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Li L, Comi TJ, Bierman RF, Akey JM. Recurrent gene flow between Neanderthals and modern humans over the past 200,000 years. Science 2024; 385:eadi1768. [PMID: 38991054 DOI: 10.1126/science.adi1768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 05/14/2024] [Indexed: 07/13/2024]
Abstract
Although it is well known that the ancestors of modern humans and Neanderthals admixed, the effects of gene flow on the Neanderthal genome are not well understood. We develop methods to estimate the amount of human-introgressed sequences in Neanderthals and apply it to whole-genome sequence data from 2000 modern humans and three Neanderthals. We estimate that Neanderthals have 2.5 to 3.7% human ancestry, and we leverage human-introgressed sequences in Neanderthals to revise estimates of Neanderthal ancestry in modern humans, show that Neanderthal population sizes were significantly smaller than previously estimated, and identify two distinct waves of modern human gene flow into Neanderthals. Our data provide insights into the genetic legacy of recurrent gene flow between modern humans and Neanderthals.
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Affiliation(s)
- Liming Li
- Department of Medical Genetics and Developmental Biology, School of Medicine, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing 210009, China
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
| | - Troy J Comi
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
| | - Rob F Bierman
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
| | - Joshua M Akey
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
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2
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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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Aneli S, Ceccatelli Berti C, Gilea AI, Birolo G, Mutti G, Pavesi A, Baruffini E, Goffrini P, Capelli C. Functional characterization of archaic-specific variants in mitonuclear genes: insights from comparative analysis in S. cerevisiae. Hum Mol Genet 2024; 33:1152-1163. [PMID: 38558123 DOI: 10.1093/hmg/ddae057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/29/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024] Open
Abstract
Neanderthal and Denisovan hybridisation with modern humans has generated a non-random genomic distribution of introgressed regions, the result of drift and selection dynamics. Cross-species genomic incompatibility and more efficient removal of slightly deleterious archaic variants have been proposed as selection-based processes involved in the post-hybridisation purge of archaic introgressed regions. Both scenarios require the presence of functionally different alleles across Homo species onto which selection operated differently according to which populations hosted them, but only a few of these variants have been pinpointed so far. In order to identify functionally divergent archaic variants removed in humans, we focused on mitonuclear genes, which are underrepresented in the genomic landscape of archaic humans. We searched for non-synonymous, fixed, archaic-derived variants present in mitonuclear genes, rare or absent in human populations. We then compared the functional impact of archaic and human variants in the model organism Saccharomyces cerevisiae. Notably, a variant within the mitochondrial tyrosyl-tRNA synthetase 2 (YARS2) gene exhibited a significant decrease in respiratory activity and a substantial reduction of Cox2 levels, a proxy for mitochondrial protein biosynthesis, coupled with the accumulation of the YARS2 protein precursor and a lower amount of mature enzyme. Our work suggests that this variant is associated with mitochondrial functionality impairment, thus contributing to the purging of archaic introgression in YARS2. While different molecular mechanisms may have impacted other mitonuclear genes, our approach can be extended to the functional screening of mitonuclear genetic variants present across species and populations.
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Affiliation(s)
- Serena Aneli
- Department of Public Health Sciences and Pediatrics, University of Turin, C.so Galileo Galilei 22, Turin 10126, Italy
| | - Camilla Ceccatelli Berti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Alexandru Ionut Gilea
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Giovanni Birolo
- Department of Medical Sciences, University of Turin, Via Santena 5, Turin 10126, Italy
| | - Giacomo Mutti
- Barcelona Supercomputing Centre (BSC-CNS), Department of Life Sciences, Plaça Eusebi Güell, 1-3, Barcelona 08034, Spain
- Institute for Research in Biomedicine (IRB Barcelona), Department of Mechanisms of Disease, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Angelo Pavesi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Enrico Baruffini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Paola Goffrini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Cristian Capelli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
- Department of Biology, University of Oxford, 11a Mansfield Rd, Oxford OX1 3SZ, United Kingdom
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Li C, Lambers H, Jing J, Zhang C, Bezemer TM, Klironomos J, Cong WF, Zhang F. Belowground cascading biotic interactions trigger crop diversity benefits. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00115-8. [PMID: 38821841 DOI: 10.1016/j.tplants.2024.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/21/2024] [Accepted: 04/30/2024] [Indexed: 06/02/2024]
Abstract
Crop diversification practices offer numerous synergistic benefits. So far, research has traditionally been confined to exploring isolated, unidirectional single-process interactions among plants, soil, and microorganisms. Here, we present a novel and systematic perspective, unveiling the intricate web of plant-soil-microbiome interactions that trigger cascading effects. Applying the principles of cascading interactions can be an alternative way to overcome soil obstacles such as soil compaction and soil pathogen pressure. Finally, we introduce a research framework comprising the design of diversified cropping systems by including commercial varieties and crops with resource-efficient traits, the exploration of cascading effects, and the innovation of field management. We propose that this provides theoretical and methodological insights that can reveal new mechanisms by which crop diversity increases productivity.
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Affiliation(s)
- Chunjie Li
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Hans Lambers
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; School of Biological Sciences and Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia
| | - Jingying Jing
- College of Grassland Science and Technology, China Agricultural University, 100193 Beijing, China
| | - Chaochun Zhang
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - T Martijn Bezemer
- Institute of Biology, Leiden University, 2333, BE, Leiden, The Netherlands
| | - John Klironomos
- Department of Biology, Chemistry and Environmental Sciences, American University of Sharjah, PO Box 26666, Sharjah, United Arab Emirates
| | - Wen-Feng Cong
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.
| | - Fusuo Zhang
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
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Pauly R, Johnson L, Feltus FA, Casanova EL. Enrichment of a subset of Neanderthal polymorphisms in autistic probands and siblings. Mol Psychiatry 2024:10.1038/s41380-024-02593-7. [PMID: 38760502 DOI: 10.1038/s41380-024-02593-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 05/19/2024]
Abstract
Homo sapiens and Neanderthals underwent hybridization during the Middle/Upper Paleolithic age, culminating in retention of small amounts of Neanderthal-derived DNA in the modern human genome. In the current study, we address the potential roles Neanderthal single nucleotide polymorphisms (SNP) may be playing in autism susceptibility in samples of black non-Hispanic, white Hispanic, and white non-Hispanic people using data from the Simons Foundation Powering Autism Research (SPARK), Genotype-Tissue Expression (GTEx), and 1000 Genomes (1000G) databases. We have discovered that rare variants are significantly enriched in autistic probands compared to race-matched controls. In addition, we have identified 25 rare and common SNPs that are significantly enriched in autism on different ethnic backgrounds, some of which show significant clinical associations. We have also identified other SNPs that share more specific genotype-phenotype correlations but which are not necessarily enriched in autism and yet may nevertheless play roles in comorbid phenotype expression (e.g., intellectual disability, epilepsy, and language regression). These results strongly suggest Neanderthal-derived DNA is playing a significant role in autism susceptibility across major populations in the United States.
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Affiliation(s)
- Rini Pauly
- Biomedical Data Science and Informatics Program, Clemson University, Clemson, SC, 29634, USA
| | - Layla Johnson
- Department of Psychology, Loyola University, New Orleans, New Orleans, LA, 70118, USA
| | - F Alex Feltus
- Biomedical Data Science and Informatics Program, Clemson University, Clemson, SC, 29634, USA
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA
- Center for Human Genetics, Clemson University, Clemson, SC, 29634, USA
| | - Emily L Casanova
- Department of Psychology, Loyola University, New Orleans, New Orleans, LA, 70118, USA.
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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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Ferreira RC, Rodrigues CR, Broach JR, Briones MRS. Convergent Mutations and Single Nucleotide Variants in Mitochondrial Genomes of Modern Humans and Neanderthals. Int J Mol Sci 2024; 25:3785. [PMID: 38612593 PMCID: PMC11012180 DOI: 10.3390/ijms25073785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 04/14/2024] Open
Abstract
The genetic contributions of Neanderthals to the modern human genome have been evidenced by the comparison of present-day human genomes with paleogenomes. Neanderthal signatures in extant human genomes are attributed to intercrosses between Neanderthals and archaic anatomically modern humans (AMHs). Although Neanderthal signatures are well documented in the nuclear genome, it has been proposed that there is no contribution of Neanderthal mitochondrial DNA to contemporary human genomes. Here we show that modern human mitochondrial genomes contain 66 potential Neanderthal signatures, or Neanderthal single nucleotide variants (N-SNVs), of which 36 lie in coding regions and 7 result in nonsynonymous changes. Seven N-SNVs are associated with traits such as cycling vomiting syndrome, Alzheimer's disease and Parkinson's disease, and two N-SNVs are associated with intelligence quotient. Based on recombination tests, principal component analysis (PCA) and the complete absence of these N-SNVs in 41 archaic AMH mitogenomes, we conclude that convergent evolution, and not recombination, explains the presence of N-SNVs in present-day human mitogenomes.
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Affiliation(s)
- Renata C. Ferreira
- Center for Medical Bioinformatics, Federal University of São Paulo, São Paulo 04039032, SP, Brazil;
| | - Camila R. Rodrigues
- Graduate Program in Microbiology and Immunology, Federal University of São Paulo, São Paulo 04039032, SP, Brazil;
| | - James R. Broach
- Department of Biochemistry, Institute for Personalized Medicine, Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA;
| | - Marcelo R. S. Briones
- Center for Medical Bioinformatics, Federal University of São Paulo, São Paulo 04039032, SP, Brazil;
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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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Zeberg H, Jakobsson M, Pääbo S. The genetic changes that shaped Neandertals, Denisovans, and modern humans. Cell 2024; 187:1047-1058. [PMID: 38367615 DOI: 10.1016/j.cell.2023.12.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/20/2023] [Accepted: 12/20/2023] [Indexed: 02/19/2024]
Abstract
Modern human ancestors diverged from the ancestors of Neandertals and Denisovans about 600,000 years ago. Until about 40,000 years ago, these three groups existed in parallel, occasionally met, and exchanged genes. A critical question is why modern humans, and not the other two groups, survived, became numerous, and developed complex cultures. Here, we discuss genetic differences among the groups and some of their functional consequences. As more present-day genome sequences become available from diverse groups, we predict that very few, if any, differences will distinguish all modern humans from all Neandertals and Denisovans. We propose that the genetic basis of what constitutes a modern human is best thought of as a combination of genetic features, where perhaps none of them is present in each and every present-day individual.
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Affiliation(s)
- Hugo Zeberg
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Physiology and Pharmacology, Karolinska Institutet, 17165 Stockholm, Sweden.
| | - Mattias Jakobsson
- Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Okinawa Institute of Science and Technology, Onnason 904-0495, Okinawa, Japan.
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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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Piszczek L, Kaczanowska J, Haubensak W. Towards correlative archaeology of the human mind. Biol Chem 2024; 405:5-12. [PMID: 37819768 PMCID: PMC10687516 DOI: 10.1515/hsz-2023-0199] [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: 05/01/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023]
Abstract
Retracing human cognitive origins started out at the systems level with the top-down interpretation of archaeological records spanning from man-made artifacts to endocasts of ancient skulls. With emerging evolutionary genetics and organoid technologies, it is now possible to deconstruct evolutionary processes on a molecular/cellular level from the bottom-up by functionally testing archaic alleles in experimental models. The current challenge is to complement these approaches with novel strategies that allow a holistic reconstruction of evolutionary patterns across human cognitive domains. We argue that computational neuroarcheology can provide such a critical mesoscale framework at the brain network-level, linking molecular/cellular (bottom-up) to systems (top-down) level data for the correlative archeology of the human mind.
