1
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Hoge C, de Manuel M, Mahgoub M, Okami N, Fuller Z, Banerjee S, Baker Z, McNulty M, Andolfatto P, Macfarlan TS, Schumer M, Tzika AC, Przeworski M. Patterns of recombination in snakes reveal a tug-of-war between PRDM9 and promoter-like features. Science 2024; 383:eadj7026. [PMID: 38386752 DOI: 10.1126/science.adj7026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 01/04/2024] [Indexed: 02/24/2024]
Abstract
In some mammals, notably humans, recombination occurs almost exclusively where the protein PRDM9 binds, whereas in vertebrates lacking an intact PRDM9, such as birds and canids, recombination rates are elevated near promoter-like features. To determine whether PRDM9 directs recombination in nonmammalian vertebrates, we focused on an exemplar species with a single, intact PRDM9 ortholog, the corn snake (Pantherophis guttatus). Analyzing historical recombination rates along the genome and crossovers in pedigrees, we found evidence that PRDM9 specifies the location of recombination events, but we also detected a separable effect of promoter-like features. These findings reveal that the uses of PRDM9 and promoter-like features need not be mutually exclusive and instead reflect a tug-of-war that is more even in some species than others.
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Affiliation(s)
- Carla Hoge
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Marc de Manuel
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Mohamed Mahgoub
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Naima Okami
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Zachary Fuller
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Shreya Banerjee
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Zachary Baker
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Morgan McNulty
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Molly Schumer
- Department of Biology, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford, CA, USA
| | - Athanasia C Tzika
- Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, Geneva, Switzerland
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
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2
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Mochales-Riaño G, Fontsere C, de Manuel M, Talavera A, Burriel-Carranza B, Tejero-Cicuéndez H, AlGethami RHM, Shobrak M, Marques-Bonet T, Carranza S. Genomics reveals introgression and purging of deleterious mutations in the Arabian leopard ( Panthera pardus nimr). iScience 2023; 26:107481. [PMID: 37601769 PMCID: PMC10432787 DOI: 10.1016/j.isci.2023.107481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/21/2023] [Accepted: 07/24/2023] [Indexed: 08/22/2023] Open
Abstract
In endangered species, low-genetic variation and inbreeding result from recent population declines. Genetic screenings in endangered populations help to assess their vulnerability to extinction and to create informed management actions toward their conservation efforts. The leopard, Panthera pardus, is a highly generalist predator with currently eight different subspecies. Yet, genomic data are still lacking for the Critically Endangered Arabian leopard (P. p. nimr). Here, we sequenced the whole genome of two Arabian leopards and assembled the most complete genomic dataset for leopards to date. Our phylogenomic analyses show that leopards are divided into two deeply divergent clades: the African and the Asian. Conservation genomic analyses indicate a prolonged population decline, which has led to an increase in inbreeding and runs of homozygosity, with consequent purging of deleterious mutations in both Arabian individuals. Our study represents the first attempt to genetically inform captive breeding programmes for this Critically Endangered subspecies.
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Affiliation(s)
| | - Claudia Fontsere
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Øster Farimagsgade 5A, 1352 Copenhagen, Denmark
| | - Marc de Manuel
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Adrián Talavera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | | | - Héctor Tejero-Cicuéndez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense de Madrid, Madrid, Spain
| | - Raed Hamoud M. AlGethami
- National Center for Wildlife, Prince Saud Al-Faisal for Wildlife Research, P. O Box 1086, Taif, Taif 21944, Saudi Arabia
| | - Mohammed Shobrak
- National Center for Wildlife, Prince Saud Al-Faisal for Wildlife Research, P. O Box 1086, Taif, Taif 21944, Saudi Arabia
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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3
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Spisak N, de Manuel M, Milligan W, Sella G, Przeworski M. Disentangling sources of clock-like mutations in germline and soma. bioRxiv 2023:2023.09.07.556720. [PMID: 37745549 PMCID: PMC10515775 DOI: 10.1101/2023.09.07.556720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The rates of mutations vary across cell types. To identify causes of this variation, mutations are often decomposed into a combination of the single base substitution (SBS) "signatures" observed in germline, soma and tumors, with the idea that each signature corresponds to one or a small number of underlying mutagenic processes. Two such signatures turn out to be ubiquitous across cell types: SBS signature 1, which consists primarily of transitions at methylated CpG sites caused by spontaneous deamination, and the more diffuse SBS signature 5, which is of unknown etiology. In cancers, the number of mutations attributed to these two signatures accumulates linearly with age of diagnosis, and thus the signatures have been termed "clock-like." To better understand this clock-like behavior, we develop a mathematical model that includes DNA replication errors, unrepaired damage, and damage repaired incorrectly. We show that mutational signatures can exhibit clock-like behavior because cell divisions occur at a constant rate and/or because damage rates remain constant over time, and that these distinct sources can be teased apart by comparing cell lineages that divide at different rates. With this goal in mind, we analyze the rate of accumulation of mutations in multiple cell types, including soma as well as male and female germline. We find no detectable increase in SBS signature 1 mutations in neurons and only a very weak increase in mutations assigned to the female germline, but a significant increase with time in rapidly-dividing cells, suggesting that SBS signature 1 is driven by rounds of DNA replication occurring at a relatively fixed rate. In contrast, SBS signature 5 increases with time in all cell types, including post-mitotic ones, indicating that it accumulates independently of cell divisions; this observation points to errors in DNA repair as the key underlying mechanism. Thus, the two "clock-like" signatures observed across cell types likely have distinct origins, one set by rates of cell division, the other by damage rates.
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Affiliation(s)
- Natanael Spisak
- Department of Biological Sciences, Columbia University, New York, United States
| | - Marc de Manuel
- Department of Biological Sciences, Columbia University, New York, United States
| | - William Milligan
- Department of Biological Sciences, Columbia University, New York, United States
| | - Guy Sella
- Department of Biological Sciences, Columbia University, New York, United States
- Program for Mathematical Genomics, Columbia University, New York, United States
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, United States
- Department of Systems Biology, Columbia University, New York, United States
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4
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Pawar H, Rymbekova A, Cuadros-Espinoza S, Huang X, de Manuel M, van der Valk T, Lobon I, Alvarez-Estape M, Haber M, Dolgova O, Han S, Esteller-Cucala P, Juan D, Ayub Q, Bautista R, Kelley JL, Cornejo OE, Lao O, Andrés AM, Guschanski K, Ssebide B, Cranfield M, Tyler-Smith C, Xue Y, Prado-Martinez J, Marques-Bonet T, Kuhlwilm M. Ghost admixture in eastern gorillas. Nat Ecol Evol 2023; 7:1503-1514. [PMID: 37500909 PMCID: PMC10482688 DOI: 10.1038/s41559-023-02145-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 06/30/2023] [Indexed: 07/29/2023]
Abstract
Archaic admixture has had a substantial impact on human evolution with multiple events across different clades, including from extinct hominins such as Neanderthals and Denisovans into modern humans. In great apes, archaic admixture has been identified in chimpanzees and bonobos but the possibility of such events has not been explored in other species. Here, we address this question using high-coverage whole-genome sequences from all four extant gorilla subspecies, including six newly sequenced eastern gorillas from previously unsampled geographic regions. Using approximate Bayesian computation with neural networks to model the demographic history of gorillas, we find a signature of admixture from an archaic 'ghost' lineage into the common ancestor of eastern gorillas but not western gorillas. We infer that up to 3% of the genome of these individuals is introgressed from an archaic lineage that diverged more than 3 million years ago from the common ancestor of all extant gorillas. This introgression event took place before the split of mountain and eastern lowland gorillas, probably more than 40 thousand years ago and may have influenced perception of bitter taste in eastern gorillas. When comparing the introgression landscapes of gorillas, humans and bonobos, we find a consistent depletion of introgressed fragments on the X chromosome across these species. However, depletion in protein-coding content is not detectable in eastern gorillas, possibly as a consequence of stronger genetic drift in this species.
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Affiliation(s)
- Harvinder Pawar
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
| | - Aigerim Rymbekova
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Wien, Austria
| | | | - Xin Huang
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Wien, Austria
| | - Marc de Manuel
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
| | - Tom van der Valk
- Department of Bioinformatics and Genetics, Scilifelab, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Irene Lobon
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
| | | | - Marc Haber
- Institute of Cancer and Genomic Sciences, University of Birmingham, Dubai, United Arab Emirates
| | - Olga Dolgova
- Integrative Genomics Lab, CIC bioGUNE-Centro de Investigación Cooperativa en Biociencias, Parque Científico Tecnológico de Bizkaia building 801A, Derio, Spain
| | - Sojung Han
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Wien, Austria
| | | | - David Juan
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
| | - Qasim Ayub
- Wellcome Sanger Institute, Hinxton, UK
- Monash University Malaysia Genomics Facility, School of Science, Monash University Malaysia, Selangor Darul Ehsan, Malaysia
| | | | - Joanna L Kelley
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Omar E Cornejo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Oscar Lao
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
| | - Aida M Andrés
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Katerina Guschanski
- Animal Ecology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Science for Life Laboratory, Uppsala, Sweden
| | | | - Mike Cranfield
- Gorilla Doctors, Karen C. Drayer Wildlife Health Center, One Health Institute, University of California Davis, School of Veterinary Medicine, Davis, CA, USA
| | | | - Yali Xue
- Wellcome Sanger Institute, Hinxton, UK
| | - Javier Prado-Martinez
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
- Wellcome Sanger Institute, Hinxton, UK
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain.
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, Barcelona, Spain.
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, Barcelona, Spain.
| | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain.
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Wien, Austria.
