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Berlioz E, Fernández-García M, Soulier MC, Agudo-Pérez L, Amorós G, Normand C, Marín-Arroyo AB. Aurignacian groups at Isturitz (France) adapted to a shifting environment upon their arrival in Western Europe ∼42,000 years ago. J Hum Evol 2025; 202:103665. [PMID: 40187118 DOI: 10.1016/j.jhevol.2025.103665] [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: 07/22/2024] [Revised: 02/07/2025] [Accepted: 02/17/2025] [Indexed: 04/07/2025]
Abstract
The Marine Isotope Stage 3 is a context of considerable climatic instability. Establishing the link between global climate changes and their impact on the local ecological contexts and prey exploited by human populations is challenging. Still, it is necessary to understand better the local conditions where humans lived to unravel how they adapted to fluctuating environmental conditions. Here, we address this question by studying 250 osteodental elements from animals hunted and consumed by human groups at Isturitz, a rich and well-documented French archaeological site and one of the earliest in Western Europe where the Aurignacian technoculture has been attested. To do so, we set up a multiproxy approach (archaeozoology, three-dimensional dental microwear texture analyses, and stable isotopic analyses of δ18O and δ13C in enamel bioapatite and δ13C, δ15N, and δ34S in bone collagen) that informs us on a timeline from the first years to the last few days of an animal's life. We reconstructed their ecologies and paleoenvironments during the different Aurignacian phases at Isturitz. Our findings indicate that the first human occupations at Isturitz occurred under cold and arid conditions, rapidly becoming even cooler and drier. Limited changes are observed in the human-environment-prey relationship despite this unstable climatic context where significant changes in rainfall, temperature, and a gradual opening of environments and some changes in the faunal assemblage occurred. Our findings suggest that human groups hunted in similar territories and utilized comparable strategies throughout the temporal sequence. Our multiproxy approach, combining complementary analyses, provides a better understanding of the adaptation strategies when the first phases of the Upper Paleolithic were emerging in Western Europe.
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Affiliation(s)
- E Berlioz
- Research Group I+D+i EvoAdapta (Evolución Humana y Adaptaciones durante La Prehistoria), Department of Historical Sciences, University of Cantabria, Santander, 39005, Spain
| | - M Fernández-García
- Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, Valencia, 46010, Spain; IPHES-CERCA (Institut Català de Paleoecologia Humana i Evolució Social), Tarragona, 43007, Spain
| | - M-C Soulier
- Laboratoire TRACES, UMR 5608, CNRS, Université de Toulouse-Jean Jaurès, F-31058, Toulouse Cedex 9, France
| | - L Agudo-Pérez
- Research Group I+D+i EvoAdapta (Evolución Humana y Adaptaciones durante La Prehistoria), Department of Historical Sciences, University of Cantabria, Santander, 39005, Spain
| | - G Amorós
- Research Group ECCE HOMO (Evolución, Cenozoico, Cuaternario, Ecología HOMO), Department of Plant Biology, Faculty of Biology, University of Murcia, Murcia, 30003, Spain
| | - C Normand
- Laboratoire TRACES, UMR 5608, CNRS, Université de Toulouse-Jean Jaurès, F-31058, Toulouse Cedex 9, France
| | - A B Marín-Arroyo
- Research Group I+D+i EvoAdapta (Evolución Humana y Adaptaciones durante La Prehistoria), Department of Historical Sciences, University of Cantabria, Santander, 39005, Spain.
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2
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Patin E, Quintana-Murci L. Tracing the Evolution of Human Immunity Through Ancient DNA. Annu Rev Immunol 2025; 43:57-82. [PMID: 39705165 DOI: 10.1146/annurev-immunol-082323-024638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2024]
Abstract
Infections have imposed strong selection pressures throughout human evolution, making the study of natural selection's effects on immunity genes highly complementary to disease-focused research. This review discusses how ancient DNA studies, which have revolutionized evolutionary genetics, increase our understanding of the evolution of human immunity. These studies have shown that interbreeding between modern humans and Neanderthals or Denisovans has influenced present-day immune responses, particularly to viruses. Additionally, ancient genomics enables the tracking of how human immunity has evolved across cultural transitions, highlighting strong selection since the Bronze Age in Europe (<4,500 years) and potential genetic adaptations to epidemics raging during the Middle Ages and the European colonization of the Americas. Furthermore, ancient genomic studies suggest that the genetic risk for noninfectious immune disorders has gradually increased over millennia because alleles associated with increased risk for autoimmunity and inflammation once conferred resistance to infections. The challenge now is to extend these findings to diverse, non-European populations and to provide a more global understanding of the evolution of human immunity.
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Affiliation(s)
- Etienne Patin
- Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Human Evolutionary Genetics Unit, Paris, France;
| | - Lluis Quintana-Murci
- Human Genomics and Evolution, Collège de France, Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Human Evolutionary Genetics Unit, Paris, France;
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3
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Degioanni A, Cabut S, Condemi S, Smith RS. Climate change in Europe between 90 and 50 kyr BP and Neanderthal territorial habitability. PLoS One 2025; 20:e0308690. [PMID: 40009574 PMCID: PMC11864554 DOI: 10.1371/journal.pone.0308690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Accepted: 01/17/2025] [Indexed: 02/28/2025] Open
Abstract
After having lived as the dominant human species in Europe for over 200 kyr, Homo neanderthalensis (the Neanderthals) disappeared around 40 kyr BP (Before Present) Higham T (2014). Competition with Homo sapiens, who arrived in Europe around the same time, is often invoked to explain this extinction. Others have argued that climate change may have reduced the living space of this population making its disappearance more rapid. In order to test the climate change hypothesis we modelled the Neanderthals' ecological niches in Europe between 90 and 50 kyr BP through paleoenvironmental reconstructions and Eco-Cultural Niche Modelling. We selected five environmental variables (orographic height, mean annual precipitation, mean temperature of the coldest month, carrying capacity and friction, see below) from climate model simulations of 5 periods between 90 and 50 kyr BP in Europe. We used Structural Similarity (SSIM) index to compare the probability maps of suitable niches to Neanderthals performed by Maxent. After a strong initial environmental change between the first (P1 = 90 to 83 kyr BP) and second (P2 = 83 to 69 kyr BP) periods, our results show that large areas highly suitable for Neanderthal occupation persisted across Europe. As our results show an increase/stability of the areas suitable to Neanderthals, the question of the cause of the decrease or displacement of the Neanderthal population towards southern Europe after this climatic change remains open.
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Affiliation(s)
- Anna Degioanni
- Aix-Marseille Universite, CNRS, Minist, Culture, LAMPEA, Aix-en-Provence, France
| | - Sandrine Cabut
- Aix-Marseille Universite, CNRS, Minist, Culture, LAMPEA, Aix-en-Provence, France
| | - Silvana Condemi
- Aix-Marseille Universite, EFS, CNRS, ADES, Marseille, France
| | - Robin S. Smith
- Department of Meteorology, NCAS, University of Reading, Reading, United Kingdom
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4
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Khouri-Farah N, Winchester EW, Schilder BM, Robinson K, Curtis SW, Skene NG, Leslie-Clarkson EJ, Cotney J. Gene expression patterns of the developing human face at single cell resolution reveal cell type contributions to normal facial variation and disease risk. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.18.633396. [PMID: 39868299 PMCID: PMC11761091 DOI: 10.1101/2025.01.18.633396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
Abstract
Craniofacial development gives rise to the complex structures of the face and involves the interplay of diverse cell types. Despite its importance, our understanding of human-specific craniofacial developmental mechanisms and their genetic underpinnings remains limited. Here, we present a comprehensive single-nucleus RNA sequencing (snRNA-seq) atlas of human craniofacial development from craniofacial tissues of 24 embryos that span six key time points during the embryonic period (4-8 post-conception weeks). This resource resolves the transcriptional dynamics of seven major cell types and uncovers distinct major cell types, including muscle progenitors and cranial neural crest cells (CNCCs), as well as dozens of subtypes of ectoderm and mesenchyme. Comparative analyses reveal substantial conservation of major cell types, alongside human biased differences in gene expression programs. CNCCs, which play a crucial role in craniofacial morphogenesis, exhibit the lowest marker gene conservation, underscoring their evolutionary plasticity. Spatial transcriptomics further localizes cell populations, providing a detailed view of their developmental roles and anatomical context. We also link these developmental processes to genetic variation, identifying cell type-specific enrichments for common variants associated with facial morphology and rare variants linked to orofacial clefts. Intriguingly, Neanderthal-introgressed sequences are enriched near genes with biased expression in cartilage and specialized ectodermal subtypes, suggesting their contribution to modern human craniofacial features. This atlas offers unprecedented insights into the cellular and genetic mechanisms shaping the human face, highlighting conserved and distinctly human aspects of craniofacial biology. Our findings illuminate the developmental origins of craniofacial disorders, the genetic basis of facial variation, and the evolutionary legacy of ancient hominins. This work provides a foundational resource for exploring craniofacial biology, with implications for developmental genetics, evolutionary biology, and clinical research into congenital anomalies.
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Affiliation(s)
| | | | - Brian M Schilder
- Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, W12 0BZ, UK
- UK Dementia Research Institute at Imperial College London, London, W12 0BZ, UK
| | - Kelsey Robinson
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sarah W Curtis
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nathan G Skene
- Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, W12 0BZ, UK
- UK Dementia Research Institute at Imperial College London, London, W12 0BZ, UK
| | | | - Justin Cotney
- Department of Surgery, Children's Hospital of Philadelphia, Philadelphia, PA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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Sümer AP, Rougier H, Villalba-Mouco V, Huang Y, Iasi LNM, Essel E, Bossoms Mesa A, Furtwaengler A, Peyrégne S, de Filippo C, Rohrlach AB, Pierini F, Mafessoni F, Fewlass H, Zavala EI, Mylopotamitaki D, Bianco RA, Schmidt A, Zorn J, Nickel B, Patova A, Posth C, Smith GM, Ruebens K, Sinet-Mathiot V, Stoessel A, Dietl H, Orschiedt J, Kelso J, Zeberg H, Bos KI, Welker F, Weiss M, McPherron SP, Schüler T, Hublin JJ, Velemínský P, Brůžek J, Peter BM, Meyer M, Meller H, Ringbauer H, Hajdinjak M, Prüfer K, Krause J. Earliest modern human genomes constrain timing of Neanderthal admixture. Nature 2025; 638:711-717. [PMID: 39667410 PMCID: PMC11839475 DOI: 10.1038/s41586-024-08420-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Accepted: 11/18/2024] [Indexed: 12/14/2024]
Abstract
Modern humans arrived in Europe more than 45,000 years ago, overlapping at least 5,000 years with Neanderthals1-4. Limited genomic data from these early modern humans have shown that at least two genetically distinct groups inhabited Europe, represented by Zlatý kůň, Czechia3 and Bacho Kiro, Bulgaria2. Here we deepen our understanding of early modern humans by analysing one high-coverage genome and five low-coverage genomes from approximately 45,000-year-old remains from Ilsenhöhle in Ranis, Germany4, and a further high-coverage genome from Zlatý kůň. We show that distant familial relationships link the Ranis and Zlatý kůň individuals and that they were part of the same small, isolated population that represents the deepest known split from the Out-of-Africa lineage. Ranis genomes harbour Neanderthal segments that originate from a single admixture event shared with all non-Africans that we date to approximately 45,000-49,000 years ago. This implies that ancestors of all non-Africans sequenced so far resided in a common population at this time, and further suggests that modern human remains older than 50,000 years from outside Africa represent different non-African populations.