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Affiliation(s)
- Lukasz Piszczek
- Department of Neuronal Cell Biology, Center for Brain Research, Medical University of Vienna, A-Vienna, Austria
| | | | - Wulf Haubensak
- Department of Neuronal Cell Biology, Center for Brain Research, Medical University of Vienna, A-Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, A-1030Vienna, Austria
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Lei H, Li J, Zhao B, Kou SH, Xiao F, Chen T, Wang SM. Evolutionary origin of germline pathogenic variants in human DNA mismatch repair genes. Hum Genomics 2024; 18:5. [PMID: 38287404 PMCID: PMC10823654 DOI: 10.1186/s40246-024-00573-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 01/17/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND Mismatch repair (MMR) system is evolutionarily conserved for genome stability maintenance. Germline pathogenic variants (PVs) in MMR genes that lead to MMR functional deficiency are associated with high cancer risk. Knowing the evolutionary origin of germline PVs in human MMR genes will facilitate understanding the biological base of MMR deficiency in cancer. However, systematic knowledge is lacking to address the issue. In this study, we performed a comprehensive analysis to know the evolutionary origin of human MMR PVs. METHODS We retrieved MMR gene variants from the ClinVar database. The genomes of 100 vertebrates were collected from the UCSC genome browser and ancient human sequencing data were obtained through comprehensive data mining. Cross-species conservation analysis was performed based on the phylogenetic relationship among 100 vertebrates. Rescaled ancient sequencing data were used to perform variant calling for archeological analysis. RESULTS Using the phylogenetic approach, we traced the 3369 MMR PVs identified in modern humans in 99 non-human vertebrate genomes but found no evidence for cross-species conservation as the source for human MMR PVs. Using the archeological approach, we searched the human MMR PVs in over 5000 ancient human genomes dated from 45,045 to 100 years before present and identified a group of MMR PVs shared between modern and ancient humans mostly within 10,000 years with similar quantitative patterns. CONCLUSION Our study reveals that MMR PVs in modern humans were arisen within the recent human evolutionary history.
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Affiliation(s)
- Huijun Lei
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310018, Zhejiang, China
- Department of Cancer Prevention, Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, China
| | - Jiaheng Li
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Bojin Zhao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Si Hoi Kou
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Fengxia Xiao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Tianhui Chen
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310018, Zhejiang, China.
- Department of Cancer Prevention, Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, China.
| | - San Ming Wang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China.
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13
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Stefanucci L, Collins J, Sims MC, Barrio-Hernandez I, Sun L, Burren OS, Perfetto L, Bender I, Callahan TJ, Fleming K, Guerrero JA, Hermjakob H, Martin MJ, Stephenson J, Paneerselvam K, Petrovski S, Porras P, Robinson PN, Wang Q, Watkins X, Frontini M, Laskowski RA, Beltrao P, Di Angelantonio E, Gomez K, Laffan M, Ouwehand WH, Mumford AD, Freson K, Carss K, Downes K, Gleadall N, Megy K, Bruford E, Vuckovic D. The effects of pathogenic and likely pathogenic variants for inherited hemostasis disorders in 140 214 UK Biobank participants. Blood 2023; 142:2055-2068. [PMID: 37647632 PMCID: PMC10733830 DOI: 10.1182/blood.2023020118] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 08/04/2023] [Accepted: 08/04/2023] [Indexed: 09/01/2023] Open
Abstract
Rare genetic diseases affect millions, and identifying causal DNA variants is essential for patient care. Therefore, it is imperative to estimate the effect of each independent variant and improve their pathogenicity classification. Our study of 140 214 unrelated UK Biobank (UKB) participants found that each of them carries a median of 7 variants previously reported as pathogenic or likely pathogenic. We focused on 967 diagnostic-grade gene (DGG) variants for rare bleeding, thrombotic, and platelet disorders (BTPDs) observed in 12 367 UKB participants. By association analysis, for a subset of these variants, we estimated effect sizes for platelet count and volume, and odds ratios for bleeding and thrombosis. Variants causal of some autosomal recessive platelet disorders revealed phenotypic consequences in carriers. Loss-of-function variants in MPL, which cause chronic amegakaryocytic thrombocytopenia if biallelic, were unexpectedly associated with increased platelet counts in carriers. We also demonstrated that common variants identified by genome-wide association studies (GWAS) for platelet count or thrombosis risk may influence the penetrance of rare variants in BTPD DGGs on their associated hemostasis disorders. Network-propagation analysis applied to an interactome of 18 410 nodes and 571 917 edges showed that GWAS variants with large effect sizes are enriched in DGGs and their first-order interactors. Finally, we illustrate the modifying effect of polygenic scores for platelet count and thrombosis risk on disease severity in participants carrying rare variants in TUBB1 or PROC and PROS1, respectively. Our findings demonstrate the power of association analyses using large population datasets in improving pathogenicity classifications of rare variants.
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Affiliation(s)
- Luca Stefanucci
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- British Heart Foundation, BHF Centre of Research Excellence, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Janine Collins
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Haematology, Barts Health NHS Trust, London, United Kingdom
| | - Matthew C. Sims
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Haematology, Sheffield Teaching Hospitals NHS Foundation Trust, Royal Hallamshire Hospital, Sheffield, United Kingdom
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - Inigo Barrio-Hernandez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Luanluan Sun
- Department of Public Health and Primary Care, BHF Cardiovascular Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Oliver S. Burren
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Livia Perfetto
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Department of Biology and Biotechnology “C.Darwin,” Sapienza University of Rome, Rome, Italy
| | - Isobel Bender
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Tiffany J. Callahan
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY
| | - Kathryn Fleming
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Jose A. Guerrero
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Haematology, Barts Health NHS Trust, London, United Kingdom
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Maria J. Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - James Stephenson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - NIHR BioResource
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- British Heart Foundation, BHF Centre of Research Excellence, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Haematology, Barts Health NHS Trust, London, United Kingdom
- Department of Haematology, Sheffield Teaching Hospitals NHS Foundation Trust, Royal Hallamshire Hospital, Sheffield, United Kingdom
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Department of Public Health and Primary Care, BHF Cardiovascular Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
- Department of Biology and Biotechnology “C.Darwin,” Sapienza University of Rome, Rome, Italy
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
- Centre for Genomics Research, Discovery Sciences, AstraZeneca, Cambridge, United Kingdom
- Department of Medicine, Austin Health, The University of Melbourne, Melbourne, Australia
- Genomic Medicine, The Jackson Laboratory, Farmington, CT
- Institute for Systems Genomics, University of Connecticut, Farmington, CT
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences RILD Building, University of Exeter Medical School, Exeter, United Kingdom
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
- Heart and Lung Research Institute, University of Cambridge, Cambridge, United Kingdom
- NIHR Blood and Transplant Research Unit in Donor Health and Behaviour, Cambridge, United Kingdom
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, United Kingdom
- Health Data Science Centre, Human Technopole, Milan, Italy
- Haemophilia Centre and Thrombosis Unit, Royal Free London NHS Foundation Trust, London, United Kingdom
- Department of Haematology, Imperial College Healthcare NHS Trust, London, United Kingdom
- Department of Immunology and Inflammation, Centre for Haematology, Imperial College London, London, United Kingdom
- Department of Haematology, University College London Hospitals NHS Trust, London, United Kingdom
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, KULeuven, Leuven, Belgium
- Cambridge Genomics Laboratory, Cambridge University Hospitals National Health Service Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
| | - Kalpana Paneerselvam
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, AstraZeneca, Cambridge, United Kingdom
- Department of Medicine, Austin Health, The University of Melbourne, Melbourne, Australia
| | - Pablo Porras
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Peter N. Robinson
- Genomic Medicine, The Jackson Laboratory, Farmington, CT
- Institute for Systems Genomics, University of Connecticut, Farmington, CT
| | - Quanli Wang
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Xavier Watkins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Mattia Frontini
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- British Heart Foundation, BHF Centre of Research Excellence, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences RILD Building, University of Exeter Medical School, Exeter, United Kingdom
| | - Roman A. Laskowski
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Pedro Beltrao
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Emanuele Di Angelantonio
- British Heart Foundation, BHF Centre of Research Excellence, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Public Health and Primary Care, BHF Cardiovascular Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
- Heart and Lung Research Institute, University of Cambridge, Cambridge, United Kingdom
- NIHR Blood and Transplant Research Unit in Donor Health and Behaviour, Cambridge, United Kingdom
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, United Kingdom
- Health Data Science Centre, Human Technopole, Milan, Italy
| | - Keith Gomez
- Haemophilia Centre and Thrombosis Unit, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Mike Laffan
- Department of Haematology, Imperial College Healthcare NHS Trust, London, United Kingdom
- Department of Immunology and Inflammation, Centre for Haematology, Imperial College London, London, United Kingdom
| | - Willem H. Ouwehand
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Haematology, University College London Hospitals NHS Trust, London, United Kingdom
| | - Andrew D. Mumford
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, KULeuven, Leuven, Belgium
| | - Keren Carss
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Cambridge Genomics Laboratory, Cambridge University Hospitals National Health Service Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Nick Gleadall
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Karyn Megy
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Elspeth Bruford
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Dragana Vuckovic
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
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14
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Houldcroft CJ, Underdown S. Infectious disease in the Pleistocene: Old friends or old foes? AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 182:513-531. [PMID: 38006200 DOI: 10.1002/ajpa.24737] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 03/01/2023] [Accepted: 03/14/2023] [Indexed: 11/26/2023]
Abstract
The impact of endemic and epidemic disease on humans has traditionally been seen as a comparatively recent historical phenomenon associated with the Neolithisation of human groups, an increase in population size led by sedentarism, and increasing contact with domesticated animals as well as species occupying opportunistic symbiotic and ectosymbiotic relationships with humans. The orthodox approach is that Neolithisation created the conditions for increasing population size able to support a reservoir of infectious disease sufficient to act as selective pressure. This orthodoxy is the result of an overly simplistic reliance on skeletal data assuming that no skeletal lesions equated to a healthy individual, underpinned by the assumption that hunter-gatherer groups were inherently healthy while agricultural groups acted as infectious disease reservoirs. The work of van Blerkom, Am. J. Phys. Anthropol., vol. suppl 37 (2003), Wolfe et al., Nature, vol. 447 (2007) and Houldcroft and Underdown, Am. J. Phys. Anthropol., vol. 160, (2016) has changed this landscape by arguing that humans and pathogens have long been fellow travelers. The package of infectious diseases experienced by our ancient ancestors may not be as dissimilar to modern infectious diseases as was once believed. The importance of DNA, from ancient and modern sources, to the study of the antiquity of infectious disease, and its role as a selective pressure cannot be overstated. Here we consider evidence of ancient epidemic and endemic infectious diseases with inferences from modern and ancient human and hominin DNA, and from circulating and extinct pathogen genomes. We argue that the pandemics of the past are a vital tool to unlock the weapons needed to fight pandemics of the future.
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Affiliation(s)
| | - Simon Underdown
- Human Origins and Palaeoenvironmental Research Group, School of Social Sciences, Oxford Brookes University, Oxford, UK
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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15
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Pollen AA, Kilik U, Lowe CB, Camp JG. Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution. Nat Rev Genet 2023; 24:687-711. [PMID: 36737647 PMCID: PMC9897628 DOI: 10.1038/s41576-022-00568-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2022] [Indexed: 02/05/2023]
Abstract
Our ancestors acquired morphological, cognitive and metabolic modifications that enabled humans to colonize diverse habitats, develop extraordinary technologies and reshape the biosphere. Understanding the genetic, developmental and molecular bases for these changes will provide insights into how we became human. Connecting human-specific genetic changes to species differences has been challenging owing to an abundance of low-effect size genetic changes, limited descriptions of phenotypic differences across development at the level of cell types and lack of experimental models. Emerging approaches for single-cell sequencing, genetic manipulation and stem cell culture now support descriptive and functional studies in defined cell types with a human or ape genetic background. In this Review, we describe how the sequencing of genomes from modern and archaic hominins, great apes and other primates is revealing human-specific genetic changes and how new molecular and cellular approaches - including cell atlases and organoids - are enabling exploration of the candidate causal factors that underlie human-specific traits.
