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Marivaux L, Negri FR, Antoine PO, Stutz NS, Condamine FL, Kerber L, Pujos F, Ventura Santos R, Alvim AMV, Hsiou AS, Bissaro MC, Adami-Rodrigues K, Ribeiro AM. An eosimiid primate of South Asian affinities in the Paleogene of Western Amazonia and the origin of New World monkeys. Proc Natl Acad Sci U S A 2023; 120:e2301338120. [PMID: 37399374 PMCID: PMC10334725 DOI: 10.1073/pnas.2301338120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/22/2023] [Indexed: 07/05/2023] Open
Abstract
Recent fossil discoveries in Western Amazonia revealed that two distinct anthropoid primate clades of African origin colonized South America near the Eocene/Oligocene transition (ca. 34 Ma). Here, we describe a diminutive fossil primate from Brazilian Amazonia and suggest that, surprisingly, a third clade of anthropoids was involved in the Paleogene colonization of South America by primates. This new taxon, Ashaninkacebus simpsoni gen. et sp. nov., has strong dental affinities with Asian African stem anthropoids: the Eosimiiformes. Morphology-based phylogenetic analyses of early Old World anthropoids and extinct and extant New World monkeys (platyrrhines) support relationships of both Ashaninkacebus and Amamria (late middle Eocene, North Africa) to the South Asian Eosimiidae. Afro-Arabia, then a mega island, played the role of a biogeographic stopover between South Asia and South America for anthropoid primates and hystricognathous rodents. The earliest primates from South America bear little adaptive resemblance to later Oligocene-early Miocene platyrrhine monkeys, and the scarcity of available paleontological data precludes elucidating firmly their affinities with or within Platyrrhini. Nonetheless, these data shed light on some of their life history traits, revealing a particularly small body size and a diet consisting primarily of insects and possibly fruit, which would have increased their chances of survival on a natural floating island during this extraordinary over-water trip to South America from Africa. Divergence-time estimates between Old and New World taxa indicate that the transatlantic dispersal(s) could source in the intense flooding events associated with the late middle Eocene climatic optimum (ca. 40.5 Ma) in Western Africa.
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Affiliation(s)
- Laurent Marivaux
- Laboratoire de Paléontologie, Institut des Sciences de l’Évolution de Montpellier (UMR 5554, CNRS/Université de Montpellier/Institut de Recherche pour le Développement), Université de Montpellier, 34095Montpellier, France
| | - Francisco R. Negri
- Laboratório de Paleontologia, Universidade Federal do Acre, 69980-000Cruzeiro do Sul, Brazil
| | - Pierre-Olivier Antoine
- Laboratoire de Paléontologie, Institut des Sciences de l’Évolution de Montpellier (UMR 5554, CNRS/Université de Montpellier/Institut de Recherche pour le Développement), Université de Montpellier, 34095Montpellier, France
| | - Narla S. Stutz
- Laboratoire de Paléontologie, Institut des Sciences de l’Évolution de Montpellier (UMR 5554, CNRS/Université de Montpellier/Institut de Recherche pour le Développement), Université de Montpellier, 34095Montpellier, France
- Programa de Pós-Graduação em Geociências, Universidade Federal do Rio Grande do Sul, 91501-970Porto Alegre, Brazil
| | - Fabien L. Condamine
- Laboratoire de Paléontologie, Institut des Sciences de l’Évolution de Montpellier (UMR 5554, CNRS/Université de Montpellier/Institut de Recherche pour le Développement), Université de Montpellier, 34095Montpellier, France
| | - Leonardo Kerber
- Centro de Apoio à Pesquisa Paleontológica da Quarta Colônia, Universidade Federal de Santa Maria, 97230-000São João do Polêsine, Brazil
| | - François Pujos
- Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales, CONICET–Universidad Nacional de Cuyo-Mendoza, 5500Mendoza, Argentina
| | - Roberto Ventura Santos
- Laboratório de Geocronologia, Instituto de Geociências, Universidade de Brasília, 70910-000Brasília, Brazil
| | - André M. V. Alvim
- Laboratório de Geocronologia, Instituto de Geociências, Universidade de Brasília, 70910-000Brasília, Brazil
| | - Annie S. Hsiou
- Laboratório de Paleontologia, Universidade de São Paulo, 14040-901Ribeirão Preto, Brazil
| | - Marcos C. Bissaro
- Laboratório de Paleontologia, Universidade de São Paulo, 14040-901Ribeirão Preto, Brazil
| | - Karen Adami-Rodrigues
- Núcleo de Estudos em Paleontologia e Estratigrafia, Centro das Engenharias, Universidade Federal de Pelotas, 96010-020Pelotas, Brazil
| | - Ana Maria Ribeiro
- Programa de Pós-Graduação em Geociências, Universidade Federal do Rio Grande do Sul, 91501-970Porto Alegre, Brazil
- Seção de Paleontologia, Museu de Ciências Naturais, Secretaria do Meio Ambiente e Infraestrutura, 90690-000Porto Alegre, Brazil
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2
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Kuderna LFK, Gao H, Janiak MC, Kuhlwilm M, Orkin JD, Bataillon T, Manu S, Valenzuela A, Bergman J, Rousselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, Schraiber JG, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, Valsecchi J, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin AD, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Rogers J, Farh KKH, Marques Bonet T. A global catalog of whole-genome diversity from 233 primate species. Science 2023; 380:906-913. [PMID: 37262161 DOI: 10.1126/science.abn7829] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 02/06/2023] [Indexed: 06/03/2023]
Abstract
The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.