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Affiliation(s)
- Arev P Sümer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Hélène Rougier
- California State University Northridge, Northridge, CA, USA
| | - Vanessa Villalba-Mouco
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Yilei Huang
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Institute of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Leonardo N M Iasi
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Elena Essel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alba Bossoms Mesa
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anja Furtwaengler
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Stéphane Peyrégne
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cesare de Filippo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Adam B Rohrlach
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Federica Pierini
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Helen Fewlass
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Francis Crick Institute, London, UK
- University of Bristol, Bristol, UK
| | - Elena I Zavala
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- University of California, Berkeley, CA, USA
| | - Dorothea Mylopotamitaki
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Chaire de Paléoanthropologie, CIRB, Collège de France, Paris, France
| | - Raffaela A Bianco
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anna Schmidt
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Julia Zorn
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Birgit Nickel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anna Patova
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Geoff M Smith
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Archaeology, University of Reading, Reading, UK
| | - Karen Ruebens
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Chaire de Paléoanthropologie, CIRB, Collège de France, Paris, France
- Department of Archaeology, University of Reading, Reading, UK
| | - Virginie Sinet-Mathiot
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- University of Bordeaux, CNRS, Ministère de la Culture, PACEA, Pessac, France
- University of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248 and Bordeaux Proteome Platform, Bordeaux, France
| | - Alexander Stoessel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Friedrich Schiller University Jena, Institute of Zoology and Evolutionary Research, Jena, Germany
| | - Holger Dietl
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt-Landesmuseum für Vorgeschichte, Halle, Germany
| | - Jörg Orschiedt
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt-Landesmuseum für Vorgeschichte, Halle, Germany
- Prähistorische Archäologie, Freie Universität, Berlin, Germany
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Hugo Zeberg
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Karolinska Institutet, Stockholm, Sweden
| | - Kirsten I Bos
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Frido Welker
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Marcel Weiss
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Institut für Ur- und Frühgeschichte, Erlangen, Germany
| | | | - Tim Schüler
- Thuringian State Office for the Preservation of Historical Monuments and Archaeology, Weimar, Germany
| | - Jean-Jacques Hublin
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Chaire de Paléoanthropologie, CIRB, Collège de France, Paris, France
| | | | | | - Benjamin M Peter
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- University of Rochester, Rochester, NY, USA
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Harald Meller
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt-Landesmuseum für Vorgeschichte, Halle, Germany
| | - Harald Ringbauer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mateja Hajdinjak
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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6
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Tournebize R, Chikhi L. Ignoring population structure in hominin evolutionary models can lead to the inference of spurious admixture events. Nat Ecol Evol 2025; 9:225-236. [PMID: 39672950 DOI: 10.1038/s41559-024-02591-6] [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: 04/25/2023] [Accepted: 10/29/2024] [Indexed: 12/15/2024]
Abstract
Genomic and ancient DNA data have revolutionized palaeoanthropology and our vision of human evolution, with indisputable landmarks like the sequencing of Neanderthal and Denisovan genomes. Yet, using genetic data to identify, date and quantify evolutionary events-such as ancient bottlenecks or admixture-is not straightforward, as inferences may depend on model assumptions. In the last two decades, the idea that Neanderthals and members of the Homo sapiens lineage interbred has gained momentum. From the status of unlikely theory, it has reached consensus among human evolutionary biologists. This theory is mainly supported by statistical approaches that depend on demographic models minimizing or ignoring population structure, despite its widespread occurrence and the fact that, when ignored, population structure can lead to the inference of spurious demographic events. We simulated genomic data under a structured and admixture-free model of human evolution, and found that all the tested admixture approaches identified long Neanderthal fragments in our simulated genomes and an admixture event that never took place. We also observed that several published admixture models failed to predict important empirical diversity or admixture statistics, and that we could identify several scenarios from our structured model that better predicted these statistics jointly. Using a simulated time series of ancient DNA, the structured scenarios could also predict the trajectory of the empirical D statistics. Our results suggest that models accounting for population structure are fundamental to improve our understanding of human evolution, and that admixture between Neanderthals and H. sapiens needs to be re-evaluated in the light of structured models. Beyond the Neanderthal case, we argue that ancient hybridization events, which are increasingly documented in many species, including with other hominins, may also benefit from such re-evaluation.
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Affiliation(s)
- Rémi Tournebize
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France.
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE) UMR 5300, Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 Paul Sabatier (UT3), Toulouse, France.
| | - Lounès Chikhi
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE) UMR 5300, Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 Paul Sabatier (UT3), Toulouse, France.
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal.
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7
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Malomane D, Williams MP, Huber C, Mangul S, Abedalthagafi M, Chiang CWK. Patterns of population structure and genetic variation within the Saudi Arabian population. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.10.632500. [PMID: 39868174 PMCID: PMC11761371 DOI: 10.1101/2025.01.10.632500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
Abstract
The Arabian Peninsula is considered the initial site of historic human migration out of Africa. The modern-day indigenous Arabians are believed to be the descendants who remained from the ancient split of the migrants into Eurasia. Here, we investigated how the population history and cultural practices such as endogamy have shaped the genetic variation of the Saudi Arabians. We genotyped 3,352 individuals and identified twelve genetic sub-clusters that corresponded to the geographical distribution of different tribal regions, differentiated by distinct components of ancestry based on comparisons to modern and ancient DNA references. These sub-clusters also showed variation across ranges of the genome covered in runs of homozygosity, as well as differences in population size changes over time. Using 25,488,981 variants found in whole genome sequencing data (WGS) from 302 individuals, we found that the Saudi tend to show proportionally more deleterious alleles than neutral alleles when compared to Africans/African Americans from gnomAD (e.g. a 13% increase of deleterious alleles annotated by AlphaMissense between 0.5 - 5% frequency in Saudi, compared to 7% decrease of the benign alleles; P < 0.001). Saudi sub-clusters with greater inbreeding and lower effective population sizes showed greater enrichment of deleterious alleles as well. Additionally, we found that approximately 10% of the variants discovered in our WGS data are not observed in gnomAD; these variants are also enriched with deleterious annotations. To accelerate studying the population-enriched deleterious alleles and their health consequences in this population, we made available the allele frequency estimates of 25,488,981 variants discovered in our samples. Taken together, our results suggest that Saudi's population history impacts its pattern of genetic variation with potential consequences to the population health. It further highlights the need to sequence diverse and unique populations so to provide a foundation on which to interpret medical- and pharmaco- genomic findings from these populations.
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Affiliation(s)
- D.K. Malomane
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - M. P. Williams
- Department of Biology, Pennsylvania State University, University Park, PA
| | - C.D. Huber
- Department of Biology, Pennsylvania State University, University Park, PA
| | - S. Mangul
- Titus Department of Clinical Pharmacy, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA
| | - M. Abedalthagafi
- Department of Pathology and Laboratory Medicine, Emory University Hospital, Atlanta, GA
- Genomics Research Department, King Fahad Medical City, Riyadh, Saudi Arabia
| | - C. W. K. Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA
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8
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Speidel L, Silva M, Booth T, Raffield B, Anastasiadou K, Barrington C, Götherström A, Heather P, Skoglund P. High-resolution genomic history of early medieval Europe. Nature 2025; 637:118-126. [PMID: 39743601 PMCID: PMC11693606 DOI: 10.1038/s41586-024-08275-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 10/23/2024] [Indexed: 01/04/2025]
Abstract
Many known and unknown historical events have remained below detection thresholds of genetic studies because subtle ancestry changes are challenging to reconstruct. Methods based on shared haplotypes1,2 and rare variants3,4 improve power but are not explicitly temporal and have not been possible to adopt in unbiased ancestry models. Here we develop Twigstats, an approach of time-stratified ancestry analysis that can improve statistical power by an order of magnitude by focusing on coalescences in recent times, while remaining unbiased by population-specific drift. We apply this framework to 1,556 available ancient whole genomes from Europe in the historical period. We are able to model individual-level ancestry using preceding genomes to provide high resolution. During the first half of the first millennium CE, we observe at least two different streams of Scandinavian-related ancestry expanding across western, central and eastern Europe. By contrast, during the second half of the first millennium CE, ancestry patterns suggest the regional disappearance or substantial admixture of these ancestries. In Scandinavia, we document a major ancestry influx by approximately 800 CE, when a large proportion of Viking Age individuals carried ancestry from groups related to central Europe not seen in individuals from the early Iron Age. Our findings suggest that time-stratified ancestry analysis can provide a higher-resolution lens for genetic history.
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Affiliation(s)
- Leo Speidel
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK.
- Genetics Institute, University College London, London, UK.
- iTHEMS, RIKEN, Wako, Japan.
| | - Marina Silva
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK
| | - Thomas Booth
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK
| | - Ben Raffield
- Department of Archaeology and Ancient History, Uppsala University, Uppsala, Sweden
| | | | | | - Anders Götherström
- Centre for Palaeogenetics, Stockholm University, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Peter Heather
- Department of History, King's College London, London, UK
| | - Pontus Skoglund
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK.
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9
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Iasi LNM, Chintalapati M, Skov L, Mesa AB, Hajdinjak M, Peter BM, Moorjani P. Neanderthal ancestry through time: Insights from genomes of ancient and present-day humans. Science 2024; 386:eadq3010. [PMID: 39666853 DOI: 10.1126/science.adq3010] [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: 05/08/2024] [Accepted: 10/22/2024] [Indexed: 12/14/2024]
Abstract
Gene flow from Neanderthals has shaped genetic and phenotypic variation in modern humans. We generated a catalog of Neanderthal ancestry segments in more than 300 genomes spanning the past 50,000 years. We examined how Neanderthal ancestry is shared among individuals over time. Our analysis revealed that the vast majority of Neanderthal gene flow is attributable to a single, shared extended period of gene flow that occurred between 50,500 to 43,500 years ago, as evidenced by ancestry correlation, colocalization of Neanderthal segments across individuals, and divergence from the sequenced Neanderthals. Most natural selection-positive and negative-on Neanderthal variants occurred rapidly after the gene flow. Our findings provide new insights into how contact with Neanderthals shaped modern human origins and adaptation.
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Affiliation(s)
- Leonardo N M Iasi
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Manjusha Chintalapati
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Laurits Skov
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Alba Bossoms Mesa
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mateja Hajdinjak
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
- The Francis Crick Institute, London, UK
| | - Benjamin M Peter
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Biology, University of Rochester, Rochester NY, USA
| | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Center for Computational Biology, University of California Berkeley, Berkeley, CA, USA
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10
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Shimada MK, Nishida T. Haplotype-Based Approach Represents Locus Specificity in the Genomic Diversification Process in Humans ( Homo sapiens). Genes (Basel) 2024; 15:1554. [PMID: 39766821 PMCID: PMC11675571 DOI: 10.3390/genes15121554] [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: 11/05/2024] [Revised: 11/23/2024] [Accepted: 11/25/2024] [Indexed: 01/11/2025] Open
Abstract
BACKGROUND/OBJECTIVES Recent progress in evolutionary genomics on human (Homo sapiens) populations has revealed complex demographic events and genomic changes. These include population expansion with complicated migration, substantial population structure, and ancient introgression from other hominins, as well as human characteristics selections. Nevertheless, the genomic regions in which such evolutionary events took place have remained unclear. METHODS Here, we focused on eight loci containing the haplotypes that were previously presented as atypical for the mutation pattern in sequence and/or geographic distribution pattern with the model of recent African origin, which constitute two major clusters: African only, and global. This was the consensus model before information regarding introgression from Neanderthal (Homo neanderthalensis) was available. We compared diversity in identical datasets of the modern human population genome, with the 1000 Genomes project among them. RESULTS/CONCLUSIONS This study identified representative genomic regions that show traces of various demographic events and genomic changes that modern humans have undergone by categorizing the relationships in sequence similarity and in worldwide geographic distribution among haplotypes.
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Affiliation(s)
- Makoto K. Shimada
- Center for Medical Science, Fujita Health University, Toyoake 470-1192, Aichi, Japan
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11
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Koppetsch T, Malinsky M, Matschiner M. Towards Reliable Detection of Introgression in the Presence of Among-Species Rate Variation. Syst Biol 2024; 73:769-788. [PMID: 38912803 PMCID: PMC11639170 DOI: 10.1093/sysbio/syae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 05/23/2024] [Accepted: 06/19/2024] [Indexed: 06/25/2024] Open
Abstract
The role of interspecific hybridization has recently seen increasing attention, especially in the context of diversification dynamics. Genomic research has now made it abundantly clear that both hybridization and introgression-the exchange of genetic material through hybridization and backcrossing-are far more common than previously thought. Besides cases of ongoing or recent genetic exchange between taxa, an increasing number of studies report "ancient introgression"- referring to results of hybridization that took place in the distant past. However, it is not clear whether commonly used methods for the detection of introgression are applicable to such old systems, given that most of these methods were originally developed for analyses at the level of populations and recently diverged species, affected by recent or ongoing genetic exchange. In particular, the assumption of constant evolutionary rates, which is implicit in many commonly used approaches, is more likely to be violated as evolutionary divergence increases. To test the limitations of introgression detection methods when being applied to old systems, we simulated thousands of genomic datasets under a wide range of settings, with varying degrees of among-species rate variation and introgression. Using these simulated datasets, we showed that some commonly applied statistical methods, including the D-statistic and certain tests based on sets of local phylogenetic trees, can produce false-positive signals of introgression between divergent taxa that have different rates of evolution. These misleading signals are caused by the presence of homoplasies occurring at different rates in different lineages. To distinguish between the patterns caused by rate variation and genuine introgression, we developed a new test that is based on the expected clustering of introgressed sites along the genome and implemented this test in the program Dsuite.
