient DNA data and in underrepresented populations with limited reference data. In this work, we introduce an accurate method for inferring effective population size variation during the past ~2000 years in both modern and ancient DNA data, called HapNe. HapNe infers recent population size fluctuations using either IBD sharing (HapNe-IBD) or linkage disequilibrium (HapNe-LD), which does not require phasing and can be computed in low coverage data, including data sets with heterogeneous sampling times. HapNe shows improved accuracy in a range of simulated demographic scenarios compared to currently available methods for IBD-based and LD-based inference of recent effective population size, while requiring fewer computational resources. We apply HapNe to several modern populations from the 1,000 Genomes Project, the UK Biobank, the Allen Ancient DNA Resource, and recently published samples from Iron Age Britain, detecting multiple instances of recent effective population size variation across these groups.
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Affiliation(s)
| | | | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Pier Francesco Palamara
- Department of Statistics, University of Oxford, Oxford, UK.
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
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23
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Silcocks M, Farlow A, Hermes A, Tsambos G, Patel HR, Huebner S, Baynam G, Jenkins MR, Vukcevic D, Easteal S, Leslie S. Indigenous Australian genomes show deep structure and rich novel variation. Nature 2023; 624:593-601. [PMID: 38093005 PMCID: PMC10733150 DOI: 10.1038/s41586-023-06831-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 11/03/2023] [Indexed: 12/20/2023]
Abstract
The Indigenous peoples of Australia have a rich linguistic and cultural history. How this relates to genetic diversity remains largely unknown because of their limited engagement with genomic studies. Here we analyse the genomes of 159 individuals from four remote Indigenous communities, including people who speak a language (Tiwi) not from the most widespread family (Pama-Nyungan). This large collection of Indigenous Australian genomes was made possible by careful community engagement and consultation. We observe exceptionally strong population structure across Australia, driven by divergence times between communities of 26,000-35,000 years ago and long-term low but stable effective population sizes. This demographic history, including early divergence from Papua New Guinean (47,000 years ago) and Eurasian groups1, has generated the highest proportion of previously undescribed genetic variation seen outside Africa and the most extended homozygosity compared with global samples. A substantial proportion of this variation is not observed in global reference panels or clinical datasets, and variation with predicted functional consequence is more likely to be homozygous than in other populations, with consequent implications for medical genomics2. Our results show that Indigenous Australians are not a single homogeneous genetic group and their genetic relationship with the peoples of New Guinea is not uniform. These patterns imply that the full breadth of Indigenous Australian genetic diversity remains uncharacterized, potentially limiting genomic medicine and equitable healthcare for Indigenous Australians.
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Affiliation(s)
- Matthew Silcocks
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- University of Melbourne, School of Biosciences, Parkville, Victoria, Australia
| | - Ashley Farlow
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- University of Melbourne, School of Mathematics and Statistics, Parkville, Victoria, Australia
| | - Azure Hermes
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Georgia Tsambos
- University of Melbourne, School of Mathematics and Statistics, Parkville, Victoria, Australia
| | - Hardip R Patel
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Sharon Huebner
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Gareth Baynam
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- Faculty of Health and Medical Sciences, Division of Paediatrics and Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital and Rare Care Centre, Perth Children's Hospital, Perth, Western Australia, Australia
| | - Misty R Jenkins
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- University of Melbourne, Department of Medical Biology, Parkville, Victoria, Australia
| | - Damjan Vukcevic
- University of Melbourne, School of Mathematics and Statistics, Parkville, Victoria, Australia
| | - Simon Easteal
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Stephen Leslie
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia.
- University of Melbourne, School of Biosciences, Parkville, Victoria, Australia.
- University of Melbourne, School of Mathematics and Statistics, Parkville, Victoria, Australia.
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24
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Biswas A, Kumari A, Gaikwad DS, Pandey DK. Revolutionizing Biological Science: The Synergy of Genomics in Health, Bioinformatics, Agriculture, and Artificial Intelligence. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:550-569. [PMID: 38100404 DOI: 10.1089/omi.2023.0197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
With climate emergency, COVID-19, and the rise of planetary health scholarship, the binary of human and ecosystem health has been deeply challenged. The interdependence of human and nonhuman animal health is increasingly acknowledged and paving the way for new frontiers in integrative biology. The convergence of genomics in health, bioinformatics, agriculture, and artificial intelligence (AI) has ushered in a new era of possibilities and applications. However, the sheer volume of genomic/multiomics big data generated also presents formidable sociotechnical challenges in extracting meaningful biological, planetary health and ecological insights. Over the past few years, AI-guided bioinformatics has emerged as a powerful tool for managing, analyzing, and interpreting complex biological datasets. The advances in AI, particularly in machine learning and deep learning, have been transforming the fields of genomics, planetary health, and agriculture. This article aims to unpack and explore the formidable range of possibilities and challenges that result from such transdisciplinary integration, and emphasizes its radically transformative potential for human and ecosystem health. The integration of these disciplines is also driving significant advancements in precision medicine and personalized health care. This presents an unprecedented opportunity to deepen our understanding of complex biological systems and advance the well-being of all life in planetary ecosystems. Notwithstanding in mind its sociotechnical, ethical, and critical policy challenges, the integration of genomics, multiomics, planetary health, and agriculture with AI-guided bioinformatics opens up vast opportunities for transnational collaborative efforts, data sharing, analysis, valorization, and interdisciplinary innovations in life sciences and integrative biology.
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Affiliation(s)
- Aakanksha Biswas
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, India
| | - Aditi Kumari
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, India
| | - D S Gaikwad
- Amity Institute of Organic Agriculture, Amity University, Noida, India
| | - Dhananjay K Pandey
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, India
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25
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Velazquez-Arcelay K, Colbran LL, McArthur E, Brand CM, Rinker DC, Siemann JK, McMahon DG, Capra JA. Archaic Introgression Shaped Human Circadian Traits. Genome Biol Evol 2023; 15:evad203. [PMID: 38095367 PMCID: PMC10719892 DOI: 10.1093/gbe/evad203] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2023] [Indexed: 12/17/2023] Open
Abstract
When the ancestors of modern Eurasians migrated out of Africa and interbred with Eurasian archaic hominins, namely, Neanderthals and Denisovans, DNA of archaic ancestry integrated into the genomes of anatomically modern humans. This process potentially accelerated adaptation to Eurasian environmental factors, including reduced ultraviolet radiation and increased variation in seasonal dynamics. However, whether these groups differed substantially in circadian biology and whether archaic introgression adaptively contributed to human chronotypes remain unknown. Here, we traced the evolution of chronotype based on genomes from archaic hominins and present-day humans. First, we inferred differences in circadian gene sequences, splicing, and regulation between archaic hominins and modern humans. We identified 28 circadian genes containing variants with potential to alter splicing in archaics (e.g., CLOCK, PER2, RORB, and RORC) and 16 circadian genes likely divergently regulated between present-day humans and archaic hominins, including RORA. These differences suggest the potential for introgression to modify circadian gene expression. Testing this hypothesis, we found that introgressed variants are enriched among expression quantitative trait loci for circadian genes. Supporting the functional relevance of these regulatory effects, we found that many introgressed alleles have associations with chronotype. Strikingly, the strongest introgressed effects on chronotype increase morningness, consistent with adaptations to high latitude in other species. Finally, we identified several circadian loci with evidence of adaptive introgression or latitudinal clines in allele frequency. These findings identify differences in circadian gene regulation between modern humans and archaic hominins and support the contribution of introgression via coordinated effects on variation in human chronotype.