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Affiliation(s)
- Alex A Pollen
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
| | - Umut Kilik
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Craig B Lowe
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
| | - J Gray Camp
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
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16
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Piccardi M, Gentiluomo M, Bertoncini S, Pezzilli R, Erőss B, Bunduc S, Uzunoglu FG, Talar-Wojnarowska R, Vanagas T, Sperti C, Oliverius M, Aoki MN, Ermini S, Hussein T, Boggi U, Jamroziak K, Maiello E, Morelli L, Vodickova L, Di Franco G, Landi S, Szentesi A, Lovecek M, Puzzono M, Tavano F, van Laarhoven HWM, Zerbi A, Mohelnikova-Duchonova B, Stocker H, Costello E, Capurso G, Ginocchi L, Lawlor RT, Vanella G, Bazzocchi F, Izbicki JR, Latiano A, Bueno-de-Mesquita B, Ponz de Leon Pisani R, Schöttker B, Soucek P, Hegyi P, Gazouli M, Hackert T, Kupcinskas J, Poskiene L, Tacelli M, Roth S, Carrara S, Perri F, Hlavac V, Theodoropoulos GE, Busch OR, Mambrini A, van Eijck CHJ, Arcidiacono P, Scarpa A, Pasquali C, Basso D, Lucchesi M, Milanetto AC, Neoptolemos JP, Cavestro GM, Janciauskas D, Chen X, Chammas R, Goetz M, Brenner H, Archibugi L, Dannemann M, Canzian F, Tofanelli S, Campa D. Exploring the Neandertal legacy of pancreatic ductal adenocarcinoma risk in Eurasians. Biol Res 2023; 56:46. [PMID: 37574541 PMCID: PMC10424372 DOI: 10.1186/s40659-023-00457-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/20/2023] [Indexed: 08/15/2023] Open
Abstract
BACKGROUND The genomes of present-day non-Africans are composed of 1-3% of Neandertal-derived DNA as a consequence of admixture events between Neandertals and anatomically modern humans about 50-60 thousand years ago. Neandertal-introgressed single nucleotide polymorphisms (aSNPs) have been associated with modern human disease-related traits, which are risk factors for pancreatic ductal adenocarcinoma (PDAC), such as obesity, type 2 diabetes, and inflammation. In this study, we aimed at investigating the role of aSNPs in PDAC in three Eurasian populations. RESULTS The high-coverage Vindija Neandertal genome was used to select aSNPs in non-African populations from 1000 Genomes project phase 3 data. Then, the association between aSNPs and PDAC risk was tested independently in Europeans and East Asians, using existing GWAS data on more than 200 000 individuals. We did not find any significant associations between aSNPs and PDAC in samples of European descent, whereas, in East Asians, we observed that the Chr10p12.1-rs117585753-T allele (MAF = 10%) increased the risk to develop PDAC (OR = 1.35, 95%CI 1.19-1.54, P = 3.59 × 10-6), with a P-value close to a threshold that takes into account multiple testing. CONCLUSIONS Our results show only a minimal contribution of Neandertal SNPs to PDAC risk.
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Affiliation(s)
- Margherita Piccardi
- Department of Biology, Unit of Genetics, University of Pisa, Via Derna 1, 56126, Pisa, Italy
| | - Manuel Gentiluomo
- Department of Biology, Unit of Genetics, University of Pisa, Via Derna 1, 56126, Pisa, Italy
| | - Stefania Bertoncini
- Department of Biology, Unit of Zoology and Anthropology, University of Pisa, Pisa, Italy
| | | | - Bálint Erőss
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Stefania Bunduc
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
- Center for Translational Medicine, Semmelweis University, Budapest, Hungary
- Division of Pancreatic Diseases, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
- Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Faik G Uzunoglu
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Tomas Vanagas
- Department of Surgery, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Cosimo Sperti
- Department DISCOG, Chirurgia Generale 1, University of Padova, Padua, Italy
| | - Martin Oliverius
- Department of Surgery, Third Faculty of Medicine, University Hospital Kralovske Vinohrady, Charles University, Prague, Czech Republic
| | - Mateus Nóbrega Aoki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Curitiba, Brazil
| | - Stefano Ermini
- Blood Transfusion Service, Azienda Ospedaliero-Universitaria Meyer, Children's Hospital, Florence, Italy
| | - Tamás Hussein
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Ugo Boggi
- Division of General and Transplantation Surgery, University of Pisa, Pisa, Italy
| | - Krzysztof Jamroziak
- Department of Hematology, Transplantation and Internal Medicine, University of Warsaw, Warsaw, Poland
| | - Evaristo Maiello
- Department of Oncology, Fondazione IRCCS "Casa Sollievo Della Sofferenza" Hospital, San Giovanni Rotondo, Foggia, Italy
| | - Luca Morelli
- Department of Translational Research and New Technologies in Medicine and Surgery, General Surgery Unit, University of Pisa, Pisa, Italy
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Gregorio Di Franco
- Department of Translational Research and New Technologies in Medicine and Surgery, General Surgery Unit, University of Pisa, Pisa, Italy
| | - Stefano Landi
- Department of Biology, Unit of Genetics, University of Pisa, Via Derna 1, 56126, Pisa, Italy
| | - Andrea Szentesi
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
- Center for Translational Medicine, Semmelweis University, Budapest, Hungary
- János Szentágothai Research Center, University of Pécs, Pécs, Hungary
| | - Martin Lovecek
- Department of Surgery I, University Hospital Olomouc, Olomouc, Czech Republic
| | - Marta Puzzono
- Gastroenterology and Gastrointestinal Endoscopy Unit, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesca Tavano
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo Della Sofferenza" Hospital, San Giovanni Rotondo, Foggia, Italy
| | - Hanneke W M van Laarhoven
- Department of Medical Oncology, Amsterdam UMC, Cancer Center Amsterdam, University of Amsterdam, Amsterdam, The Netherlands
| | - Alessandro Zerbi
- Pancreatic Unit, IRCCS Humanitas Research Hospital, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | | | - Hannah Stocker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Network Aging Research (NAR), Heidelberg University, Heidelberg, Germany
| | - Eithne Costello
- Department of Molecular & Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Gabriele Capurso
- Digestive and Liver Disease Unit, S Andrea Hospital, Rome, Italy
- Pancreas Translational and Clinical Research Center, Pancreato-Biliary Endoscopy and Endoscopic Ultrasound, San Raffaele Scientific Institute IRCCS, Milan, Italy
| | - Laura Ginocchi
- Oncological Department, Oncology of Massa Carrara, ASL Toscana Nord Ovest, Massa Carrara, Italy
| | - Rita T Lawlor
- ARC-NET Research Centre and Department of Diagnostics and Public Health, Section of Pathology, University of Verona, Verona, Italy
| | - Giuseppe Vanella
- Digestive and Liver Disease Unit, S Andrea Hospital, Rome, Italy
- Pancreas Translational and Clinical Research Center, Pancreato-Biliary Endoscopy and Endoscopic Ultrasound, San Raffaele Scientific Institute IRCCS, Milan, Italy
| | - Francesca Bazzocchi
- Department of Surgery, Fondazione IRCCS "Casa Sollievo Della Sofferenza" Hospital, San Giovanni Rotondo, Foggia, Italy
| | - Jakob R Izbicki
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna Latiano
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo Della Sofferenza" Hospital, San Giovanni Rotondo, Foggia, Italy
| | - Bas Bueno-de-Mesquita
- Centre for Nutrition, Prevention and Health Services, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Ruggero Ponz de Leon Pisani
- Pancreato-Biliary Endoscopy and Endoscopic Ultrasound, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute IRCCS, Milan, Italy
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Network Aging Research (NAR), Heidelberg University, Heidelberg, Germany
| | - Pavel Soucek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Péter Hegyi
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
- Center for Translational Medicine, Semmelweis University, Budapest, Hungary
- Division of Pancreatic Diseases, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
- János Szentágothai Research Center, University of Pécs, Pécs, Hungary
| | - Maria Gazouli
- Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Thilo Hackert
- Department of General, Visceral, and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Juozas Kupcinskas
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Lina Poskiene
- Department of Pathology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Matteo Tacelli
- Pancreato-Biliary Endoscopy and Endoscopic Ultrasound, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute IRCCS, Milan, Italy
| | - Susanne Roth
- Department of General, Visceral, and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Silvia Carrara
- Department of Gastroenterology, Endoscopic Unit, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Francesco Perri
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo Della Sofferenza" Hospital, San Giovanni Rotondo, Foggia, Italy
| | - Viktor Hlavac
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - George E Theodoropoulos
- First Department of Propaedeutic Surgery, Hippocration General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Olivier R Busch
- Department of Surgery, Amsterdam UMC, Cancer Center Amsterdam, University of Amsterdam, Amsterdam, the Netherlands
| | - Andrea Mambrini
- Oncological Department, Oncology of Massa Carrara, ASL Toscana Nord Ovest, Massa Carrara, Italy
| | - Casper H J van Eijck
- Department of Surgery, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Paolo Arcidiacono
- Pancreato-Biliary Endoscopy and Endoscopic Ultrasound, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute IRCCS, Milan, Italy
| | - Aldo Scarpa
- ARC-NET Research Centre and Department of Diagnostics and Public Health, Section of Pathology, University of Verona, Verona, Italy
| | - Claudio Pasquali
- Department DISCOG, Chirurgia Generale 3, University of Padova, Padua, Italy
| | - Daniela Basso
- Department DIMED, Laboratory Medicine, University of Padova, Padua, Italy
| | - Maurizio Lucchesi
- Oncological Department, Oncology of Massa Carrara, ASL Toscana Nord Ovest, Massa Carrara, Italy
| | | | - John P Neoptolemos
- Department of General, Visceral, and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Giulia Martina Cavestro
- Gastroenterology and Gastrointestinal Endoscopy Unit, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Dainius Janciauskas
- Department of Pathology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Xuechen Chen
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Roger Chammas
- Department of Radiology and Oncology, Institute of Cancer of São Paulo (ICESP) São Paulo, Sao Paulo, Brazil
- Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Mara Goetz
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Livia Archibugi
- Digestive and Liver Disease Unit, S Andrea Hospital, Rome, Italy
- Pancreas Translational and Clinical Research Center, Pancreato-Biliary Endoscopy and Endoscopic Ultrasound, San Raffaele Scientific Institute IRCCS, Milan, Italy
| | - Michael Dannemann
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sergio Tofanelli
- Department of Biology, Unit of Zoology and Anthropology, University of Pisa, Pisa, Italy
| | - Daniele Campa
- Department of Biology, Unit of Genetics, University of Pisa, Via Derna 1, 56126, Pisa, Italy.
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17
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Rong S, Neil CR, Welch A, Duan C, Maguire S, Meremikwu IC, Meyerson M, Evans BJ, Fairbrother WG. Large-scale functional screen identifies genetic variants with splicing effects in modern and archaic humans. Proc Natl Acad Sci U S A 2023; 120:e2218308120. [PMID: 37192163 PMCID: PMC10214146 DOI: 10.1073/pnas.2218308120] [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: 11/07/2022] [Accepted: 04/12/2023] [Indexed: 05/18/2023] Open
Abstract
Humans coexisted and interbred with other hominins which later became extinct. These archaic hominins are known to us only through fossil records and for two cases, genome sequences. Here, we engineer Neanderthal and Denisovan sequences into thousands of artificial genes to reconstruct the pre-mRNA processing patterns of these extinct populations. Of the 5,169 alleles tested in this massively parallel splicing reporter assay (MaPSy), we report 962 exonic splicing mutations that correspond to differences in exon recognition between extant and extinct hominins. Using MaPSy splicing variants, predicted splicing variants, and splicing quantitative trait loci, we show that splice-disrupting variants experienced greater purifying selection in anatomically modern humans than that in Neanderthals. Adaptively introgressed variants were enriched for moderate-effect splicing variants, consistent with positive selection for alternative spliced alleles following introgression. As particularly compelling examples, we characterized a unique tissue-specific alternative splicing variant at the adaptively introgressed innate immunity gene TLR1, as well as a unique Neanderthal introgressed alternative splicing variant in the gene HSPG2 that encodes perlecan. We further identified potentially pathogenic splicing variants found only in Neanderthals and Denisovans in genes related to sperm maturation and immunity. Finally, we found splicing variants that may contribute to variation among modern humans in total bilirubin, balding, hemoglobin levels, and lung capacity. Our findings provide unique insights into natural selection acting on splicing in human evolution and demonstrate how functional assays can be used to identify candidate causal variants underlying differences in gene regulation and phenotype.