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Affiliation(s)
- Thore Koppetsch
- Natural History Museum, University of Oslo, 0318 Oslo, Norway
| | - Milan Malinsky
- Institute of Ecology and Evolution, Department of Biology, University of Bern, 3012 Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
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12
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Higgins OA, Modi A, Cannariato C, Diroma MA, Lugli F, Ricci S, Zaro V, Vai S, Vazzana A, Romandini M, Yu H, Boschin F, Magnone L, Rossini M, Di Domenico G, Baruffaldi F, Oxilia G, Bortolini E, Dellù E, Moroni A, Ronchitelli A, Talamo S, Müller W, Calattini M, Nava A, Posth C, Lari M, Bondioli L, Benazzi S, Caramelli D. Life history and ancestry of the late Upper Palaeolithic infant from Grotta delle Mura, Italy. Nat Commun 2024; 15:8248. [PMID: 39304646 PMCID: PMC11415373 DOI: 10.1038/s41467-024-51150-x] [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: 07/14/2023] [Accepted: 07/30/2024] [Indexed: 09/22/2024] Open
Abstract
The biological aspects of infancy within late Upper Palaeolithic populations and the role of southern refugia at the end of the Last Glacial Maximum are not yet fully understood. This study presents a multidisciplinary, high temporal resolution investigation of an Upper Palaeolithic infant from Grotta delle Mura (Apulia, southern Italy) combining palaeogenomics, dental palaeohistology, spatially-resolved geochemical analyses, direct radiocarbon dating, and traditional anthropological studies. The skeletal remains of the infant - Le Mura 1 - were directly dated to 17,320-16,910 cal BP. The results portray a biological history of the infant's development, early life, health and death (estimated at ~72 weeks). They identify, several phenotypic traits and a potential congenital disease in the infant, the mother's low mobility during gestation, and a high level of endogamy. Furthermore, the genomic data indicates an early spread of the Villabruna-like components along the Italian peninsula, confirming a population turnover around the time of the Last Glacial Maximum, and highlighting a general reduction in genetic variability from northern to southern Italy. Overall, Le Mura 1 contributes to our better understanding of the early stages of life and the genetic puzzle in the Italian peninsula at the end of the Last Glacial Maximum.
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Affiliation(s)
- Owen Alexander Higgins
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy.
- Department of Odontostomatological and Maxillofacial Sciences, Sapienza University of Rome, Rome, Italy.
| | - Alessandra Modi
- Department of Biology, University of Florence, Florence, Italy.
| | | | | | - Federico Lugli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Stefano Ricci
- Department of Physical Sciences, Earth and Environment - RU of Prehistory and Anthropology, University of Siena, Siena, Italy
| | - Valentina Zaro
- Department of Biology, University of Florence, Florence, Italy
| | - Stefania Vai
- Department of Biology, University of Florence, Florence, Italy
| | - Antonino Vazzana
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Matteo Romandini
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - He Yu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Francesco Boschin
- Department of Physical Sciences, Earth and Environment - RU of Prehistory and Anthropology, University of Siena, Siena, Italy
| | - Luigi Magnone
- Department of Physical Sciences, Earth and Environment - RU of Prehistory and Anthropology, University of Siena, Siena, Italy
| | - Matteo Rossini
- Department of Physical Sciences, Earth and Environment - RU of Prehistory and Anthropology, University of Siena, Siena, Italy
| | | | - Fabio Baruffaldi
- Laboratory of Medical Technology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Gregorio Oxilia
- Department of Translational Medicine and for Romagna, University of Ferrara, Ferrara, Italy
| | - Eugenio Bortolini
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Elena Dellù
- Institute Villa Adriana e Villa d'Este, Superintendence of Archeology, Fine Arts and Landscape for the metropolitan city of Bari - Ministry of Culture, Bari, Italy
| | - Adriana Moroni
- Department of Physical Sciences, Earth and Environment - RU of Prehistory and Anthropology, University of Siena, Siena, Italy
| | - Annamaria Ronchitelli
- Department of Physical Sciences, Earth and Environment - RU of Prehistory and Anthropology, University of Siena, Siena, Italy
| | - Sahra Talamo
- Department of Chemistry G. Ciamician, University of Bologna, Bologna, Italy
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Wolfgang Müller
- Institut für Geowissenschaften, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
- Frankfurt Isotope and Element Research Center (FIERCE), Goethe University Frankfurt, Frankfurt, Frankfurt am Main, Germany
| | - Mauro Calattini
- Department of History and Cultural Heritage, University of Siena, Siena, Italy
| | - Alessia Nava
- Department of Odontostomatological and Maxillofacial Sciences, Sapienza University of Rome, Rome, Italy
| | - Cosimo Posth
- Archaeo- and Palaeogenetics, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen, Tübingen, Germany
| | - Martina Lari
- Department of Biology, University of Florence, Florence, Italy
| | - Luca Bondioli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
- Department of Cultural Heritage, University of Padua, Padova, Italy
| | - Stefano Benazzi
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - David Caramelli
- Department of Biology, University of Florence, Florence, Italy
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13
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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] [Grants] [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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14
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Conde-Valverde M, Martínez I, Quam R, Arsuaga JL. The ear of the Sima de los Huesos hominins (Atapuerca, Spain). Anat Rec (Hoboken) 2024; 307:2410-2424. [PMID: 36825485 DOI: 10.1002/ar.25181] [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: 12/21/2022] [Revised: 02/08/2023] [Accepted: 02/08/2023] [Indexed: 02/25/2023]
Abstract
Previous studies on the morphology of the inner ear (semicircular canals and cochlea) in the Sima de los Huesos hominin sample have provided important results on the evolution of these structures in the Neandertal lineage. Similarly, studies of the anatomy of the external and middle ear cavities of the Sima de los Huesos hominins have also provided important data on the auditory capacities of this European Middle Pleistocene population. The present contribution provides unpublished data on three new middle ear variables from the Sima de los Huesos fossils and compares these data with values from samples of Pan troglodytes, Homo neanderthalensis and Homo sapiens. The results of this analysis are combined with those obtained in previous studies to characterize the anatomy of the outer, middle and inner ear in the Sima de los Huesos fossils, as well as to establish the order of appearance of the features that characterize Neandertal ears. As in other cranial structures, the ear region in the Sima de los Huesos show a mosaic evolutionary pattern that includes primitive traits, others shared exclusively with Neandertals, and others that are specific to the Sima de los Huesos hominins. Neandertals and Sima de los Huesos hominins share two exclusive features of the middle ear that are among the first characteristics of the Neandertal lineage: a long tympanic cavity and a large entrance and exit of the mastoid antrum. Along with these traits, the Sima de los Huesos hominins present two specialized features: large volumes of the tympanic cavity and the mastoid antrum. Finally, the middle ear of the Neandertals is characterized by the presence of small angles between the tympanic axis and the plane of the oval window.
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Affiliation(s)
- Mercedes Conde-Valverde
- Universidad de Alcalá, Departamento de Ciencias de la Vida, Cátedra de Otoacústica Evolutiva y Paleoantropología (HM Hospitales-Universidad de Alcalá), Alcalá de Henares, Spain
- Department of Anthropology, Binghamton University (SUNY), New York, USA
- Centro de Investigación Francisco Javier Muñiz, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Ignacio Martínez
- Universidad de Alcalá, Departamento de Ciencias de la Vida, Cátedra de Otoacústica Evolutiva y Paleoantropología (HM Hospitales-Universidad de Alcalá), Alcalá de Henares, Spain
- Centro de Investigación Francisco Javier Muñiz, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Rolf Quam
- Universidad de Alcalá, Departamento de Ciencias de la Vida, Cátedra de Otoacústica Evolutiva y Paleoantropología (HM Hospitales-Universidad de Alcalá), Alcalá de Henares, Spain
- Department of Anthropology, Binghamton University (SUNY), New York, USA
- Centro Mixto (UCM-ISCIII) de Evolución y Comportamiento Humanos, Madrid, Spain
- Division of Anthropology, American Museum of Natural History, New York, USA
| | - Juan Luis Arsuaga
- Centro Mixto (UCM-ISCIII) de Evolución y Comportamiento Humanos, Madrid, Spain
- Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, Madrid, Spain
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15
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Yermakovich D, André M, Brucato N, Kariwiga J, Leavesley M, Pankratov V, Mondal M, Ricaut FX, Dannemann M. Denisovan admixture facilitated environmental adaptation in Papua New Guinean populations. Proc Natl Acad Sci U S A 2024; 121:e2405889121. [PMID: 38889149 PMCID: PMC11214076 DOI: 10.1073/pnas.2405889121] [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: 03/21/2024] [Accepted: 05/16/2024] [Indexed: 06/20/2024] Open
Abstract
Neandertals and Denisovans, having inhabited distinct regions in Eurasia and possibly Oceania for over 200,000 y, experienced ample time to adapt to diverse environmental challenges these regions presented. Among present-day human populations, Papua New Guineans (PNG) stand out as one of the few carrying substantial amounts of both Neandertal and Denisovan DNA, a result of past admixture events with these archaic human groups. This study investigates the distribution of introgressed Denisovan and Neandertal DNA within two distinct PNG populations, residing in the highlands of Mt Wilhelm and the lowlands of Daru Island. These locations exhibit unique environmental features, some of which may parallel the challenges that archaic humans once confronted and adapted to. Our results show that PNG highlanders carry higher levels of Denisovan DNA compared to PNG lowlanders. Among the Denisovan-like haplotypes with higher frequencies in highlander populations, those exhibiting the greatest frequency difference compared to lowlander populations also demonstrate more pronounced differences in population frequencies than frequency-matched nonarchaic variants. Two of the five most highly differentiated of those haplotypes reside in genomic areas linked to brain development genes. Conversely, Denisovan-like haplotypes more frequent in lowlanders overlap with genes associated with immune response processes. Our findings suggest that Denisovan DNA has provided genetic variation associated with brain biology and immune response to PNG genomes, some of which might have facilitated adaptive processes to environmental challenges.
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Affiliation(s)
- Danat Yermakovich
- Center of Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, Tartu51010, Estonia
| | - Mathilde André
- Center of Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, Tartu51010, Estonia
| | - Nicolas Brucato
- Centre de Recherche sur la Biodiversité et l'Environnement, Université de Toulouse, Centre National de la Recherche Scientifique, Institut de Recherche pour le Développement, Toulouse Institut National Polytechnique, Université Toulouse 3–Paul Sabatier, cedex 9, Toulouse31062, France
| | - Jason Kariwiga
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea
- School of Social Science, University of Queensland, St. Lucia, QLD4072, Australia
| | - Matthew Leavesley
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea
- The Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage & College of Arts, Society and Education, James Cook University, Cairns, QLD4870, Australia
| | - Vasili Pankratov
- Center of Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, Tartu51010, Estonia
| | - Mayukh Mondal
- Center of Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, Tartu51010, Estonia
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Kiel24118, Germany
| | - François-Xavier Ricaut
- Centre de Recherche sur la Biodiversité et l'Environnement, Université de Toulouse, Centre National de la Recherche Scientifique, Institut de Recherche pour le Développement, Toulouse Institut National Polytechnique, Université Toulouse 3–Paul Sabatier, cedex 9, Toulouse31062, France
| | - Michael Dannemann
- Center of Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, Tartu51010, Estonia
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16
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Iasi LNM, Chintalapati M, Skov L, Mesa AB, Hajdinjak M, Peter BM, Moorjani P. Neandertal ancestry through time: Insights from genomes of ancient and present-day humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.593955. [PMID: 38798350 PMCID: PMC11118355 DOI: 10.1101/2024.05.13.593955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Gene flow from Neandertals has shaped the landscape of genetic and phenotypic variation in modern humans. We identify the location and size of introgressed Neandertal ancestry segments in more than 300 genomes spanning the last 50,000 years. We study how Neandertal ancestry is shared among individuals to infer the time and duration of the Neandertal gene flow. We find the correlation of Neandertal segment locations across individuals and their divergence to sequenced Neandertals, both support a model of single major Neandertal gene flow. Our catalog of introgressed segments through time confirms that most natural selection-positive and negative-on Neandertal ancestry variants occurred immediately after the gene flow, and provides new insights into how the contact with Neandertals shaped human origins and adaptation.