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Affiliation(s)
| | - Laura L Colbran
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Evonne McArthur
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Colin M Brand
- Department of Epidemiology and Biostatistics, University of California, SanFrancisco, California, USA
- Bakar Computational Health Sciences Institute, University of California, SanFrancisco, California, USA
| | - David C Rinker
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Justin K Siemann
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Douglas G McMahon
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - John A Capra
- Department of Epidemiology and Biostatistics, University of California, SanFrancisco, California, USA
- Bakar Computational Health Sciences Institute, University of California, SanFrancisco, California, USA
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26
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Leung JG. Ethnopsychopharmacology: Clinical and scientific writing pearls. Ment Health Clin 2023; 13:276-288. [PMID: 38058595 PMCID: PMC10696167 DOI: 10.9740/mhc.2023.12.276] [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: 04/03/2023] [Accepted: 09/26/2023] [Indexed: 12/08/2023] Open
Abstract
The concept of ethnopsychopharmacology aims to predict or explain the pharmacologic response to psychiatric medications based on the influence of biologic and nonbiologic factors. Interactions involving these factors are complex and influence patient outcomes in health care. Pharmacists and other clinicians working in patient care environments, research, or medical education should engage in lifelong learning to enhance ethnopsychopharmacologic knowledge gaps, which ultimately may improve and individualize care across diverse populations. Through two cases, this paper provides pearls on how biogeographical ancestry and cytochrome P450 status may influence pharmacotherapy selection, dosing, or response. A third scenario highlights a publication, like many other published works, with deficiencies in how data on ancestry, race, and ethnicity are collected or reported. Current recommendations on the use of inclusive language in scientific writing are reviewed, with attention to specific examples.
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Guevara E, Gopalan S, Massey DJ, Adegboyega M, Zhou W, Solis A, Anaya AD, Churchill SE, Feldblum J, Lawler RR. Getting it right: Teaching undergraduate biology to undermine racial essentialism. Biol Methods Protoc 2023; 8:bpad032. [PMID: 38023347 PMCID: PMC10674104 DOI: 10.1093/biomethods/bpad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/03/2023] [Accepted: 11/10/2023] [Indexed: 12/01/2023] Open
Abstract
How we teach human genetics matters for social equity. The biology curriculum appears to be a crucial locus of intervention for either reinforcing or undermining students' racial essentialist views. The Mendelian genetic models dominating textbooks, particularly in combination with racially inflected language sometimes used when teaching about monogenic disorders, can increase middle and high school students' racial essentialism and opposition to policies to increase equity. These findings are of particular concern given the increasing spread of racist misinformation online and the misappropriation of human genomics research by white supremacists, who take advantage of low levels of genetics literacy in the general public. Encouragingly, however, teaching updated information about the geographical distribution of human genetic variation and the complex, multifactorial basis of most human traits, reduces students' endorsement of racial essentialism. The genetics curriculum is therefore a key tool in combating misinformation and scientific racism. Here, we describe a framework and example teaching materials for teaching students key concepts in genetics, human evolutionary history, and human phenotypic variation at the undergraduate level. This framework can be flexibly applied in biology and anthropology classes and adjusted based on time availability. Our goal is to provide undergraduate-level instructors with varying levels of expertise with a set of evidence-informed tools for teaching human genetics to combat scientific racism, including an evolving set of instructional resources, as well as learning goals and pedagogical approaches. Resources can be found at https://noto.li/YIlhZ5. Additionally, we hope to generate conversation about integrating modern genetics into the undergraduate curriculum, in light of recent findings about the risks and opportunities associated with teaching genetics.
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Affiliation(s)
- Elaine Guevara
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Shyamalika Gopalan
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Dashiell J Massey
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Mayowa Adegboyega
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Wen Zhou
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
- Department of Evolutionary Anthropology, Duke Kunshan University, Kunshan, Jiangsu 215316, China
| | - Alma Solis
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Alisha D Anaya
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Steven E Churchill
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Joseph Feldblum
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27713, United States
| | - Richard R Lawler
- Department of Sociology and Anthropology, James Madison University, Harrisonburg, Virginia 22807, United States
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Ascunce MS, Toloza AC, González-Oliver A, Reed DL. Nuclear genetic diversity of head lice sheds light on human dispersal around the world. PLoS One 2023; 18:e0293409. [PMID: 37939041 PMCID: PMC10631634 DOI: 10.1371/journal.pone.0293409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 09/26/2023] [Indexed: 11/10/2023] Open
Abstract
The human louse, Pediculus humanus, is an obligate blood-sucking ectoparasite that has coevolved with humans for millennia. Given the intimate relationship between this parasite and the human host, the study of human lice has the potential to shed light on aspects of human evolution that are difficult to interpret using other biological evidence. In this study, we analyzed the genetic variation in 274 human lice from 25 geographic sites around the world by using nuclear microsatellite loci and female-inherited mitochondrial DNA sequences. Nuclear genetic diversity analysis revealed the presence of two distinct genetic clusters I and II, which are subdivided into subclusters: Ia-Ib and IIa-IIb, respectively. Among these samples, we observed the presence of the two most common louse mitochondrial haplogroups: A and B that were found in both nuclear Clusters I and II. Evidence of nuclear admixture was uncommon (12%) and was predominate in the New World potentially mirroring the history of colonization in the Americas. These findings were supported by novel DIYABC simulations that were built using both host and parasite data to define parameters and models suggesting that admixture between cI and cII was very recent. This pattern could also be the result of a reproductive barrier between these two nuclear genetic clusters. In addition to providing new evolutionary knowledge about this human parasite, our study could guide the development of new analyses in other host-parasite systems.
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Affiliation(s)
- Marina S. Ascunce
- Department of Plant Pathology, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- USDA-ARS Center for Medical, Agricultural, and Veterinary Entomology, Gainesville, Florida, United States of America
| | - Ariel C. Toloza
- Centro de Investigaciones de Plagas e Insecticidas (CONICET-UNIDEF), Villa Martelli, Buenos Aires, Argentina
| | - Angélica González-Oliver
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - David L. Reed
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America
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Flouri T, Jiao X, Huang J, Rannala B, Yang Z. Efficient Bayesian inference under the multispecies coalescent with migration. Proc Natl Acad Sci U S A 2023; 120:e2310708120. [PMID: 37871206 PMCID: PMC10622872 DOI: 10.1073/pnas.2310708120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 08/15/2023] [Indexed: 10/25/2023] Open
Abstract
Analyses of genome sequence data have revealed pervasive interspecific gene flow and enriched our understanding of the role of gene flow in speciation and adaptation. Inference of gene flow using genomic data requires powerful statistical methods. Yet current likelihood-based methods involve heavy computation and are feasible for small datasets only. Here, we implement the multispecies-coalescent-with-migration model in the Bayesian program bpp, which can be used to test for gene flow and estimate migration rates, as well as species divergence times and population sizes. We develop Markov chain Monte Carlo algorithms for efficient sampling from the posterior, enabling the analysis of genome-scale datasets with thousands of loci. Implementation of both introgression and migration models in the same program allows us to test whether gene flow occurred continuously over time or in pulses. Analyses of genomic data from Anopheles mosquitoes demonstrate rich information in typical genomic datasets about the mode and rate of gene flow.