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Affiliation(s)
- Stephen Rong
- Center for Computational Molecular Biology, Brown University, Providence, RI02912
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
| | - Christopher R. Neil
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
| | - Anastasia Welch
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
| | - Chaorui Duan
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
| | - Samantha Maguire
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
| | - Ijeoma C. Meremikwu
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
| | - Malcolm Meyerson
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
| | - Ben J. Evans
- Department of Biology, McMaster University, Hamilton, ONL8S 4K1, Canada
| | - William G. Fairbrother
- Center for Computational Molecular Biology, Brown University, Providence, RI02912
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
- Hassenfeld Child Health Innovation Institute of Brown University, Providence, RI02912
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18
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Chen Z, Reynolds RH, Pardiñas AF, Gagliano Taliun SA, van Rheenen W, Lin K, Shatunov A, Gustavsson EK, Fogh I, Jones AR, Robberecht W, Corcia P, Chiò A, Shaw PJ, Morrison KE, Veldink JH, van den Berg LH, Shaw CE, Powell JF, Silani V, Hardy JA, Houlden H, Owen MJ, Turner MR, Ryten M, Al-Chalabi A. The contribution of Neanderthal introgression and natural selection to neurodegenerative diseases. Neurobiol Dis 2023; 180:106082. [PMID: 36925053 DOI: 10.1016/j.nbd.2023.106082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
Humans are thought to be more susceptible to neurodegeneration than equivalently-aged primates. It is not known whether this vulnerability is specific to anatomically-modern humans or shared with other hominids. The contribution of introgressed Neanderthal DNA to neurodegenerative disorders remains uncertain. It is also unclear how common variants associated with neurodegenerative disease risk are maintained by natural selection in the population despite their deleterious effects. In this study, we aimed to quantify the genome-wide contribution of Neanderthal introgression and positive selection to the heritability of complex neurodegenerative disorders to address these questions. We used stratified-linkage disequilibrium score regression to investigate the relationship between five SNP-based signatures of natural selection, reflecting different timepoints of evolution, and genome-wide associated variants of the three most prevalent neurodegenerative disorders: Alzheimer's disease, amyotrophic lateral sclerosis and Parkinson's disease. We found no evidence for enrichment of positively-selected SNPs in the heritability of Alzheimer's disease, amyotrophic lateral sclerosis and Parkinson's disease, suggesting that common deleterious disease variants are unlikely to be maintained by positive selection. There was no enrichment of Neanderthal introgression in the SNP-heritability of these disorders, suggesting that Neanderthal admixture is unlikely to have contributed to disease risk. These findings provide insight into the origins of neurodegenerative disorders within the evolution of Homo sapiens and addresses a long-standing debate, showing that Neanderthal admixture is unlikely to have contributed to common genetic risk of neurodegeneration in anatomically-modern humans.
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Affiliation(s)
- Zhongbo Chen
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London (UCL), London, UK; Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, UCL, London, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL, London, UK.
| | - Regina H Reynolds
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, UCL, London, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL, London, UK
| | - Antonio F Pardiñas
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Sarah A Gagliano Taliun
- Department of Medicine & Department of Neurosciences, Université de Montréal, Montréal, Québec, Canada; Montréal Heart Institute, Montréal, Québec, Canada
| | - Wouter van Rheenen
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, the Netherlands
| | - Kuang Lin
- Nuffield Department of Population Health, Oxford University, Oxford, UK
| | - Aleksey Shatunov
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Emil K Gustavsson
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, UCL, London, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL, London, UK
| | - Isabella Fogh
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Ashley R Jones
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Wim Robberecht
- Department of Neurology, University Hospital Leuven, Leuven, Belgium; Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease, Leuven, Belgium; Vesalius Research Center, Laboratory of Neurobiology, Leuven, Belgium
| | - Philippe Corcia
- ALS Center, Department of Neurology, CHRU Bretonneau, Tours, France
| | - Adriano Chiò
- Rita Levi Montalcini Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy; Azienda Ospedaliera Universitaria Città della Salute e della Scienza, Torino, Italy
| | - Pamela J Shaw
- Academic Neurology Unit, Department of Neuroscience, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, UK
| | - Karen E Morrison
- School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Jan H Veldink
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, the Netherlands
| | - Leonard H van den Berg
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, the Netherlands
| | - Christopher E Shaw
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - John F Powell
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Vincenzo Silani
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milano, Italy; Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, 20122 Milano, Italy
| | - John A Hardy
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London (UCL), London, UK; Reta Lila Weston Institute, Queen Square Institute of Neurology, UCL, London, UK; UK Dementia Research Institute, Queen Square Institute of Neurology, UCL, London, UK; NIHR University College London Hospitals Biomedical Research Centre, London, UK; Institute for Advanced Study, The Hong Kong University of Science and Technology, Hong Kong, SAR, China
| | - Henry Houlden
- Department of Neuromuscular Disease, Queen Square Institute of Neurology, UCL, London, UK
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Martin R Turner
- Nuffield Department of Clinical Neurosciences, Oxford University, Oxford, UK
| | - Mina Ryten
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, UCL, London, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL, London, UK
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
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19
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Wei X, Robles CR, Pazokitoroudi A, Ganna A, Gusev A, Durvasula A, Gazal S, Loh PR, Reich D, Sankararaman S. The lingering effects of Neanderthal introgression on human complex traits. eLife 2023; 12:e80757. [PMID: 36939312 PMCID: PMC10076017 DOI: 10.7554/elife.80757] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 03/17/2023] [Indexed: 03/21/2023] Open
Abstract
The genetic variants introduced into the ancestors of modern humans from interbreeding with Neanderthals have been suggested to contribute an unexpected extent to complex human traits. However, testing this hypothesis has been challenging due to the idiosyncratic population genetic properties of introgressed variants. We developed rigorous methods to assess the contribution of introgressed Neanderthal variants to heritable trait variation and applied these methods to analyze 235,592 introgressed Neanderthal variants and 96 distinct phenotypes measured in about 300,000 unrelated white British individuals in the UK Biobank. Introgressed Neanderthal variants make a significant contribution to trait variation (explaining 0.12% of trait variation on average). However, the contribution of introgressed variants tends to be significantly depleted relative to modern human variants matched for allele frequency and linkage disequilibrium (about 59% depletion on average), consistent with purifying selection on introgressed variants. Different from previous studies (McArthur et al., 2021), we find no evidence for elevated heritability across the phenotypes examined. We identified 348 independent significant associations of introgressed Neanderthal variants with 64 phenotypes. Previous work (Skov et al., 2020) has suggested that a majority of such associations are likely driven by statistical association with nearby modern human variants that are the true causal variants. Applying a customized fine-mapping led us to identify 112 regions across 47 phenotypes containing 4303 unique genetic variants where introgressed variants are highly likely to have a phenotypic effect. Examination of these variants reveals their substantial impact on genes that are important for the immune system, development, and metabolism.
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Affiliation(s)
- Xinzhu Wei
- Department of Computational Biology, Cornell UniversityNew YorkUnited States
| | - Christopher R Robles
- Department of Human Genetics, University of California, Los AngelesLos AngelesUnited States
| | - Ali Pazokitoroudi
- Department of Computer Science, University of California, Los AngelesLos AngelesUnited States
| | - Andrea Ganna
- Analytical and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
- Stanley Center for Psychiatric Research, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Alexander Gusev
- Dana-Farber Cancer Institute, Harvard Medical SchoolBostonUnited States
| | - Arun Durvasula
- Department of Genetics, Harvard Medical SchoolBostonUnited States
- Department of Human Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Steven Gazal
- Center for Genetic Epidemiology, Department of Public and Population Health Sciences, University of Southern CaliforniaLos AngelesUnited States
- Division of Genetics,Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Po-Ru Loh
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| | - David Reich
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Genetics, Harvard Medical SchoolBostonUnited States
- Department of Human Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Howard Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
| | - Sriram Sankararaman
- Department of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Department of Computer Science, University of California, Los AngelesLos AngelesUnited States
- Department of Computational Medicine, University of California, Los AngelesLos AngelesUnited States
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20
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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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21
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Yermakovich D, Pankratov V, Võsa U, Yunusbayev B, Dannemann M. Long-range regulatory effects of Neandertal DNA in modern humans. Genetics 2023; 223:6957427. [PMID: 36560850 PMCID: PMC9991505 DOI: 10.1093/genetics/iyac188] [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: 10/13/2022] [Revised: 10/13/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
The admixture between modern humans and Neandertals has resulted in ∼2% of the genomes of present-day non-Africans being composed of Neandertal DNA. Introgressed Neandertal DNA has been demonstrated to significantly affect the transcriptomic landscape in people today and via this molecular mechanism influence phenotype variation as well. However, little is known about how much of that regulatory impact is mediated through long-range regulatory effects that have been shown to explain ∼20% of expression variation. Here we identified 60 transcription factors (TFs) with their top cis-eQTL SNP in GTEx being of Neandertal ancestry and predicted long-range Neandertal DNA-induced regulatory effects by screening for the predicted target genes of those TFs. We show that the TFs form a significantly connected protein-protein interaction network. Among them are JUN and PRDM5, two brain-expressed TFs that have their predicted target genes enriched in regions devoid of Neandertal DNA. Archaic cis-eQTLs for the 60 TFs include multiple candidates for local adaptation, some of which show significant allele frequency increases over the last ∼10,000 years. A large proportion of the cis-eQTL-associated archaic SNPs have additional associations with various immune traits, schizophrenia, blood cell type composition and anthropometric measures. Finally, we demonstrate that our results are consistent with those of Neandertal DNA-associated empirical trans-eQTLs. Our results suggest that Neandertal DNA significantly influences regulatory networks, that its regulatory reach goes beyond the 40% of genomic sequence it still covers in present-day non-Africans and that via the investigated mechanism Neandertal DNA influences the phenotypic variation in people today.
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Affiliation(s)
- Danat Yermakovich
- Centre for Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Vasili Pankratov
- Centre for Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Urmo Võsa
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Bayazit Yunusbayev
- Centre for Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | | | - Michael Dannemann
- Centre for Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
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22
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Evolutionary Origin of Germline Pathogenic MUTYH Variations in Modern Humans. Biomolecules 2023; 13:biom13030429. [PMID: 36979362 PMCID: PMC10046817 DOI: 10.3390/biom13030429] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/30/2022] [Accepted: 01/04/2023] [Indexed: 03/02/2023] Open
Abstract
MUTYH plays an essential role in preventing oxidation-caused DNA damage. Pathogenic germline variations in MUTYH damage its function, causing intestinal polyposis and colorectal cancer. Determination of the evolutionary origin of the variation is essential to understanding the etiological relationship between MUTYH variation and cancer development. In this study, we analyzed the origins of pathogenic germline variants in human MUTYH. Using a phylogenic approach, we searched pathogenic MUTYH variants in modern humans in the MUTYH of 99 vertebrates across eight clades. We did not find pathogenic variants shared between modern humans and the non-human vertebrates following the evolutionary tree, ruling out the possibility of cross-species conservation as the origin of human pathogenic variants in MUTYH. We then searched the variants in the MUTYH of 5031 ancient humans and extinct Neanderthals and Denisovans. We identified 24 pathogenic variants in 42 ancient humans dated between 30,570 and 480 years before present (BP), and three pathogenic variants in Neanderthals dated between 65,000 and 38,310 years BP. Data from our study revealed that human pathogenic MUTYH variants mostly arose in recent human history and were partially inherited from Neanderthals.