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Affiliation(s)
- Leonardo N. M. Iasi
- Department for Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology; Leipzig, 04301, Germany
| | - Manjusha Chintalapati
- Department of Molecular and Cell Biology, University of California Berkeley; Berkeley, CA 94720, USA
| | - Laurits Skov
- Department of Molecular and Cell Biology, University of California Berkeley; Berkeley, CA 94720, USA
| | - Alba Bossoms Mesa
- Department for Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology; Leipzig, 04301, Germany
| | - Mateja Hajdinjak
- Department for Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology; Leipzig, 04301, Germany
- The Francis Crick Institute; London, NW1 1AT, UK
| | - Benjamin M. Peter
- Department for Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology; Leipzig, 04301, Germany
- Department of Biology, University of Rochester; Rochester NY, 14620,USA
| | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California Berkeley; Berkeley, CA 94720, USA
- Center for Computational Biology, University of California Berkeley; Berkeley, CA 94720, USA
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17
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Goli RC, Chishi KG, Ganguly I, Singh S, Dixit S, Rathi P, Diwakar V, Sree C C, Limbalkar OM, Sukhija N, Kanaka K. Global and Local Ancestry and its Importance: A Review. Curr Genomics 2024; 25:237-260. [PMID: 39156729 PMCID: PMC11327809 DOI: 10.2174/0113892029298909240426094055] [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: 01/13/2024] [Revised: 03/02/2024] [Accepted: 03/11/2024] [Indexed: 08/20/2024] Open
Abstract
The fastest way to significantly change the composition of a population is through admixture, an evolutionary mechanism. In animal breeding history, genetic admixture has provided both short-term and long-term advantages by utilizing the phenomenon of complementarity and heterosis in several traits and genetic diversity, respectively. The traditional method of admixture analysis by pedigree records has now been replaced greatly by genome-wide marker data that enables more precise estimations. Among these markers, SNPs have been the popular choice since they are cost-effective, not so laborious, and automation of genotyping is easy. Certain markers can suggest the possibility of a population's origin from a sample of DNA where the source individual is unknown or unwilling to disclose their lineage, which are called Ancestry-Informative Markers (AIMs). Revealing admixture level at the locus-specific level is termed as local ancestry and can be exploited to identify signs of recent selective response and can account for genetic drift. Considering the importance of genetic admixture and local ancestry, in this mini-review, both concepts are illustrated, encompassing basics, their estimation/identification methods, tools/software used and their applications.
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Affiliation(s)
| | - Kiyevi G. Chishi
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Indrajit Ganguly
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Sanjeev Singh
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - S.P. Dixit
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Pallavi Rathi
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Vikas Diwakar
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Chandana Sree C
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | | | - Nidhi Sukhija
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
- Central Tasar Research and Training Institute, Ranchi, 835303, Jharkhand, India
| | - K.K Kanaka
- ICAR- Indian Institute of Agricultural Biotechnology, Ranchi, 834010, Jharkhand, India
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18
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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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19
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Peyrégne S, Slon V, Kelso J. More than a decade of genetic research on the Denisovans. Nat Rev Genet 2024; 25:83-103. [PMID: 37723347 DOI: 10.1038/s41576-023-00643-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2023] [Indexed: 09/20/2023]
Abstract
Denisovans, a group of now extinct humans who lived in Eastern Eurasia in the Middle and Late Pleistocene, were first identified from DNA sequences just over a decade ago. Only ten fragmentary remains from two sites have been attributed to Denisovans based entirely on molecular information. Nevertheless, there has been great interest in using genetic data to understand Denisovans and their place in human history. From the reconstruction of a single high-quality genome, it has been possible to infer their population history, including events of admixture with other human groups. Additionally, the identification of Denisovan DNA in the genomes of present-day individuals has provided insights into the timing and routes of dispersal of ancient modern humans into Asia and Oceania, as well as the contributions of archaic DNA to the physiology of present-day people. In this Review, we synthesize more than a decade of research on Denisovans, reconcile controversies and summarize insights into their population history and phenotype. We also highlight how our growing knowledge about Denisovans has provided insights into our own evolutionary history.
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Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Viviane Slon
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anatomy and Anthropology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, Tel Aviv, Israel
| | - Janet Kelso
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
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20
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Di Santo LN, Quilodrán CS, Currat M. Temporal Variation in Introgressed Segments' Length Statistics Computed from a Limited Number of Ancient Genomes Sheds Light on Past Admixture Pulses. Mol Biol Evol 2023; 40:msad252. [PMID: 37992125 PMCID: PMC10715198 DOI: 10.1093/molbev/msad252] [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: 04/18/2023] [Revised: 10/16/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023] Open
Abstract
Hybridization is recognized as an important evolutionary force, but identifying and timing admixture events between divergent lineages remain a major aim of evolutionary biology. While this has traditionally been done using inferential tools on contemporary genomes, the latest advances in paleogenomics have provided a growing wealth of temporally distributed genomic data. Here, we used individual-based simulations to generate chromosome-level genomic data for a 2-population system and described temporal neutral introgression patterns under a single- and 2-pulse admixture model. We computed 6 summary statistics aiming to inform the timing and number of admixture pulses between interbreeding entities: lengths of introgressed sequences and their variance within genomes, as well as genome-wide introgression proportions and related measures. The first 2 statistics could confidently be used to infer interlineage hybridization history, peaking at the beginning and shortly after an admixture pulse. Temporal variation in introgression proportions and related statistics provided more limited insights, particularly when considering their application to ancient genomes still scant in number. Lastly, we computed these statistics on Homo sapiens paleogenomes and successfully inferred the hybridization pulse from Neanderthal that occurred approximately 40 to 60 kya. The scarce number of genomes dating from this period prevented more precise inferences, but the accumulation of paleogenomic data opens promising perspectives as our approach only requires a limited number of ancient genomes.
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Affiliation(s)
- Lionel N Di Santo
- Department of Genetics and Evolution, University of Geneva, Geneva CH-1205
| | | | - Mathias Currat
- Department of Genetics and Evolution, University of Geneva, Geneva CH-1205
- Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva CH-1205
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21
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Wroblewski TH, Witt KE, Lee SB, Malhi RS, Peede D, Huerta-Sánchez E, Villanea FA, Claw KG. Pharmacogenetic Variation in Neanderthals and Denisovans and Implications for Human Health and Response to Medications. Genome Biol Evol 2023; 15:evad222. [PMID: 38051947 PMCID: PMC10727477 DOI: 10.1093/gbe/evad222] [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: 04/03/2023] [Revised: 11/08/2023] [Accepted: 11/16/2023] [Indexed: 12/07/2023] Open
Abstract
Modern humans carry both Neanderthal and Denisovan (archaic) genome elements that are part of the human gene pool and affect the life and health of living individuals. The impact of archaic DNA may be particularly evident in pharmacogenes-genes responsible for the processing of exogenous substances such as food, pollutants, and medications-as these can relate to changing environmental effects, and beneficial variants may have been retained as modern humans encountered new environments. However, the health implications and contribution of archaic ancestry in pharmacogenes of modern humans remain understudied. Here, we explore 11 key cytochrome P450 genes (CYP450) involved in 75% of all drug metabolizing reactions in three Neanderthal and one Denisovan individuals and examine archaic introgression in modern human populations. We infer the metabolizing efficiency of these 11 CYP450 genes in archaic individuals and find important predicted phenotypic differences relative to modern human variants. We identify several single nucleotide variants shared between archaic and modern humans in each gene, including some potentially function-altering mutations in archaic CYP450 genes, which may result in altered metabolism in living people carrying these variants. We also identified several variants in the archaic CYP450 genes that are novel and unique to archaic humans as well as one gene, CYP2B6, that shows evidence for a gene duplication found only in Neanderthals and modern Africans. Finally, we highlight CYP2A6, CYP2C9, and CYP2J2, genes which show evidence for archaic introgression into modern humans and posit evolutionary hypotheses that explain their allele frequencies in modern populations.
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Affiliation(s)
- Tadeusz H Wroblewski
- Department of Biomedical Informatics, Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kelsey E Witt
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, South Carolina, USA
| | - Seung-been Lee
- Precision Medicine Institute, Macrogen Inc., Seoul, Republic of Korea
| | - Ripan S Malhi
- Department of Anthropology and Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Illinois, USA
| | - David Peede
- Department of Ecology, Evolution, and Organismal Biology and Center for Computational and Molecular Biology, Brown University, Providence, Rhode Island, USA
- Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, USA
| | - Emilia Huerta-Sánchez
- Department of Ecology, Evolution, and Organismal Biology and Center for Computational and Molecular Biology, Brown University, Providence, Rhode Island, USA
| | | | - Katrina G Claw
- Department of Biomedical Informatics, Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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22
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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: 0.5] [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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23
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Harris DN, Platt A, Hansen MEB, Fan S, McQuillan MA, Nyambo T, Mpoloka SW, Mokone GG, Belay G, Fokunang C, Njamnshi AK, Tishkoff SA. Diverse African genomes reveal selection on ancient modern human introgressions in Neanderthals. Curr Biol 2023; 33:4905-4916.e5. [PMID: 37837965 PMCID: PMC10841429 DOI: 10.1016/j.cub.2023.09.066] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/18/2023] [Accepted: 09/26/2023] [Indexed: 10/16/2023]
Abstract
Comparisons of Neanderthal genomes to anatomically modern human (AMH) genomes show a history of Neanderthal-to-AMH introgression stemming from interbreeding after the migration of AMHs from Africa to Eurasia. All non-sub-Saharan African AMHs have genomic regions genetically similar to Neanderthals that descend from this introgression. Regions of the genome with Neanderthal similarities have also been identified in sub-Saharan African populations, but their origins have been unclear. To better understand how these regions are distributed across sub-Saharan Africa, the source of their origin, and what their distribution within the genome tells us about early AMH and Neanderthal evolution, we analyzed a dataset of high-coverage, whole-genome sequences from 180 individuals from 12 diverse sub-Saharan African populations. In sub-Saharan African populations with non-sub-Saharan African ancestry, as much as 1% of their genomes can be attributed to Neanderthal sequence introduced by recent migration, and subsequent admixture, of AMH populations originating from the Levant and North Africa. However, most Neanderthal homologous regions in sub-Saharan African populations originate from migration of AMH populations from Africa to Eurasia ∼250 kya, and subsequent admixture with Neanderthals, resulting in ∼6% AMH ancestry in Neanderthals. These results indicate that there have been multiple migration events of AMHs out of Africa and that Neanderthal and AMH gene flow has been bi-directional. Observing that genomic regions where AMHs show a depletion of Neanderthal introgression are also regions where Neanderthal genomes show a depletion of AMH introgression points to deleterious interactions between introgressed variants and background genomes in both groups-a hallmark of incipient speciation.