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5
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Hoge C, de Manuel M, Mahgoub M, Okami N, Fuller Z, Banerjee S, Baker Z, McNulty M, Andolfatto P, Macfarlan TS, Schumer M, Tzika AC, Przeworski M. Patterns of recombination in snakes reveal a tug of war between PRDM9 and promoter-like features. bioRxiv 2023:2023.07.11.548536. [PMID: 37502971 PMCID: PMC10369914 DOI: 10.1101/2023.07.11.548536] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
In vertebrates, there are two known mechanisms by which meiotic recombination is directed to the genome: in humans, mice, and other mammals, recombination occurs almost exclusively where the protein PRDM9 binds, while in species lacking an intact PRDM9, such as birds and canids, recombination rates are elevated near promoter-like features. To test if PRDM9 also directs recombination in non-mammalian vertebrates, we focused on an exemplar species, the corn snake (Pantherophis guttatus). Unlike birds, this species possesses a single, intact PRDM9 ortholog. By inferring historical recombination rates along the genome from patterns of linkage disequilibrium and identifying crossovers in pedigrees, we found that PRDM9 specifies the location of recombination events outside of mammals. However, we also detected an independent effect of promoter-like features on recombination, which is more pronounced on macro- than microchromosomes. Thus, our findings reveal that the uses of PRDM9 and promoter-like features are not mutually-exclusive, and instead reflect a tug of war, which varies in strength along the genome and is more lopsided in some species than others.
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Affiliation(s)
- Carla Hoge
- Dept. of Biological Sciences, Columbia University
| | | | - Mohamed Mahgoub
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health
| | - Naima Okami
- Dept. of Biological Sciences, Columbia University
| | | | | | | | | | | | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health
| | - Molly Schumer
- Dept. of Biology, Stanford University
- Howard Hughes Medical Institute, Stanford, CA
| | - Athanasia C Tzika
- Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva
| | - Molly Przeworski
- Dept. of Biological Sciences, Columbia University
- Howard Hughes Medical Institute, Stanford, CA
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6
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de Manuel M, Wu FL, Przeworski M. A paternal bias in germline mutation is widespread in amniotes and can arise independently of cell divisions. eLife 2022; 11:80008. [PMID: 35916372 PMCID: PMC9439683 DOI: 10.7554/elife.80008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
In humans and other mammals, germline mutations are more likely to arise in fathers than in mothers. Although this sex bias has long been attributed to DNA replication errors in spermatogenesis, recent evidence from humans points to the importance of mutagenic processes that do not depend on cell division, calling into question our understanding of this basic phenomenon. Here, we infer the ratio of paternal-to-maternal mutations, α, in 42 species of amniotes, from putatively neutral substitution rates of sex chromosomes and autosomes. Despite marked differences in gametogenesis, physiologies and environments across species, fathers consistently contribute more mutations than mothers in all the species examined, including mammals, birds, and reptiles. In mammals, α is as high as 4 and correlates with generation times; in birds and snakes, α appears more stable around 2. These observations are consistent with a simple model, in which mutations accrue at equal rates in both sexes during early development and at a higher rate in the male germline after sexual differentiation, with a conserved paternal-to-maternal ratio across species. Thus, α may reflect the relative contributions of two or more developmental phases to total germline mutations, and is expected to depend on generation time even if mutations do not track cell divisions.
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Affiliation(s)
- Marc de Manuel
- Department of Biological Sciences, Columbia University, New York, United States
| | - Felix L Wu
- Department of Biological Sciences, Columbia University, New York, United States
| | - Molly Przeworski
- Department of Systems Biology, Columbia University, New York, United States
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7
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Khan N, de Manuel M, Peyregne S, Do R, Prufer K, Marques-Bonet T, Varki N, Gagneux P, Varki A. Multiple Genomic Events Altering Hominin SIGLEC Biology and Innate Immunity Predated the Common Ancestor of Humans and Archaic Hominins. Genome Biol Evol 2021; 12:1040-1050. [PMID: 32556248 PMCID: PMC7379906 DOI: 10.1093/gbe/evaa125] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2020] [Indexed: 12/11/2022] Open
Abstract
Human-specific pseudogenization of the CMAH gene eliminated the mammalian sialic acid (Sia) Neu5Gc (generating an excess of its precursor Neu5Ac), thus changing ubiquitous cell surface “self-associated molecular patterns” that modulate innate immunity via engagement of CD33-related-Siglec receptors. The Alu-fusion-mediated loss-of-function of CMAH fixed ∼2–3 Ma, possibly contributing to the origins of the genus Homo. The mutation likely altered human self-associated molecular patterns, triggering multiple events, including emergence of human-adapted pathogens with strong preference for Neu5Ac recognition and/or presenting Neu5Ac-containing molecular mimics of human glycans, which can suppress immune responses via CD33-related-Siglec engagement. Human-specific alterations reported in some gene-encoding Sia-sensing proteins suggested a “hotspot” in hominin evolution. The availability of more hominid genomes including those of two extinct hominins now allows full reanalysis and evolutionary timing. Functional changes occur in 8/13 members of the human genomic cluster encoding CD33-related Siglecs, all predating the human common ancestor. Comparisons with great ape genomes indicate that these changes are unique to hominins. We found no evidence for strong selection after the Human–Neanderthal/Denisovan common ancestor, and these extinct hominin genomes include almost all major changes found in humans, indicating that these changes in hominin sialobiology predate the Neanderthal–human divergence ∼0.6 Ma. Multiple changes in this genomic cluster may also explain human-specific expression of CD33rSiglecs in unexpected locations such as amnion, placental trophoblast, pancreatic islets, ovarian fibroblasts, microglia, Natural Killer(NK) cells, and epithelia. Taken together, our data suggest that innate immune interactions with pathogens markedly altered hominin Siglec biology between 0.6 and 2 Ma, potentially affecting human evolution.
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Affiliation(s)
- Naazneen Khan
- Glycobiology Research and Training Center, Department of Medicine, University of California San Diego.,Center for Academic Research and Training in Anthropogeny (CARTA),University of California San Diego
| | - Marc de Manuel
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
| | - Stephane Peyregne
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Raymond Do
- Glycobiology Research and Training Center, Department of Medicine, University of California San Diego.,Center for Academic Research and Training in Anthropogeny (CARTA),University of California San Diego
| | - Kay Prufer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, Barcelona, Spain
| | - Nissi Varki
- Glycobiology Research and Training Center, Department of Medicine, University of California San Diego.,Center for Academic Research and Training in Anthropogeny (CARTA),University of California San Diego
| | - Pascal Gagneux
- Glycobiology Research and Training Center, Department of Medicine, University of California San Diego.,Center for Academic Research and Training in Anthropogeny (CARTA),University of California San Diego
| | - Ajit Varki
- Glycobiology Research and Training Center, Department of Medicine, University of California San Diego.,Center for Academic Research and Training in Anthropogeny (CARTA),University of California San Diego
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8
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Sánchez-Barreiro F, Gopalakrishnan S, Ramos-Madrigal J, Westbury MV, de Manuel M, Margaryan A, Ciucani MM, Vieira FG, Patramanis Y, Kalthoff DC, Timmons Z, Sicheritz-Pontén T, Dalén L, Ryder OA, Zhang G, Marquès-Bonet T, Moodley Y, Gilbert MTP. Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum). Mol Ecol 2021; 30:6355-6369. [PMID: 34176179 PMCID: PMC9291831 DOI: 10.1111/mec.16043] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 06/11/2021] [Accepted: 06/21/2021] [Indexed: 01/08/2023]
Abstract
Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore has suffered a remarkable decline in the last 150 years due to human activities. Its subspecies, the northern (NWR) and the southern white rhinoceros (SWR), however, underwent opposite fates: the NWR vanished quickly, while the SWR recovered after the severe decline. Such demographic events are predicted to have an erosive effect at the genomic level, linked to the extirpation of diversity, and increased genetic drift and inbreeding. However, there is little empirical data available to directly reconstruct the subtleties of such processes in light of distinct demographic histories. Therefore, we generated a whole-genome, temporal data set consisting of 52 resequenced white rhinoceros genomes, representing both subspecies at two time windows: before and during/after the bottleneck. Our data reveal previously unknown population structure within both subspecies, as well as quantifiable genomic erosion. Genome-wide heterozygosity decreased significantly by 10% in the NWR and 36% in the SWR, and inbreeding coefficients rose significantly by 11% and 39%, respectively. Despite the remarkable loss of genomic diversity and recent inbreeding it suffered, the only surviving subspecies, the SWR, does not show a significant accumulation of genetic load compared to its historical counterpart. Our data provide empirical support for predictions about the genomic consequences of shrinking populations, and our findings have the potential to inform the conservation efforts of the remaining white rhinoceroses.
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Affiliation(s)
| | - Shyam Gopalakrishnan
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,DTU Bioinformatics, Kongens Lyngby, Hovedstaden, Denmark.,Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Marc de Manuel
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Barcelona, Spain
| | - Ashot Margaryan
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
| | - Marta M Ciucani
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Filipe G Vieira
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Daniela C Kalthoff
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Zena Timmons
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK
| | - Thomas Sicheritz-Pontén
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA, USA
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.,BGI-Shenzhen, Shenzhen, China
| | - Tomás Marquès-Bonet
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Barcelona, Spain.,National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Yoshan Moodley
- Department of Zoology, University of Venda, Thohoyandou, South Africa
| | - M Thomas P Gilbert
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark.,Norwegian University of Science and Technology, University Museum, Trondheim, Norway
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9
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Westbury MV, Barnett R, Sandoval-Velasco M, Gower G, Vieira FG, de Manuel M, Hansen AJ, Yamaguchi N, Werdelin L, Marques-Bonet T, Gilbert MTP, Lorenzen ED. A genomic exploration of the early evolution of extant cats and their sabre-toothed relatives. Open Res Eur 2021; 1:25. [PMID: 35098251 PMCID: PMC7612286 DOI: 10.12688/openreseurope.13104.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 06/10/2021] [Indexed: 12/03/2022]
Abstract
Background: The evolutionary relationships of Felidae during their Early-Middle Miocene radiation is contentious. Although the early common ancestors have been subsumed under the grade-group Pseudaelurus, this group is thought to be paraphyletic, including the early ancestors of both modern cats and extinct sabretooths. Methods: Here, we sequenced a draft nuclear genome of Smilodon populator, dated to 13,182 ± 90 cal BP, making this the oldest palaeogenome from South America to date, a region known to be problematic for ancient DNA preservation. We analysed this genome, together with genomes from other extinct and extant cats to investigate their phylogenetic relationships. Results: We confirm a deep divergence (~20.65 Ma) within sabre-toothed cats. Through the analysis of both simulated and empirical data, we show a lack of gene flow between Smilodon and contemporary Felidae. Conclusions: Given that some species traditionally assigned to Pseudaelurus originated in the Early Miocene ~20 Ma, this indicates that some species of Pseudaelurus may be younger than the lineages they purportedly gave rise to, further supporting the hypothesis that Pseudaelurus was paraphyletic.