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Affiliation(s)
- Tomáš Flouri
- Department of Genetics, Evolution, and Environment, University College London, LondonWC1E 6BT, United Kingdom
| | - Xiyun Jiao
- Department of Statistics and Data Science, China Southern University of Science and Technology, Shenzhen518055, China
| | - Jun Huang
- Department of Intelligent Medical Engineering, School of Biomedical Engineering, Capital Medical University, Beijing100069, China
| | - Bruce Rannala
- Department of Evolution and Ecology, University of California, Davis, CA95616
| | - Ziheng Yang
- Department of Genetics, Evolution, and Environment, University College London, LondonWC1E 6BT, United Kingdom
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Quilodrán CS, Rio J, Tsoupas A, Currat M. Past human expansions shaped the spatial pattern of Neanderthal ancestry. SCIENCE ADVANCES 2023; 9:eadg9817. [PMID: 37851812 PMCID: PMC10584333 DOI: 10.1126/sciadv.adg9817] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 09/11/2023] [Indexed: 10/20/2023]
Abstract
The worldwide expansion of modern humans (Homo sapiens) started before the extinction of Neanderthals (Homo neanderthalensis). Both species coexisted and interbred, leading to slightly higher introgression in East Asians than in Europeans. This distinct ancestry level has been argued to result from selection, but range expansions of modern humans could provide an alternative explanation. This hypothesis would lead to spatial introgression gradients, increasing with distance from the expansion source. We investigate the presence of Neanderthal introgression gradients after past human expansions by analyzing Eurasian paleogenomes. We show that the out-of-Africa expansion resulted in spatial gradients of Neanderthal ancestry that persisted through time. While keeping the same gradient orientation, the expansion of early Neolithic farmers contributed decisively to reducing the Neanderthal introgression in European populations compared to Asian populations. This is because Neolithic farmers carried less Neanderthal DNA than preceding Paleolithic hunter-gatherers. This study shows that inferences about past human population dynamics can be made from the spatiotemporal variation in archaic introgression.
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Affiliation(s)
| | - Jérémy Rio
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Alexandros Tsoupas
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Mathias Currat
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland
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Medina-Muñoz SG, Ortega-Del Vecchyo D, Cruz-Hervert LP, Ferreyra-Reyes L, García-García L, Moreno-Estrada A, Ragsdale AP. Demographic modeling of admixed Latin American populations from whole genomes. Am J Hum Genet 2023; 110:1804-1816. [PMID: 37725976 PMCID: PMC10577084 DOI: 10.1016/j.ajhg.2023.08.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 08/17/2023] [Accepted: 08/23/2023] [Indexed: 09/21/2023] Open
Abstract
Demographic models of Latin American populations often fail to fully capture their complex evolutionary history, which has been shaped by both recent admixture and deeper-in-time demographic events. To address this gap, we used high-coverage whole-genome data from Indigenous American ancestries in present-day Mexico and existing genomes from across Latin America to infer multiple demographic models that capture the impact of different timescales on genetic diversity. Our approach, which combines analyses of allele frequencies and ancestry tract length distributions, represents a significant improvement over current models in predicting patterns of genetic variation in admixed Latin American populations. We jointly modeled the contribution of European, African, East Asian, and Indigenous American ancestries into present-day Latin American populations. We infer that the ancestors of Indigenous Americans and East Asians diverged ∼30 thousand years ago, and we characterize genetic contributions of recent migrations from East and Southeast Asia to Peru and Mexico. Our inferred demographic histories are consistent across different genomic regions and annotations, suggesting that our inferences are robust to the potential effects of linked selection. In conjunction with published distributions of fitness effects for new nonsynonymous mutations in humans, we show in large-scale simulations that our models recover important features of both neutral and deleterious variation. By providing a more realistic framework for understanding the evolutionary history of Latin American populations, our models can help address the historical under-representation of admixed groups in genomics research and can be a valuable resource for future studies of populations with complex admixture and demographic histories.
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Affiliation(s)
- Santiago G Medina-Muñoz
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | - Diego Ortega-Del Vecchyo
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de Mexico, Juriquilla, Querétaro 76230, Mexico
| | | | | | | | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico.
| | - Aaron P Ragsdale
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico; Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Yang C, Zhou Y, Song Y, Wu D, Zeng Y, Nie L, Liu P, Zhang S, Chen G, Xu J, Zhou H, Zhou L, Qian X, Liu C, Tan S, Zhou C, Dai W, Xu M, Qi Y, Wang X, Guo L, Fan G, Wang A, Deng Y, Zhang Y, Jin J, He Y, Guo C, Guo G, Zhou Q, Xu X, Yang H, Wang J, Xu S, Mao Y, Jin X, Ruan J, Zhang G. The complete and fully-phased diploid genome of a male Han Chinese. Cell Res 2023; 33:745-761. [PMID: 37452091 PMCID: PMC10542383 DOI: 10.1038/s41422-023-00849-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023] Open
Abstract
Since the release of the complete human genome, the priority of human genomic study has now been shifting towards closing gaps in ethnic diversity. Here, we present a fully phased and well-annotated diploid human genome from a Han Chinese male individual (CN1), in which the assemblies of both haploids achieve the telomere-to-telomere (T2T) level. Comparison of this diploid genome with the CHM13 haploid T2T genome revealed significant variations in the centromere. Outside the centromere, we discovered 11,413 structural variations, including numerous novel ones. We also detected thousands of CN1 alleles that have accumulated high substitution rates and a few that have been under positive selection in the East Asian population. Further, we found that CN1 outperforms CHM13 as a reference genome in mapping and variant calling for the East Asian population owing to the distinct structural variants of the two references. Comparison of SNP calling for a large cohort of 8869 Chinese genomes using CN1 and CHM13 as reference respectively showed that the reference bias profoundly impacts rare SNP calling, with nearly 2 million rare SNPs miss-called with different reference genomes. Finally, applying the CN1 as a reference, we discovered 5.80 Mb and 4.21 Mb putative introgression sequences from Neanderthal and Denisovan, respectively, including many East Asian specific ones undetected using CHM13 as the reference. Our analyses reveal the advances of using CN1 as a reference for population genomic studies and paleo-genomic studies. This complete genome will serve as an alternative reference for future genomic studies on the East Asian population.
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Affiliation(s)
- Chentao Yang
- Center for Genomic Research, International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
- Center for Evolutionary & Organismal Biology, & Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Yang Zhou
- BGI-Shenzhen, Shenzhen, Guangdong, China
- BGI Research-Wuhan, BGI, Wuhan, Hubei, China
| | - Yanni Song
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Dongya Wu
- Center for Genomic Research, International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
- Center for Evolutionary & Organismal Biology, & Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yan Zeng
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Lei Nie
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | | | - Shilong Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Guangji Chen
- BGI-Shenzhen, Shenzhen, Guangdong, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jinjin Xu
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Hongling Zhou
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Long Zhou
- Center for Evolutionary & Organismal Biology, & Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaobo Qian
- BGI-Shenzhen, Shenzhen, Guangdong, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chenlu Liu
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | | | | | - Wei Dai
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Mengyang Xu
- BGI-Shenzhen, Shenzhen, Guangdong, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, China
| | - Yanwei Qi
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, China
| | - Xiaobo Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Lidong Guo
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, China
| | - Aijun Wang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, China
| | - Yuan Deng
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Yong Zhang
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | | | - Yunqiu He
- Center for Genomic Research, International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
- Center for Evolutionary & Organismal Biology, & Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Chunxue Guo
- BGI-Shenzhen, Shenzhen, Guangdong, China
- BGI-Hangzhou, Hangzhou, Zhejiang, China
| | - Guoji Guo
- School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qing Zhou
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | | | - Jian Wang
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, China
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, International Joint Center of Genomics of Jiangsu Province School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
- Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yafei Mao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Jue Ruan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China.
| | - Guojie Zhang
- Center for Genomic Research, International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China.