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Affiliation(s)
- Daniel N Harris
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexander Platt
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew E B Hansen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shaohua Fan
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai 200438, China
| | - Michael A McQuillan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Thomas Nyambo
- Department of Biochemistry and Molecular Biology, Hubert Kairuki Memorial University, Dar es Salaam, Tanzania
| | - Sununguko Wata Mpoloka
- Department of Biological Sciences, Faculty of Science, University of Botswana, Private Bag UB 0022, Gaborone, Botswana
| | - Gaonyadiwe George Mokone
- Department of Biomedical Sciences, Faculty of Medicine, University of Botswana, Private Bag UB 0022, Gaborone, Botswana
| | - Gurja Belay
- Department of Microbial Cellular and Molecular Biology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Charles Fokunang
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, P.O. Box 337, Yaoundé, Cameroon
| | - Alfred K Njamnshi
- Brain Research Africa Initiative (BRAIN), P.O. Box 25625, Yaoundé, Cameroon; Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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24
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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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25
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Moorjani P, Hellenthal G. Methods for Assessing Population Relationships and History Using Genomic Data. Annu Rev Genomics Hum Genet 2023; 24:305-332. [PMID: 37220313 PMCID: PMC11040641 DOI: 10.1146/annurev-genom-111422-025117] [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: 05/25/2023]
Abstract
Genetic data contain a record of our evolutionary history. The availability of large-scale datasets of human populations from various geographic areas and timescales, coupled with advances in the computational methods to analyze these data, has transformed our ability to use genetic data to learn about our evolutionary past. Here, we review some of the widely used statistical methods to explore and characterize population relationships and history using genomic data. We describe the intuition behind commonly used approaches, their interpretation, and important limitations. For illustration, we apply some of these techniques to genome-wide autosomal data from 929 individuals representing 53 worldwide populations that are part of the Human Genome Diversity Project. Finally, we discuss the new frontiers in genomic methods to learn about population history. In sum, this review highlights the power (and limitations) of DNA to infer features of human evolutionary history, complementing the knowledge gleaned from other disciplines, such as archaeology, anthropology, and linguistics.
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Affiliation(s)
- Priya Moorjani
- Department of Molecular and Cell Biology and Center for Computational Biology, University of California, Berkeley, California, USA;
| | - Garrett Hellenthal
- UCL Genetics Institute and Research Department of Genetics, Evolution, and Environment, University College London, London, United Kingdom;
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26
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Tozzi A. Non-ultrametric phylogenetic trees shed new light on Neanderthal introgression. ORG DIVERS EVOL 2023:1-9. [PMID: 37359819 PMCID: PMC10256575 DOI: 10.1007/s13127-023-00613-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 04/28/2023] [Indexed: 06/28/2023]
Abstract
Ultrametric spaces are widely used to depict evolutionary times in phylogenetic trees since they assume that every population/species is located at the tips of bifurcating branches of the same length. The discrete branching of ultrametric trees permits the measurement of distances between pairs of individuals that are proportional to their divergence time. Here the traditional ultrametric concept of bifurcating and divergent phylogenetic tree is overturned and a new type of non-ultrametric diagram is introduced. The objective of this study is the description of gene flows in branching species/populations in terms of converging trees instead of bifurcating trees. To provide an operational example, the paleoanthropological issue of the date of Neanderthal genome's introgression in non-African humans is examined. Neanderthals and ancient humans are not anymore two species that exchange chunks of DNA, rather become a single, novel cluster of extant hominins that must be considered by itself. The novel converging, non-ultrametric phylogenetic trees permit the calibration of molecular clocks with a twofold benefit. When the date of the branching of two population/species from a common ancestor is known, the novel approach allows to calculate the time of subsequent introgressions. On the contrary, when the date of the introgression between two population/species is known, the novel approach allows to detect the time of their previous branching from a common ancestor.
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Affiliation(s)
- Arturo Tozzi
- Center for Nonlinear Science, Department of Physics, University of North Texas, 1155 Union Circle, Denton, TX #31142776203-5017 USA
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27
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Pereson MJ, Sanabria DJ, Torres C, Liotta DJ, Campos RH, Schurr TG, Di Lello FA, Badano I. Evolutionary analysis of JC polyomavirus in Misiones' population yields insight into the population dynamics of the early human dispersal in the Americas. Virology 2023; 585:100-108. [PMID: 37327595 DOI: 10.1016/j.virol.2023.05.009] [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: 03/14/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND JC polyomavirus (JCV) has an ethno-geographical distribution across human populations. OBJECTIVE Study the origins of the population of Misiones (Argentina) by using JCV as genetic marker. METHODS Viral detection and characterization was conducted by PCR amplification and evolutionary analysis of the intergenic region sequences. RESULTS 22 out of 121 samples were positive for JCV, including 5 viral lineages: MY (n = 8), Eu-a (n = 7), B1-c (n = 4), B1-b (n = 2) and Af2 (n = 1). MY sequences clustered within a branch of Native American origin that diverged from its Asian counterpart about 21,914 years ago (HPD 95% interval 15,383-30,177), followed by a sustained demographic expansion around 5000 years ago. CONCLUSIONS JCV in Misiones reflects the multiethnic origin of the current population, with an important Amerindian contribution. Analysis of the MY viral lineage shows a pattern consistent with the arrival of early human migrations to the Americas and a population expansion by the pre-Columbian native societies.
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Affiliation(s)
- Matias J Pereson
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina
| | - Daiana J Sanabria
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina; Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Laboratorio de Biología Molecular Aplicada (LaBiMAp). Posadas, Misiones, Argentina
| | - Carolina Torres
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina
| | - Domingo J Liotta
- Instituto Nacional de Medicina Tropical-ANLIS ''Dr. Malbrán'', Neuquén y Jujuy S/n, N3370, Puerto Iguazú, Misiones, Argentina
| | - Rodolfo H Campos
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina
| | - Theodore G Schurr
- Laboratory of Molecular Anthropology, Department of Anthropology, University of Pennsylvania. Philadelphia, PA 19104-6398, USA
| | - Federico A Di Lello
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina
| | - Inés Badano
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina; Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Laboratorio de Biología Molecular Aplicada (LaBiMAp). Posadas, Misiones, Argentina; Universidad Nacional de Misiones. Red de Laboratorios. Laboratorio de Antropología Biológica y Bioinformática Aplicada (LABBA). Misiones, Argentina.
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28
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Ågren R, Patil S, Zhou X, Sahlholm K, Pääbo S, Zeberg H. Major Genetic Risk Factors for Dupuytren's Disease Are Inherited From Neandertals. Mol Biol Evol 2023; 40:msad130. [PMID: 37315093 DOI: 10.1093/molbev/msad130] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023] Open
Abstract
Dupuytren's disease is characterized by fingers becoming permanently bent in a flexed position. Whereas people of African ancestry are rarely afflicted by Dupuytren's disease, up to ∼30% of men over 60 years suffer from this condition in northern Europe. Here, we meta-analyze 3 biobanks comprising 7,871 cases and 645,880 controls and find 61 genome-wide significant variants associated with Dupuytren's disease. We show that 3 of the 61 loci harbor alleles of Neandertal origin, including the second and third most strongly associated ones (P = 6.4 × 10-132 and P = 9.2 × 10-69, respectively). For the most strongly associated Neandertal variant, we identify EPDR1 as the causal gene. Dupuytren's disease is an example of how admixture with Neandertals has shaped regional differences in disease prevalence.
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Affiliation(s)
- Richard Ågren
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Snehal Patil
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Kristoffer Sahlholm
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Department of Integrative Medical Biology, Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Human Evolutionary Genomics Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Hugo Zeberg
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Human Evolutionary Genomics Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
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29
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Pathogenic Variants Associated with Rare Monogenic Diseases Established in Ancient Neanderthal and Denisovan Genome-Wide Data. Genes (Basel) 2023; 14:genes14030727. [PMID: 36980999 PMCID: PMC10048696 DOI: 10.3390/genes14030727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
Ancient anatomically modern humans (AMHs) encountered other archaic human species, most notably Neanderthals and Denisovans, when they left Africa and spread across Europe and Asia ~60,000 years ago. They interbred with them, and modern human genomes retain DNA inherited from these interbreeding events. High quality (high coverage) ancient human genomes have recently been sequenced allowing for a direct estimation of individual heterozygosity, which has shown that genetic diversity in these archaic human groups was very low, indicating low population sizes. In this study, we analyze ten ancient human genome-wide data, including four sequenced with high-coverage. We screened these ancient genome-wide data for pathogenic mutations associated with monogenic diseases, and established unusual aggregation of pathogenic mutations in individual subjects, including quadruple homozygous cases of pathogenic variants in the PAH gene associated with the condition phenylketonuria in a ~120,000 years old Neanderthal. Such aggregation of pathogenic mutations is extremely rare in contemporary populations, and their existence in ancient humans could be explained by less significant clinical manifestations coupled with small community sizes, leading to higher inbreeding levels. Our results suggest that pathogenic variants associated with rare diseases might be the result of introgression from other archaic human species, and archaic admixture thus could have influenced disease risk in modern humans.
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30
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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: 2] [Impact Index Per Article: 1.0] [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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31
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Profile of Svante Pääbo: 2022 Nobel laureate in physiology or medicine. Proc Natl Acad Sci U S A 2023; 120:e2217025119. [PMID: 36580591 PMCID: PMC9910432 DOI: 10.1073/pnas.2217025119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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Keeling BA, Quam R, Martínez I, Arsuaga JL, Maroto J. Reassessment of the human mandible from Banyoles (Girona, Spain). J Hum Evol 2023; 174:103291. [PMID: 36493597 DOI: 10.1016/j.jhevol.2022.103291] [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: 11/09/2021] [Revised: 10/18/2022] [Accepted: 10/21/2022] [Indexed: 12/12/2022]
Abstract
Since the discovery of a human mandible in 1887 near the present-day city of Banyoles, northeastern Spain, researchers have generally emphasized its archaic features, including the lack of chin structures, and suggested affinities with the Neandertals or European Middle Pleistocene (Chibanian) specimens. Uranium-series and electron spin resonance dating suggest the mandible dates to the Late Pleistocene (Tarantian), approximately ca. 45-66 ka. In this study, we reassessed the taxonomic affinities of the Banyoles mandible by comparing it to samples of Middle Pleistocene fossils from Africa and Europe, Neandertals, Early and Upper Paleolithic modern humans, and recent modern humans. We evaluated the frequencies and expressions of morphological features and performed a three-dimensional geometric morphometric analysis on a virtual reconstruction of Banyoles to capture overall mandibular shape. Our results revealed no derived Neandertal morphological features in Banyoles. While a principal component analysis based on Euclidean distances from the first two principal components clearly grouped Banyoles with both fossil and recent Homo sapiens individuals, an analysis of the Procrustes residuals demonstrated that Banyoles did not fit into any of the comparative groups. The lack of Neandertal features in Banyoles is surprising considering its Late Pleistocene age. A consideration of the Middle Pleistocene fossil record in Europe and southwest Asia suggests that Banyoles is unlikely to represent a late-surviving Middle Pleistocene population. The lack of chin structures also complicates an assignment to H. sapiens, although early fossil H. sapiens do show somewhat variable development of the chin structures. Thus, Banyoles represents a non-Neandertal Late Pleistocene European individual and highlights the continuing signal of diversity in the hominin fossil record. The present situation makes Banyoles a prime candidate for ancient DNA or proteomic analyses, which may shed additional light on its taxonomic affinities.