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Affiliation(s)
- Michael V Westbury
- The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Ross Barnett
- The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | | | - Graham Gower
- The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Filipe Garrett Vieira
- The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Marc de Manuel
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Anders J Hansen
- The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Nobuyuki Yamaguchi
- Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | - Lars Werdelin
- Department of Palaeobiology, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - M Thomas P Gilbert
- The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway
| | - Eline D Lorenzen
- The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
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10
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Barnett R, Westbury MV, Sandoval-Velasco M, Vieira FG, Jeon S, Zazula G, Martin MD, Ho SYW, Mather N, Gopalakrishnan S, Ramos-Madrigal J, de Manuel M, Zepeda-Mendoza ML, Antunes A, Baez AC, De Cahsan B, Larson G, O'Brien SJ, Eizirik E, Johnson WE, Koepfli KP, Wilting A, Fickel J, Dalén L, Lorenzen ED, Marques-Bonet T, Hansen AJ, Zhang G, Bhak J, Yamaguchi N, Gilbert MTP. Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens. Curr Biol 2020; 30:5018-5025.e5. [PMID: 33065008 PMCID: PMC7762822 DOI: 10.1016/j.cub.2020.09.051] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/10/2020] [Accepted: 09/15/2020] [Indexed: 12/17/2022]
Abstract
Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1, 2, 3, 4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of which were key characteristics for predation on Pleistocene megafauna [5]. Previous mitochondrial DNA phylogenies suggested that it was a highly divergent sister lineage to all extant cat species [6, 7, 8]. However, mitochondrial phylogenies can be misled by hybridization [9], incomplete lineage sorting (ILS), or sex-biased dispersal patterns [10], which might be especially relevant for Homotherium since widespread mito-nuclear discrepancies have been uncovered in modern cats [10]. To examine the evolutionary history of Homotherium, we generated a ∼7x nuclear genome and a ∼38x exome from H. latidens using shotgun and target-capture sequencing approaches. Phylogenetic analyses reveal Homotherium as highly divergent (∼22.5 Ma) from living cat species, with no detectable signs of gene flow. Comparative genomic analyses found signatures of positive selection in several genes, including those involved in vision, cognitive function, and energy consumption, putatively consistent with diurnal activity, well-developed social behavior, and cursorial hunting [5]. Finally, we uncover relatively high levels of genetic diversity, suggesting that Homotherium may have been more abundant than the limited fossil record suggests [3, 4, 11, 12, 13, 14]. Our findings complement and extend previous inferences from both the fossil record and initial molecular studies, enhancing our understanding of the evolution and ecology of this remarkable lineage. Nuclear genome and exome analyses of extinct scimitar-toothed cat, Homotherium latidens Homotherium was a highly divergent lineage from all living cat species (∼22.5 Ma) Genetic adaptations to cursorial and diurnal hunting behaviors Relatively high levels of genetic diversity in this individual
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Affiliation(s)
- Ross Barnett
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Michael V Westbury
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark.
| | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Filipe Garrett Vieira
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Sungwon Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Grant Zazula
- Yukon Palaeontology Program, Department of Tourism and Culture, Government of Yukon, PO Box 2703, Whitehorse, YT Y1A 2C6, Canada
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim NO-7491, Norway
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Niklas Mather
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1352, Denmark
| | - Jazmín Ramos-Madrigal
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1352, Denmark
| | - Marc de Manuel
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, Barcelona 08003, Spain
| | - M Lisandra Zepeda-Mendoza
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark; School of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, Porto 4450-208, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Porto 4169-007, Portugal
| | - Aldo Carmona Baez
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Binia De Cahsan
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
| | - Stephen J O'Brien
- Laboratory of Genomic Diversity, Center for Computer Technologies, ITMO University, 49 Kronverkskiy Pr., St. Petersburg 197101, Russia; Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, 8000 North Ocean Drive. Ft Lauderdale, FL 33004, USA
| | - Eduardo Eizirik
- Laboratory of Genomics and Molecular Biology, Escola de Ciências da Saúde e da Vida, PUCRS, Porto Alegre, RS, Brazil; INCT Ecologia, Evolução e Conservação da Biodiversidade (INCT-EECBio), Goiânia, GO, Brazil; Instituto Pró-Carnívoros, Atibaia, SP, Brazil
| | - Warren E Johnson
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA 22630, USA; The Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, 4210 Silver Hill Rd., Suitland, MD 20746-2863, USA; Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA 22630, USA
| | - Andreas Wilting
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, Berlin 10315, Germany
| | - Jörns Fickel
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, Berlin 10315, Germany; Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, Potsdam 14476, Germany
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, Stockholm SE-10691, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, Stockholm 10405, Sweden
| | - Eline D Lorenzen
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1352, Denmark
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, Barcelona 08003, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain; Institució Catalana de Recerca i Estudis Avançats, ICREA, Barcelona 08003, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, Cerdanyola del Vallès, Barcelona 08193, Spain
| | - Anders J Hansen
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1352, Denmark; Section for GeoGenetics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Guojie Zhang
- BGI-Shenzhen, Shenzhen 518083, China; Section for Ecology and Evolution, Department of Biology, Faculty of Science, University of Copenhagen, Universitetsparken 15, Copenhagen, Denmark; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Jong Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; Clinomics, Inc., Ulsan 44919, Republic of Korea; Personal Genomics Institute (PGI), Genome Research Foundation (GRF), Osong 28160, Republic of Korea
| | - Nobuyuki Yamaguchi
- Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark; Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim NO-7491, Norway; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1352, Denmark.
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11
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Welker F, Ramos-Madrigal J, Gutenbrunner P, Mackie M, Tiwary S, Jersie-Christensen RR, Chiva C, Dickinson MR, Kuhlwilm M, de Manuel M, Gelabert P, Martinón-Torres M, Margvelashvili A, Arsuaga JL, Carbonell E, Marques-Bonet T, Penkman K, Sabidó E, Cox J, Olsen JV, Lordkipanidze D, Racimo F, Lalueza-Fox C, de Castro JMB, Willerslev E, Cappellini E. Author Correction: The dental proteome of Homo antecessor. Nature 2020; 584:E19. [PMID: 32724207 DOI: 10.1038/s41586-020-2580-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Frido Welker
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Jazmín Ramos-Madrigal
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Petra Gutenbrunner
- Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Meaghan Mackie
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Shivani Tiwary
- Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | - Cristina Chiva
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.,Proteomics Unit, University Pompeu Fabra, Barcelona, Spain
| | | | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC), University Pompeu Fabra, Barcelona, Spain
| | - Marc de Manuel
- Institute of Evolutionary Biology (UPF-CSIC), University Pompeu Fabra, Barcelona, Spain
| | - Pere Gelabert
- Institute of Evolutionary Biology (UPF-CSIC), University Pompeu Fabra, Barcelona, Spain
| | - María Martinón-Torres
- Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), Burgos, Spain.,Anthropology Department, University College London, London, UK
| | | | - Juan Luis Arsuaga
- Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Madrid, Spain.,Departamento de Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Eudald Carbonell
- Departamento d'Història i Història de l'Art, Universidad Rovira i Virgili, Tarragona, Spain.,Institut Català de Paleoecologia Humana i Evolució Social (IPHES), Tarragona, Spain
| | - Tomas Marques-Bonet
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.,Institute of Evolutionary Biology (UPF-CSIC), University Pompeu Fabra, Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Eduard Sabidó
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.,Proteomics Unit, University Pompeu Fabra, Barcelona, Spain
| | - Jürgen Cox
- Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jesper V Olsen
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - David Lordkipanidze
- Georgian National Museum, Tbilisi, Georgia.,Tbilisi State University, Tbilisi, Georgia
| | - Fernando Racimo
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (UPF-CSIC), University Pompeu Fabra, Barcelona, Spain
| | - José María Bermúdez de Castro
- Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), Burgos, Spain. .,Anthropology Department, University College London, London, UK.
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Zoology, University of Cambridge, Cambridge, UK. .,Wellcome Sanger Institute, Hinxton, UK. .,Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark.
| | - Enrico Cappellini
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
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12
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Sinding MHS, Gopalakrishnan S, Ramos-Madrigal J, de Manuel M, Pitulko VV, Kuderna L, Feuerborn TR, Frantz LAF, Vieira FG, Niemann J, Samaniego Castruita JA, Carøe C, Andersen-Ranberg EU, Jordan PD, Pavlova EY, Nikolskiy PA, Kasparov AK, Ivanova VV, Willerslev E, Skoglund P, Fredholm M, Wennerberg SE, Heide-Jørgensen MP, Dietz R, Sonne C, Meldgaard M, Dalén L, Larson G, Petersen B, Sicheritz-Pontén T, Bachmann L, Wiig Ø, Marques-Bonet T, Hansen AJ, Gilbert MTP. Arctic-adapted dogs emerged at the Pleistocene-Holocene transition. Science 2020; 368:1495-1499. [PMID: 32587022 DOI: 10.1126/science.aaz8599] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 05/06/2020] [Indexed: 12/18/2022]
Abstract
Although sled dogs are one of the most specialized groups of dogs, their origin and evolution has received much less attention than many other dog groups. We applied a genomic approach to investigate their spatiotemporal emergence by sequencing the genomes of 10 modern Greenland sled dogs, an ~9500-year-old Siberian dog associated with archaeological evidence for sled technology, and an ~33,000-year-old Siberian wolf. We found noteworthy genetic similarity between the ancient dog and modern sled dogs. We detected gene flow from Pleistocene Siberian wolves, but not modern American wolves, to present-day sled dogs. The results indicate that the major ancestry of modern sled dogs traces back to Siberia, where sled dog-specific haplotypes of genes that potentially relate to Arctic adaptation were established by 9500 years ago.