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23
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Zhang X, Kim B, Singh A, Sankararaman S, Durvasula A, Lohmueller KE. MaLAdapt Reveals Novel Targets of Adaptive Introgression From Neanderthals and Denisovans in Worldwide Human Populations. Mol Biol Evol 2023; 40:msad001. [PMID: 36617238 PMCID: PMC9887621 DOI: 10.1093/molbev/msad001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 12/25/2022] [Accepted: 12/28/2022] [Indexed: 01/09/2023] Open
Abstract
Adaptive introgression (AI) facilitates local adaptation in a wide range of species. Many state-of-the-art methods detect AI with ad-hoc approaches that identify summary statistic outliers or intersect scans for positive selection with scans for introgressed genomic regions. Although widely used, approaches intersecting outliers are vulnerable to a high false-negative rate as the power of different methods varies, especially for complex introgression events. Moreover, population genetic processes unrelated to AI, such as background selection or heterosis, may create similar genomic signals to AI, compromising the reliability of methods that rely on neutral null distributions. In recent years, machine learning (ML) methods have been increasingly applied to population genetic questions. Here, we present a ML-based method called MaLAdapt for identifying AI loci from genome-wide sequencing data. Using an Extra-Trees Classifier algorithm, our method combines information from a large number of biologically meaningful summary statistics to capture a powerful composite signature of AI across the genome. In contrast to existing methods, MaLAdapt is especially well-powered to detect AI with mild beneficial effects, including selection on standing archaic variation, and is robust to non-AI selective sweeps, heterosis from deleterious mutations, and demographic misspecification. Furthermore, MaLAdapt outperforms existing methods for detecting AI based on the analysis of simulated data and the validation of empirical signals through visual inspection of haplotype patterns. We apply MaLAdapt to the 1000 Genomes Project human genomic data and discover novel AI candidate regions in non-African populations, including genes that are enriched in functionally important biological pathways regulating metabolism and immune responses.
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Affiliation(s)
- Xinjun Zhang
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA
| | - Bernard Kim
- Department of Biology, Stanford University, Palo Alto, CA
| | - Armaan Singh
- Department of Computer Science, UCLA, Los Angeles, CA
| | - Sriram Sankararaman
- Department of Computer Science, UCLA, Los Angeles, CA
- Department of Computational Medicine, UCLA, Los Angeles, CA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA
| | - Arun Durvasula
- Department of Genetics, Harvard Medical School, Boston, MA
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA
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24
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Lemaitre H, Le Guen Y, Tilot AK, Stein JL, Philippe C, Mangin JF, Fisher SE, Frouin V. Genetic variations within human gained enhancer elements affect human brain sulcal morphology. Neuroimage 2023; 265:119773. [PMID: 36442731 DOI: 10.1016/j.neuroimage.2022.119773] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/07/2022] [Accepted: 11/24/2022] [Indexed: 11/26/2022] Open
Abstract
The expansion of the cerebral cortex is one of the most distinctive changes in the evolution of the human brain. Cortical expansion and related increases in cortical folding may have contributed to emergence of our capacities for high-order cognitive abilities. Molecular analysis of humans, archaic hominins, and non-human primates has allowed identification of chromosomal regions showing evolutionary changes at different points of our phylogenetic history. In this study, we assessed the contributions of genomic annotations spanning 30 million years to human sulcal morphology measured via MRI in more than 18,000 participants from the UK Biobank. We found that variation within brain-expressed human gained enhancers, regulatory genetic elements that emerged since our last common ancestor with Old World monkeys, explained more trait heritability than expected for the left and right calloso-marginal posterior fissures and the right central sulcus. Intriguingly, these are sulci that have been previously linked to the evolution of locomotion in primates and later on bipedalism in our hominin ancestors.
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Affiliation(s)
- Herve Lemaitre
- Institut des Maladies Neurodégénératives, CNRS UMR 5293, Université de bordeaux, Centre Broca Nouvelle-Aquitaine, Bordeaux, France.
| | - Yann Le Guen
- Université Paris-Saclay, CEA, CNRS, Neurospin, Baobab UMR 9027, Gif-sur-Yvette, France
| | - Amanda K Tilot
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
| | - Jason L Stein
- Department of Genetics and the UNC Neuroscience Center, UNC-Chapel Hill, Chapel Hill, NC, United States of America
| | - Cathy Philippe
- Université Paris-Saclay, CEA, CNRS, Neurospin, Baobab UMR 9027, Gif-sur-Yvette, France
| | - Jean-François Mangin
- Université Paris-Saclay, CEA, CNRS, Neurospin, Baobab UMR 9027, Gif-sur-Yvette, France
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands
| | - Vincent Frouin
- Université Paris-Saclay, CEA, CNRS, Neurospin, Baobab UMR 9027, Gif-sur-Yvette, France
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25
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Schroeder L, Ackermann RR. Moving beyond the adaptationist paradigm for human evolution, and why it matters. J Hum Evol 2023; 174:103296. [PMID: 36527977 DOI: 10.1016/j.jhevol.2022.103296] [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: 04/25/2022] [Revised: 11/12/2022] [Accepted: 11/12/2022] [Indexed: 12/23/2022]
Abstract
The Journal of Human Evolution (JHE) was founded 50 years ago when much of the foundation for how we think about human evolution was in place or being put in place, providing the main framework for how we consider our origins today. Here, we will explore historical developments, including early JHE outputs, as they relate to our understanding of the relationship between phenotypic variation and evolutionary process, and use that as a springboard for considering our current understanding of these links as applied to human evolution. We will focus specifically on how the study of variation itself has shifted us away from taxonomic and adaptationist perspectives toward a richer understanding of the processes shaping human evolutionary history, using literature searches and specific test cases to highlight this. We argue that natural selection, gene exchange, genetic drift, and mutation should not be considered individually when considering the production of hominin diversity. In this context, we offer suggestions for future research directions and reflect on this more complex understanding of human evolution and its broader relevance to society. Finally, we end by considering authorship demographics and practices in the last 50 years within JHE and how a shift in these demographics has the potential to reshape the science of human evolution going forward.
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Affiliation(s)
- Lauren Schroeder
- Department of Anthropology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada; Human Evolution Research Institute, University of Cape Town, Rondebosch, 7701, South Africa.
| | - Rebecca Rogers Ackermann
- Human Evolution Research Institute, University of Cape Town, Rondebosch, 7701, South Africa; Department of Archaeology, University of Cape Town, Rondebosch, 7701, South Africa.
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26
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Taravella Oill AM, Buetow KH, Wilson MA. The role of Neanderthal introgression in liver cancer. BMC Med Genomics 2022; 15:255. [PMID: 36503519 PMCID: PMC9743633 DOI: 10.1186/s12920-022-01405-7] [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: 07/25/2022] [Accepted: 11/25/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Neanderthal introgressed DNA has been linked to different normal and disease traits including immunity and metabolism-two important functions that are altered in liver cancer. However, there is limited understanding of the relationship between Neanderthal introgression and liver cancer risk. The aim of this study was to investigate the relationship between Neanderthal introgression and liver cancer risk. METHODS Using germline and somatic DNA and tumor RNA from liver cancer patients from The Cancer Genome Atlas, along with ancestry-match germline DNA from unaffected individuals from the 1000 Genomes Resource, and allele specific expression data from normal liver tissue from The Genotype-Tissue Expression project we investigated whether Neanderthal introgression impacts cancer etiology. Using a previously generated set of Neanderthal alleles, we identified Neanderthal introgressed haplotypes. We then tested whether somatic mutations are enriched or depleted on Neanderthal introgressed haplotypes compared to modern haplotypes. We also computationally assessed whether somatic mutations have a functional effect or show evidence of regulating expression of Neanderthal haplotypes. Finally, we compared patterns of Neanderthal introgression in liver cancer patients and the general population. RESULTS We find Neanderthal introgressed haplotypes exhibit an excess of somatic mutations compared to modern haplotypes. Variant Effect Predictor analysis revealed that most of the somatic mutations on these Neanderthal introgressed haplotypes are not functional. We did observe expression differences of Neanderthal alleles between tumor and normal for four genes that also showed a pattern of enrichment of somatic mutations on Neanderthal haplotypes. However, gene expression was similar between liver cancer patients with modern ancestry and liver cancer patients with Neanderthal ancestry at these genes. Provocatively, when analyzing all genes, we find evidence of Neanderthal introgression regulating expression in tumor from liver cancer patients in two genes, ARK1C4 and OAS1. Finally, we find that most genes do not show a difference in the proportion of Neanderthal introgression between liver cancer patients and the general population. CONCLUSION Our results suggest that Neanderthal introgression provides opportunity for somatic mutations to accumulate, and that some Neanderthal introgression may impact liver cancer risk.
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Affiliation(s)
- Angela M Taravella Oill
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.
- School of Life Sciences, Arizona State University, Tempe, AZ, USA.
| | - Kenneth H Buetow
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Melissa A Wilson
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
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27
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Vespasiani DM, Jacobs GS, Cook LE, Brucato N, Leavesley M, Kinipi C, Ricaut FX, Cox MP, Gallego Romero I. Denisovan introgression has shaped the immune system of present-day Papuans. PLoS Genet 2022; 18:e1010470. [PMID: 36480515 PMCID: PMC9731433 DOI: 10.1371/journal.pgen.1010470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 10/10/2022] [Indexed: 12/13/2022] Open
Abstract
Modern humans have admixed with multiple archaic hominins. Papuans, in particular, owe up to 5% of their genome to Denisovans, a sister group to Neanderthals whose remains have only been identified in Siberia and Tibet. Unfortunately, the biological and evolutionary significance of these introgression events remain poorly understood. Here we investigate the function of both Denisovan and Neanderthal alleles characterised within a set of 56 genomes from Papuan individuals. By comparing the distribution of archaic and non-archaic variants we assess the consequences of archaic admixture across a multitude of different cell types and functional elements. We observe an enrichment of archaic alleles within cis-regulatory elements and transcribed regions of the genome, with Denisovan variants strongly affecting elements active within immune-related cells. We identify 16,048 and 10,032 high-confidence Denisovan and Neanderthal variants that fall within annotated cis-regulatory elements and with the potential to alter the affinity of multiple transcription factors to their cognate DNA motifs, highlighting a likely mechanism by which introgressed DNA can impact phenotypes. Lastly, we experimentally validate these predictions by testing the regulatory potential of five Denisovan variants segregating within Papuan individuals, and find that two are associated with a significant reduction of transcriptional activity in plasmid reporter assays. Together, these data provide support for a widespread contribution of archaic DNA in shaping the present levels of modern human genetic diversity, with different archaic ancestries potentially affecting multiple phenotypic traits within non-Africans.
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Affiliation(s)
- Davide M. Vespasiani
- Melbourne Integrative Genomics, University of Melbourne, Parkville, Australia
- School of Biosciences, University of Melbourne, Parkville, Australia
| | - Guy S. Jacobs
- Department of Archaeology, University of Cambridge, Cambridge, Uniteed Kingdom
| | - Laura E. Cook
- Melbourne Integrative Genomics, University of Melbourne, Parkville, Australia
- School of Biosciences, University of Melbourne, Parkville, Australia
| | - Nicolas Brucato
- Laboratoire de Evolution et Diversite Biologique, Université de Toulouse Midi-Pyrénées, Toulouse, France
| | - Matthew Leavesley
- School of Humanities and Social Sciences, University of Papua New Guinea, Port Moresby, Papua New Guinea
- College of Arts, Society and Education, James Cook University, Cairns, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, Australia
| | - Christopher Kinipi
- School of Humanities and Social Sciences, University of Papua New Guinea, Port Moresby, Papua New Guinea
| | - François-Xavier Ricaut
- Laboratoire de Evolution et Diversite Biologique, Université de Toulouse Midi-Pyrénées, Toulouse, France
| | - Murray P. Cox
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Irene Gallego Romero
- Melbourne Integrative Genomics, University of Melbourne, Parkville, Australia
- School of Biosciences, University of Melbourne, Parkville, Australia
- Center for Stem Cell Systems, University of Melbourne, Parkville, Australia
- Center for Genomics, Evolution and Medicine, University of Tartu, Tartu, Estonia
- * E-mail:
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28
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Koller D, Wendt FR, Pathak GA, De Lillo A, De Angelis F, Cabrera-Mendoza B, Tucci S, Polimanti R. Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations. BMC Biol 2022; 20:249. [PMID: 36344982 PMCID: PMC9641937 DOI: 10.1186/s12915-022-01449-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 10/24/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Introgression from extinct Neanderthal and Denisovan human species has been shown to contribute to the genetic pool of modern human populations and their phenotypic spectrum. Evidence of how Neanderthal introgression shaped the genetics of human traits and diseases has been extensively studied in populations of European descent, with signatures of admixture reported for instance in genes associated with pigmentation, immunity, and metabolic traits. However, limited information is currently available about the impact of archaic introgression on other ancestry groups. Additionally, to date, no study has been conducted with respect to the impact of Denisovan introgression on the health and disease of modern populations. Here, we compare the way evolutionary pressures shaped the genetics of complex traits in East Asian and European populations, and provide evidence of the impact of Denisovan introgression on the health of East Asian and Central/South Asian populations. RESULTS Leveraging genome-wide association statistics from the Biobank Japan and UK Biobank, we assessed whether Denisovan and Neanderthal introgression together with other evolutionary genomic signatures were enriched for the heritability of physiological and pathological conditions in populations of East Asian and European descent. In EAS, Denisovan-introgressed loci were enriched for coronary artery disease heritability (1.69-fold enrichment, p=0.003). No enrichment for archaic introgression was observed in EUR. We also performed a phenome-wide association study of Denisovan and Neanderthal alleles in six ancestry groups available in the UK Biobank. In EAS, the Denisovan-introgressed SNP rs62391664 in the major histocompatibility complex region was associated with albumin/globulin ratio (beta=-0.17, p=3.57×10-7). Neanderthal-introgressed alleles were associated with psychiatric and cognitive traits in EAS (e.g., "No Bipolar or Depression"-rs79043717 beta=-1.5, p=1.1×10-7), and with blood biomarkers (e.g., alkaline phosphatase-rs11244089 beta=0.1, p=3.69×10-116) and red hair color (rs60733936 beta=-0.86, p=4.49×10-165) in EUR. In the other ancestry groups, Neanderthal alleles were associated with several traits, also including the use of certain medications (e.g., Central/South East Asia: indapamide - rs732632 beta=-2.38, p=5.22×10-7). CONCLUSIONS Our study provides novel evidence regarding the impact of archaic introgression on the genetics of complex traits in worldwide populations, highlighting the specific contribution of Denisovan introgression in EAS populations.