- Center for Evolutionary & Organismal Biology, & Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China.
- Innovation Center of Yangtze River Delta, Zhejiang University, Hangzhou, Zhejiang, China.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
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Nanjala R, Mbiyavanga M, Hashim S, de Villiers S, Mulder N. Assessing HLA imputation accuracy in a West African population. PLoS One 2023; 18:e0291437. [PMID: 37768905 PMCID: PMC10538777 DOI: 10.1371/journal.pone.0291437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/28/2023] [Indexed: 09/30/2023] Open
Abstract
The Human Leukocyte Antigen (HLA) region plays an important role in autoimmune and infectious diseases. HLA is a highly polymorphic region and thus difficult to impute. We, therefore, sought to evaluate HLA imputation accuracy, specifically in a West African population, since they are understudied and are known to harbor high genetic diversity. The study sets were selected from 315 Gambian individuals within the Gambian Genome Variation Project (GGVP) Whole Genome Sequence datasets. Two different arrays, Illumina Omni 2.5 and Human Hereditary and Health in Africa (H3Africa), were assessed for the appropriateness of their markers, and these were used to test several imputation panels and tools. The reference panels were chosen from the 1000 Genomes (1kg-All), 1000 Genomes African (1kg-Afr), 1000 Genomes Gambian (1kg-Gwd), H3Africa, and the HLA Multi-ethnic datasets. HLA-A, HLA-B, and HLA-C alleles were imputed using HIBAG, SNP2HLA, CookHLA, and Minimac4, and concordance rate was used as an assessment metric. The best performing tool was found to be HIBAG, with a concordance rate of 0.84, while the best performing reference panel was the H3Africa panel, with a concordance rate of 0.62. Minimac4 (0.75) was shown to increase HLA-B allele imputation accuracy compared to HIBAG (0.71), SNP2HLA (0.51) and CookHLA (0.17). The H3Africa and Illumina Omni 2.5 array performances were comparable, showing that genotyping arrays have less influence on HLA imputation in West African populations. The findings show that using a larger population-specific reference panel and the HIBAG tool improves the accuracy of HLA imputation in a West African population.
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Affiliation(s)
- Ruth Nanjala
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, University of Cape Town, Cape Town, South Africa
| | - Mamana Mbiyavanga
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, University of Cape Town, Cape Town, South Africa
| | - Suhaila Hashim
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
- Pwani University Biosciences Research Centre, Pwani University, Kilifi, Kenya
| | - Santie de Villiers
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
- Pwani University Biosciences Research Centre, Pwani University, Kilifi, Kenya
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, University of Cape Town, Cape Town, South Africa
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Dumesic DA, Abbott DH, Chazenbalk GD. An Evolutionary Model for the Ancient Origins of Polycystic Ovary Syndrome. J Clin Med 2023; 12:6120. [PMID: 37834765 PMCID: PMC10573644 DOI: 10.3390/jcm12196120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
Polycystic ovary syndrome (PCOS) is a common endocrinopathy of reproductive-aged women, characterized by hyperandrogenism, oligo-anovulation and insulin resistance and closely linked with preferential abdominal fat accumulation. As an ancestral primate trait, PCOS was likely further selected in humans when scarcity of food in hunter-gatherers of the late Pleistocene additionally programmed for enhanced fat storage to meet the metabolic demands of reproduction in later life. As an evolutionary model for PCOS, healthy normal-weight women with hyperandrogenic PCOS have subcutaneous (SC) abdominal adipose stem cells that favor fat storage through exaggerated lipid accumulation during development to adipocytes in vitro. In turn, fat storage is counterbalanced by reduced insulin sensitivity and preferential accumulation of highly lipolytic intra-abdominal fat in vivo. This metabolic adaptation in PCOS balances energy storage with glucose availability and fatty acid oxidation for optimal energy use during reproduction; its accompanying oligo-anovulation allowed PCOS women from antiquity sufficient time and strength for childrearing of fewer offspring with a greater likelihood of childhood survival. Heritable PCOS characteristics are affected by today's contemporary environment through epigenetic events that predispose women to lipotoxicity, with excess weight gain and pregnancy complications, calling for an emphasis on preventive healthcare to optimize the long-term, endocrine-metabolic health of PCOS women in today's obesogenic environment.
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Affiliation(s)
- Daniel A. Dumesic
- Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, 10833 Le Conte Ave, Los Angeles, CA 90095, USA;
| | - David H. Abbott
- Department of Obstetrics and Gynecology, Wisconsin National Primate Research Center, University of Wisconsin, 1223 Capitol Court, Madison, WI 53715, USA;
| | - Gregorio D. Chazenbalk
- Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, 10833 Le Conte Ave, Los Angeles, CA 90095, USA;
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Velazquez-Arcelay K, Colbran LL, McArthur E, Brand C, Rinker D, Siemann J, McMahon D, Capra JA. Archaic Introgression Shaped Human Circadian Traits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.03.527061. [PMID: 36778254 PMCID: PMC9915721 DOI: 10.1101/2023.02.03.527061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Introduction When the ancestors of modern Eurasians migrated out of Africa and interbred with Eurasian archaic hominins, namely Neanderthals and Denisovans, DNA of archaic ancestry integrated into the genomes of anatomically modern humans. This process potentially accelerated adaptation to Eurasian environmental factors, including reduced ultra-violet radiation and increased variation in seasonal dynamics. However, whether these groups differed substantially in circadian biology, and whether archaic introgression adaptively contributed to human chronotypes remains unknown. Results Here we traced the evolution of chronotype based on genomes from archaic hominins and present-day humans. First, we inferred differences in circadian gene sequences, splicing, and regulation between archaic hominins and modern humans. We identified 28 circadian genes containing variants with potential to alter splicing in archaics (e.g., CLOCK, PER2, RORB, RORC), and 16 circadian genes likely divergently regulated between present-day humans and archaic hominins, including RORA. These differences suggest the potential for introgression to modify circadian gene expression. Testing this hypothesis, we found that introgressed variants are enriched among eQTLs for circadian genes. Supporting the functional relevance of these regulatory effects, we found that many introgressed alleles have associations with chronotype. Strikingly, the strongest introgressed effects on chronotype increase morningness, consistent with adaptations to high latitude in other species. Finally, we identified several circadian loci with evidence of adaptive introgression or latitudinal clines in allele frequency. Conclusions These findings identify differences in circadian gene regulation between modern humans and archaic hominins and support the contribution of introgression via coordinated effects on variation in human chronotype.