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Affiliation(s)
- Mikkel-Holger S Sinding
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Natural History Museum, University of Oslo, Oslo, Norway.,The Qimmeq Project, University of Greenland, Nuussuaq, Greenland.,Greenland Institute of Natural Resources, Nuuk, Greenland.,Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | | | | | - Marc de Manuel
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain
| | - Vladimir V Pitulko
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | - Lukas Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain
| | - Tatiana R Feuerborn
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,The Qimmeq Project, University of Greenland, Nuussuaq, Greenland.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Laurent A F Frantz
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.,School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Filipe G Vieira
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Niemann
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,BioArch, Department of Archaeology, University of York, York, UK
| | | | - Christian Carøe
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Emilie U Andersen-Ranberg
- The Qimmeq Project, University of Greenland, Nuussuaq, Greenland.,Department of Clinical Veterinary Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Peter D Jordan
- Arctic Centre and Groningen Institute of Archaeology, University of Groningen, Netherlands
| | - Elena Y Pavlova
- Arctic and Antarctic Research Institute, St. Petersburg, Russia
| | | | - Aleksei K Kasparov
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | - Varvara V Ivanova
- VNIIOkeangeologia Research Institute (The All-Russian Research Institute of Geology and Mineral Resources of the World Ocean), St. Petersburg, Russia
| | - Eske Willerslev
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Danish Institute for Advanced Study (D-IAS), University of Southern Denmark, Odense, Denmark.,Department of Zoology, University of Cambridge, Cambridge, UK.,Wellcome Trust Sanger Institute, University of Cambridge, Cambridge, UK
| | - Pontus Skoglund
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Francis Crick Institute, London, UK
| | - Merete Fredholm
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Sanne Eline Wennerberg
- Ministry of Fisheries, Hunting and Agriculture, Government of Greenland, Nuuk, Greenland
| | | | - Rune Dietz
- Department of Bioscience, Arctic Research Centre, Aarhus University, Roskilde, Denmark
| | - Christian Sonne
- The Qimmeq Project, University of Greenland, Nuussuaq, Greenland.,Department of Bioscience, Arctic Research Centre, Aarhus University, Roskilde, Denmark.,Henan Province Engineering Research Center for Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou, Henan, China
| | - Morten Meldgaard
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,The Qimmeq Project, University of Greenland, Nuussuaq, Greenland
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Bent Petersen
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Thomas Sicheritz-Pontén
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Lutz Bachmann
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Øystein Wiig
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain. .,Catalan Institution of Research and Advanced Studies, Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Anders J Hansen
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,The Qimmeq Project, University of Greenland, Nuussuaq, Greenland
| | - M Thomas P Gilbert
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,University Museum, Norwegian University of Science and Technology, Trondheim, Norway
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13
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de Manuel M, Barnett R, Sandoval-Velasco M, Yamaguchi N, Garrett Vieira F, Zepeda Mendoza ML, Liu S, Martin MD, Sinding MHS, Mak SST, Carøe C, Liu S, Guo C, Zheng J, Zazula G, Baryshnikov G, Eizirik E, Koepfli KP, Johnson WE, Antunes A, Sicheritz-Ponten T, Gopalakrishnan S, Larson G, Yang H, O'Brien SJ, Hansen AJ, Zhang G, Marques-Bonet T, Gilbert MTP. The evolutionary history of extinct and living lions. Proc Natl Acad Sci U S A 2020; 117:10927-10934. [PMID: 32366643 PMCID: PMC7245068 DOI: 10.1073/pnas.1919423117] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Lions are one of the world's most iconic megafauna, yet little is known about their temporal and spatial demographic history and population differentiation. We analyzed a genomic dataset of 20 specimens: two ca. 30,000-y-old cave lions (Panthera leo spelaea), 12 historic lions (Panthera leo leo/Panthera leo melanochaita) that lived between the 15th and 20th centuries outside the current geographic distribution of lions, and 6 present-day lions from Africa and India. We found that cave and modern lions shared an ancestor ca. 500,000 y ago and that the 2 lineages likely did not hybridize following their divergence. Within modern lions, we found 2 main lineages that diverged ca. 70,000 y ago, with clear evidence of subsequent gene flow. Our data also reveal a nearly complete absence of genetic diversity within Indian lions, probably due to well-documented extremely low effective population sizes in the recent past. Our results contribute toward the understanding of the evolutionary history of lions and complement conservation efforts to protect the diversity of this vulnerable species.
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Affiliation(s)
- Marc de Manuel
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
| | - Ross Barnett
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Nobuyuki Yamaguchi
- Institute of Tropical Biodiversity and Sustainable Development, University Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia;
| | - Filipe Garrett Vieira
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - M Lisandra Zepeda Mendoza
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
- School of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, B15 2TT Edgbaston, Birmingham, United Kingdom
| | | | - Michael D Martin
- Norwegian University of Science and Technology (NTNU) University Museum, 7012 Trondheim, Norway
| | - Mikkel-Holger S Sinding
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Sarah S T Mak
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Christian Carøe
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Shanlin Liu
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
- BGI-Shenzhen, 518083 Shenzhen, China
| | | | - Jiao Zheng
- BGI-Shenzhen, 518083 Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, 518083 Shenzhen, China
| | - Grant Zazula
- Yukon Palaeontology Program, Department of Tourism and Culture, Government of Yukon, Y1A 2C6 Whitehorse, Yukon, Canada
| | - Gennady Baryshnikov
- Zoological Institute, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Eduardo Eizirik
- Laboratory of Genomics and Molecular Biology, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS 90619-900, Brazil
- Instituto Nacional de Ciência e Tecnologia - Ecologia Evolução e Conservação da Biodiversidade (INCT-EECBio), Goiânia, GO 74690-900, Brazil
- Instituto Pró-Carnívoros, Atibaia, SP 12945-010, Brazil
| | - Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630
| | - Warren E Johnson
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630
- The Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, MD 20746-2863
- Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Agostinho Antunes
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, 4450-208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Thomas Sicheritz-Ponten
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, Asian Institute of Medicine, Science and Technology (AIMST), 08100 Bedong, Kedah, Malaysia
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, OX1 3QY Oxford, United Kingdom
| | - Huanming Yang
- BGI-Shenzhen, 518083 Shenzhen, China
- James D. Watson Institute of Genome Science, 310008 Hangzhou, China
| | - Stephen J O'Brien
- Laboratory of Genomic Diversity, Center for Computer Technologies, ITMO (Information Technologies, Mechanics and Optics) University, 197101 St. Petersburg, Russia;
- Guy Harvey Oceanographic Center Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Ft. Lauderdale, FL 33004
| | - Anders J Hansen
- Section for GeoGenetics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Guojie Zhang
- BGI-Shenzhen, 518083 Shenzhen, China
- Section for Ecology and Evolution, Department of Biology, Faculty of Science, University of Copenhagen, 2100 Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, China
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain;
- Centre Nacional d'Anàlisi Genòmica, Centre for Genomic Regulation (CNAG-CRG), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark;
- Norwegian University of Science and Technology (NTNU) University Museum, 7012 Trondheim, Norway
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14
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van Dorp L, Gelabert P, Rieux A, de Manuel M, de-Dios T, Gopalakrishnan S, Carøe C, Sandoval-Velasco M, Fregel R, Olalde I, Escosa R, Aranda C, Huijben S, Mueller I, Marquès-Bonet T, Balloux F, Gilbert MTP, Lalueza-Fox C. Plasmodium vivax Malaria Viewed through the Lens of an Eradicated European Strain. Mol Biol Evol 2020; 37:773-785. [PMID: 31697387 PMCID: PMC7038659 DOI: 10.1093/molbev/msz264] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The protozoan Plasmodium vivax is responsible for 42% of all cases of malaria outside Africa. The parasite is currently largely restricted to tropical and subtropical latitudes in Asia, Oceania, and the Americas. Though, it was historically present in most of Europe before being finally eradicated during the second half of the 20th century. The lack of genomic information on the extinct European lineage has prevented a clear understanding of historical population structuring and past migrations of P. vivax. We used medical microscope slides prepared in 1944 from malaria-affected patients from the Ebro Delta in Spain, one of the last footholds of malaria in Europe, to generate a genome of a European P. vivax strain. Population genetics and phylogenetic analyses placed this strain basal to a cluster including samples from the Americas. This genome allowed us to calibrate a genomic mutation rate for P. vivax, and to estimate the mean age of the last common ancestor between European and American strains to the 15th century. This date points to an introduction of the parasite during the European colonization of the Americas. In addition, we found that some known variants for resistance to antimalarial drugs, including Chloroquine and Sulfadoxine, were already present in this European strain, predating their use. Our results shed light on the evolution of an important human pathogen and illustrate the value of antique medical collections as a resource for retrieving genomic information on pathogens from the past.