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Affiliation(s)
- Lukas F K Kuderna
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Mareike C Janiak
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Martin Kuhlwilm
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Austria
| | - Joseph D Orkin
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Département d'anthropologie, Université de Montréal, 3150 Jean-Brillant, Montréal, QC H3T 1N8, Canada
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Alejandro Valenzuela
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Estrada da Bexiga 2584, CEP 69553-225, Tefé, Amazonas, Brazil
- Evolutionary Biology and Ecology (EBE), Département de Biologie des Organismes, Université libre de Bruxelles (ULB), Av. Franklin D. Roosevelt 50, CP 160/12, B-1050 Brussels Belgium
| | - Lidia Agueda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Julie Blanc
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Ian Goodhead
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
| | | | - Julie E Horvath
- North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC 27707, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - David Juan
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
| | | | - Joshua G Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | | | - Fabrício Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah, Salt Lake City. UT 84102, USA
| | | | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
| | - João Valsecchi
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development, Tefé, Amazonas, Brazil
- Rede de Pesquisa para Estudos sobre Diversidade, Conservação e Uso da Fauna na Amazônia - RedeFauna, Manaus, Amazonas, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica - ComFauna, Iquitos, Loreto, Peru
| | - Malu Messias
- Universidade Federal de Rondônia, Porto Velho, Rondônia, Brazil
| | | | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Rogerio Rossi
- Instituto de Biociências, Universidade Federal do Mato Grosso, Cuiabá, MT, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
- Department of Biology, Trinity University, San Antonio, TX 78212, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clément J Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clifford J Jolly
- Department of Anthropology, New York University, New York, NY 10003, USA
| | - Jane Phillips-Conroy
- Department of Neuroscience, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | - Christian Abee
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | - Joe H Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | | | - Sree Kanthaswamy
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ 85004, USA
| | - Fekadu Shiferaw
- Guinea Worm Eradication Program, The Carter Center Ethiopia, Addis Ababa, Ethiopia
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Long Zhou
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Guojie Zhang
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
- Women's Hospital, School of Medicine, Zhejiang University, 1 Xueshi Road, Shangcheng District, Hangzhou 310006, China
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Head Office, P.O. Box 661, Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany
| | - Minh D Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, Vietnam
| | - Esther Lizano
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, Stuttgart, Germany
| | - Arcadi Navarro
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra. Pg. Luís Companys 23, 08010 Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Av. Doctor Aiguader, N88, 08003 Barcelona, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, C. Wellington 30, 08005 Barcelona, Spain
| | - Tilo Nadler
- Cuc Phuong Commune, Nho Quan District, Ninh Binh Province, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Jessica Lee
- Mandai Nature, 80 Mandai Lake Road, Singapore
| | - Patrick Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK, and School of Geosciences, Drummond Street, Edinburgh EH8 9XP, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37077 Göttingen, Germany
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
- Department of Medical Genetics, University of Calgary, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Jean P Boubli
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Tomas Marques Bonet
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 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, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra. Pg. Luís Companys 23, 08010 Barcelona, Spain
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Storer JM, Walker JA, Baker JN, Hossain S, Roos C, Wheeler TJ, Batzer MA. Framework of the Alu Subfamily Evolution in the Platyrrhine Three-Family Clade of Cebidae, Callithrichidae, and Aotidae. Genes (Basel) 2023; 14:249. [PMID: 36833175 PMCID: PMC9956951 DOI: 10.3390/genes14020249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/10/2023] [Accepted: 01/14/2023] [Indexed: 01/20/2023] Open
Abstract
The history of Alu retroposons has been choreographed by the systematic accumulation of inherited diagnostic nucleotide substitutions to form discrete subfamilies, each having a distinct nucleotide consensus sequence. The oldest subfamily, AluJ, gave rise to AluS after the split between Strepsirrhini and what would become Catarrhini and Platyrrhini. The AluS lineage gave rise to AluY in catarrhines and to AluTa in platyrrhines. Platyrrhine Alu subfamilies Ta7, Ta10, and Ta15 were assigned names based on a standardized nomenclature. However, with the subsequent intensification of whole genome sequencing (WGS), large scale analyses to characterize Alu subfamilies using the program COSEG identified entire lineages of subfamilies simultaneously. The first platyrrhine genome with WGS, the common marmoset (Callithrix jacchus; [caljac3]), resulted in Alu subfamily names sf0 to sf94 in an arbitrary order. Although easily resolved by alignment of the consensus sequences, this naming convention can become increasingly confusing as more genomes are independently analyzed. In this study, we reported Alu subfamily characterization for the platyrrhine three-family clade of Cebidae, Callithrichidae, and Aotidae. We investigated one species/genome from each recognized family of Callithrichidae and Aotidae and of both subfamilies (Cebinae and Saimiriinae) of the family Cebidae. Furthermore, we constructed a comprehensive network of Alu subfamily evolution within the three-family clade of platyrrhines to provide a working framework for future research. Alu expansion in the three-family clade has been dominated by AluTa15 and its derivatives.
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Affiliation(s)
- Jessica M. Storer
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA; (J.M.S.); (J.A.W.)
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Jerilyn A. Walker
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA; (J.M.S.); (J.A.W.)
| | - Jasmine N. Baker
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Shifat Hossain
- Department of Pharmacy Practice & Science, University of Arizona, Tucson, AZ 85721, USA; (S.H.); (T.J.W.)
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany;
| | - Travis J. Wheeler
- Department of Pharmacy Practice & Science, University of Arizona, Tucson, AZ 85721, USA; (S.H.); (T.J.W.)
| | - Mark A. Batzer
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA; (J.M.S.); (J.A.W.)
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4
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Beck RMD, de Vries D, Janiak MC, Goodhead IB, Boubli JP. Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches. J Hum Evol 2023; 174:103293. [PMID: 36493598 DOI: 10.1016/j.jhevol.2022.103293] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 10/21/2022] [Accepted: 10/21/2022] [Indexed: 12/12/2022]
Abstract
There have been multiple published phylogenetic analyses of platyrrhine primates (New World monkeys) using both morphological and molecular data, but relatively few that have integrated both types of data into a total evidence approach. Here, we present phylogenetic analyses of recent and fossil platyrrhines, based on a total evidence data set of 418 morphological characters and 10.2 kilobases of DNA sequence data from 17 nuclear genes taken from previous studies, using undated and tip-dating approaches in a Bayesian framework. We compare the results of these analyses with molecular scaffold analyses using maximum parsimony and Bayesian approaches, and we use a formal information theoretic approach to identify unstable taxa. After a posteriori pruning of unstable taxa, the undated and tip-dating topologies appear congruent with recent molecular analyses and support largely similar relationships, with strong support for Stirtonia as a stem alouattine, Neosaimiri as a stem saimirine, Cebupithecia as a stem pitheciine, and Lagonimico as a stem callitrichid. Both analyses find three Greater Antillean subfossil platyrrhines (Xenothrix, Antillothrix, and Paralouatta) to form a clade that is related to Callicebus, congruent with a single dispersal event by the ancestor of this clade to the Greater Antilles. They also suggest that the fossil Proteropithecia may not be closely related to pitheciines, and that all known platyrrhines older than the Middle Miocene are stem taxa. Notably, the undated analysis found the Early Miocene Panamacebus (currently recognized as the oldest known cebid) to be unstable, and the tip-dating analysis placed it outside crown Platyrrhini. Our tip-dating analysis supports a late Oligocene or earliest Miocene (20.8-27.0 Ma) age for crown Platyrrhini, congruent with recent molecular clock analyses.