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Affiliation(s)
- Dora Koller
- Department of Psychiatry, Yale University School of Medicine, West Haven, CT, 06516, USA
- VA CT Healthcare Center, West Haven, CT, 06516, USA
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, 08028, Spain
| | - Frank R Wendt
- Department of Psychiatry, Yale University School of Medicine, West Haven, CT, 06516, USA
- VA CT Healthcare Center, West Haven, CT, 06516, USA
| | - Gita A Pathak
- Department of Psychiatry, Yale University School of Medicine, West Haven, CT, 06516, USA
- VA CT Healthcare Center, West Haven, CT, 06516, USA
| | - Antonella De Lillo
- Department of Psychiatry, Yale University School of Medicine, West Haven, CT, 06516, USA
- Department of Biology, University of Rome "Tor Vergata", Rome, 00133, Italy
| | - Flavio De Angelis
- Department of Psychiatry, Yale University School of Medicine, West Haven, CT, 06516, USA
- VA CT Healthcare Center, West Haven, CT, 06516, USA
- Department of Biology, University of Rome "Tor Vergata", Rome, 00133, Italy
| | - Brenda Cabrera-Mendoza
- Department of Psychiatry, Yale University School of Medicine, West Haven, CT, 06516, USA
- VA CT Healthcare Center, West Haven, CT, 06516, USA
| | - Serena Tucci
- Department of Anthropology, Yale University, New Haven, CT, 06511, USA
| | - Renato Polimanti
- Department of Psychiatry, Yale University School of Medicine, West Haven, CT, 06516, USA.
- VA CT Healthcare Center, West Haven, CT, 06516, USA.
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29
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Doust C, Fontanillas P, Eising E, Gordon SD, Wang Z, Alagöz G, Molz B, Pourcain BS, Francks C, Marioni RE, Zhao J, Paracchini S, Talcott JB, Monaco AP, Stein JF, Gruen JR, Olson RK, Willcutt EG, DeFries JC, Pennington BF, Smith SD, Wright MJ, Martin NG, Auton A, Bates TC, Fisher SE, Luciano M. Discovery of 42 genome-wide significant loci associated with dyslexia. Nat Genet 2022; 54:1621-1629. [PMID: 36266505 PMCID: PMC9649434 DOI: 10.1038/s41588-022-01192-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 08/23/2022] [Indexed: 12/11/2022]
Abstract
Reading and writing are crucial life skills but roughly one in ten children are affected by dyslexia, which can persist into adulthood. Family studies of dyslexia suggest heritability up to 70%, yet few convincing genetic markers have been found. Here we performed a genome-wide association study of 51,800 adults self-reporting a dyslexia diagnosis and 1,087,070 controls and identified 42 independent genome-wide significant loci: 15 in genes linked to cognitive ability/educational attainment, and 27 new and potentially more specific to dyslexia. We validated 23 loci (13 new) in independent cohorts of Chinese and European ancestry. Genetic etiology of dyslexia was similar between sexes, and genetic covariance with many traits was found, including ambidexterity, but not neuroanatomical measures of language-related circuitry. Dyslexia polygenic scores explained up to 6% of variance in reading traits, and might in future contribute to earlier identification and remediation of dyslexia.
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Affiliation(s)
- Catherine Doust
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | | | - Else Eising
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - Scott D Gordon
- Genetic Epidemiology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Zhengjun Wang
- School of Psychology, Shaanxi Normal University and Shaanxi Key Research Center of Child Mental and Behavioral Health, Xi'an, China
| | - Gökberk Alagöz
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - Barbara Molz
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | | | | | - Beate St Pourcain
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Clyde Francks
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Jingjing Zhao
- School of Psychology, Shaanxi Normal University and Shaanxi Key Research Center of Child Mental and Behavioral Health, Xi'an, China
| | | | - Joel B Talcott
- Institute of Health and Neurodevelopment, Aston University, Birmingham, UK
| | | | - John F Stein
- Department of Physiology, Anatomy and Genetics, Oxford University, Oxford, UK
| | - Jeffrey R Gruen
- Departments of Pediatrics and Genetics, Yale Medical School, New Haven, CT, USA
| | - Richard K Olson
- Department of Psychology and Neuroscience, University of Colorado, Boulder, CO, USA
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO, USA
| | - Erik G Willcutt
- Department of Psychology and Neuroscience, University of Colorado, Boulder, CO, USA
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO, USA
| | - John C DeFries
- Department of Psychology and Neuroscience, University of Colorado, Boulder, CO, USA
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO, USA
| | | | - Shelley D Smith
- Department of Neurological Sciences, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Margaret J Wright
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Nicholas G Martin
- Genetic Epidemiology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | | | - Timothy C Bates
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Michelle Luciano
- Department of Psychology, University of Edinburgh, Edinburgh, UK.
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30
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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: 0.5] [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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31
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Harvati K, Ackermann RR. Merging morphological and genetic evidence to assess hybridization in Western Eurasian late Pleistocene hominins. Nat Ecol Evol 2022; 6:1573-1585. [PMID: 36064759 DOI: 10.1038/s41559-022-01875-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/08/2022] [Indexed: 11/09/2022]
Abstract
Previous scientific consensus saw human evolution as defined by adaptive differences (behavioural and/or biological) and the emergence of Homo sapiens as the ultimate replacement of non-modern groups by a modern, adaptively more competitive group. However, recent research has shown that the process underlying our origins was considerably more complex. While archaeological and fossil evidence suggests that behavioural complexity may not be confined to the modern human lineage, recent palaeogenomic work shows that gene flow between distinct lineages (for example, Neanderthals, Denisovans, early H. sapiens) occurred repeatedly in the late Pleistocene, probably contributing elements to our genetic make-up that might have been crucial to our success as a diverse, adaptable species. Following these advances, the prevailing human origins model has shifted from one of near-complete replacement to a more nuanced view of partial replacement with considerable reticulation. Here we provide a brief introduction to the current genetic evidence for hybridization among hominins, its prevalence in, and effects on, comparative mammal groups, and especially how it manifests in the skull. We then explore the degree to which cranial variation seen in the fossil record of late Pleistocene hominins from Western Eurasia corresponds with our current genetic and comparative data. We are especially interested in understanding the degree to which skeletal data can reflect admixture. Our findings indicate some correspondence between these different lines of evidence, flag individual fossils as possibly admixed, and suggest that different cranial regions may preserve hybridization signals differentially. We urge further studies of the phenotype to expand our ability to detect the ways in which migration, interaction and genetic exchange have shaped the human past, beyond what is currently visible with the lens of ancient DNA.
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Affiliation(s)
- K Harvati
- Paleoanthropology section, Senckenberg Centre for Human Evolution and Palaeoenvironment, Institute for Archaeological Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany.
- DFG Centre for Advanced Studies 'Words, Bones, Genes, Tools', Eberhard Karls Universität Tübingen, Tübingen, Germany.
| | - R R Ackermann
- Human Evolution Research Institute, University of Cape Town, Cape Town, South Africa.
- Department of Archaeology, University of Cape Town, Cape Town, South Africa.
- DFG Centre for Advanced Studies 'Words, Bones, Genes, Tools', Eberhard Karls Universität Tübingen, Tübingen, Germany.
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32
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Reilly PF, Tjahjadi A, Miller SL, Akey JM, Tucci S. The contribution of Neanderthal introgression to modern human traits. Curr Biol 2022; 32:R970-R983. [PMID: 36167050 PMCID: PMC9741939 DOI: 10.1016/j.cub.2022.08.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Neanderthals, our closest extinct relatives, lived in western Eurasia from 400,000 years ago until they went extinct around 40,000 years ago. DNA retrieved from ancient specimens revealed that Neanderthals mated with modern human contemporaries. As a consequence, introgressed Neanderthal DNA survives scattered across the human genome such that 1-4% of the genome of present-day people outside Africa are inherited from Neanderthal ancestors. Patterns of Neanderthal introgressed genomic sequences suggest that Neanderthal alleles had distinct fates in the modern human genetic background. Some Neanderthal alleles facilitated human adaptation to new environments such as novel climate conditions, UV exposure levels and pathogens, while others had deleterious consequences. Here, we review the body of work on Neanderthal introgression over the past decade. We describe how evolutionary forces shaped the genomic landscape of Neanderthal introgression and highlight the impact of introgressed alleles on human biology and phenotypic variation.
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Affiliation(s)
| | - Audrey Tjahjadi
- Department of Anthropology, Yale University, New Haven, CT, USA
| | | | - Joshua M Akey
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
| | - Serena Tucci
- Department of Anthropology, Yale University, New Haven, CT, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
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33
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Vilgalys TP, Fogel AS, Anderson JA, Mututua RS, Warutere JK, Siodi IL, Kim SY, Voyles TN, Robinson JA, Wall JD, Archie EA, Alberts SC, Tung J. Selection against admixture and gene regulatory divergence in a long-term primate field study. Science 2022; 377:635-641. [PMID: 35926022 PMCID: PMC9682493 DOI: 10.1126/science.abm4917] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genetic admixture is central to primate evolution. We combined 50 years of field observations of immigration and group demography with genomic data from ~9 generations of hybrid baboons to investigate the consequences of admixture in the wild. Despite no obvious fitness costs to hybrids, we found signatures of selection against admixture similar to those described for archaic hominins. These patterns were concentrated near genes where ancestry is strongly associated with gene expression. Our analyses also show that introgression is partially predictable across the genome. This study demonstrates the value of integrating genomic and field data for revealing how "genomic signatures of selection" (e.g., reduced introgression in low-recombination regions) manifest in nature; moreover, it underscores the importance of other primates as living models for human evolution.