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Affiliation(s)
- Brian A Keeling
- Department of Anthropology, Binghamton University, SUNY, New York, USA.
| | - Rolf Quam
- Department of Anthropology, Binghamton University, SUNY, New York, USA; Centro UCM-ISCIII de Evolución y Comportamiento Humanos, Madrid, Spain; Division of Anthropology, American Museum of Natural History, New York, USA; Cátedra de Otoacústica Evolutiva y Paleoantropología (HM Hospitales-Universidad de Alcalá), Departamento de Ciencias de la Vida, Universidad de Alcalá, Madrid, Spain
| | - Ignacio Martínez
- Cátedra de Otoacústica Evolutiva y Paleoantropología (HM Hospitales-Universidad de Alcalá), Departamento de Ciencias de la Vida, Universidad de Alcalá, Madrid, Spain; Centro de Investigación Francisco Javier Muñiz, Universidad de Buenos Aires, Calle Paraguay 2155, Primer piso, Ciudad Autónoma de Buenos Aires, 1121, Argentina
| | - Juan Luis Arsuaga
- Centro UCM-ISCIII de Evolución y Comportamiento Humanos, Madrid, Spain; Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Julià Maroto
- Grup d'Arqueologia i Prehistòria, Universitat de Girona, pl. Ferrater Mora, 1, 17071 Girona, Spain
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Neandertal introgression partitions the genetic landscape of neuropsychiatric disorders and associated behavioral phenotypes. Transl Psychiatry 2022; 12:433. [PMID: 36198681 PMCID: PMC9534885 DOI: 10.1038/s41398-022-02196-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 09/13/2022] [Accepted: 09/20/2022] [Indexed: 11/08/2022] Open
Abstract
Despite advances in identifying the genetic basis of psychiatric and neurological disorders, fundamental questions about their evolutionary origins remain elusive. Here, introgressed variants from archaic humans such as Neandertals can serve as an intriguing research paradigm. We compared the number of associations for Neandertal variants to the number of associations of frequency-matched non-archaic variants with regard to human CNS disorders (neurological and psychiatric), nervous system drug prescriptions (as a proxy for disease), and related, non-disease phenotypes in the UK biobank (UKBB). While no enrichment for Neandertal genetic variants were observed in the UKBB for psychiatric or neurological disease categories, we found significant associations with certain behavioral phenotypes including pain, chronotype/sleep, smoking and alcohol consumption. In some instances, the enrichment signal was driven by Neandertal variants that represented the strongest association genome-wide. SNPs within a Neandertal haplotype that was associated with smoking in the UKBB could be replicated in four independent genomics datasets.Our data suggest that evolutionary processes in recent human evolution like admixture with Neandertals significantly contribute to behavioral phenotypes but not psychiatric and neurological diseases. These findings help to link genetic variants in a population to putative past beneficial effects, which likely only indirectly contribute to pathology in modern day humans.
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34
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Reilly PF, Tjahjadi A, Miller SL, Akey JM, Tucci S. The contribution of Neanderthal introgression to modern human traits. Curr Biol 2022; 32:R970-R983. [PMID: 36167050 PMCID: PMC9741939 DOI: 10.1016/j.cub.2022.08.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Neanderthals, our closest extinct relatives, lived in western Eurasia from 400,000 years ago until they went extinct around 40,000 years ago. DNA retrieved from ancient specimens revealed that Neanderthals mated with modern human contemporaries. As a consequence, introgressed Neanderthal DNA survives scattered across the human genome such that 1-4% of the genome of present-day people outside Africa are inherited from Neanderthal ancestors. Patterns of Neanderthal introgressed genomic sequences suggest that Neanderthal alleles had distinct fates in the modern human genetic background. Some Neanderthal alleles facilitated human adaptation to new environments such as novel climate conditions, UV exposure levels and pathogens, while others had deleterious consequences. Here, we review the body of work on Neanderthal introgression over the past decade. We describe how evolutionary forces shaped the genomic landscape of Neanderthal introgression and highlight the impact of introgressed alleles on human biology and phenotypic variation.
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Affiliation(s)
| | - Audrey Tjahjadi
- Department of Anthropology, Yale University, New Haven, CT, USA
| | | | - Joshua M Akey
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
| | - Serena Tucci
- Department of Anthropology, Yale University, New Haven, CT, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
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35
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Phillips C, de la Puente M, Ruiz-Ramirez J, Staniewska A, Ambroa-Conde A, Freire-Aradas A, Mosquera-Miguel A, Rodriguez A, Lareu MV. Eurasiaplex-2: Shifting the focus to SNPs with high population specificity increases the power of forensic ancestry marker sets. Forensic Sci Int Genet 2022; 61:102780. [PMID: 36174251 DOI: 10.1016/j.fsigen.2022.102780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/16/2022] [Accepted: 09/18/2022] [Indexed: 11/27/2022]
Abstract
To compile a new South Asian-informative panel of forensic ancestry SNPs, we changed the strategy for selecting the most powerful markers for this purpose by targeting polymorphisms with near absolute specificity - when the South Asian-informative allele identified is absent from all other populations or present at frequencies below 0.001 (one in a thousand). More than 120 candidate SNPs were identified from 1000 Genomes datasets satisfying an allele frequency screen of ≥ 0.1 (10 % or more) allele frequency in South Asians, and ≤ 0.001 (0.1 % or less) in African, East Asian, and European populations. From the candidate pool of markers, a final panel of 36 SNPs, widely distributed across most autosomes, were selected that had allele frequencies in the five 1000 Genomes South Asian populations ranging from 0.4 to 0.15. Slightly lower average allele frequencies, but consistent patterns of informativeness were observed in gnomAD South Asian datasets used to validate the 1000 Genomes variant annotations. We named the panel of 36 South Asian-specific SNPs Eurasiaplex-2, and the informativeness of the panel was evaluated by compiling worldwide population data from 4097 samples in four genome variation databases that largely complement the global sampling of 1000 Genomes. Consistent patterns of allele frequency distribution, which were specific to South Asia, were observed in all populations in, or closely sited to, the Indian sub-continent. Pakistani populations from the HGDP-CEPH panel had markedly lower allele frequencies, highlighting the need to develop a statistical system to evaluate the ancestry inference value of counting the number of population-specific alleles present in an individual.
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Affiliation(s)
- C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain; Institute of Anthropology and Ethnology, Adam Mickiewicz University in Poznań, Poland..
| | - M de la Puente
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - J Ruiz-Ramirez
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - A Staniewska
- Institute of Anthropology and Ethnology, Adam Mickiewicz University in Poznań, Poland
| | - A Ambroa-Conde
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - A Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - A Mosquera-Miguel
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - A Rodriguez
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - M V Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
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36
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Churchill SE, Keys K, Ross AH. Midfacial Morphology and Neandertal-Modern Human Interbreeding. BIOLOGY 2022; 11:1163. [PMID: 36009790 PMCID: PMC9404802 DOI: 10.3390/biology11081163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/29/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
Ancient DNA from, Neandertal and modern human fossils, and comparative morphological analyses of them, reveal a complex history of interbreeding between these lineages and the introgression of Neandertal genes into modern human genomes. Despite substantial increases in our knowledge of these events, the timing and geographic location of hybridization events remain unclear. Six measures of facial size and shape, from regional samples of Neandertals and early modern humans, were used in a multivariate exploratory analysis to try to identify regions in which early modern human facial morphology was more similar to that of Neandertals, which might thus represent regions of greater introgression of Neandertal genes. The results of canonical variates analysis and hierarchical cluster analysis suggest important affinities in facial morphology between both Middle and Upper Paleolithic early modern humans of the Near East with Neandertals, highlighting the importance of this region for interbreeding between the two lineages.
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Affiliation(s)
- Steven E. Churchill
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA;
- Centre for the Exploration of the Deep Human Journey, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Kamryn Keys
- Human Identification & Forensic Analysis Laboratory, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA;
| | - Ann H. Ross
- Human Identification & Forensic Analysis Laboratory, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA;
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37
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Pfennig A, Lachance J. Hybrid fitness effects modify fixation probabilities of introgressed alleles. G3 GENES|GENOMES|GENETICS 2022; 12:6583188. [PMID: 35536195 PMCID: PMC9258535 DOI: 10.1093/g3journal/jkac113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 04/28/2022] [Indexed: 11/12/2022]
Abstract
Hybridization is a common occurrence in natural populations, and introgression is a major source of genetic variation. Despite the evolutionary importance of adaptive introgression, classical population genetics theory does not take into account hybrid fitness effects. Specifically, heterosis (i.e. hybrid vigor) and Dobzhansky–Muller incompatibilities influence the fates of introgressed alleles. Here, we explicitly account for polygenic, unlinked hybrid fitness effects when tracking a rare introgressed marker allele. These hybrid fitness effects quickly decay over time due to repeated backcrossing, enabling a separation-of-timescales approach. Using diffusion and branching process theory in combination with computer simulations, we formalize the intuition behind how hybrid fitness effects affect introgressed alleles. We find that hybrid fitness effects can significantly hinder or boost the fixation probability of introgressed alleles, depending on the relative strength of heterosis and Dobzhansky–Muller incompatibilities effects. We show that the inclusion of a correction factor (α, representing the compounded effects of hybrid fitness effects over time) into classic population genetics theory yields accurate fixation probabilities. Despite having a strong impact on the probability of fixation, hybrid fitness effects only subtly change the distribution of fitness effects of introgressed alleles that reach fixation. Although strong Dobzhansky–Muller incompatibility effects may expedite the loss of introgressed alleles, fixation times are largely unchanged by hybrid fitness effects.
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Affiliation(s)
- Aaron Pfennig
- School of Biological Sciences, Georgia Institute of Technology , Atlanta, GA 30332, USA
| | - Joseph Lachance
- School of Biological Sciences, Georgia Institute of Technology , Atlanta, GA 30332, USA
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38
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Slimak L, Zanolli C, Higham T, Frouin M, Schwenninger JL, Arnold LJ, Demuro M, Douka K, Mercier N, Guérin G, Valladas H, Yvorra P, Giraud Y, Seguin-Orlando A, Orlando L, Lewis JE, Muth X, Camus H, Vandevelde S, Buckley M, Mallol C, Stringer C, Metz L. Modern human incursion into Neanderthal territories 54,000 years ago at Mandrin, France. SCIENCE ADVANCES 2022; 8:eabj9496. [PMID: 35138885 PMCID: PMC8827661 DOI: 10.1126/sciadv.abj9496] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Determining the extent of overlap between modern humans and other hominins in Eurasia, such as Neanderthals and Denisovans, is fundamental to understanding the nature of their interactions and what led to the disappearance of archaic hominins. Apart from a possible sporadic pulse recorded in Greece during the Middle Pleistocene, the first settlements of modern humans in Europe have been constrained to ~45,000 to 43,000 years ago. Here, we report hominin fossils from Grotte Mandrin in France that reveal the earliest known presence of modern humans in Europe between 56,800 and 51,700 years ago. This early modern human incursion in the Rhône Valley is associated with technologies unknown in any industry of that age outside Africa or the Levant. Mandrin documents the first alternating occupation of Neanderthals and modern humans, with a modern human fossil and associated Neronian lithic industry found stratigraphically between layers containing Neanderthal remains associated with Mousterian industries.
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Affiliation(s)
- Ludovic Slimak
- CNRS, UMR 5608, TRACES, Université de Toulouse Jean Jaurès, 5 Allées Antonio Machado, 31058 Toulouse Cedex 9, France
- Corresponding author. (L.S.); (C.Z.)
| | - Clément Zanolli
- Université de Bordeaux, CNRS, MCC, PACEA, UMR 5199, 33600 Pessac, France
- Corresponding author. (L.S.); (C.Z.)