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Affiliation(s)
- Lucy van Dorp
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Pere Gelabert
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Adrien Rieux
- CIRAD, UMR PVBMT, St. Pierre de la Réunion, France
| | - Marc de Manuel
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Toni de-Dios
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Christian Carøe
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rosa Fregel
- Department of Genetics, Stanford University, Stanford, CA
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Spain
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA
| | - Raül Escosa
- Consorci de Polítiques Ambientals de les Terres de l'Ebre (COPATE), Deltebre, Spain
| | - Carles Aranda
- Servei de Control de Mosquits, Consell Comarcal del Baix Llobregat, Sant Feliu de Llobregat, Spain
| | - Silvie Huijben
- School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ
- ISGlobal, Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Ivo Mueller
- ISGlobal, Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Population Health and Immunity Division, Walter & Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Barcelona Institute of Science and Technology, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - François Balloux
- UCL Genetics Institute, University College London, London, United Kingdom
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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15
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Gelabert P, Sandoval-Velasco M, Serres A, de Manuel M, Renom P, Margaryan A, Stiller J, de-Dios T, Fang Q, Feng S, Mañosa S, Pacheco G, Ferrando-Bernal M, Shi G, Hao F, Chen X, Petersen B, Olsen RA, Navarro A, Deng Y, Dalén L, Marquès-Bonet T, Zhang G, Antunes A, Gilbert MTP, Lalueza-Fox C. Evolutionary History, Genomic Adaptation to Toxic Diet, and Extinction of the Carolina Parakeet. Curr Biol 2019; 30:108-114.e5. [PMID: 31839456 DOI: 10.1016/j.cub.2019.10.066] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/03/2019] [Accepted: 10/30/2019] [Indexed: 12/13/2022]
Abstract
As the only endemic neotropical parrot to have recently lived in the northern hemisphere, the Carolina parakeet (Conuropsis carolinensis) was an iconic North American bird. The last surviving specimen died in the Cincinnati Zoo in 1918 [1]. The cause of its extinction remains contentious: besides excessive mortality associated to habitat destruction and active hunting, their survival could have been negatively affected by its range having become increasingly patchy [2] or by the exposure to poultry pathogens [3, 4]. In addition, the Carolina parakeet showed a predilection for cockleburs, an herbaceous plant that contains a powerful toxin, carboxyatractyloside, or CAT [5], which did not seem to affect them but made the birds notoriously toxic to most predators [3]. To explore the demographic history of this bird, we generated the complete genomic sequence of a preserved specimen held in a private collection in Espinelves (Girona, Spain), as well as of a close extant relative, Aratinga solstitialis. We identified two non-synonymous genetic changes in two highly conserved proteins known to interact with CAT that could underlie a specific dietary adaptation to this toxin. Our genomic analyses did not reveal evidence of a dramatic past demographic decline in the Carolina parakeet; also, its genome did not exhibit the long runs of homozygosity that are signals of recent inbreeding and are typically found in endangered species. As such, our results suggest its extinction was an abrupt process and thus likely solely attributable to human causes.
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Affiliation(s)
- Pere Gelabert
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Dr. Aiguader 88, 08003 Barcelona, Spain; Department of Evolutionary Anthropology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Aitor Serres
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Marc de Manuel
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Pere Renom
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Ashot Margaryan
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Josefin Stiller
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Toni de-Dios
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Qi Fang
- BGI-Shenzhen, Beishan Industrial Zone, Building 11, Shenzhen 518083, China
| | - Shaohong Feng
- BGI-Shenzhen, Beishan Industrial Zone, Building 11, Shenzhen 518083, China
| | - Santi Mañosa
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Facultat de Biologia, Avinguda Diagonal 643, 08028 Barcelona, Spain
| | - George Pacheco
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Manuel Ferrando-Bernal
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Guolin Shi
- Center of Special Environmental Biomechanics & Biomedical Engineering, School of Life Sciences, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Fei Hao
- Center of Special Environmental Biomechanics & Biomedical Engineering, School of Life Sciences, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Xianqing Chen
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Bent Petersen
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Semeling Road, 08100 Kedah, Malaysia
| | - Remi-André Olsen
- ScieLifeLab, Department of Biochemistry and Biophysics, Stockholm University, Frescativägen 40, SE-17121 Solna, Sweden
| | - Arcadi Navarro
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Dr. Aiguader 88, 08003 Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys 23, 08010 Barcelona, Spain; CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08036 Barcelona, Spain
| | - Yuan Deng
- BGI-Shenzhen, Beishan Industrial Zone, Building 11, Shenzhen 518083, China
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Frescativägen 40, 10405 Stockholm, Sweden
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Dr. Aiguader 88, 08003 Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys 23, 08010 Barcelona, Spain; CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08036 Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, c. de les Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark; China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming 650223, China
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark; NTNU University Museum, Erling Skakkes gate 47c, 7012 Trondheim, Norway.
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Dr. Aiguader 88, 08003 Barcelona, Spain.
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Schmidt JM, de Manuel M, Marques-Bonet T, Castellano S, Andrés AM. The impact of genetic adaptation on chimpanzee subspecies differentiation. PLoS Genet 2019; 15:e1008485. [PMID: 31765391 PMCID: PMC6901233 DOI: 10.1371/journal.pgen.1008485] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 12/09/2019] [Accepted: 10/17/2019] [Indexed: 12/25/2022] Open
Abstract
Chimpanzees, humans' closest relatives, are in danger of extinction. Aside from direct human impacts such as hunting and habitat destruction, a key threat is transmissible disease. As humans continue to encroach upon their habitats, which shrink in size and grow in density, the risk of inter-population and cross-species viral transmission increases, a point dramatically made in the reverse with the global HIV/AIDS pandemic. Inhabiting central Africa, the four subspecies of chimpanzees differ in demographic history and geographical range, and are likely differentially adapted to their particular local environments. To quantitatively explore genetic adaptation, we investigated the genic enrichment for SNPs highly differentiated between chimpanzee subspecies. Previous analyses of such patterns in human populations exhibited limited evidence of adaptation. In contrast, chimpanzees show evidence of recent positive selection, with differences among subspecies. Specifically, we observe strong evidence of recent selection in eastern chimpanzees, with highly differentiated SNPs being uniquely enriched in genic sites in a way that is expected under recent adaptation but not under neutral evolution or background selection. These sites are enriched for genes involved in immune responses to pathogens, and for genes inferred to differentiate the immune response to infection by simian immunodeficiency virus (SIV) in natural vs. non-natural host species. Conversely, central chimpanzees exhibit an enrichment of signatures of positive selection only at cytokine receptors, due to selective sweeps in CCR3, CCR9 and CXCR6 -paralogs of CCR5 and CXCR4, the two major receptors utilized by HIV to enter human cells. Thus, our results suggest that positive selection has contributed to the genetic and phenotypic differentiation of chimpanzee subspecies, and that viruses likely play a predominate role in this differentiation, with SIV being a likely selective agent. Interestingly, our results suggest that SIV has elicited distinctive adaptive responses in these two chimpanzee subspecies.
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MESH Headings
- Adaptation, Physiological/genetics
- Adaptation, Physiological/immunology
- Animals
- Demography
- Genetic Drift
- Genetic Speciation
- HIV/genetics
- HIV/immunology
- HIV/pathogenicity
- Humans
- Immunity, Innate/genetics
- Pan troglodytes/genetics
- Pan troglodytes/immunology
- Pan troglodytes/virology
- Polymorphism, Single Nucleotide/genetics
- Receptors, CCR/genetics
- Receptors, CCR3/genetics
- Receptors, CCR5/genetics
- Receptors, CXCR4/genetics
- Receptors, CXCR6/immunology
- Selection, Genetic/genetics
- Simian Immunodeficiency Virus/genetics
- Simian Immunodeficiency Virus/immunology
- Simian Immunodeficiency Virus/pathogenicity
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Affiliation(s)
- Joshua M. Schmidt
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics, Leipzig, Germany
- * E-mail: (JMS); (AMA)
| | - Marc de Manuel
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas–Universitat Pompeu Fabra), Barcelona, Spain
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas–Universitat Pompeu Fabra), Barcelona, Spain
- National Centre for Genomic Analysis–Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Sergi Castellano
- Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics, Leipzig, Germany
- Genetics and Genomic Medicine Programme, Great Ormond Street Institute of Child Health, University College London (UCL), London, United Kingdom
- UCL Genomics, London, United Kingdom
| | - Aida M. Andrés
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics, Leipzig, Germany
- * E-mail: (JMS); (AMA)
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17
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de Manuel M, Shiina T, Suzuki S, Dereuddre-Bosquet N, Garchon HJ, Tanaka M, Congy-Jolivet N, Aarnink A, Le Grand R, Marques-Bonet T, Blancher A. Whole genome sequencing in the search for genes associated with the control of SIV infection in the Mauritian macaque model. Sci Rep 2018; 8:7131. [PMID: 29739964 PMCID: PMC5940699 DOI: 10.1038/s41598-018-25071-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 04/11/2018] [Indexed: 11/09/2022] Open
Abstract
In the Mauritian macaque experimentally inoculated with SIV, gene polymorphisms potentially associated with the plasma virus load at a set point, approximately 100 days post inoculation, were investigated. Among the 42 animals inoculated with 50 AID50 of the same strain of SIV, none of which received any preventive or curative treatment, nine individuals were selected: three with a plasma virus load (PVL) among the lowest, three with intermediate PVL values and three among the highest PVL values. The complete genomes of these nine animals were then analyzed. Initially, attention was focused on variants with a potential functional impact on protein encoding genes (non-synonymous SNPs (NS-SNPs) and splicing variants). Thus, 424 NS-SNPs possibly associated with PVL were detected. The 424 candidates SNPs were genotyped in these 42 SIV experimentally infected animals (including the nine animals subjected to whole genome sequencing). The genes containing variants most probably associated with PVL at a set time point are analyzed herein.