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Affiliation(s)
| | - Laura L. Colbran
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania
| | | | - Colin Brand
- Department of Epidemiology and Biostatistics, University of California, San Francisco
- Bakar Computational Health Sciences Institute, University of California, San Francisco
| | - David Rinker
- Department of Biological Sciences, Vanderbilt University
| | - Justin Siemann
- Department of Biological Sciences, Vanderbilt University
| | | | - John A. Capra
- Department of Epidemiology and Biostatistics, University of California, San Francisco
- Bakar Computational Health Sciences Institute, University of California, San Francisco
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Hu W, Hao Z, Du P, Di Vincenzo F, Manzi G, Cui J, Fu YX, Pan YH, Li H. Genomic inference of a severe human bottleneck during the Early to Middle Pleistocene transition. Science 2023; 381:979-984. [PMID: 37651513 DOI: 10.1126/science.abq7487] [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: 04/28/2022] [Accepted: 07/11/2023] [Indexed: 09/02/2023]
Abstract
Population size history is essential for studying human evolution. However, ancient population size history during the Pleistocene is notoriously difficult to unravel. In this study, we developed a fast infinitesimal time coalescent process (FitCoal) to circumvent this difficulty and calculated the composite likelihood for present-day human genomic sequences of 3154 individuals. Results showed that human ancestors went through a severe population bottleneck with about 1280 breeding individuals between around 930,000 and 813,000 years ago. The bottleneck lasted for about 117,000 years and brought human ancestors close to extinction. This bottleneck is congruent with a substantial chronological gap in the available African and Eurasian fossil record. Our results provide new insights into our ancestry and suggest a coincident speciation event.
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Affiliation(s)
- Wangjie Hu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Brain Functional Genomics of Ministry of Education, School of Life Science, East China Normal University, Shanghai, China
| | - Ziqian Hao
- College of Artificial Intelligence and Big Data for Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Pengyuan Du
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- College of Artificial Intelligence and Big Data for Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | | | - Giorgio Manzi
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Jialong Cui
- Key Laboratory of Brain Functional Genomics of Ministry of Education, School of Life Science, East China Normal University, Shanghai, China
| | - Yun-Xin Fu
- Department of Biostatistics and Data Science, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
- Key Laboratory for Conservation and Utilization of Bioresources, Yunnan University, Kunming, China
| | - Yi-Hsuan Pan
- Key Laboratory of Brain Functional Genomics of Ministry of Education, School of Life Science, East China Normal University, Shanghai, China
| | - Haipeng Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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37
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Hernández CL. Mitochondrial DNA in Human Diversity and Health: From the Golden Age to the Omics Era. Genes (Basel) 2023; 14:1534. [PMID: 37628587 PMCID: PMC10453943 DOI: 10.3390/genes14081534] [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: 06/19/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Mitochondrial DNA (mtDNA) is a small fraction of our hereditary material. However, this molecule has had an overwhelming presence in scientific research for decades until the arrival of high-throughput studies. Several appealing properties justify the application of mtDNA to understand how human populations are-from a genetic perspective-and how individuals exhibit phenotypes of biomedical importance. Here, I review the basics of mitochondrial studies with a focus on the dawn of the field, analysis methods and the connection between two sides of mitochondrial genetics: anthropological and biomedical. The particularities of mtDNA, with respect to inheritance pattern, evolutionary rate and dependence on the nuclear genome, explain the challenges of associating mtDNA composition and diseases. Finally, I consider the relevance of this single locus in the context of omics research. The present work may serve as a tribute to a tool that has provided important insights into the past and present of humankind.
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Affiliation(s)
- Candela L Hernández
- Department of Biodiversity, Ecology and Evolution, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain
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38
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Reitz C, Pericak-Vance MA, Foroud T, Mayeux R. A global view of the genetic basis of Alzheimer disease. Nat Rev Neurol 2023; 19:261-277. [PMID: 37024647 PMCID: PMC10686263 DOI: 10.1038/s41582-023-00789-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2023] [Indexed: 04/08/2023]
Abstract
The risk of Alzheimer disease (AD) increases with age, family history and informative genetic variants. Sadly, there is still no cure or means of prevention. As in other complex diseases, uncovering genetic causes of AD could identify underlying pathological mechanisms and lead to potential treatments. Rare, autosomal dominant forms of AD occur in middle age as a result of highly penetrant genetic mutations, but the most common form of AD occurs later in life. Large-scale, genome-wide analyses indicate that 70 or more genes or loci contribute to AD. One of the major factors limiting progress is that most genetic data have been obtained from non-Hispanic white individuals in Europe and North America, preventing the development of personalized approaches to AD in individuals of other ethnicities. Fortunately, emerging genetic data from other regions - including Africa, Asia, India and South America - are now providing information on the disease from a broader range of ethnicities. Here, we summarize the current knowledge on AD genetics in populations across the world. We predominantly focus on replicated genetic discoveries but also include studies in ethnic groups where replication might not be feasible. We attempt to identify gaps that need to be addressed to achieve a complete picture of the genetic and molecular factors that drive AD in individuals across the globe.
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Affiliation(s)
- Christiane Reitz
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA
- The Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA
- Department of Neurology, Columbia University, New York, NY, USA
- Department of Epidemiology, Columbia University, New York, NY, USA
| | - Margaret A Pericak-Vance
- The John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- National Centralized Repository for Alzheimer's Disease and Related Dementias, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Richard Mayeux
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA.
- The Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA.
- Department of Neurology, Columbia University, New York, NY, USA.
- Department of Epidemiology, Columbia University, New York, NY, USA.
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Kim BJ, Choi J, Kim SH. On whole-genome demography of world's ethnic groups and individual genomic identity. Sci Rep 2023; 13:6316. [PMID: 37072456 PMCID: PMC10113208 DOI: 10.1038/s41598-023-32325-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 03/25/2023] [Indexed: 05/03/2023] Open
Abstract
All current categorizations of human population, such as ethnicity, ancestry and race, are based on various selections and combinations of complex and dynamic common characteristics, that are mostly societal and cultural in nature, perceived by the members within or from outside of the categorized group. During the last decade, a massive amount of a new type of characteristics, that are exclusively genomic in nature, became available that allows us to analyze the inherited whole-genome demographics of extant human, especially in the fields such as human genetics, health sciences and medical practices (e.g., 1,2,3), where such health-related characteristics can be related to whole-genome-based categorization. Here we show the feasibility of deriving such whole-genome-based categorization. We observe that, within the available genomic data at present, (a) the study populations form about 14 genomic groups, each consisting of multiple ethnic groups; and (b), at an individual level, approximately 99.8%, on average, of the whole autosomal-genome contents are identical between any two individuals regardless of their genomic or ethnic groups.
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Affiliation(s)
- Byung-Ju Kim
- Department of Chemistry and Center for Computational Biology, University of California, Berkeley, CA, 94720, USA
- Human Genome Research Center, Incheon National University, Incheon, 22012, Republic of Korea
- Convergence Research Center for Insect Vectors, Incheon National University, Incheon, 22012, Republic of Korea
| | - JaeJin Choi
- Department of Chemistry and Center for Computational Biology, University of California, Berkeley, CA, 94720, USA
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Sung-Hou Kim
- Department of Chemistry and Center for Computational Biology, University of California, Berkeley, CA, 94720, USA.
- Human Genome Research Center, Incheon National University, Incheon, 22012, Republic of Korea.