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Affiliation(s)
- Robin M D Beck
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK.
| | - Dorien de Vries
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Mareike C Janiak
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Ian B Goodhead
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Jean P Boubli
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
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5
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Storer JM, Walker JA, Brown MA, Batzer MA. Cebidae Alu Element Alignments and a Complex Non-Human Primate Radiation. Life (Basel) 2022; 12:1655. [PMID: 36295090 PMCID: PMC9605045 DOI: 10.3390/life12101655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/17/2022] Open
Abstract
Phylogenetic relationships among Cebidae species of platyrrhine primates are presently under debate. Studies prior to whole genome sequence (WGS) availability utilizing unidirectional Alu repeats linked Callithrix and Saguinus as sister taxa, based on a limited number of genetic markers and specimens, while the relative positions of Cebus, Saimiri and Aotus remained controversial. Multiple WGS allowed computational detection of Alu-genome junctions, however random mutation and evolutionary decay of these short-read segments prevented phylogenetic resolution. In this study, WGS for four Cebidae genomes of marmoset, squirrel monkey, owl monkey and capuchin were analyzed for full-length Alu elements and each locus was compared to the other three genomes in all possible combinations using orthologous region sequence alignments. Over 2000 candidates were aligned and subjected to visual inspection. Approximately 34% passed inspection and were considered shared in their respective category, 48% failed due to the target being present in all four genomes, having N's in the sequence or other sequence quality anomalies, and 18% were determined to represent near parallel insertions (NP). Wet bench locus specific PCR confirmed the presence of shared Alu insertions in all phylogenetically informative categories, providing evidence of extensive incomplete lineage sorting (ILS) and an abundance of Alu proliferation during the complex radiation of Cebidae taxa.
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Affiliation(s)
- Jessica M. Storer
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Jerilyn A. Walker
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
| | - Morgan A. Brown
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
| | - Mark A. Batzer
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
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6
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de La Salles AYF, de Andrade JK, de Souza JG, Freitas KDB, Carreiro ADN, Veloso EVL, Rocha EF, Klem MAP, Mendonça FTM, de Menezes DJA. Anatomy applied to image diagnosis of the hind limb in the black-striped capuchin (Sapajus libidinosus Spix, 1823). Am J Primatol 2022; 84:e23416. [PMID: 35848101 DOI: 10.1002/ajp.23416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/27/2022] [Accepted: 06/15/2022] [Indexed: 11/09/2022]
Abstract
The knowledge of anatomy and imaging exams emerges as an important tool in the study of evolutionary processes of a species, in the elaboration of diagnosis, and the successful choice of the appropriate clinical and surgical procedures. Therefore, this study aims to describe the osteology of the hind limb of Sapajus libidinosus by means of gross, radiographic, and tomographic images. Four cadavers were used in the macroscopic analysis and five animals for the imaging exams, of which four were eventually euthanized and added to the macroscopic study. For imaging exams, they were kept anesthetized. All bones of the hind limb were documented, their structures were described, and compared with data in the literature from human and nonhuman primates. We have performed Student's t test for independent samples. There was no statistical difference between the sexes regarding the length of the hind limb bones. The coxal bone was largely well described using imaging methods. A small penile bone was present at the tip of the penis and it could be identified by all analysis methods. The femur, as well as the tibia and fibula, were not well portrayed in their proximal and distal epiphyses by radiography (Rx). However, they were well identified on tomography. No third trochanter was observed in the femur and the patella had a triangular shape. All the structures described by gross anatomy of the tarsus and metatarsus could be identified by Rx and tomography. More subtle structures, such as the popliteal notch on the tibia, and the gluteal tuberosity pectineal line and facies aspera on the coxal bone, were not identified by medical imaging. S. libidinosus presented anatomical characteristics that were similar to those of larger New World and Old World monkeys, including man. This suggests it's value as an experimental model for studies in recent primates.