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Affiliation(s)
- Marc de Manuel
- Institute of Evolutionary Biology, UPF-CSIC, PRBB, Dr. Aiguader 88, 08003, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies, ICREA, Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation, CRG, Barcelona Institute of Science and Technology (BIST, Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Takashi Shiina
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Shingo Suzuki
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Nathalie Dereuddre-Bosquet
- CEA - Université Paris-Sud 11 - INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases, IDMIT Department, IBFJ, 92265, Fontenay-aux-Roses, France
| | - Henri-Jean Garchon
- Inserm U1173, Simone Veil School of Health Sciences, University of Versailles Saint-Quentin-en-Yvelines, Montigny-le-Bretonneux, France
- Genetics Division, Ambroise Paré Hospital (AP-HP), Boulogne-Billancourt, France
| | - Masayuki Tanaka
- Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa, Japan
| | - Nicolas Congy-Jolivet
- Laboratoire d'immunogénétique moléculaire (LIMT, EA 3034, Faculté de médecine Purpan, Université Toulouse 3 (Université Paul Sabatier, UPS), Toulouse, France
- Laboratoire d'immunologie, CHU de Toulouse, France
| | - Alice Aarnink
- Laboratoire d'immunogénétique moléculaire (LIMT, EA 3034, Faculté de médecine Purpan, Université Toulouse 3 (Université Paul Sabatier, UPS), Toulouse, France
| | - Roger Le Grand
- CEA - Université Paris-Sud 11 - INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases, IDMIT Department, IBFJ, 92265, Fontenay-aux-Roses, France
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology, UPF-CSIC, PRBB, Dr. Aiguader 88, 08003, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies, ICREA, Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation, CRG, Barcelona Institute of Science and Technology (BIST, Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Antoine Blancher
- Laboratoire d'immunogénétique moléculaire (LIMT, EA 3034, Faculté de médecine Purpan, Université Toulouse 3 (Université Paul Sabatier, UPS), Toulouse, France.
- Laboratoire d'immunologie, CHU de Toulouse, France.
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18
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Solis-Moruno M, de Manuel M, Hernandez-Rodriguez J, Fontsere C, Gomara-Castaño A, Valsera-Naranjo C, Crailsheim D, Navarro A, Llorente M, Riera L, Feliu-Olleta O, Marques-Bonet T. Potential damaging mutation in LRP5 from genome sequencing of the first reported chimpanzee with the Chiari malformation. Sci Rep 2017; 7:15224. [PMID: 29123202 PMCID: PMC5680330 DOI: 10.1038/s41598-017-15544-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/30/2017] [Indexed: 12/29/2022] Open
Abstract
The genus Pan is the closest related to humans (Homo sapiens) and it includes two species: Pan troglodytes (chimpanzees) and Pan paniscus (bonobos). Different characteristics, some of biomedical aspect, separate them from us. For instance, some common human medical conditions are rare in chimpanzees (menopause, Alzheimer disease) although it is unclear to which extent longevity plays an active role in these differences. However, both humans and chimpanzees present similar pathologies, thus, understanding traits in chimpanzees can help unravel the molecular basis of human conditions. Here, we sequenced the genome of Nico, a central chimpanzee diagnosed with a particular biomedical condition, the Chiari malformation. We performed a variant calling analysis comparing his genome to 25 whole genomes from healthy individuals (bonobos and chimpanzees), and after predicting the effects of the genetic variants, we looked for genes within the OMIM database. We found a novel, private, predicted as damaging mutation in Nico in LRP5, a gene related to bone density alteration pathologies, and we suggest a link between this mutation and his Chiari malformation as previously shown in humans. Our results reinforce the idea that a comparison between humans and chimpanzees can be established in this genetic frame of common diseases.
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Affiliation(s)
- Manuel Solis-Moruno
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, 08003, Spain.
| | - Marc de Manuel
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, 08003, Spain
| | - Jessica Hernandez-Rodriguez
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, 08003, Spain
| | - Claudia Fontsere
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, 08003, Spain
| | - Alba Gomara-Castaño
- Fundació Mona, Carretera C-25, s/n, Riudellots de la Selva, 17457, Girona, Spain
| | | | - Dietmar Crailsheim
- Fundació Mona, Carretera C-25, s/n, Riudellots de la Selva, 17457, Girona, Spain
| | - Arcadi Navarro
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, 08003, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, Barcelona, 08010, Spain
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona, 08028, Spain
| | - Miquel Llorente
- Fundació Mona, Carretera C-25, s/n, Riudellots de la Selva, 17457, Girona, Spain
| | - Laura Riera
- Fundació Mona, Carretera C-25, s/n, Riudellots de la Selva, 17457, Girona, Spain
| | - Olga Feliu-Olleta
- Fundació Mona, Carretera C-25, s/n, Riudellots de la Selva, 17457, Girona, Spain
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, 08003, Spain.
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, Barcelona, 08010, Spain.
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona, 08028, Spain.
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Nater A, Mattle-Greminger MP, Nurcahyo A, Nowak MG, de Manuel M, Desai T, Groves C, Pybus M, Sonay TB, Roos C, Lameira AR, Wich SA, Askew J, Davila-Ross M, Fredriksson G, de Valles G, Casals F, Prado-Martinez J, Goossens B, Verschoor EJ, Warren KS, Singleton I, Marques DA, Pamungkas J, Perwitasari-Farajallah D, Rianti P, Tuuga A, Gut IG, Gut M, Orozco-terWengel P, van Schaik CP, Bertranpetit J, Anisimova M, Scally A, Marques-Bonet T, Meijaard E, Krützen M. Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species. Curr Biol 2017; 27:3487-3498.e10. [PMID: 29103940 DOI: 10.1016/j.cub.2017.09.047] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 07/17/2017] [Accepted: 09/20/2017] [Indexed: 12/30/2022]
Abstract
Six extant species of non-human great apes are currently recognized: Sumatran and Bornean orangutans, eastern and western gorillas, and chimpanzees and bonobos [1]. However, large gaps remain in our knowledge of fine-scale variation in hominoid morphology, behavior, and genetics, and aspects of great ape taxonomy remain in flux. This is particularly true for orangutans (genus: Pongo), the only Asian great apes and phylogenetically our most distant relatives among extant hominids [1]. Designation of Bornean and Sumatran orangutans, P. pygmaeus (Linnaeus 1760) and P. abelii (Lesson 1827), as distinct species occurred in 2001 [1, 2]. Here, we show that an isolated population from Batang Toru, at the southernmost range limit of extant Sumatran orangutans south of Lake Toba, is distinct from other northern Sumatran and Bornean populations. By comparing cranio-mandibular and dental characters of an orangutan killed in a human-animal conflict to those of 33 adult male orangutans of a similar developmental stage, we found consistent differences between the Batang Toru individual and other extant Ponginae. Our analyses of 37 orangutan genomes provided a second line of evidence. Model-based approaches revealed that the deepest split in the evolutionary history of extant orangutans occurred ∼3.38 mya between the Batang Toru population and those to the north of Lake Toba, whereas both currently recognized species separated much later, about 674 kya. Our combined analyses support a new classification of orangutans into three extant species. The new species, Pongo tapanuliensis, encompasses the Batang Toru population, of which fewer than 800 individuals survive. VIDEO ABSTRACT.
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Affiliation(s)
- Alexander Nater
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland; Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland; Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.
| | - Maja P Mattle-Greminger
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland; Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Anton Nurcahyo
- School of Archaeology and Anthropology, Australian National University, Canberra, ACT, Australia
| | - Matthew G Nowak
- Sumatran Orangutan Conservation Programme (PanEco-YEL), Jalan Wahid Hasyim 51/74, Medan 20154, Indonesia; Department of Anthropology, Southern Illinois University, 1000 Faner Drive, Carbondale, IL 62901, USA
| | - Marc de Manuel
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona 08003, Spain
| | - Tariq Desai
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Colin Groves
- School of Archaeology and Anthropology, Australian National University, Canberra, ACT, Australia
| | - Marc Pybus
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona 08003, Spain
| | - Tugce Bilgin Sonay
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Adriano R Lameira
- Department of Anthropology, Durham University, Dawson Building, South Road, Durham DH1 3LE, UK; School of Psychology & Neuroscience, St. Andrews University, St. Mary's Quad, South Street, St. Andrews, Fife KY16 9JP, Scotland, UK
| | - Serge A Wich
- School of Natural Sciences and Psychology, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, UK; Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, Amsterdam 1098, the Netherlands
| | - James Askew
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA
| | - Marina Davila-Ross
- Department of Psychology, University of Portsmouth, King Henry Building, King Henry 1(st) Street, Portsmouth PO1 2DY, UK
| | - Gabriella Fredriksson
- Sumatran Orangutan Conservation Programme (PanEco-YEL), Jalan Wahid Hasyim 51/74, Medan 20154, Indonesia; Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, Amsterdam 1098, the Netherlands
| | - Guillem de Valles
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona 08003, Spain
| | - Ferran Casals
- Servei de Genòmica, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona 08003, Spain
| | | | - Benoit Goossens
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK; Danau Girang Field Centre, c/o Sabah Wildlife Department, Wisma Muis, 88100 Kota Kinabalu, Sabah, Malaysia; Sabah Wildlife Department, Wisma Muis, 88100 Kota Kinabalu, Sabah, Malaysia; Sustainable Places Research Institute, Cardiff University, 33 Park Place, Cardiff CF10 3BA, UK
| | - Ernst J Verschoor
- Department of Virology, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288GJ Rijswijk, the Netherlands
| | - Kristin S Warren
- Conservation Medicine Program, College of Veterinary Medicine, Murdoch University, South Street, Murdoch, WA 6150, Australia
| | - Ian Singleton
- Sumatran Orangutan Conservation Programme (PanEco-YEL), Jalan Wahid Hasyim 51/74, Medan 20154, Indonesia; Foundation for a Sustainable Ecosystem (YEL), Medan, Indonesia
| | - David A Marques
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland; Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
| | - Joko Pamungkas
- Primate Research Center, Bogor Agricultural University, Bogor 16151, Indonesia; Faculty of Veterinary Medicine, Bogor Agricultural University, Darmaga Campus, Bogor 16680, Indonesia
| | - Dyah Perwitasari-Farajallah
- Primate Research Center, Bogor Agricultural University, Bogor 16151, Indonesia; Animal Biosystematics and Ecology Division, Department of Biology, Bogor Agricultural University, Jalan Agatis, Dramaga Campus, Bogor 16680, Indonesia
| | - Puji Rianti
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland; Primate Research Center, Bogor Agricultural University, Bogor 16151, Indonesia; Animal Biosystematics and Ecology Division, Department of Biology, Bogor Agricultural University, Jalan Agatis, Dramaga Campus, Bogor 16680, Indonesia
| | - Augustine Tuuga
- Sabah Wildlife Department, Wisma Muis, 88100 Kota Kinabalu, Sabah, Malaysia
| | - Ivo G Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Plaça de la Mercè 10, 08002 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Plaça de la Mercè 10, 08002 Barcelona, Spain
| | - Pablo Orozco-terWengel
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK
| | - Carel P van Schaik
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Jaume Bertranpetit
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona 08003, Spain; Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Cambridge, UK
| | - Maria Anisimova
- Institute of Applied Simulations, School of Life Sciences and Facility Management, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31a, 8820 Wädenswil, Switzerland; Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, 1015 Lausanne, Switzerland
| | - Aylwyn Scally
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona 08003, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| | - Erik Meijaard
- School of Archaeology and Anthropology, Australian National University, Canberra, ACT, Australia; Borneo Futures, Bandar Seri Begawan, Brunei Darussalam.