| | - Tom Higham
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK
- Department of Evolutionary Anthropology, University of Vienna, University Biology Building, Djerassiplatz 1, A-1030 Vienna, Austria
| | - Marine Frouin
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK
- Department of Geosciences, Stony Brook University, 255 Earth and Space Sciences Building, Stony Brook, NY 11794-2100, USA
- Turkana Basin Institute, Stony Brook University, Stony Brook, NY 11794-4364, USA
| | - Jean-Luc Schwenninger
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK
| | - Lee J. Arnold
- School of Physical Sciences, Environment Institute, Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, North Terrace Campus, Adelaide, SA 5005, Australia
| | - Martina Demuro
- School of Physical Sciences, Environment Institute, Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, North Terrace Campus, Adelaide, SA 5005, Australia
| | - Katerina Douka
- Department of Evolutionary Anthropology, University of Vienna, University Biology Building, Djerassiplatz 1, A-1030 Vienna, Austria
- Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische, Str. 10, 07745 Jena, Germany
| | - Norbert Mercier
- CNRS, UMR 5060, Institut de Recherche sur les Archéomatériaux and Centre de Recherche en Physique Appliquée à l’Archéologie (CRP2A), Maison de l’Archéologie, Université Bordeaux Montaigne, 33607 Pessac, France
| | - Gilles Guérin
- Laboratoire des Sciences du Climat et de l’Environnement, LSCE/IPSL, UMR 8212 CEA CNRS UVSQ, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Hélène Valladas
- Laboratoire des Sciences du Climat et de l’Environnement, LSCE/IPSL, UMR 8212 CEA CNRS UVSQ, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Pascale Yvorra
- Aix-Marseille Université, CNRS, Min. Culture, UMR 7269, LAMPEA, Maison Méditerranéenne des Sciences de l’Homme, BP 647, 5 rue du Château de l’Horloge, F-13094, Aix-en-Provence Cedex 2, France
| | - Yves Giraud
- Aix-Marseille Université, CNRS, Min. Culture, UMR 7269, LAMPEA, Maison Méditerranéenne des Sciences de l’Homme, BP 647, 5 rue du Château de l’Horloge, F-13094, Aix-en-Provence Cedex 2, France
| | | | - Ludovic Orlando
- CNRS, UMR 5288, CAGT, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Jason E. Lewis
- Turkana Basin Institute, Stony Brook University, Stony Brook, NY 11794-4364, USA
- Department of Anthropology, Stony Brook University, Stony Brook, NY 11794-4364, USA
| | | | - Hubert Camus
- PROTEE-EXPERT, 4 rue des Aspholdèles, 34750 Villeneuve-lès-Maguelone, France
| | - Ségolène Vandevelde
- Laboratoire des Sciences du Climat et de l’Environnement, LSCE/IPSL, UMR 8212 CEA CNRS UVSQ, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
- Université Paris 1–Panthéon-Sorbonne, Équipe Archéologies Environnementales, UMR 7041, ArScAn, Équipe Archéologies Environnementales, 21 allée de l’Université, 92023 Nanterre Cedex, France
| | - Mike Buckley
- Department of Earth and Environmental Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Carolina Mallol
- Archaeological Micromorphology and Biomarkers Laboratory (AMBI Lab), Instituto Universitario de Bio-Orgánica Antonio González, Departamento de Geografía e Historia, UDI Prehistoria, Arqueología e Historia Antigua, Facultad de Geografía e Historia, Universidad de La Laguna, Tenerife, Spain
| | - Chris Stringer
- Centre for Human Evolution Research (CHER), Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Laure Metz
- Aix-Marseille Université, CNRS, Min. Culture, UMR 7269, LAMPEA, Maison Méditerranéenne des Sciences de l’Homme, BP 647, 5 rue du Château de l’Horloge, F-13094, Aix-en-Provence Cedex 2, France
- College of Liberal Arts and Sciences, University of Connecticut, 215 Glenbrook Road, U-4098, Storrs, CT 06269-4098, USA
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Huffman JE, Butler-Laporte G, Khan A, Pairo-Castineira E, Drivas TG, Peloso GM, Nakanishi T, Ganna A, Verma A, Baillie JK, Kiryluk K, Richards JB, Zeberg H. Multi-ancestry fine mapping implicates OAS1 splicing in risk of severe COVID-19. Nat Genet 2022; 54:125-127. [PMID: 35027740 PMCID: PMC8837537 DOI: 10.1038/s41588-021-00996-8] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 11/29/2021] [Indexed: 01/18/2023]
Abstract
The OAS1/2/3 cluster has been identified as a risk locus for severe COVID-19 among individuals of European ancestry, with a protective haplotype of approximately 75 kilobases (kb) derived from Neanderthals in the chromosomal region 12q24.13. This haplotype contains a splice variant of OAS1, which occurs in people of African ancestry independently of gene flow from Neanderthals. Using trans-ancestry fine-mapping approaches in 20,779 hospitalized cases, we demonstrate that this splice variant is likely to be the SNP responsible for the association at this locus, thus strongly implicating OAS1 as an effector gene influencing COVID-19 severity.
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Affiliation(s)
- Jennifer E Huffman
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA, USA
| | - Guillaume Butler-Laporte
- Departments of Medicine, Human Genetics, Epidemiology, Biostatistics and Occupational Health, McGill University, Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Erola Pairo-Castineira
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Theodore G Drivas
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania,, Philadelphia, PA, USA
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gina M Peloso
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Tomoko Nakanishi
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Anurag Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania,, Philadelphia, PA, USA
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Corporal Michael Crescenz VA Medical Center, Philadelphia, PA, USA
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - J Brent Richards
- Departments of Medicine, Human Genetics, Epidemiology, Biostatistics and Occupational Health, McGill University, Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada
- Department of Twin Research, King's College London, London, UK
| | - Hugo Zeberg
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
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40
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Hayakawa T, Terahara M, Fujito NT, Matsunaga T, Teshima KM, Hane M, Kitajima K, Sato C, Takahata N, Satta Y. Lower promoter activity of the ST8SIA2 gene has been favored in evolving human collective brains. PLoS One 2021; 16:e0259897. [PMID: 34914745 PMCID: PMC8675693 DOI: 10.1371/journal.pone.0259897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 10/28/2021] [Indexed: 11/18/2022] Open
Abstract
ST8SIA2 is an important molecule regulating expression of the phenotype involved in schizophrenia. Lowered promoter activity of the ST8SIA2 gene is considered to be protective against schizophrenia by conferring tolerance to psychosocial stress. Here, we examined the promoter-type composition of anatomically modern humans (AMHs) and archaic humans (AHs; Neanderthals and Denisovans), and compared the promoter activity at the population level (population promoter activity; PPA) between them. In AMHs, the TCT-type, showing the second lowest promoter activity, was most prevalent in the ancestral population of non-Africans. However, the detection of only the CGT-type from AH samples and recombination tracts in AH sequences showed that the CGT- and TGT-types, exhibiting the two highest promoter activities, were common in AH populations. Furthermore, interspecies gene flow occurred into AMHs from AHs and into Denisovans from Neanderthals, influencing promoter-type compositions independently in both AMHs and AHs. The difference of promoter-type composition makes PPA unique in each population. East and Southeast Asian populations show the lowest PPA. This results from the selective increase of the CGC-type, showing the lowest promoter activity, in these populations. Every non-African population shows significantly lower PPA than African populations, resulting from the TCT-type having the highest prevalence in the ancestral population of non-Africans. In addition, PPA reduction is also found among subpopulations within Africa via a slight increase of the TCT-type. These findings indicate a trend toward lower PPA in the spread of AMHs, interpreted as a continuous adaptation to psychosocial stress arising in migration. This trend is considered as genetic tuning for the evolution of collective brains. The inferred promoter-type composition of AHs differed markedly from that of AMHs, resulting in higher PPA in AHs than in AMHs. This suggests that the trend toward lower PPA is a unique feature in AMH spread.
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Affiliation(s)
- Toshiyuki Hayakawa
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
- Faculty of Arts and Science, Kyushu University, Fukuoka, Japan
- * E-mail:
| | - Masahiro Terahara
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Naoko T. Fujito
- School of Advanced Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan
| | - Takumi Matsunaga
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | | | - Masaya Hane
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi, Japan
| | - Ken Kitajima
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Aichi, Japan
| | - Chihiro Sato
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Aichi, Japan
| | - Naoyuki Takahata
- School of Advanced Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan
| | - Yoko Satta
- School of Advanced Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan
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41
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White S, Pope M, Hillson S, Soligo C. Geometric morphometric variability in the supraorbital and orbital region of Middle Pleistocene hominins: Implications for the taxonomy and evolution of later Homo. J Hum Evol 2021; 162:103095. [PMID: 34847365 DOI: 10.1016/j.jhevol.2021.103095] [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: 10/15/2020] [Revised: 10/10/2021] [Accepted: 10/11/2021] [Indexed: 11/26/2022]
Abstract
This study assessed variation in the supraorbital and orbital region of the Middle Pleistocene hominins (MPHs), sometimes called Homo heidelbergensis s.l., to test whether it matched the expectations of intraspecific variation. The morphological distinctiveness and relative variation of this region, which is relatively well represented in the hominin fossil record, was analyzed quantitatively in a comparative taxonomic framework. Coordinates of 230 3D landmarks (20) and sliding semilandmarks (210) were collected from 704 specimens from species of Homo, Australopithecus, Paranthropus, Gorilla, Pan, Papio, and Macaca. Results showed that the MPHs had expected levels of morphological distinctiveness and intragroup and intergroup variation in supraorbital and orbital morphology, relative to commonly recognized non-hominin catarrhine species. However, the Procrustes distances between this group and H. sapiens were significantly higher than expected for two closely related catarrhine species. Furthermore, this study showed that variation within the MPH could be similarly well contained within existing hypodigms of H. sapiens, H. neanderthalensis, and H. erectus s.l. Although quantitative assessment of supraorbital and orbital morphology did not allow differentiation between taxonomic hypotheses in later Homo, it could be used to test individual taxonomic affiliation and identify potentially anomalous individuals. This study confirmed a complicated pattern of supraorbital and orbital morphology in the MPH fossil record and raises further questions over our understanding of the speciation of H. sapiens and H. neanderthalensis and taxonomic diversity in later Homo.
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Affiliation(s)
- Suzanna White
- Department of Anthropology, University College London, 14 Taviton Street, London, WC1H 0BW, UK.
| | - Matt Pope
- Institute of Archaeology, University College London, 31-34 Gordon Square, London, WC1H 0PY, UK
| | - Simon Hillson
- Institute of Archaeology, University College London, 31-34 Gordon Square, London, WC1H 0PY, UK
| | - Christophe Soligo
- Department of Anthropology, University College London, 14 Taviton Street, London, WC1H 0BW, UK
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42
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Iasi LNM, Ringbauer H, Peter BM. An Extended Admixture Pulse Model Reveals the Limitations to Human-Neandertal Introgression Dating. Mol Biol Evol 2021; 38:5156-5174. [PMID: 34254144 PMCID: PMC8557420 DOI: 10.1093/molbev/msab210] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Neandertal DNA makes up 2-3% of the genomes of all non-African individuals. The patterns of Neandertal ancestry in modern humans have been used to estimate that this is the result of gene flow that occurred during the expansion of modern humans into Eurasia, but the precise dates of this event remain largely unknown. Here, we introduce an extended admixture pulse model that allows joint estimation of the timing and duration of gene flow. This model leads to simple expressions for both the admixture segment distribution and the decay curve of ancestry linkage disequilibrium, and we show that these two statistics are closely related. In simulations, we find that estimates of the mean time of admixture are largely robust to details in gene flow models, but that the duration of the gene flow can only be recovered if gene flow is very recent and the exact recombination map is known. These results imply that gene flow from Neandertals into modern humans could have happened over hundreds of generations. Ancient genomes from the time around the admixture event are thus likely required to resolve the question when, where, and for how long humans and Neandertals interacted.
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Affiliation(s)
- Leonardo N M Iasi
- Department of Evloutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benjamin M Peter
- Department of Evloutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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43
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An etiology of human modernity. ANTHROPOLOGICAL REVIEW 2021. [DOI: 10.2478/anre-2021-0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Following the refutation of the replacement hypothesis, which had proposed that a ‘superior’ hominin species arose in Africa and replaced all other humans existing at the time, the auto-domestication hypothesis remains the only viable explanation for the relatively abrupt change from robust to gracile humans in the Late Pleistocene. It invokes the incidental institution of the domestication syndrome in humans, most probably by newly introduced cultural practices. It also postulates that the induction of exograms compensated for the atrophy of the brain caused by domestication. This new explanation of the origins of modernity in humans elucidates practically all its many aspects, in stark contrast to the superseded replacement hypothesis, which explained virtually nothing. The first results of the domestication syndrome’s genetic exploration have become available in recent years, and they endorse the human self-domestication hypothesis.
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44
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Yan SM, Sherman RM, Taylor DJ, Nair DR, Bortvin AN, Schatz MC, McCoy RC. Local adaptation and archaic introgression shape global diversity at human structural variant loci. eLife 2021; 10:e67615. [PMID: 34528508 PMCID: PMC8492059 DOI: 10.7554/elife.67615] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 09/14/2021] [Indexed: 12/13/2022] Open
Abstract
Large genomic insertions and deletions are a potent source of functional variation, but are challenging to resolve with short-read sequencing, limiting knowledge of the role of such structural variants (SVs) in human evolution. Here, we used a graph-based method to genotype long-read-discovered SVs in short-read data from diverse human genomes. We then applied an admixture-aware method to identify 220 SVs exhibiting extreme patterns of frequency differentiation - a signature of local adaptation. The top two variants traced to the immunoglobulin heavy chain locus, tagging a haplotype that swept to near fixation in certain southeast Asian populations, but is rare in other global populations. Further investigation revealed evidence that the haplotype traces to gene flow from Neanderthals, corroborating the role of immune-related genes as prominent targets of adaptive introgression. Our study demonstrates how recent technical advances can help resolve signatures of key evolutionary events that remained obscured within technically challenging regions of the genome.