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Affiliation(s)
- Ana Y F de La Salles
- Postgraduate Program in Animal Science and Health, Center for Rural Health and Technology, Federal University of Campina Grande, Patos, Paraíba, Brazil
| | | | - Joyce G de Souza
- Postgraduate Program in Animal Science and Health, Center for Rural Health and Technology, Federal University of Campina Grande, Patos, Paraíba, Brazil
| | - Kelvis de B Freitas
- Postgraduate Program in Structural and Functional Biology, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Artur da N Carreiro
- Postgraduate Program in Animal Science and Health, Center for Rural Health and Technology, Federal University of Campina Grande, Patos, Paraíba, Brazil
| | - Edson V L Veloso
- Postgraduate Program in Animal Science and Health, Center for Rural Health and Technology, Federal University of Campina Grande, Patos, Paraíba, Brazil
| | - Ediane F Rocha
- Postgraduate Program in Animal Science and Health, Center for Rural Health and Technology, Federal University of Campina Grande, Patos, Paraíba, Brazil
| | - Marcius A P Klem
- Institute of Veterinary Radiology, Natal, Rio Grande do Norte, Brazil
| | - Fábio T M Mendonça
- Veterinary Health Center, Universidade Potiguar, Natal, Rio Grande do Norte, Brazil
| | - Danilo J A de Menezes
- Postgraduate Program in Animal Science and Health, Center for Rural Health and Technology, Federal University of Campina Grande, Patos, Paraíba, Brazil.,Department of Morphology, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
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7
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Ramírez-Chaves H, Morales-Martínez DM, Rodríguez-Posada ME, Suárez-Castro AF. Checklist of the mammals (Mammalia) of Colombia. MAMMALOGY NOTES 2022. [DOI: 10.47603/mano.v7n2.253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
La actualización de la lista de especies presentes en un país es una tarea continua que llena vacíos de información y apoya la toma de decisiones. En los últimos cinco años, ha habido un aumento del número de especies de mamíferos descritas como nuevas en Colombia, así como primeros registros y cambios taxonómicos. Con el fin de actualizar la información de las especies de mamíferos de Colombia, realizamos una revisión exhaustiva de los cambios taxonómicos de las 528 especies registradas en listas previas. Agregamos nuevas especies descritas, así como nuevos registros de especies ya descritas. Discutimos especies cuya presencia ha sido sugerida recientemente en Colombia, pero que no es respaldada por especímenes de museo. La lista actual de mamíferos en Colombia tiene 543 especies, con cuatro descritas en el último año. Esperamos que la lista sea una herramienta apoyar las necesidades de investigación, en especial las extensiones de distribución, los problemas taxonómicos y la conservación de los mamíferos del país. Finalmente, recomendamos que las actualizaciones de la lista sigan estándares nacionales e internacionales como Darwin Core, utilizado por el Repositorio de Información Global sobre Biodiversidad - GBIF, y el Sistema de Información sobre Biodiversidad de Colombia – SiB.
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8
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Distinguishing primate taxa with enamel incremental variables. J Hum Evol 2022; 164:103139. [PMID: 35123173 DOI: 10.1016/j.jhevol.2021.103139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 12/23/2021] [Accepted: 12/23/2021] [Indexed: 11/23/2022]
Abstract
Enamel has long been of interest for its functional and phylogenetic significance among fossil hominins and other primates. Previous studies demonstrated that enamel incremental features distinguish among hominin fossil taxa, suggesting utility for highlighting taxonomy. However, not all features appear to be useful in mixed samples of fossils, living humans, and apes. Here we tested enamel incremental data from closely related primate taxa to determine which features, if any, distinguish among them. Enamel incremental variables were measured from the M2 of 40 living primate taxa, and we tested our variables using discriminant function analysis at the taxonomic ranks of parvorder, family, tribe, and genus. We then included enamel incremental data from Australopithecus afarensis, Australopithecus africanus, Paranthropus aethiopicus, Paranthropus boisei, and Paranthropus robustus to determine if these features distinguished fossil taxa from living humans and apes. Our initial results show that enamel incremental variables distinguish among primate taxa, but with low classification rates. Further testing with jackknifing methods shows overlap between groups at all taxonomic ranks, suggesting enamel incremental variables are unreliable for taxonomy. The addition of many common enamel incremental growth variables also resulted in multicollinearity in our multivariate analysis. As the dentition and isolated teeth remain a significant portion of the hominin fossil record, verifying enamel incremental features as a useful taxonomic tool is fundamentally important for hominin paleobiology.
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9
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Li H, Chen C, Wang Z, Wang K, Li Y, Wang W. Pattern of New Gene Origination in a Special Fish Lineage, the Flatfishes. Genes (Basel) 2021; 12:genes12111819. [PMID: 34828425 PMCID: PMC8618825 DOI: 10.3390/genes12111819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 12/14/2022] Open
Abstract
Origination of new genes are of inherent interest of evolutionary geneticists for decades, but few studies have addressed the general pattern in a fish lineage. Using our recent released whole genome data of flatfishes, which evolved one of the most specialized body plans in vertebrates, we identified 1541 (6.9% of the starry flounder genes) flatfish-lineage-specific genes. The origination pattern of these flatfish new genes is largely similar to those observed in other vertebrates, as shown by the proportion of DNA-mediated duplication (1317; 85.5%), RNA-mediated duplication (retrogenes; 96; 6.2%), and de novo-origination (128; 8.3%). The emergence rate of species-specific genes is 32.1 per Mya and the whole average level rate for the flatfish-lineage-specific genes is 20.9 per Mya. A large proportion (31.4%) of these new genes have been subjected to selection, in contrast to the 4.0% in primates, while the old genes remain quite similar (66.4% vs. 65.0%). In addition, most of these new genes (70.8%) are found to be expressed, indicating their functionality. This study not only presents one example of systematic new gene identification in a teleost taxon based on comprehensive phylogenomic data, but also shows that new genes may play roles in body planning.
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10
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Nishihara H, Stanyon R, Tanabe H, Koga A. Replacement of owl monkey centromere satellite by a newly evolved variant was a recent and rapid process. Genes Cells 2021; 26:979-986. [PMID: 34570411 DOI: 10.1111/gtc.12898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/16/2021] [Accepted: 09/23/2021] [Indexed: 11/29/2022]
Abstract
Alpha satellite DNA is a major DNA component of primate centromeres. We previously reported that Azara's owl monkey has two types of alpha satellite DNA, OwlAlp1 and OwlAlp2. OwlAlp2 (344 bp) exhibits a sequence similarity throughout its entire length with alpha satellite DNA of closely related species. OwlAlp1 (185 bp) corresponds to the part of OwlAlp2. Based on the observation that the CENP-A protein binds to OwlAlp1, we proposed that OwlAlp1 is a relatively new repetitive DNA that replaced OwlAlp2 as the centromeric satellite DNA. However, a detailed picture of the evolutionary process of this centromere DNA replacement remains largely unknown. Here, we performed a phylogenetic analysis of OwlAlp1 and OwlAlp2 sequences, and also compared our results to alpha satellite DNA sequences of other primate species. We found that: (i) OwlAlp1 exhibits a higher similarity to OwlAlp2 than to alpha satellite DNA of other species, (ii) OwlAlp1 has a single origin, and (iii) sequence variation is lower in OwlAlp1 than in OwlAlp2. We conclude that OwlAlp1 underwent a recent and rapid expansion in the owl monkey lineage. This centromere DNA replacement could have been facilitated by the heterochromatin reorganization that is associated with the adaptation of owl monkeys to a nocturnal lifestyle.