| | - Michael Krützen
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
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Abstract
The Eurasian sympatry of Neandertals and anatomically modern humans - beginning at least 45,000 years ago and possibly lasting for more than 5000 years - has sparked immense anthropological interest into the factors that potentially contributed to Neandertal extinction. Among many different hypotheses, the "differential pathogen resistance" extinction model posits that Neandertals were disproportionately affected by exposure to novel infectious diseases that were transmitted during the period of spatiotemporal sympatry with modern humans. Comparisons of new archaic hominin paleogenome sequences with modern human genomes have confirmed a history of genetic admixture - and thus direct contact - between humans and Neandertals. Analyses of these data have also shown that Neandertal nuclear genome genetic diversity was likely considerably lower than that of the Eurasian anatomically modern humans with whom they came into contact, perhaps leaving Neandertal innate immune systems relatively more susceptible to novel pathogens. In this study, we compared levels of genetic diversity in genes for which genetic variation is hypothesized to benefit pathogen defense among Neandertals and African, European, and Asian modern humans, using available exome sequencing data (three individuals, or six chromosomes, per population). We observed that Neandertals had only 31-39% as many nonsynonymous (amino acid changing) polymorphisms across 73 innate immune system genes compared to modern human populations. We also found that Neandertal genetic diversity was relatively low in an unbiased set of balancing selection candidate genes for primates, those genes with the highest 1% genetic diversity genome-wide in non-human hominoids (apes). In contrast, Neandertals had similar or higher levels of genetic diversity than humans in 12 major histocompatibility complex (MHC) genes. Thus, while Neandertals may have been relatively more susceptible to some novel pathogens and differential pathogen resistance could be considered as one potential contributing factor in their extinction, the expectations of this model are not universally met.
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Affiliation(s)
- Alexis P Sullivan
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Marc de Manuel
- Institut de Biologia Evolutiva (CSIC/UPF), Parque de Investigación Biomédica de Barcelona (PRBB), Barcelona, Catalonia 08003, Spain
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (CSIC/UPF), Parque de Investigación Biomédica de Barcelona (PRBB), Barcelona, Catalonia 08003, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
| | - George H Perry
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA; Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA.
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21
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de Manuel M, Kuhlwilm M, Frandsen P, Sousa VC, Desai T, Prado-Martinez J, Hernandez-Rodriguez J, Dupanloup I, Lao O, Hallast P, Schmidt JM, Heredia-Genestar JM, Benazzo A, Barbujani G, Peter BM, Kuderna LFK, Casals F, Angedakin S, Arandjelovic M, Boesch C, Kühl H, Vigilant L, Langergraber K, Novembre J, Gut M, Gut I, Navarro A, Carlsen F, Andrés AM, Siegismund HR, Scally A, Excoffier L, Tyler-Smith C, Castellano S, Xue Y, Hvilsom C, Marques-Bonet T. Chimpanzee genomic diversity reveals ancient admixture with bonobos. Science 2016; 354:477-481. [PMID: 27789843 DOI: 10.1126/science.aag2602] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/09/2016] [Indexed: 12/13/2022]
Abstract
Our closest living relatives, chimpanzees and bonobos, have a complex demographic history. We analyzed the high-coverage whole genomes of 75 wild-born chimpanzees and bonobos from 10 countries in Africa. We found that chimpanzee population substructure makes genetic information a good predictor of geographic origin at country and regional scales. Multiple lines of evidence suggest that gene flow occurred from bonobos into the ancestors of central and eastern chimpanzees between 200,000 and 550,000 years ago, probably with subsequent spread into Nigeria-Cameroon chimpanzees. Together with another, possibly more recent contact (after 200,000 years ago), bonobos contributed less than 1% to the central chimpanzee genomes. Admixture thus appears to have been widespread during hominid evolution.
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Affiliation(s)
- Marc de Manuel
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Martin Kuhlwilm
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Peter Frandsen
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark. Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark
| | - Vitor C Sousa
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Berne, 3012 Berne, Switzerland. Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Tariq Desai
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Javier Prado-Martinez
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain. Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Jessica Hernandez-Rodriguez
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Isabelle Dupanloup
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Berne, 3012 Berne, Switzerland. Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Oscar Lao
- National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain. Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Pille Hallast
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK. Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Joshua M Schmidt
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - José María Heredia-Genestar
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Andrea Benazzo
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Guido Barbujani
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Benjamin M Peter
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Lukas F K Kuderna
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Ferran Casals
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Samuel Angedakin
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Mimi Arandjelovic
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Christophe Boesch
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Hjalmar Kühl
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Linda Vigilant
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Kevin Langergraber
- School of Human Evolution and Social Change and Institute of Human Origins, Arizona State University, Tempe, AZ 85287, USA
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Marta Gut
- National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Ivo Gut
- National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Arcadi Navarro
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain. National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain. Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain
| | - Frands Carlsen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark
| | - Aida M Andrés
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Hans R Siegismund
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Aylwyn Scally
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Laurent Excoffier
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Berne, 3012 Berne, Switzerland. Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Sergi Castellano
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Yali Xue
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Christina Hvilsom
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark.
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain. National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain. Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain.
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22
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Kuhlwilm M, de Manuel M, Nater A, Greminger MP, Krützen M, Marques-Bonet T. Evolution and demography of the great apes. Curr Opin Genet Dev 2016; 41:124-129. [PMID: 27716526 DOI: 10.1016/j.gde.2016.09.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 09/03/2016] [Accepted: 09/12/2016] [Indexed: 01/27/2023]
Abstract
The great apes are the closest living relatives of humans. Chimpanzees and bonobos group together with humans, while gorillas and orangutans are more divergent from humans. Here, we review insights into their evolution pertaining to the topology of species and subspecies and the reconstruction of their demography based on genome-wide variation. These advances have only become possible recently through next-generation sequencing technologies. Given the close relationship to humans, they provide an important evolutionary context for human genetics.
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Affiliation(s)
- Martin Kuhlwilm
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Marc de Manuel
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Alexander Nater
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Maja P Greminger
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland; Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Michael Krützen
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.
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23
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Lobon I, Tucci S, de Manuel M, Ghirotto S, Benazzo A, Prado-Martinez J, Lorente-Galdos B, Nam K, Dabad M, Hernandez-Rodriguez J, Comas D, Navarro A, Schierup MH, Andres AM, Barbujani G, Hvilsom C, Marques-Bonet T. Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions. Genome Biol Evol 2016; 8:2020-30. [PMID: 27345955 PMCID: PMC4943195 DOI: 10.1093/gbe/evw124] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2016] [Indexed: 01/02/2023] Open
Abstract
The genus Pan is the closest genus to our own and it includes two species, Pan paniscus (bonobos) and Pan troglodytes (chimpanzees). The later is constituted by four subspecies, all highly endangered. The study of the Pan genera has been incessantly complicated by the intricate relationship among subspecies and the statistical limitations imposed by the reduced number of samples or genomic markers analyzed. Here, we present a new method to reconstruct complete mitochondrial genomes (mitogenomes) from whole genome shotgun (WGS) datasets, mtArchitect, showing that its reconstructions are highly accurate and consistent with long-range PCR mitogenomes. We used this approach to build the mitochondrial genomes of 20 newly sequenced samples which, together with available genomes, allowed us to analyze the hitherto most complete Pan mitochondrial genome dataset including 156 chimpanzee and 44 bonobo individuals, with a proportional contribution from all chimpanzee subspecies. We estimated the separation time between chimpanzees and bonobos around 1.15 million years ago (Mya) [0.81-1.49]. Further, we found that under the most probable genealogical model the two clades of chimpanzees, Western + Nigeria-Cameroon and Central + Eastern, separated at 0.59 Mya [0.41-0.78] with further internal separations at 0.32 Mya [0.22-0.43] and 0.16 Mya [0.17-0.34], respectively. Finally, for a subset of our samples, we compared nuclear versus mitochondrial genomes and we found that chimpanzee subspecies have different patterns of nuclear and mitochondrial diversity, which could be a result of either processes affecting the mitochondrial genome, such as hitchhiking or background selection, or a result of population dynamics.