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Affiliation(s)
- Tauras P. Vilgalys
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA,Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - Arielle S. Fogel
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA,University Program in Genetics and Genomics, Duke University, Durham, NC, USA
| | - Jordan A. Anderson
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
| | | | | | | | - Sang Yoon Kim
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
| | - Tawni N. Voyles
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
| | | | - Jeffrey D. Wall
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Elizabeth A. Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Susan C. Alberts
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA,Department of Biology, Duke University, Durham, NC, USA,Duke University Population Research Institute, Duke University, Durham, NC, USA
| | - Jenny Tung
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA,Department of Biology, Duke University, Durham, NC, USA,Duke University Population Research Institute, Duke University, Durham, NC, USA,Canadian Institute for Advanced Research, Toronto, Canada,Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany,Corresponding author
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34
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Collins AM, Watson CT, Breden F. Immunoglobulin genes, reproductive isolation and vertebrate speciation. Immunol Cell Biol 2022; 100:497-506. [PMID: 35781330 PMCID: PMC9545137 DOI: 10.1111/imcb.12567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/19/2022] [Accepted: 06/21/2022] [Indexed: 12/15/2022]
Abstract
Reproductive isolation drives the formation of new species, and many genes contribute to this through Dobzhansky–Muller incompatibilities (DMIs). These incompatibilities occur when gene divergence affects loci encoding interacting products such as receptors and their ligands. We suggest here that the nature of vertebrate immunoglobulin (IG) genes must make them prone to DMIs. The genes of these complex loci form functional genes through the process of recombination, giving rise to a repertoire of heterodimeric receptors of incredible diversity. This repertoire, within individuals and within species, must defend against pathogens but must also avoid pathogenic self‐reactivity. We suggest that this avoidance of autoimmunity is only achieved through a coordination of evolution between heavy‐ and light‐chain genes, and between these genes and the rest of the genome. Without coordinated evolution, the hybrid offspring of two diverging populations will carry a heavy burden of DMIs, resulting in a loss of fitness. Critical incompatibilities could manifest as incompatibilities between a mother and her divergent offspring. During fetal development, biochemical differences between the parents of hybrid offspring could make their offspring a target of the maternal immune system. This hypothesis was conceived in the light of recent insights into the population genetics of IG genes. This has suggested that antibody genes are probably as susceptible to evolutionary forces as other parts of the genome. Further repertoire studies in human and nonhuman species should now help determine whether antibody genes have been part of the evolutionary forces that drive the development of species.
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Affiliation(s)
- Andrew M Collins
- School of Biotechnology and Biomolecular Sciences University of New South Wales Sydney NSW Australia
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics University of Louisville School of Medicine Louisville KY USA
| | - Felix Breden
- Department of Biological Sciences Simon Fraser University Burnaby BC Canada
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35
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Jing J, Cong WF, Bezemer TM. Legacies at work: plant-soil-microbiome interactions underpinning agricultural sustainability. TRENDS IN PLANT SCIENCE 2022; 27:781-792. [PMID: 35701291 DOI: 10.1016/j.tplants.2022.05.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 03/29/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Agricultural intensification has had long-lasting negative legacies largely because of excessive inputs of agrochemicals (e.g., fertilizers) and simplification of cropping systems (e.g., continuous monocropping). Conventional agricultural management focuses on suppressing these negative legacies. However, there is now increasing attention for creating positive above- and belowground legacies through selecting crop species/genotypes, optimizing temporal and spatial crop combinations, improving nutrient inputs, developing intelligent fertilizers, and applying soil or microbiome inoculations. This can lead to enhanced yields and reduced pest and disease pressure in cropping systems, and can also mitigate greenhouse gas emissions and enhance carbon sequestration in soils. Strengthening positive legacies requires a deeper understanding of plant-soil-microbiome interactions and innovative crop, input, and soil management which can help to achieve agricultural sustainability.
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Affiliation(s)
- Jingying Jing
- College of Grass Science and Technology, China Agricultural University, 100193 Beijing, China.
| | - Wen-Feng Cong
- College of Resources and Environmental Sciences, Laboratory of Plant-Soil Interactions, Ministry of Education, National Observation and Research Station of Agriculture Green Development at Quzhou, China Agricultural University, 100193 Beijing, China.
| | - T Martijn Bezemer
- Institute of Biology, Above-Belowground Interactions Group, Leiden University, 2333 BE Leiden, The Netherlands; Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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36
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Haeggström S, Ingelman-Sundberg M, Pääbo S, Zeberg H. The clinically relevant CYP2C8*3 and CYP2C9*2 haplotype is inherited from Neandertals. THE PHARMACOGENOMICS JOURNAL 2022; 22:247-249. [PMID: 35780191 PMCID: PMC9363273 DOI: 10.1038/s41397-022-00284-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/13/2022] [Accepted: 06/10/2022] [Indexed: 11/23/2022]
Abstract
Genetic variation in genes encoding cytochrome P450 enzymes influences the metabolism of drugs and endogenous compounds. The locus containing the cytochrome genes CYP2C8 and CYP2C9 on chromosome 10 exhibits linkage disequilibrium between the CYP2C8*3 and CYP2C9*2 alleles, forming a haplotype of ~300 kilobases. This haplotype is associated with altered metabolism of several drugs, most notably reduced metabolism of warfarin and phenytoin, leading to toxicity at otherwise therapeutic doses. Here we show that this haplotype is inherited from Neandertals.
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Brand CM, Colbran LL, Capra JA. Predicting Archaic Hominin Phenotypes from Genomic Data. Annu Rev Genomics Hum Genet 2022; 23:591-612. [PMID: 35440148 DOI: 10.1146/annurev-genom-111521-121903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ancient DNA provides a powerful window into the biology of extant and extinct species, including humans' closest relatives: Denisovans and Neanderthals. Here, we review what is known about archaic hominin phenotypes from genomic data and how those inferences have been made. We contend that understanding the influence of variants on lower-level molecular phenotypes-such as gene expression and protein function-is a promising approach to using ancient DNA to learn about archaic hominin traits. Molecular phenotypes have simpler genetic architectures than organism-level complex phenotypes, and this approach enables moving beyond association studies by proposing hypotheses about the effects of archaic variants that are testable in model systems. The major challenge to understanding archaic hominin phenotypes is broadening our ability to accurately map genotypes to phenotypes, but ongoing advances ensure that there will be much more to learn about archaic hominin phenotypes from their genomes. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Colin M Brand
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA; , .,Bakar Computational Health Sciences Institute, University of California, San Francisco, California, USA
| | - Laura L Colbran
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John A Capra
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA; , .,Bakar Computational Health Sciences Institute, University of California, San Francisco, California, USA
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38
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Jagoda E, Xue JR, Reilly SK, Dannemann M, Racimo F, Huerta-Sanchez E, Sankararaman S, Kelso J, Pagani L, Sabeti PC, Capellini TD. Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells. Mol Biol Evol 2022; 39:msab304. [PMID: 34662402 PMCID: PMC8760939 DOI: 10.1093/molbev/msab304] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Although some variation introgressed from Neanderthals has undergone selective sweeps, little is known about its functional significance. We used a Massively Parallel Reporter Assay (MPRA) to assay 5,353 high-frequency introgressed variants for their ability to modulate the gene expression within 170 bp of endogenous sequence. We identified 2,548 variants in active putative cis-regulatory elements (CREs) and 292 expression-modulating variants (emVars). These emVars are predicted to alter the binding motifs of important immune transcription factors, are enriched for associations with neutrophil and white blood cell count, and are associated with the expression of genes that function in innate immune pathways including inflammatory response and antiviral defense. We combined the MPRA data with other data sets to identify strong candidates to be driver variants of positive selection including an emVar that may contribute to protection against severe COVID-19 response. We endogenously deleted two CREs containing expression-modulation variants linked to immune function, rs11624425 and rs80317430, identifying their primary genic targets as ELMSAN1, and PAN2 and STAT2, respectively, three genes differentially expressed during influenza infection. Overall, we present the first database of experimentally identified expression-modulating Neanderthal-introgressed alleles contributing to potential immune response in modern humans.
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Affiliation(s)
- Evelyn Jagoda
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - James R Xue
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Steven K Reilly
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael Dannemann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Fernando Racimo
- Lundbeck GeoGenetics Centre, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Emilia Huerta-Sanchez
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Sriram Sankararaman
- Department of Computer Science, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, UCLA, Los Angeles, CA, USA
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Biology, University of Padova, Padova, Italy
| | - Pardis C Sabeti
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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39
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Kerley CI, Chaganti S, Nguyen TQ, Bermudez C, Cutting LE, Beason-Held LL, Lasko T, Landman BA. pyPheWAS: A Phenome-Disease Association Tool for Electronic Medical Record Analysis. Neuroinformatics 2022; 20:483-505. [PMID: 34981404 PMCID: PMC9250547 DOI: 10.1007/s12021-021-09553-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2021] [Indexed: 11/29/2022]
Abstract
Along with the increasing availability of electronic medical record (EMR) data, phenome-wide association studies (PheWAS) and phenome-disease association studies (PheDAS) have become a prominent, first-line method of analysis for uncovering the secrets of EMR. Despite this recent growth, there is a lack of approachable software tools for conducting these analyses on large-scale EMR cohorts. In this article, we introduce pyPheWAS, an open-source python package for conducting PheDAS and related analyses. This toolkit includes 1) data preparation, such as cohort censoring and age-matching; 2) traditional PheDAS analysis of ICD-9 and ICD-10 billing codes; 3) PheDAS analysis applied to a novel EMR phenotype mapping: current procedural terminology (CPT) codes; and 4) novelty analysis of significant disease-phenotype associations found through PheDAS. The pyPheWAS toolkit is approachable and comprehensive, encapsulating data prep through result visualization all within a simple command-line interface. The toolkit is designed for the ever-growing scale of available EMR data, with the ability to analyze cohorts of 100,000 + patients in less than 2 h. Through a case study of Down Syndrome and other intellectual developmental disabilities, we demonstrate the ability of pyPheWAS to discover both known and potentially novel disease-phenotype associations across different experiment designs and disease groups. The software and user documentation are available in open source at https://github.com/MASILab/pyPheWAS .
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Affiliation(s)
- Cailey I Kerley
- Department of Electrical Engineering, Vanderbilt University, Nashville, TN, USA.
| | - Shikha Chaganti
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Tin Q Nguyen
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA.,Department of Special Education, Peabody College of Education and Human Development, Nashville, TN, USA
| | - Camilo Bermudez
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Laurie E Cutting
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA.,Department of Special Education, Peabody College of Education and Human Development, Nashville, TN, USA.,Vanderbilt Kennedy Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA
| | - Lori L Beason-Held
- Laboratory of Behavioral Neuroscience, National Institute On Aging, NIH, Baltimore, MD, USA
| | - Thomas Lasko
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bennett A Landman
- Department of Electrical Engineering, Vanderbilt University, Nashville, TN, USA.,Department of Computer Science, Vanderbilt University, Nashville, TN, USA.,Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA.,Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.,Vanderbilt Kennedy Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
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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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Rodríguez-Frías F, Quer J, Tabernero D, Cortese MF, Garcia-Garcia S, Rando-Segura A, Pumarola T. Microorganisms as Shapers of Human Civilization, from Pandemics to Even Our Genomes: Villains or Friends? A Historical Approach. Microorganisms 2021; 9:2518. [PMID: 34946123 PMCID: PMC8708650 DOI: 10.3390/microorganisms9122518] [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] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/23/2021] [Accepted: 11/30/2021] [Indexed: 02/07/2023] Open
Abstract
Universal history is characterized by continuous evolution, in which civilizations are born and die. This evolution is associated with multiple factors, among which the role of microorganisms is often overlooked. Viruses and bacteria have written or decisively contributed to terrible episodes of history, such as the Black Death in 14th century Europe, the annihilation of pre-Columbian American civilizations, and pandemics such as the 1918 Spanish flu or the current COVID-19 pandemic caused by the coronavirus SARS-CoV-2. Nevertheless, it is clear that we could not live in a world without these tiny beings. Endogenous retroviruses have been key to our evolution and for the regulation of gene expression, and the gut microbiota helps us digest compounds that we could not otherwise process. In addition, we have used microorganisms to preserve or prepare food for millennia and more recently to obtain drugs such as antibiotics or to develop recombinant DNA technologies. Due to the enormous importance of microorganisms for our survival, they have significantly influenced the population genetics of different human groups. This paper will review the role of microorganisms as "villains" who have been responsible for tremendous mortality throughout history but also as "friends" who help us survive and evolve.