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Affiliation(s)
- Hidenori Nishihara
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Roscoe Stanyon
- Department of Biology, University of Florence, Florence, Italy
| | - Hideyuki Tanabe
- Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies, Hayama, Japan
| | - Akihiko Koga
- Primate Research Institute, Kyoto University, Inuyama, Japan
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11
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Henriques LD, Hauzman E, Bonci DMO, Chang BSW, Muniz JAPC, da Silva Souza G, de Lima Silveira LC, de Faria Galvão O, Goulart PRK, Ventura DF. Uniform trichromacy in Alouatta caraya and Alouatta seniculus: behavioural and genetic colour vision evaluation. Front Zool 2021; 18:36. [PMID: 34238318 PMCID: PMC8268213 DOI: 10.1186/s12983-021-00421-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 06/15/2021] [Indexed: 11/25/2022] Open
Abstract
Primate colour vision depends on a matrix of photoreceptors, a neuronal post receptoral structure and a combination of genes that culminate in different sensitivity through the visual spectrum. Along with a common cone opsin gene for short wavelengths (sws1), Neotropical primates (Platyrrhini) have only one cone opsin gene for medium-long wavelengths (mws/lws) per X chromosome while Paleotropical primates (Catarrhini), including humans, have two active genes. Therefore, while female platyrrhines may be trichromats, males are always dichromats. The genus Alouatta is inferred to be an exception to this rule, as electrophysiological, behavioural and molecular analyses indicated a potential for male trichromacy in this genus. However, it is very important to ascertain by a combination of genetic and behavioural analyses whether this potential translates in terms of colour discrimination capability. We evaluated two howler monkeys (Alouatta spp.), one male A. caraya and one female A. seniculus, using a combination of genetic analysis of the opsin gene sequences and a behavioral colour discrimination test not previously used in this genus. Both individuals completed the behavioural test with performances typical of trichromatic colour vision and the genetic analysis of the sws1, mws, and lws opsin genes revealed three different opsin sequences in both subjects. These results are consistent with uniform trichromacy in both male and female, with presumed spectral sensitivity peaks similar to Catarrhini, at ~ 430 nm, 532 nm, and 563 nm for S-, M- and L-cones, respectively.
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Affiliation(s)
- Leonardo Dutra Henriques
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, Brazil.
| | - Einat Hauzman
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, Brazil.,Instituto de Ensino e Pesquisa, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | | | - Belinda S W Chang
- Department of Cell and System Biology, University of Toronto, Toronto, Canada
| | | | - Givago da Silva Souza
- Núcleo de Medicina Tropical, Universidade Federal do Pará, Belém, Pará, Brazil.,Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Luiz Carlos de Lima Silveira
- Núcleo de Medicina Tropical, Universidade Federal do Pará, Belém, Pará, Brazil.,Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Olavo de Faria Galvão
- Núcleo de Teoria e Pesquisa do Comportamento, Universidade Federal do Pará, Belém, Pará, Brazil
| | | | - Dora Fix Ventura
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, Brazil.,Instituto de Ensino e Pesquisa, Hospital Israelita Albert Einstein, São Paulo, Brazil
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12
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Heymann E. Book review: New World Monkeys. The Evolutionary Odyssey. Primate Biol 2021. [PMCID: PMC8200681 DOI: 10.5194/pb-8-15-2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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13
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Maruyama SR, Rogerio LA, Freitas PD, Teixeira MMG, Ribeiro JMC. Total Ortholog Median Matrix as an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes. Sci Rep 2021; 11:3791. [PMID: 33589693 PMCID: PMC7884790 DOI: 10.1038/s41598-021-81926-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 01/05/2021] [Indexed: 11/09/2022] Open
Abstract
The increasing number of available genomic data allowed the development of phylogenomic analytical tools. Current methods compile information from single gene phylogenies, whether based on topologies or multiple sequence alignments. Generally, phylogenomic analyses elect gene families or genomic regions to construct phylogenomic trees. Here, we presented an alternative approach for Phylogenomics, named TOMM (Total Ortholog Median Matrix), to construct a representative phylogram composed by amino acid distance measures of all pairwise ortholog protein sequence pairs from desired species inside a group of organisms. The procedure is divided two main steps, (1) ortholog detection and (2) creation of a matrix with the median amino acid distance measures of all pairwise orthologous sequences. We tested this approach within three different group of organisms: Kinetoplastida protozoa, hematophagous Diptera vectors and Primates. Our approach was robust and efficacious to reconstruct the phylogenetic relationships for the three groups. Moreover, novel branch topologies could be achieved, providing insights about some phylogenetic relationships between some taxa.
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Affiliation(s)
- Sandra Regina Maruyama
- Department of Genetics and Evolution, Center for Biological Sciences and Health, Federal University of São Carlos (UFSCar), São Carlos, SP, 13565-905, Brazil.
| | - Luana Aparecida Rogerio
- Department of Genetics and Evolution, Center for Biological Sciences and Health, Federal University of São Carlos (UFSCar), São Carlos, SP, 13565-905, Brazil
| | - Patricia Domingues Freitas
- Department of Genetics and Evolution, Center for Biological Sciences and Health, Federal University of São Carlos (UFSCar), São Carlos, SP, 13565-905, Brazil
| | | | - José Marcos Chaves Ribeiro
- Vector Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 12735 Twinbrook Parkway rm 2E32, Rockville, MD, 20852, USA.