- Department of Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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Mairbäurl H, Kilian S, Seide S, Muckenthaler MU, Gassmann M, Benedict RK. The Increase in Hemoglobin Concentration With Altitude Differs Between World Regions and Is Less in Children Than in Adults. Hemasphere 2023; 7:e854. [PMID: 37038466 PMCID: PMC10082317 DOI: 10.1097/hs9.0000000000000854] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 01/28/2023] [Indexed: 04/12/2023] Open
Abstract
To compensate for decreased oxygen partial pressure, high-altitude residents increase hemoglobin concentrations [Hb]. The elevation varies between world regions, posing problems in defining cutoff values for anemia or polycythemia. The currently used altitude adjustments (World Health Organization [WHO]), however, do not account for regional differences. Data from The Demographic and Health Survey (DHS) Program were analyzed from 32 countries harboring >4% of residents at altitudes above 1000 m. [Hb]-increase, (ΔHb/km altitude) was calculated by linear regression analysis. Tables show 95% reference intervals (RIs) for different altitude ranges, world regions, and age groups. The prevalence of anemia and polycythemia was calculated using regressions in comparison to WHO adjustments. The most pronounced Δ[Hb]/km was found in East Africans and South Americans while [Hb] increased least in South/South-East Asia. In African regions and Middle East, [Hb] was decreased in some altitude regions showing inconsistent changes in different age groups. Of note, in all regions, the Δ[Hb]/km was lower in children than in adults, and in the Middle East, it was even negative. Overall, the Δ[Hb]/km from our analysis differed from the region-independent adjustments currently suggested by the WHO resulting in a lower anemia prevalence at very high altitudes. The distinct patterns of Δ[Hb] with altitude in residents from different world regions imply that one single, region-independent correction factor for altitude is not be applicable for diagnosing abnormal [Hb]. Therefore, we provide regression coefficients and reference-tables that are specific for world regions and altitude ranges to improve diagnosing abnormal [Hb].
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Affiliation(s)
- Heimo Mairbäurl
- Translational Pneumology, University Hospital Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research, Heidelberg, Germany
| | - Samuel Kilian
- Institute of Medical Biometry and Informatics (IMBI), University of Heidelberg, Germany
| | - Svenja Seide
- Institute of Medical Biometry and Informatics (IMBI), University of Heidelberg, Germany
| | - Martina U. Muckenthaler
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research, Heidelberg, Germany
- Pediatric Oncology, Hematology & Immunology, University Hospital Heidelberg, Germany
| | - Max Gassmann
- Institute of Veterinary Physiology, Vetsuisse Faculty, and Zurich Center for Integrative Human Physiology (ZIHP), University of Zürich, Switzerland
- Universidad Peruana Cayetano Heredia (UPCH), Lima, Peru
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dos Santos ALC, Sullasi HSL, Gokcumen O, Lindo J, DeGiorgio M. Spatiotemporal fluctuations of population structure in the Americas revealed by a meta-analysis of the first decade of archaeogenomes. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 180:703-714. [PMID: 39081397 PMCID: PMC11288623 DOI: 10.1002/ajpa.24673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/15/2022] [Indexed: 08/02/2024]
Abstract
Objectives Since 2010, genome-wide data from hundreds of ancient Native Americans have contributed to the understanding of Americas' prehistory. However, these samples have never been studied as a single dataset, and distinct relationships among themselves and with present-day populations may have never come to light. Here, we reassess genomic diversity and population structure of 223 ancient Native Americans published between 2010 and 2019. Materials and Methods The genomic data from ancient Americas was merged with a worldwide reference panel of 278 present-day genomes from the Simons Genome Diversity Project and then analyzed through ADMIXTURE, D-statistics, PCA, t-SNE, and UMAP. Results We find largely similar population structures in ancient and present-day Americas. However, the population structure of contemporary Native Americans, traced here to at least 10,000 years before present, is noticeably less diverse than their ancient counterparts, a possible outcome of the European contact. Additionally, in the past there were greater levels of population structure in North than in South America, except for ancient Brazil, which harbors comparatively high degrees of structure. Moreover, we find a component of genetic ancestry in the ancient dataset that is closely related to that of present-day Oceanic populations but does not correspond to the previously reported Australasian signal. Lastly, we report an expansion of the Ancient Beringian ancestry, previously reported for only one sample. Discussion Overall, our findings support a complex scenario for the settlement of the Americas, accommodating the occurrence of founder effects and the emergence of ancestral mixing events at the regional level.
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Affiliation(s)
- Andre Luiz Campelo dos Santos
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida, USA
- Department of Archaeology, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | | | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA
| | - John Lindo
- Department of Anthropology, Emory University, Atlanta, Georgia, USA
| | - Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida, USA
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42
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Watanabe Y, Ohashi J. Modern Japanese ancestry-derived variants reveal the formation process of the current Japanese regional gradations. iScience 2023; 26:106130. [PMID: 36879818 PMCID: PMC9984562 DOI: 10.1016/j.isci.2023.106130] [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: 09/26/2022] [Revised: 12/02/2022] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Modern Japanese people have two major ancestral populations: indigenous Jomon hunter-gatherers and continental East Asian farmers. To determine the formation process of the current Japanese population, we developed a detection method for variants derived from ancestral populations using a summary statistic, the ancestry marker index (AMI). We applied AMI to modern Japanese population samples and identified 208,648 single nucleotide polymorphisms (SNPs) that were likely derived from the Jomon people (Jomon-derived variants). Analysis of Jomon-derived variants in 10,842 modern Japanese individuals recruited from all over Japan revealed that the admixture proportions of the Jomon people varied between prefectures, probably owing to the prehistoric population size difference. The estimated allele frequencies of genome-wide SNPs in the ancestral populations of the modern Japanese suggested their adaptive phenotypic characteristics to their respective livelihoods. Based on our findings, we propose a formation model for the genotypic and phenotypic gradations of the current Japanese archipelago populations.
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Affiliation(s)
- Yusuke Watanabe
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.,Genome Medical Science Project Toyama Project, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
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de Leon J. Reflections on the Lack of Consideration of Ethnic Ancestry to Stratify Clozapine Dosing. Psychiatry Investig 2023; 20:183-195. [PMID: 36850057 PMCID: PMC10064212 DOI: 10.30773/pi.2022.0293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 12/17/2022] [Accepted: 12/26/2022] [Indexed: 03/01/2023] Open
Abstract
This review article argues against trusting standard clozapine references, including the US package insert, because they do not include advances in the sciences of pharmacokinetics and pharmacovigilance and ignore the effects of ethnic ancestry on therapeutic dosing. The minimum therapeutic dose leading to the minimum therapeutic concentration of 350 ng/mL in serum/plasma can be used to compare individuals/groups with treatment-resistant schizophrenia. The US clozapine package insert recommends targeting doses of 300-450 mg/day and, subsequently, increments of up to 100 mg with a maximum dose of 900 mg/day. Ethnic ancestry is defined by DNA ancestry group. Asians (people with ancestry ranging from Pakistan to Japan) and Indigenous Americans are similar in clozapine dosing; their average clozapine minimum therapeutic dose ranged from 166 mg/day (female non-smokers) to 270 mg/day (male smokers). For those with European ancestry, average clozapine minimum therapeutic doses ranged from 236 mg/day (female non-smokers) to 368 mg/day (male smokers). Based on limited studies, Black (African sub-Saharan ancestry) patients may be treated with typical US doses (300-600 mg/day), assuming no poor metabolism (PM) status. Ancestry's impact on clozapine lethality in four countries is discussed (two countries with highly homogenous populations, Denmark and Japan, and two countries with increasingly heterogenous populations due to immigration, Australia and the UK). An international guideline with 104 authors from 50 countries/regions was recently published, providing 6 personalized clozapine titration schedules for adult inpatients (3 ancestry groups and PM/non-PM schedules) and recommending c-reactive protein monitoring at baseline and weekly for 4 weeks.