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Affiliation(s)
- Stephanie M Yan
- Department of Biology, Johns Hopkins University, BaltimoreBaltimoreUnited States
| | - Rachel M Sherman
- Department of Computer Science, Johns Hopkins UniversityBaltimoreUnited States
| | - Dylan J Taylor
- Department of Biology, Johns Hopkins University, BaltimoreBaltimoreUnited States
| | - Divya R Nair
- Department of Biology, Johns Hopkins University, BaltimoreBaltimoreUnited States
| | - Andrew N Bortvin
- Department of Biology, Johns Hopkins University, BaltimoreBaltimoreUnited States
| | - Michael C Schatz
- Department of Biology, Johns Hopkins University, BaltimoreBaltimoreUnited States
- Department of Computer Science, Johns Hopkins UniversityBaltimoreUnited States
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins University, BaltimoreBaltimoreUnited States
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45
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Buck LT, Katz DC, Ackermann RR, Hlusko LJ, Kanthaswamy S, Weaver TD. Effects of hybridization on pelvic morphology: A macaque model. J Hum Evol 2021; 159:103049. [PMID: 34455262 DOI: 10.1016/j.jhevol.2021.103049] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 11/28/2022]
Abstract
Ancient DNA analyses have shown that interbreeding between hominin taxa occurred multiple times. Although admixture is often reflected in skeletal phenotype, the relationship between the two remains poorly understood, hampering interpretation of the hominin fossil record. Direct study of this relationship is often impossible due to the paucity of hominin fossils and difficulties retrieving ancient genetic material. Here, we use a sample of known ancestry hybrids between two closely related nonhuman primate taxa (Indian and Chinese Macaca mulatta) to investigate the effect of admixture on skeletal morphology. We focus on pelvic shape, which has potential fitness implications in hybrids, as mismatches between maternal pelvic and fetal cranial morphology are often fatal to mother and offspring. As the pelvis is also one of the skeletal regions that differs most between Homo sapiens and Neanderthals, investigating the pelvic consequences of interbreeding could be informative regarding the viability of their hybrids. We find that the effect of admixture in M. mulatta is small and proportional to the relatively small morphological difference between the parent taxa. Sexual dimorphism appears to be the main determinant of pelvic shape in M. mulatta. The lack of difference in pelvic shape between Chinese and Indian M. mulatta is in contrast to that between Neanderthals and H. sapiens, despite a similar split time (in generations) between the hybridizing pairs. Greater phenotypic divergence between hominins may relate to adaptations to disparate environments but may also highlight how the unique degree of cultural buffering in hominins allowed for greater neutral divergence. In contrast to some previous work identifying extreme morphologies in first- and second-generation hybrids, here the relationship between pelvic shape and admixture is linear. This linearity may be because most sampled animals have a multigenerational admixture history or because of relatively high constraints on the pelvis compared with other skeletal regions.
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Affiliation(s)
- Laura T Buck
- School of Biological and Environmental Sciences, Liverpool John Moores University, UK; Department of Anthropology, University of California Davis, USA.
| | - David C Katz
- Department of Anthropology, University of California Davis, USA; University of Calgary, Cumming School of Medicine, Canada
| | - Rebecca Rogers Ackermann
- Department of Archaeology, University of Cape Town, South Africa; Human Evolution Research Institute, University of Cape Town, South Africa
| | - Leslea J Hlusko
- Department of Integrative Biology, University of California Berkeley, USA; Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), Burgos, Spain
| | - Sree Kanthaswamy
- School of Natural and Mathematical Sciences, Arizona State University, USA
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46
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Irving-Pease EK, Muktupavela R, Dannemann M, Racimo F. Quantitative Human Paleogenetics: What can Ancient DNA Tell us About Complex Trait Evolution? Front Genet 2021; 12:703541. [PMID: 34422004 PMCID: PMC8371751 DOI: 10.3389/fgene.2021.703541] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/08/2021] [Indexed: 12/13/2022] Open
Abstract
Genetic association data from national biobanks and large-scale association studies have provided new prospects for understanding the genetic evolution of complex traits and diseases in humans. In turn, genomes from ancient human archaeological remains are now easier than ever to obtain, and provide a direct window into changes in frequencies of trait-associated alleles in the past. This has generated a new wave of studies aiming to analyse the genetic component of traits in historic and prehistoric times using ancient DNA, and to determine whether any such traits were subject to natural selection. In humans, however, issues about the portability and robustness of complex trait inference across different populations are particularly concerning when predictions are extended to individuals that died thousands of years ago, and for which little, if any, phenotypic validation is possible. In this review, we discuss the advantages of incorporating ancient genomes into studies of trait-associated variants, the need for models that can better accommodate ancient genomes into quantitative genetic frameworks, and the existing limits to inferences about complex trait evolution, particularly with respect to past populations.
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Affiliation(s)
- Evan K. Irving-Pease
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rasa Muktupavela
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Michael Dannemann
- Center for Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Fernando Racimo
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
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47
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Ancient DNA and multimethod dating confirm the late arrival of anatomically modern humans in southern China. Proc Natl Acad Sci U S A 2021; 118:2019158118. [PMID: 33558418 DOI: 10.1073/pnas.2019158118] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The expansion of anatomically modern humans (AMHs) from Africa around 65,000 to 45,000 y ago (ca. 65 to 45 ka) led to the establishment of present-day non-African populations. Some paleoanthropologists have argued that fossil discoveries from Huanglong, Zhiren, Luna, and Fuyan caves in southern China indicate one or more prior dispersals, perhaps as early as ca. 120 ka. We investigated the age of the human remains from three of these localities and two additional early AMH sites (Yangjiapo and Sanyou caves, Hubei) by combining ancient DNA (aDNA) analysis with a multimethod geological dating strategy. Although U-Th dating of capping flowstones suggested they lie within the range ca. 168 to 70 ka, analyses of aDNA and direct AMS 14C dating on human teeth from Fuyan and Yangjiapo caves showed they derive from the Holocene. OSL dating of sediments and AMS 14C analysis of mammal teeth and charcoal also demonstrated major discrepancies from the flowstone ages; the difference between them being an order of magnitude or more at most of these localities. Our work highlights the surprisingly complex depositional history recorded at these subtropical caves which involved one or more episodes of erosion and redeposition or intrusion as recently as the late Holocene. In light of our findings, the first appearance datum for AMHs in southern China should probably lie within the timeframe set by molecular data of ca. 50 to 45 ka.
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48
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Ahlquist KD, Bañuelos MM, Funk A, Lai J, Rong S, Villanea FA, Witt KE. Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture. Genome Biol Evol 2021; 13:evab115. [PMID: 34028527 PMCID: PMC8480178 DOI: 10.1093/gbe/evab115] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/07/2021] [Accepted: 05/22/2021] [Indexed: 11/30/2022] Open
Abstract
The archaic ancestry present in the human genome has captured the imagination of both scientists and the wider public in recent years. This excitement is the result of new studies pushing the envelope of what we can learn from the archaic genetic information that has survived for over 50,000 years in the human genome. Here, we review the most recent ten years of literature on the topic of archaic introgression, including the current state of knowledge on Neanderthal and Denisovan introgression, as well as introgression from other as-yet unidentified archaic populations. We focus this review on four topics: 1) a reimagining of human demographic history, including evidence for multiple admixture events between modern humans, Neanderthals, Denisovans, and other archaic populations; 2) state-of-the-art methods for detecting archaic ancestry in population-level genomic data; 3) how these novel methods can detect archaic introgression in modern African populations; and 4) the functional consequences of archaic gene variants, including how those variants were co-opted into novel function in modern human populations. The goal of this review is to provide a simple-to-access reference for the relevant methods and novel data, which has changed our understanding of the relationship between our species and its siblings. This body of literature reveals the large degree to which the genetic legacy of these extinct hominins has been integrated into the human populations of today.
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Affiliation(s)
- K D Ahlquist
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Mayra M Bañuelos
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Alyssa Funk
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Jiaying Lai
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Brown Center for Biomedical Informatics, Brown University, Providence, Rhode Island, USA
| | - Stephen Rong
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Fernando A Villanea
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Department of Anthropology, University of Colorado Boulder, Colorado, USA
| | - Kelsey E Witt
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, USA
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49
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Gregory MD, Eisenberg DP, Hamborg M, Kippenhan JS, Kohn P, Kolachana B, Dickinson D, Berman KF. Neanderthal-derived genetic variation in living humans relates to schizophrenia diagnosis, to psychotic symptom severity, and to dopamine synthesis. Am J Med Genet B Neuropsychiatr Genet 2021; 186:329-338. [PMID: 34487600 PMCID: PMC8454493 DOI: 10.1002/ajmg.b.32872] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/30/2021] [Accepted: 08/10/2021] [Indexed: 11/12/2022]
Abstract
Schizophrenia has been hypothesized to be a human-specific condition, but experimental approaches to testing this idea have been limited. Because Neanderthals, our closest evolutionary relatives, interbred with modern humans prior to their disappearance from the fossil record, leaving a residual echo that survives in our DNA today, we leveraged new discoveries about ancient hominid DNA to explore this hypothesis in living people in three converging ways. First, in four independent case-control datasets totaling 9,362 individuals, individuals with schizophrenia had less Neanderthal-derived genetic variation than controls (p = .044). Second, in 49 unmedicated inpatients with schizophrenia, having more Neanderthal admixture predicted less severe positive symptoms (p = .046). Finally, using 18 F-fluorodopa PET scanning in 172 healthy individuals, having greater Neanderthal introgression was significantly associated with lower dopamine synthesis capacity in the striatum and pons (p's < 2 × 10-5 ), which is fundamentally important in the pathophysiology and treatment of psychosis. These results may help to elucidate the evolutionary history of a devastating neuropsychiatric disease by supporting the notion of schizophrenia as a human-specific condition. Additionally, the relationship between Neanderthal admixture and dopamine function suggests a potential mechanism whereby Neanderthal admixture may have affected our gene pool to alter schizophrenia risk and/or course.
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Affiliation(s)
- Michael D. Gregory
- Section on Integrative Neuroimaging, Clinical and Translational Neuroscience Branch, National Institute of Mental Health, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Daniel P. Eisenberg
- Section on Integrative Neuroimaging, Clinical and Translational Neuroscience Branch, National Institute of Mental Health, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Madeline Hamborg
- Section on Integrative Neuroimaging, Clinical and Translational Neuroscience Branch, National Institute of Mental Health, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - J. Shane Kippenhan
- Section on Integrative Neuroimaging, Clinical and Translational Neuroscience Branch, National Institute of Mental Health, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Philip Kohn
- Section on Integrative Neuroimaging, Clinical and Translational Neuroscience Branch, National Institute of Mental Health, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Bhaskar Kolachana
- Human Brain Collection Core, National Institute of Mental Health, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Dwight Dickinson
- Psychosis and Cognitive Studies Section, Clinical and Translational Neuroscience Branch, National Institute of Mental Health, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Karen F. Berman
- Section on Integrative Neuroimaging, Clinical and Translational Neuroscience Branch, National Institute of Mental Health, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
- Psychosis and Cognitive Studies Section, Clinical and Translational Neuroscience Branch, National Institute of Mental Health, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
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50
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Abstract
The detection of introgression from genomic data is transforming our view of species and the origins of adaptive variation. Among the most widely used approaches to detect introgression is the so-called ABBA-BABA test or D-statistic, which identifies excess allele sharing between nonsister taxa. Part of the appeal of D is its simplicity, but this also limits its informativeness, particularly about the timing and direction of introgression. Here we present a simple extension, D frequency spectrum or DFS, in which D is partitioned according to the frequencies of derived alleles. We use simulations over a large parameter space to show how DFS carries information about various factors. In particular, recent introgression reliably leads to a peak in DFS among low-frequency derived alleles, whereas violation of model assumptions can lead to a lack of signal at low frequencies. We also reanalyze published empirical data from six different animal and plant taxa, and interpret the results in the light of our simulations, showing how DFS provides novel insights. We currently see DFS as a descriptive tool that will augment both simple and sophisticated tests for introgression, but in the future it may be usefully incorporated into probabilistic inference frameworks.
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Affiliation(s)
- Simon H Martin
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - William Amos
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
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