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14
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Norconk MA. Historical antecedents and recent innovations in pitheciid (titi, saki, and uakari) feeding ecology. Am J Primatol 2020; 83:e23177. [PMID: 32720418 DOI: 10.1002/ajp.23177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 07/03/2020] [Indexed: 11/07/2022]
Abstract
The modern pitheciids (titis, sakis, and uakaris) of northern South America represent one of the earliest radiations of platyrrhines and demonstrate morphological adaptations and ecological strategies for seed eating. While seeds can provide reliable resources for relatively long periods of time, they are often well protected by thick husks and hard seed coverings. Seeds also tend to be rich in lipids, but they may also be high in indigestible fiber. Even though seed eaters are found in each major primate radiation, only the pitheciids demonstrate primary adaptations for eating seeds. In this partly historical, partly contemporary review, I examine the ecological and anatomical correlates of seed eating. It is dedicated to two well-known field primatologists: ecologist and conservationist J. Márcio Ayres; and anatomist and ecologist Warren G. Kinzey. Using observations in Kinzey (1992, Am J Phys Anthropol, 88, pp. 499-514) as a framework, I provide context and analysis for the intervening three decades of pitheciid research to identify what we know about this understudied group of primates and propose directions for future work.
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15
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Fordham G, Shanee S, Peck M. Effect of river size on Amazonian primate community structure: A biogeographic analysis using updated taxonomic assessments. Am J Primatol 2020; 82:e23136. [PMID: 32323350 DOI: 10.1002/ajp.23136] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 11/05/2022]
Abstract
The mechanisms that underlie the diversification of Neotropical primates remain contested. One mechanism that has found support is the riverine barrier hypothesis (RBH), which postulates that large rivers impede gene flow between populations on opposite riverbanks and promote allopatric speciation. Ayres and Clutton-Brock (1992) demonstrated that larger Amazonian rivers acted as barriers, delineating the distribution limits of primate species. However, profound changes in taxonomy and species concepts have led to the proliferation of Neotropical primate taxa, which may have reduced support for their results. Using the most recent taxonomic assessments and distribution maps, we tested the effect of increasing river size on the similarity of opposite riverbank primate communities in the Amazon. First, we conducted a literature review of primate taxonomy and developed a comprehensive spatial database, then applied geographical information system to query mapped primate ranges against the riverine geography of the Amazon watershed to produce a similarity index for opposite riverbank communities. Finally, we ran models to test how measures of river size predicted levels of similarity. We found that, almost without exception, similarity scores were lower than scores from Ayres and Clutton-Brock (1992) for the same rivers. Our model showed a significant negative relationship between streamflow and similarity in all tests, and found river width significant for the segmented Amazon, but not for multiple Amazon watershed rivers. Our results support the RBH insofar as they provide evidence for the prediction that rivers with higher streamflow act as more substantial barriers to dispersal, and accordingly exhibit greater variation in community composition between riverbanks.
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Affiliation(s)
- Gail Fordham
- School of Life Sciences, University of Sussex, Brighton, UK
| | - Sam Shanee
- Neotropical Primate Conservation, Torpoint, Cornwall, UK
| | - Mika Peck
- School of Life Sciences, University of Sussex, Brighton, UK.,Neotropical Primate Conservation, Torpoint, Cornwall, UK
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16
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Storer JM, Walker JA, Jordan VE, Batzer MA. Sensitivity of the polyDetect computational pipeline for phylogenetic analyses. Anal Biochem 2020; 593:113516. [PMID: 31794702 DOI: 10.1016/j.ab.2019.113516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/19/2019] [Accepted: 11/25/2019] [Indexed: 01/16/2023]
Abstract
Alu elements are powerful phylogenetic markers. The combination of a recently-developed computational pipeline, polyDetect, with high copy number Alu insertions has previously been utilized to help resolve the Papio baboon phylogeny with high statistical support. Here, the polyDetect method was applied to the highly contentious Cebidae phylogeny within New World monkeys (NWM). The polyDetect method relies on conserved homology/identity of short read sequence data among the species being compared to accurately map predicted shared Alu insertions to each unique flanking sequence. The results of this comprehensive assessment indicate that there were insufficient sequence homology/identity stretches in non-repeated DNA sequences among the four Cebidae genera analyzed in this study to make this strategy phylogenetically viable. The ~20 million years of evolutionary divergence of the Cebidae genera has resulted in random sequence decay within the short read data, obscuring potentially orthologous elements in the species tested. These analyses suggest that the polyDetect pipeline is best suited to resolving phylogenies of more recently diverged lineages when high-quality assembled genomes are not available for the taxa of interest.
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Affiliation(s)
- Jessica M Storer
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA
| | - Jerilyn A Walker
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA
| | - Vallmer E Jordan
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA
| | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA.
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17
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Preuss TM. Critique of Pure Marmoset. BRAIN, BEHAVIOR AND EVOLUTION 2019; 93:92-107. [PMID: 31416070 PMCID: PMC6711801 DOI: 10.1159/000500500] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/22/2019] [Indexed: 12/16/2022]
Abstract
The common marmoset, a New World (platyrrhine) monkey, is currently being fast-tracked as a non-human primate model species, especially for genetic modification but also as a general-purpose model for research on the brain and behavior bearing on the human condition. Compared to the currently dominant primate model, the catarrhine macaque monkey, marmosets are notable for certain evolutionary specializations, including their propensity for twin births, their very small size (a result of phyletic dwarfism), and features related to their small size (rapid development and relatively short lifespan), which result in these animals yielding experimental results more rapidly and at lower cost. Macaques, however, have their own advantages. Importantly, macaques are more closely related to humans (which are also catarrhine primates) than are marmosets, sharing approximately 20 million more years of common descent, and are demonstrably more similar to humans in a variety of genomic, molecular, and neurobiological characteristics. Furthermore, the very specializations of marmosets that make them attractive as experimental subjects, such as their rapid development and short lifespan, are ways in which marmosets differ from humans and in which macaques more closely resemble humans. These facts warrant careful consideration of the trade-offs between convenience and cost, on the one hand, and biological realism, on the other, in choosing between non-human primate models of human biology. Notwithstanding the advantages marmosets offer as models, prudence requires continued commitment to research on macaques and other primate species.