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Affiliation(s)
- Francisco Rodríguez-Frías
- Clinical Biochemistry Research Group, Department of Biochemistry, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (M.F.C.); (S.G.-G.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain;
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain;
| | - Josep Quer
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain;
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Vall d’Hebron Institut Recerca, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - David Tabernero
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain;
| | - Maria Francesca Cortese
- Clinical Biochemistry Research Group, Department of Biochemistry, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (M.F.C.); (S.G.-G.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain;
| | - Selene Garcia-Garcia
- Clinical Biochemistry Research Group, Department of Biochemistry, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (M.F.C.); (S.G.-G.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain;
| | - Ariadna Rando-Segura
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain;
- Department of Microbiology, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain;
| | - Tomas Pumarola
- Department of Microbiology, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain;
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42
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Sohail M, Izarraras-Gomez A, Ortega-Del Vecchyo D. Populations, Traits, and Their Spatial Structure in Humans. Genome Biol Evol 2021; 13:evab272. [PMID: 34894236 PMCID: PMC8715524 DOI: 10.1093/gbe/evab272] [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] [Accepted: 12/06/2021] [Indexed: 11/16/2022] Open
Abstract
The spatial distribution of genetic variants is jointly determined by geography, past demographic processes, natural selection, and its interplay with environmental variation. A fraction of these genetic variants are "causal alleles" that affect the manifestation of a complex trait. The effect exerted by these causal alleles on complex traits can be independent or dependent on the environment. Understanding the evolutionary processes that shape the spatial structure of causal alleles is key to comprehend the spatial distribution of complex traits. Natural selection, past population size changes, range expansions, consanguinity, assortative mating, archaic introgression, admixture, and the environment can alter the frequencies, effect sizes, and heterozygosities of causal alleles. This provides a genetic axis along which complex traits can vary. However, complex traits also vary along biogeographical and sociocultural axes which are often correlated with genetic axes in complex ways. The purpose of this review is to consider these genetic and environmental axes in concert and examine the ways they can help us decipher the variation in complex traits that is visible in humans today. This initiative necessarily implies a discussion of populations, traits, the ability to infer and interpret "genetic" components of complex traits, and how these have been impacted by adaptive events. In this review, we provide a history-aware discussion on these topics using both the recent and more distant past of our academic discipline and its relevant contexts.
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Affiliation(s)
- Mashaal Sohail
- Department of Human Genetics, University of Chicago, USA
- Centro de Ciencias Genómicas (CCG), Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | - Alan Izarraras-Gomez
- Laboratorio Internacional de Investigación sobre el Genoma Humano (LIIGH), Universidad Nacional Autónoma de México (UNAM), Juriquilla, Querétaro, México
| | - Diego Ortega-Del Vecchyo
- Laboratorio Internacional de Investigación sobre el Genoma Humano (LIIGH), Universidad Nacional Autónoma de México (UNAM), Juriquilla, Querétaro, México
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Levi G, de Lombares C, Giuliani C, Iannuzzi V, Aouci R, Garagnani P, Franceschi C, Grimaud-Hervé D, Narboux-Nême N. DLX5/6 GABAergic Expression Affects Social Vocalization: Implications for Human Evolution. Mol Biol Evol 2021; 38:4748-4764. [PMID: 34132815 PMCID: PMC8557472 DOI: 10.1093/molbev/msab181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
DLX5 and DLX6 are two closely related transcription factors involved in brain development and in GABAergic differentiation. The DLX5/6 locus is regulated by FoxP2, a gene involved in language evolution and has been associated with neurodevelopmental disorders and mental retardation. Targeted inactivation of Dlx5/6 in mouse GABAergic neurons (Dlx5/6VgatCre mice) results in behavioral and metabolic phenotypes notably increasing lifespan by 33%. Here, we show that Dlx5/6VgatCre mice present a hyper-vocalization and hyper-socialization phenotype. While only 7% of control mice emitted more than 700 vocalizations/10 min, 30% and 56% of heterozygous or homozygous Dlx5/6VgatCre mice emitted more than 700 and up to 1,400 calls/10 min with a higher proportion of complex and modulated calls. Hyper-vocalizing animals were more sociable: the time spent in dynamic interactions with an unknown visitor was more than doubled compared to low-vocalizing individuals. The characters affected by Dlx5/6 in the mouse (sociability, vocalization, skull, and brain shape…) overlap those affected in the "domestication syndrome". We therefore explored the possibility that DLX5/6 played a role in human evolution and "self-domestication" comparing DLX5/6 genomic regions from Neanderthal and modern humans. We identified an introgressed Neanderthal haplotype (DLX5/6-N-Haplotype) present in 12.6% of European individuals that covers DLX5/6 coding and regulatory sequences. The DLX5/6-N-Haplotype includes the binding site for GTF2I, a gene associated with Williams-Beuren syndrome, a hyper-sociability and hyper-vocalization neurodevelopmental disorder. The DLX5/6-N-Haplotype is significantly underrepresented in semi-supercentenarians (>105 years of age), a well-established human model of healthy aging and longevity, suggesting their involvement in the coevolution of longevity, sociability, and speech.
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Affiliation(s)
- Giovanni Levi
- Physiologie Moléculaire et Adaptation, CNRS UMR7221, Département AVIV, Muséum National d'Histoire Naturelle, Paris, France
| | - Camille de Lombares
- Physiologie Moléculaire et Adaptation, CNRS UMR7221, Département AVIV, Muséum National d'Histoire Naturelle, Paris, France
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy
| | - Vincenzo Iannuzzi
- Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, Italy
| | - Rym Aouci
- Physiologie Moléculaire et Adaptation, CNRS UMR7221, Département AVIV, Muséum National d'Histoire Naturelle, Paris, France
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhniy Novgorod, Russia
| | - Dominique Grimaud-Hervé
- Histoire Naturelle de l’Homme Préhistorique, CNRS UMR 7194, Département H&E, Muséum National d'Histoire Naturelle, Paris, France
| | - Nicolas Narboux-Nême
- Physiologie Moléculaire et Adaptation, CNRS UMR7221, Département AVIV, Muséum National d'Histoire Naturelle, Paris, France
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44
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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: 14] [Impact Index Per Article: 4.7] [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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45
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McArthur E, Rinker DC, Capra JA. Quantifying the contribution of Neanderthal introgression to the heritability of complex traits. Nat Commun 2021; 12:4481. [PMID: 34294692 PMCID: PMC8298587 DOI: 10.1038/s41467-021-24582-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 06/24/2021] [Indexed: 11/15/2022] Open
Abstract
Eurasians have ~2% Neanderthal ancestry, but we lack a comprehensive understanding of the genome-wide influence of Neanderthal introgression on modern human diseases and traits. Here, we quantify the contribution of introgressed alleles to the heritability of more than 400 diverse traits. We show that genomic regions in which detectable Neanderthal ancestry remains are depleted of heritability for all traits considered, except those related to skin and hair. Introgressed variants themselves are also depleted for contributions to the heritability of most traits. However, introgressed variants shared across multiple Neanderthal populations are enriched for heritability and have consistent directions of effect on several traits with potential relevance to human adaptation to non-African environments, including hair and skin traits, autoimmunity, chronotype, bone density, lung capacity, and menopause age. Integrating our results, we propose a model in which selection against introgressed functional variation was the dominant trend (especially for cognitive traits); however, for a few traits, introgressed variants provided beneficial variation via uni-directional (e.g., lightening skin color) or bi-directional (e.g., modulating immune response) effects. We lack a comprehensive understanding of how Neanderthal ancestry influences human traits. This study finds that regions with Neanderthal ancestry are broadly depleted of trait-associated variation; yet, introgressed variants likely contributed to human adaptation in a few traits, like skin color and immune response modulation.
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Affiliation(s)
- Evonne McArthur
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
| | - David C Rinker
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - John A Capra
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, 37235, USA. .,Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA. .,Bakar Computational Health Sciences Institute and Department of Epidemiology and Statistics, University of California San Francisco, San Francisco, CA, 94107, USA.
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46
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Hollox EJ, Zuccherato LW, Tucci S. Genome structural variation in human evolution. Trends Genet 2021; 38:45-58. [PMID: 34284881 DOI: 10.1016/j.tig.2021.06.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 01/01/2023]
Abstract
Structural variation (SV) is a large difference (typically >100 bp) in the genomic structure of two genomes and includes both copy number variation and variation that does not change copy number of a genomic region, such as an inversion. Improved reference genomes, combined with widespread genome sequencing using short-read sequencing technology, and increasingly using long-read sequencing, have reignited interest in SV. Recent large-scale studies and functional focused analyses have highlighted the role of SV in human evolution. In this review, we highlight human-specific SVs involved in changes in the brain, population-specific SVs that affect response to the environment, including adaptation to diet and infectious diseases, and summarise the contribution of archaic hominin admixture to present-day human SV.
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Affiliation(s)
- Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, UK.
| | - Luciana W Zuccherato
- Núcleo de Ensino e Pesquisa, Instituto Mário Penna, Belo Horizonte, Brazil; Departmento de Bioquímica e Imunologia, Universidade de Minas Gerais, Belo Horizonte, Brazil
| | - Serena Tucci
- Department of Anthropology, Yale University, New Haven, CT, USA
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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: 3.7] [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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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: 8] [Impact Index Per Article: 2.7] [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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Abstract
Recent studies suggest that admixture with archaic hominins played an important role in facilitating biological adaptations to new environments. For example, interbreeding with Denisovans facilitated the adaptation to high-altitude environments on the Tibetan Plateau. Specifically, the EPAS1 gene, a transcription factor that regulates the response to hypoxia, exhibits strong signatures of both positive selection and introgression from Denisovans in Tibetan individuals. Interestingly, despite being geographically closer to the Denisova Cave, East Asian populations do not harbor as much Denisovan ancestry as populations from Melanesia. Recently, two studies have suggested two independent waves of Denisovan admixture into East Asians, one of which is shared with South Asians and Oceanians. Here, we leverage data from EPAS1 in 78 Tibetan individuals to interrogate which of these two introgression events introduced the EPAS1 beneficial sequence into the ancestral population of Tibetans, and we use the distribution of introgressed segment lengths at this locus to infer the timing of the introgression and selection event. We find that the introgression event unique to East Asians most likely introduced the beneficial haplotype into the ancestral population of Tibetans around 48,700 (16,000-59,500) y ago, and selection started around 9,000 (2,500-42,000) y ago. Our estimates suggest that one of the most convincing examples of adaptive introgression is in fact selection acting on standing archaic variation.
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Gopalan S, Atkinson EG, Buck LT, Weaver TD, Henn BM. Inferring archaic introgression from hominin genetic data. Evol Anthropol 2021; 30:199-220. [PMID: 33951239 PMCID: PMC8360192 DOI: 10.1002/evan.21895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 08/03/2020] [Accepted: 03/29/2021] [Indexed: 01/05/2023]
Abstract
Questions surrounding the timing, extent, and evolutionary consequences of archaic admixture into human populations have a long history in evolutionary anthropology. More recently, advances in human genetics, particularly in the field of ancient DNA, have shed new light on the question of whether or not Homo sapiens interbred with other hominin groups. By the late 1990s, published genetic work had largely concluded that archaic groups made no lasting genetic contribution to modern humans; less than a decade later, this conclusion was reversed following the successful DNA sequencing of an ancient Neanderthal. This reversal of consensus is noteworthy, but the reasoning behind it is not widely understood across all academic communities. There remains a communication gap between population geneticists and paleoanthropologists. In this review, we endeavor to bridge this gap by outlining how technological advancements, new statistical methods, and notable controversies ultimately led to the current consensus.
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Affiliation(s)
- Shyamalika Gopalan
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA.,Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
| | - Elizabeth G Atkinson
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital and Stanley Center for Psychiatric Research, Broad Institute, Boston, Massachusetts, USA
| | - Laura T Buck
- Research Centre in Evolutionary Anthropology and Palaeoecology, Liverpool John Moores University, Liverpool, UK
| | - Timothy D Weaver
- Department of Anthropology, University of California, Davis, California, USA
| | - Brenna M Henn
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA.,Department of Anthropology, University of California, Davis, California, USA.,UC Davis Genome Center, University of California, Davis, California, USA
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