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Affiliation(s)
- Jose de Leon
- Mental Health Research Center, Eastern State Hospital, Lexington, KY, USA
- Biomedical Research Centre in Mental Health Net (CIBERSAM), Santiago Apostol Hospital, University of the Basque Country, Vitoria, Spain
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Burley JT, Orzechowski SCM, Sin SYW, Edwards SV. Whole-genome phylogeography of the blue-faced honeyeater (Entomyzon cyanotis) and discovery and characterization of a neo-Z chromosome. Mol Ecol 2023; 32:1248-1270. [PMID: 35797346 DOI: 10.1111/mec.16604] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 06/22/2022] [Accepted: 07/04/2022] [Indexed: 11/28/2022]
Abstract
Whole-genome surveys of genetic diversity and geographic variation often yield unexpected discoveries of novel structural variation, which long-read DNA sequencing can help clarify. Here, we report on whole-genome phylogeography of a bird exhibiting classic vicariant geographies across Australia and New Guinea, the blue-faced honeyeater (Entomyzon cyanotis), and the discovery and characterization of a novel neo-Z chromosome by long-read sequencing. Using short-read genome-wide SNPs, we inferred population divergence events within E. cyanotis across the Carpentarian and other biogeographic barriers during the Pleistocene (~0.3-1.7 Ma). Evidence for introgression between nonsister populations supports a hypothesis of reticulate evolution around a triad of dynamic barriers around Pleistocene Lake Carpentaria between Australia and New Guinea. During this phylogeographic survey, we discovered a large (134 Mbp) neo-Z chromosome and we explored its diversity, divergence and introgression landscape. We show that, as in some sylvioid passerine birds, a fusion occurred between chromosome 5 and the Z chromosome to form a neo-Z chromosome; and in E. cyanotis, the ancestral pseudoautosomal region (PAR) appears nonrecombinant between Z and W, along with most of the fused chromosome 5. The added recombination-suppressed portion of the neo-Z (~37.2 Mbp) displays reduced diversity and faster population genetic differentiation compared with the ancestral-Z. Yet, the new PAR (~17.4 Mbp) shows elevated diversity and reduced differentiation compared to autosomes, potentially resulting from introgression. In our case, long-read sequencing helped clarify the genomic landscape of population divergence on autosomes and sex chromosomes in a species where prior knowledge of genome structure was still incomplete.
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Affiliation(s)
- John T Burley
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA.,Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden.,Department of Ecology Evolution and Organismal Biology, Brown University, Providence, Rhode Island, USA.,Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, USA
| | | | - Simon Yung Wa Sin
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA.,School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Scott V Edwards
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA
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Dalal V, Pasupuleti N, Chaubey G, Rai N, Shinde V. Advancements and Challenges in Ancient DNA Research: Bridging the Global North-South Divide. Genes (Basel) 2023; 14:479. [PMID: 36833406 PMCID: PMC9956214 DOI: 10.3390/genes14020479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
Ancient DNA (aDNA) research first began in 1984 and ever since has greatly expanded our understanding of evolution and migration. Today, aDNA analysis is used to solve various puzzles about the origin of mankind, migration patterns, and the spread of infectious diseases. The incredible findings ranging from identifying the new branches within the human family to studying the genomes of extinct flora and fauna have caught the world by surprise in recent times. However, a closer look at these published results points out a clear Global North and Global South divide. Therefore, through this research, we aim to emphasize encouraging better collaborative opportunities and technology transfer to support researchers in the Global South. Further, the present research also focuses on expanding the scope of the ongoing conversation in the field of aDNA by reporting relevant literature published around the world and discussing the advancements and challenges in the field.
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Affiliation(s)
- Vasundhra Dalal
- Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | | | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Niraj Rai
- Ancient DNA Lab, Birbal Sahni Institute of Palaeosciences, Lucknow 226007, Uttar Pradesh, India
| | - Vasant Shinde
- Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
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Lucock MD. The evolution of human skin pigmentation: A changing medley of vitamins, genetic variability, and UV radiation during human expansion. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 180:252-271. [PMID: 36790744 PMCID: PMC10083917 DOI: 10.1002/ajpa.24564] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/19/2022] [Accepted: 05/25/2022] [Indexed: 04/12/2023]
Abstract
This review examines putative, yet likely critical evolutionary pressures contributing to human skin pigmentation and subsequently, depigmentation phenotypes. To achieve this, it provides a synthesis of ideas that frame contemporary thinking, without limiting the narrative to pigmentation genes alone. It examines how geography and hence the quality and quantity of UV exposure, pigmentation genes, diet-related genes, vitamins, anti-oxidant nutrients, and cultural practices intersect and interact to facilitate the evolution of human skin color. The article has a strong focus on the vitamin D-folate evolutionary model, with updates on the latest biophysical research findings to support this paradigm. This model is examined within a broad canvas that takes human expansion out of Africa and genetic architecture into account. A thorough discourse on the biology of melanization is provided (includes relationship to BH4 and DNA damage repair), with the relevance of this to the UV sensitivity of folate and UV photosynthesis of vitamin D explained in detail, including the relevance of these vitamins to reproductive success. It explores whether we might be able to predict vitamin-related gene polymorphisms that pivot metabolism to the prevailing UVR exposome within the vitamin D-folate evolutionary hypothesis context. This is discussed in terms of a primary adaptive phenotype (pigmentation/depigmentation), a secondary adaptive phenotype (flexible metabolic phenotype based on vitamin-related gene polymorphism profile), and a tertiary adaptive strategy (dietary anti-oxidants to support the secondary adaptive phenotype). Finally, alternative evolutionary models for pigmentation are discussed, as are challenges to future research in this area.
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Affiliation(s)
- Mark D. Lucock
- School of Environmental & Life SciencesUniversity of NewcastleOurimbahNew South WalesAustralia
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47
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Nanjala R, Mbiyavanga M, Hashim S, de Villiers S, Mulder N. Assessing HLA imputation accuracy in a West African population. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.23.525129. [PMID: 36747714 PMCID: PMC9900754 DOI: 10.1101/2023.01.23.525129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The Human Leukocyte Antigen (HLA) region plays an important role in autoimmune and infectious diseases. HLA is a highly polymorphic region and thus difficult to impute. We therefore sought to evaluate HLA imputation accuracy, specifically in a West African population, since they are understudied and are known to harbor high genetic diversity. The study sets were selected from Gambian individuals within the Gambian Genome Variation Project (GGVP) Whole Genome Sequence datasets. Two different arrays, Illumina Omni 2.5 and Human Hereditary and Health in Africa (H3Africa), were assessed for the appropriateness of their markers, and these were used to test several imputation panels and tools. The reference panels were chosen from the 1000 Genomes dataset (1kg-All), 1000 Genomes African dataset (1kg-Afr), 1000 Genomes Gambian dataset (1kg-Gwd), H3Africa dataset and the HLA Multi-ethnic dataset. HLA-A, HLA-B and HLA-C alleles were imputed using HIBAG, SNP2HLA, CookHLA and Minimac4, and concordance rate was used as an assessment metric. Overall, the best performing tool was found to be HIBAG, with a concordance rate of 0.84, while the best performing reference panel was the H3Africa panel with a concordance rate of 0.62. Minimac4 (0.75) was shown to increase HLA-B allele imputation accuracy compared to HIBAG (0.71), SNP2HLA (0.51) and CookHLA (0.17). The H3Africa and Illumina Omni 2.5 array performances were comparable, showing that genotyping arrays have less influence on HLA imputation in West African populations. The findings show that using a larger population-specific reference panel and the HIBAG tool improves the accuracy of HLA imputation in West African populations. Author Summary For studies that associate a particular HLA type to a phenotypic trait for instance HIV susceptibility or control, genotype imputation remains the main method for acquiring a larger sample size. Genotype imputation, process of inferring unobserved genotypes, is a statistical technique and thus deals with probabilities. Also, the HLA region is highly variable and therefore difficult to impute. In view of this, it is important to assess HLA imputation accuracy especially in African populations. This is because the African genome has high diversity, and such studies have hardly been conducted in African populations. This work highlights that using HIBAG imputation tool and a larger population-specific reference panel increases HLA imputation accuracy in an African population.