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Affiliation(s)
- Todd M Preuss
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA,
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18
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Fam BSO, Reales G, Vargas-Pinilla P, Paré P, Viscardi LH, Sortica VA, Felkl AB, de O Franco Á, Lucion AB, Costa-Neto CM, Pissinatti A, Salzano FM, Paixão-Côrtes VR, Bortolini MC. AVPR1b variation and the emergence of adaptive phenotypes in Platyrrhini primates. Am J Primatol 2019; 81:e23028. [PMID: 31318063 DOI: 10.1002/ajp.23028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/31/2019] [Accepted: 06/16/2019] [Indexed: 12/14/2022]
Abstract
Platyrrhini (New World monkeys, NWm) are a group of primates characterized by behavioral and reproductive traits that are otherwise uncommon among primates, including social monogamy, direct paternal care, and twin births. As a consequence, the study of Platyrrhine primates is an invaluable tool for the discovery of the genetic repertoire underlying these taxon-specific traits. Recently, high conservation of vasopressin (AVP) sequence, in contrast with high variability of oxytocin (OXT), has been described in NWm. AVP and OXT functions are possible due to interaction with their receptors: AVPR1a, AVPR1b, AVPR2, and OXTR; and the variability in this system is associated with the traits mentioned above. Understanding the variability in the receptors is thus fundamental to understand the function and evolution of the system as a whole. Here we describe the variability of AVPR1b coding region in 20 NWm species, which is well-known to influence behavioral traits such as aggression, anxiety, and stress control in placental mammals. Our results indicate that 4% of AVPR1b sites may be under positive selection and a significant number of sites under relaxed selective constraint. Considering the known role of AVPR1b, we suggest that some of the changes described here for the Platyrrhini may be a part of the genetic repertoire connected with the complex network of neuroendocrine mechanisms of AVP-OXT system in the modulation of the HPA axis. Thus, these changes may have promoted the emergence of social behaviors such as direct paternal care in socially monogamous species that are also characterized by small body size and twin births.
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Affiliation(s)
- Bibiana S O Fam
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Guillermo Reales
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,INAGEMP - Instituto de Genética Médica e Populacional, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Pedro Vargas-Pinilla
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Pamela Paré
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Lucas H Viscardi
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Vinicius A Sortica
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Aline B Felkl
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Álvaro de O Franco
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Aldo B Lucion
- Departamento de Fisiologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Claudio M Costa-Neto
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | | | - Francisco M Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Vanessa R Paixão-Côrtes
- Departamento de Biologia Geral, Instituto de Biologia, Universidade Federal da Bahia, Salvador, Brazil
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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Oizumi Y, Koga A, Kanoh J. Alpha satellite DNA-repeat OwlAlp1 forms centromeres in Azara's owl monkey. Genes Cells 2019; 24:511-517. [PMID: 31095817 DOI: 10.1111/gtc.12701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 12/19/2022]
Abstract
Centromeres play crucial roles in faithful chromosome segregation and genome integrity. In simian primates, centromeres possess tandem array of alpha satellite DNA (also referred to as alphoid DNA). Average sizes of alpha satellite repeat units vary between species, for example, 171 bp in human and 343-344 bp in many platyrrhini species (New World monkeys). Interestingly, Azara's owl monkey (Aotus azarae), a platyrrhini species, possesses alpha satellite DNA of two distinct unit sizes, OwlAlp1 (185 bp) and OwlAlp2 (344 bp), both of which present as megasatellite DNAs in the genome. It is, however, unknown which repeat sequence is responsible for functional centromere formation. To investigate the localization of centromeres in vivo, we carried out chromatin immunoprecipitation (ChIP) assay using Azara's owl monkey cells. We found that CENP-A, a histone H3 variant essential for centromere formation, was enriched at OwlAlp1, but not at OwlAlp2. Moreover, CENP-A was detected only at constricted regions of chromosomes by immunofluorescent microscopy. In contrast, trimethylation of histone H3-K9 (H3K9me3), a marker of heterochromatin, was enriched at both OwlAlp1 and OwlAlp2. Our results show that the shorter alpha satellite repeat, OwlAlp1, is selectively used for centromere formation in this monkey.
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Affiliation(s)
- Yusuke Oizumi
- Institute for Protein Research, Osaka University, Suita, Japan
| | - Akihiko Koga
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Junko Kanoh
- Institute for Protein Research, Osaka University, Suita, Japan
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20
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Storer JM, Mierl JR, Brantley SA, Threeton B, Sukharutski Y, Rewerts LC, St Romain CP, Foreman MM, Baker JN, Walker JA, Orkin JD, Melin AD, Phillips KA, Konkel MK, Batzer MA. Amplification Dynamics of Platy-1 Retrotransposons in the Cebidae Platyrrhine Lineage. Genome Biol Evol 2019; 11:1105-1116. [PMID: 30888417 PMCID: PMC6464705 DOI: 10.1093/gbe/evz062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2019] [Indexed: 12/11/2022] Open
Abstract
Platy-1 elements are Platyrrhine-specific, short interspersed elements originally discovered in the Callithrix jacchus (common marmoset) genome. To date, only the marmoset genome has been analyzed for Platy-1 repeat content. Here, we report full-length Platy-1 insertions in other New World monkey (NWM) genomes (Saimiri boliviensis, squirrel monkey; Cebus imitator, capuchin monkey; and Aotus nancymaae, owl monkey) and analyze the amplification dynamics of lineage-specific Platy-1 insertions. A relatively small number of full-length and lineage-specific Platy-1 elements were found in the squirrel, capuchin, and owl monkey genomes compared with the marmoset genome. In addition, only a few older Platy-1 subfamilies were recovered in this study, with no Platy-1 subfamilies younger than Platy-1-6. By contrast, 62 Platy-1 subfamilies were discovered in the marmoset genome. All of the lineage-specific insertions found in the squirrel and capuchin monkeys were fixed present. However, ∼15% of the lineage-specific Platy-1 loci in Aotus were polymorphic for insertion presence/absence. In addition, two new Platy-1 subfamilies were identified in the owl monkey genome with low nucleotide divergences compared with their respective consensus sequences, suggesting minimal ongoing retrotransposition in the Aotus genus and no current activity in the Saimiri, Cebus, and Sapajus genera. These comparative analyses highlight the finding that the high number of Platy-1 elements discovered in the marmoset genome is an exception among NWM analyzed thus far, rather than the rule. Future studies are needed to expand upon our knowledge of Platy-1 amplification in other NWM genomes.