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Affiliation(s)
- Irene Lobon
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
| | - Serena Tucci
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Marc de Manuel
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
| | - Silvia Ghirotto
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Andrea Benazzo
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | | | | | - Kiwoong Nam
- Bioinformatics Research Center, C.F. Møllers Alle, Aarhus University, Denmark
| | - Marc Dabad
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jessica Hernandez-Rodriguez
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
| | - Arcadi Navarro
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, Barcelona, Spain CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Mikkel H Schierup
- Bioinformatics Research Center, C.F. Møllers Alle, Aarhus University, Denmark
| | - Aida M Andres
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Guido Barbujani
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | | | - Tomas Marques-Bonet
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, Barcelona, Spain CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
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24
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Dobrynin P, Liu S, Tamazian G, Xiong Z, Yurchenko AA, Krasheninnikova K, Kliver S, Schmidt-Küntzel A, Koepfli KP, Johnson W, Kuderna LFK, García-Pérez R, Manuel MD, Godinez R, Komissarov A, Makunin A, Brukhin V, Qiu W, Zhou L, Li F, Yi J, Driscoll C, Antunes A, Oleksyk TK, Eizirik E, Perelman P, Roelke M, Wildt D, Diekhans M, Marques-Bonet T, Marker L, Bhak J, Wang J, Zhang G, O'Brien SJ. Genomic legacy of the African cheetah, Acinonyx jubatus. Genome Biol 2015; 16:277. [PMID: 26653294 PMCID: PMC4676127 DOI: 10.1186/s13059-015-0837-4] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/17/2015] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations. RESULTS Here the genome sequence of wild-born African cheetahs reveals extreme genomic depletion in SNV incidence, SNV density, SNVs of coding genes, MHC class I and II genes, and mitochondrial DNA SNVs. Cheetah genomes are on average 95 % homozygous compared to the genomes of the outbred domestic cat (24.08 % homozygous), Virunga Mountain Gorilla (78.12 %), inbred Abyssinian cat (62.63 %), Tasmanian devil, domestic dog and other mammalian species. Demographic estimators impute two ancestral population bottlenecks: one >100,000 years ago coincident with cheetah migrations out of the Americas and into Eurasia and Africa, and a second 11,084-12,589 years ago in Africa coincident with late Pleistocene large mammal extinctions. MHC class I gene loss and dramatic reduction in functional diversity of MHC genes would explain why cheetahs ablate skin graft rejection among unrelated individuals. Significant excess of non-synonymous mutations in AKAP4 (p<0.02), a gene mediating spermatozoon development, indicates cheetah fixation of five function-damaging amino acid variants distinct from AKAP4 homologues of other Felidae or mammals; AKAP4 dysfunction may cause the cheetah's extremely high (>80 %) pleiomorphic sperm. CONCLUSIONS The study provides an unprecedented genomic perspective for the rare cheetah, with potential relevance to the species' natural history, physiological adaptations and unique reproductive disposition.
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Affiliation(s)
- Pavel Dobrynin
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 41A Sredniy Avenue, St. Petersburg, 199004, Russia.
| | - Shiping Liu
- National Genbank, BGI-Shenzhen, Shenzhen, 518083, China. .,State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, PR China.
| | - Gaik Tamazian
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 41A Sredniy Avenue, St. Petersburg, 199004, Russia.
| | - Zijun Xiong
- National Genbank, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Andrey A Yurchenko
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 41A Sredniy Avenue, St. Petersburg, 199004, Russia.
| | - Ksenia Krasheninnikova
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 41A Sredniy Avenue, St. Petersburg, 199004, Russia.
| | - Sergey Kliver
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 41A Sredniy Avenue, St. Petersburg, 199004, Russia.
| | - Anne Schmidt-Küntzel
- Life Technologies Conservation Genetics Laboratory, Cheetah Conservation Fund, Otjiwarongo, Otjiwarongo, 9000, Namibia.
| | - Klaus-Peter Koepfli
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 41A Sredniy Avenue, St. Petersburg, 199004, Russia. .,National Zoological Park, Smithsonian Conservation Biology Institute, Washington DC, 20007, USA.
| | - Warren Johnson
- National Zoological Park, Smithsonian Conservation Biology Institute, Washington DC, 20007, USA.
| | - Lukas F K Kuderna
- Institut de Biologia Evolutiva (CSIC/UPF), Dr. Aiguader, 88, Barcelona, 08003, Spain.
| | - Raquel García-Pérez
- Institut de Biologia Evolutiva (CSIC/UPF), Dr. Aiguader, 88, Barcelona, 08003, Spain.
| | - Marc de Manuel
- Institut de Biologia Evolutiva (CSIC/UPF), Dr. Aiguader, 88, Barcelona, 08003, Spain.
| | - Ricardo Godinez
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, 02138, Massachusetts, USA.
| | - Aleksey Komissarov
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 41A Sredniy Avenue, St. Petersburg, 199004, Russia.
| | - Alexey Makunin
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 41A Sredniy Avenue, St. Petersburg, 199004, Russia. .,Institute of Molecular and Cellular Biology of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - Vladimir Brukhin
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 41A Sredniy Avenue, St. Petersburg, 199004, Russia.
| | - Weilin Qiu
- National Genbank, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Long Zhou
- National Genbank, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Fang Li
- National Genbank, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Jian Yi
- National Genbank, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Carlos Driscoll
- Laboratory of Neurogenetics, NIAAA, 5625 Fishers Lane, Rockville, 20852, Maryland, USA.
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas, 177, Porto, 4050-123, Portugal. .,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, Porto, 4169-007, Portugal.
| | - Taras K Oleksyk
- Biology Department, University of Puerto-Rico at Mayaguez, Mayaguez, Puerto Rico.
| | - Eduardo Eizirik
- PUCRS, Faculdade de Biociencias, Laboratorio de Biología Genómica e Molecular, Porto Alegre, 90619-900, Brazil.
| | - Polina Perelman
- Institute of Molecular and Cellular Biology of the Russian Academy of Sciences, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Novosibirsk, 630090, Russia.
| | - Melody Roelke
- Laboratory of Animal Sciences Progras, Leídos Biomedical Research Inc., Frederick National Laboratory, Frederick, 21702, Maryland, USA.
| | - David Wildt
- National Zoological Park, Smithsonian Conservation Biology Institute, Washington DC, 20007, USA.
| | - Mark Diekhans
- Center for Biomolecular Science and Engineering, University of California, Santa-Cruz, USA.
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (CSIC/UPF), Dr. Aiguader, 88, Barcelona, 08003, Spain. .,Centro Nacional de Analisis Genomics (CNAG), Baldiri Reixach 4, Barcelona, 08013, Spain. .,State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, PR China.
| | - Laurie Marker
- Cheetah Conservation Fund, Otjiwarongo, Otjiwarongo, 9000, Namibia.
| | - Jong Bhak
- Biomedical Engineering Department, UNIST, Ulsan National Institute of Science and Technology, Ulsan, Korea.
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, 518083, China. .,Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, 2200, Denmark. .,Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, 21589, Saudi Arabia. .,Macau University of Science and Technology, Taipa, 999078, Macau, China.
| | - Guojie Zhang
- National Genbank, BGI-Shenzhen, Shenzhen, 518083, China. .,Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen, DK-2100, Denmark.
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 41A Sredniy Avenue, St. Petersburg, 199004, Russia. .,Oceanographic Center, Nova Southeastern University Ft Lauderdale, 8000 N. Ocean Drive, Ft Lauderdale, 33004, Florida, USA.
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25
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Xue Y, Prado-Martinez J, Sudmant PH, Narasimhan V, Ayub Q, Szpak M, Frandsen P, Chen Y, Yngvadottir B, Cooper DN, de Manuel M, Hernandez-Rodriguez J, Lobon I, Siegismund HR, Pagani L, Quail MA, Hvilsom C, Mudakikwa A, Eichler EE, Cranfield MR, Marques-Bonet T, Tyler-Smith C, Scally A. Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding. Science 2015; 348:242-245. [PMID: 25859046 PMCID: PMC4668944 DOI: 10.1126/science.aaa3952] [Citation(s) in RCA: 221] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 03/03/2015] [Indexed: 12/30/2022]
Abstract
Mountain gorillas are an endangered great ape subspecies and a prominent focus for conservation, yet we know little about their genomic diversity and evolutionary past. We sequenced whole genomes from multiple wild individuals and compared the genomes of all four Gorilla subspecies. We found that the two eastern subspecies have experienced a prolonged population decline over the past 100,000 years, resulting in very low genetic diversity and an increased overall burden of deleterious variation. A further recent decline in the mountain gorilla population has led to extensive inbreeding, such that individuals are typically homozygous at 34% of their sequence, leading to the purging of severely deleterious recessive mutations from the population. We discuss the causes of their decline and the consequences for their future survival.
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Affiliation(s)
- Yali Xue
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Javier Prado-Martinez
- Institut de Biologia Evolutiva (CSIC/UPF), Parque de Investigación Biomédica de Barcelona (PRBB), Barcelona, Catalonia 08003, Spain
| | - Peter H. Sudmant
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Vagheesh Narasimhan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0WA, UK
| | - Qasim Ayub
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Michal Szpak
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Peter Frandsen
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Yuan Chen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Bryndis Yngvadottir
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - David N. Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff CF14 4XN, UK
| | - Marc de Manuel
- Institut de Biologia Evolutiva (CSIC/UPF), Parque de Investigación Biomédica de Barcelona (PRBB), Barcelona, Catalonia 08003, Spain
| | - Jessica Hernandez-Rodriguez
- Institut de Biologia Evolutiva (CSIC/UPF), Parque de Investigación Biomédica de Barcelona (PRBB), Barcelona, Catalonia 08003, Spain
| | - Irene Lobon
- Institut de Biologia Evolutiva (CSIC/UPF), Parque de Investigación Biomédica de Barcelona (PRBB), Barcelona, Catalonia 08003, Spain
| | - Hans R. Siegismund
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Luca Pagani
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40134 Bologna, Italy
| | - Michael A. Quail
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Christina Hvilsom
- Research and Conservation, Copenhagen Zoo, DK-2000 Frederiksberg, Denmark
| | | | - Evan E. Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 91895, USA
| | - Michael R. Cranfield
- Gorilla Doctors, Karen C. Drayer Wildlife Health Center, University of California, Davis, CA 95616, USA
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (CSIC/UPF), Parque de Investigación Biomédica de Barcelona (PRBB), Barcelona, Catalonia 08003, Spain
- Centro Nacional de Análisis Genómico (Parc Cientific de Barcelona), Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Aylwyn Scally
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
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