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Affiliation(s)
- Ruth Nanjala
- Department of Biochemistry and Biotechnology, Pwani University, Kenya
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, University of Cape Town, South Africa
| | - Mamana Mbiyavanga
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, University of Cape Town, South Africa
| | - Suhaila Hashim
- Department of Biochemistry and Biotechnology, Pwani University, Kenya
- Pwani University Biosciences Research Centre, Pwani University, Kenya
| | - Santie de Villiers
- Department of Biochemistry and Biotechnology, Pwani University, Kenya
- Pwani University Biosciences Research Centre, Pwani University, Kenya
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, University of Cape Town, South Africa
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De Oliveira TC, Secolin R, Lopes-Cendes I. A review of ancestrality and admixture in Latin America and the caribbean focusing on native American and African descendant populations. Front Genet 2023; 14:1091269. [PMID: 36741309 PMCID: PMC9893294 DOI: 10.3389/fgene.2023.1091269] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/09/2023] [Indexed: 01/21/2023] Open
Abstract
Genomics can reveal essential features about the demographic evolution of a population that may not be apparent from historical elements. In recent years, there has been a significant increase in the number of studies applying genomic epidemiological approaches to understand the genetic structure and diversity of human populations in the context of demographic history and for implementing precision medicine. These efforts have traditionally been applied predominantly to populations of European origin. More recently, initiatives in the United States and Africa are including more diverse populations, establishing new horizons for research in human populations with African and/or Native ancestries. Still, even in the most recent projects, the under-representation of genomic data from Latin America and the Caribbean (LAC) is remarkable. In addition, because the region presents the most recent global miscegenation, genomics data from LAC may add relevant information to understand population admixture better. Admixture in LAC started during the colonial period, in the 15th century, with intense miscegenation between European settlers, mainly from Portugal and Spain, with local indigenous and sub-Saharan Africans brought through the slave trade. Since, there are descendants of formerly enslaved and Native American populations in the LAC territory; they are considered vulnerable populations because of their history and current living conditions. In this context, studying LAC Native American and African descendant populations is important for several reasons. First, studying human populations from different origins makes it possible to understand the diversity of the human genome better. Second, it also has an immediate application to these populations, such as empowering communities with the knowledge of their ancestral origins. Furthermore, because knowledge of the population genomic structure is an essential requirement for implementing genomic medicine and precision health practices, population genomics studies may ensure that these communities have access to genomic information for risk assessment, prevention, and the delivery of optimized treatment; thus, helping to reduce inequalities in the Western Hemisphere. Hoping to set the stage for future studies, we review different aspects related to genetic and genomic research in vulnerable populations from LAC countries.
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Affiliation(s)
- Thais C. De Oliveira
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
- The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Rodrigo Secolin
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
- The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Iscia Lopes-Cendes
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
- The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
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Nyland J, Pyle B, Krupp R, Kittle G, Richards J, Brey J. ACL microtrauma: healing through nutrition, modified sports training, and increased recovery time. J Exp Orthop 2022; 9:121. [PMID: 36515744 PMCID: PMC9751252 DOI: 10.1186/s40634-022-00561-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022] Open
Abstract
PURPOSE Sports injuries among youth and adolescent athletes are a growing concern, particularly at the knee. Based on our current understanding of microtrauma and anterior cruciate ligament (ACL) healing characteristics, this clinical commentary describes a comprehensive plan to better manage ACL microtrauma and mitigate the likelihood of progression to a non-contact macrotraumatic ACL rupture. METHODS Medical literature related to non-contact ACL injuries among youth and adolescent athletes, collagen and ACL extracellular matrix metabolism, ACL microtrauma and sudden failure, and concerns related to current sports training were reviewed and synthesized into a comprehensive intervention plan. RESULTS With consideration for biopsychosocial model health factors, proper nutrition and modified sports training with increased recovery time, a comprehensive primary ACL injury prevention plan is described for the purpose of better managing ACL microtrauma, thereby reducing the incidence of non-contact macrotraumatic ACL rupture among youth and adolescent athletes. CONCLUSION Preventing non-contact ACL injuries may require greater consideration for reducing accumulated ACL microtrauma. Proper nutrition including glycine-rich collagen peptides, or gelatin-vitamin C supplementation in combination with healthy sleep, and adjusted sports training periodization with increased recovery time may improve ACL extracellular matrix collagen deposition homeostasis, decreasing sudden non-contact ACL rupture incidence likelihood in youth and adolescent athletes. Successful implementation will require compliance from athletes, parents, coaches, the sports medicine healthcare team, and event organizers. Studies are needed to confirm the efficacy of these concepts. LEVEL OF EVIDENCE V.
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Affiliation(s)
- J Nyland
- Norton Orthopedic Institute, 9880 Angies Way, Louisville, KY, 40241, USA.
- MSAT Program, Spalding University, 901 South Third St, Louisville, KY, USA.
- Department of Orthopaedic Surgery, University of Louisville, Louisville, KY, USA.
| | - B Pyle
- MSAT Program, Spalding University, 901 South Third St, Louisville, KY, USA
| | - R Krupp
- Norton Orthopedic Institute, 9880 Angies Way, Louisville, KY, 40241, USA
- Department of Orthopaedic Surgery, University of Louisville, Louisville, KY, USA
| | - G Kittle
- MSAT Program, Spalding University, 901 South Third St, Louisville, KY, USA
| | - J Richards
- Department of Orthopaedic Surgery, University of Louisville, Louisville, KY, USA
| | - J Brey
- Norton Orthopedic Institute, 9880 Angies Way, Louisville, KY, 40241, USA
- Department of Orthopaedic Surgery, University of Louisville, Louisville, KY, USA
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Forni D, Cagliani R, Clerici M, Sironi M. Disease-causing human viruses: novelty and legacy. Trends Microbiol 2022; 30:1232-1242. [PMID: 35902319 DOI: 10.1016/j.tim.2022.07.002] [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: 01/26/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 01/13/2023]
Abstract
About 270 viruses are known to infect humans. Some of these viruses have been known for centuries, whereas others have recently emerged. During their evolutionary history, humans have moved out of Africa to populate the world. In historical times, human migrations resulted in the displacement of large numbers of people. All these events determined the movement and dispersal of human-infecting viruses. Technological advances have resulted in the characterization of the genetic variability of human viruses, both in extant and in archaeological samples. Field studies investigated the diversity of viruses hosted by other animals. In turn, these advances provided insight into the evolutionary history of human viruses back in time and defined the key events through which they originated and spread.
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Affiliation(s)
- Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy; Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy.
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