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Affiliation(s)
| | - Jackson R Mierl
- Department of Biological Sciences, Louisiana State University
| | | | | | | | - Lydia C Rewerts
- Department of Biological Sciences, Louisiana State University
| | | | | | - Jasmine N Baker
- Department of Biological Sciences, Louisiana State University
| | | | - Joseph D Orkin
- Department of Anthropology and Archaeology & Department of Medical Genetics, University of Calgary, Alberta, Canada
| | - Amanda D Melin
- Department of Anthropology and Archaeology & Department of Medical Genetics, University of Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute, N.W. Calgary, Alberta, Canada
| | - Kimberley A Phillips
- Department of Psychology, Trinity University.,Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas
| | - Miriam K Konkel
- Department of Biological Sciences, Louisiana State University.,Department of Genetics & Biochemistry, Clemson University
| | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University
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21
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Schrago CG, Seuánez HN. Large ancestral effective population size explains the difficult phylogenetic placement of owl monkeys. Am J Primatol 2019; 81:e22955. [PMID: 30779198 DOI: 10.1002/ajp.22955] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 12/05/2018] [Accepted: 12/15/2018] [Indexed: 11/07/2022]
Abstract
The phylogenetic position of owl monkeys, grouped in the genus Aotus, has been a controversial issue for understanding Neotropical primate evolution. Explanations of the difficult phylogenetic assignment of owl monkeys have been elusive, frequently relying on insufficient data (stochastic error) or scenarios of rapid speciation (adaptive radiation) events. Using a coalescent-based approach, we explored the population-level mechanisms likely explaining these topological discrepancies. We examined the topological variance of 2,192 orthologous genes shared between representatives of the three major Cebidae lineages and the outgroup. By employing a methodological framework that allows for reticulated tree topologies, our analysis explicitly tested for non-dichotomous evolutionary processes impacting the finding of the position of owl monkeys in the cebid phylogeny. Our findings indicated that Aotus is a sister lineage of the callitrichines. Most gene trees (>50%) failed to recover the species tree topology, although the distribution of gene trees mismatching the true species topology followed the standard expectation of the multispecies coalescent without reticulation. We showed that the large effective population size of the common ancestor of Aotus and callitrichines was the most likely factor responsible for generating phylogenetic uncertainty. On the other hand, fast speciation scenarios or introgression played minor roles. We propose that the difficult phylogenetic placement of Aotus is explained by population-level processes associated with the large ancestral effective size. These results shed light on the biogeography of the early cebid diversification in the Miocene, highlighting the relevance of evaluating phylogenetic relationships employing population-aware approaches.
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Affiliation(s)
- Carlos G Schrago
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Hector N Seuánez
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Division of Genetics, National Cancer Institute, Rio de Janeiro, Brazil
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22
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Burrows AM, Nash LT, Hartstone‐Rose A, Silcox MT, López‐Torres S, Selig KR. Dental Signatures for Exudativory in Living Primates, with Comparisons to Other Gouging Mammals. Anat Rec (Hoboken) 2019; 303:265-281. [DOI: 10.1002/ar.24048] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 06/03/2018] [Accepted: 06/11/2018] [Indexed: 01/18/2023]
Affiliation(s)
- Anne M. Burrows
- Department of Physical TherapyDuquesne University Pittsburgh Pennsylvania
- Department of AnthropologyUniversity of Pittsburgh Pittsburgh Pennsylvania
| | - Leanne T. Nash
- School of Human Evolution and Social ChangeArizona State University Tempe Arizona
| | | | - Mary T. Silcox
- Department of AnthropologyUniversity of Toronto Scarborough Toronto Canada
| | - Sergi López‐Torres
- Department of Evolutionary PaleobiologyRoman Kozłowski Institute of Paleobiology, Polish Academy of Sciences Warsaw Poland
| | - Keegan R. Selig
- Department of AnthropologyUniversity of Toronto Scarborough Toronto Canada
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23
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Valeri MP, Dias GB, Pereira VDS, Campos Silva Kuhn G, Svartman M. An eutherian intronic sequence gave rise to a major satellite DNA in Platyrrhini. Biol Lett 2018; 14:rsbl.2017.0686. [PMID: 29386361 DOI: 10.1098/rsbl.2017.0686] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/08/2018] [Indexed: 11/12/2022] Open
Abstract
Satellite DNAs (satDNAs) are major components of eukaryote genomes. However, because of their quick divergence, the evolutionary origin of a given satDNA family can rarely be determined. Herein we took advantage of available primate sequenced genomes to determine the origin of the CapA satDNA (approx. 1500 bp long monomers), first described in the tufted capuchin monkey Sapajus apella We show that CapA is an abundant satDNA in Platyrrhini, whereas in the genomes of most eutherian mammals, including humans, this sequence is present only as a single copy located within a large intron of the NOS1AP (nitric oxide synthase 1 adaptor protein) gene. Our data suggest that this intronic CapA-like sequence gave rise to the CapA satDNA and we discuss possible mechanisms implicated in this event. This is the first report to our knowledge of a single copy intronic sequence giving origin to a satDNA that reaches up to 100 000 copies in some genomes.
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Affiliation(s)
- Mirela Pelizaro Valeri
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Guilherme Borges Dias
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | | | - Gustavo Campos Silva Kuhn
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Marta Svartman
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
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24
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Monson TA, Coleman JL, Hlusko LJ. Craniodental Allometry, Prenatal Growth Rates, and the Evolutionary Loss of the Third Molars in New World Monkeys. Anat Rec (Hoboken) 2018; 302:1419-1433. [PMID: 30315641 DOI: 10.1002/ar.23979] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/06/2018] [Accepted: 06/14/2018] [Indexed: 11/12/2022]
Abstract
A growing body of literature demonstrates that genetic patterning mechanisms underlie the relative proportions of the mammalian postcanine dentition with the third molar being key to understanding variation within the molar row. With this relatively recent insight, there has been renewed interest in mammalian taxa that have lost the third molars. Within platyrrhines, the marmosets and tamarins (Callitrichidae family) are characterized by small body size, claw-like nails, twinning, and reduced molar number. Small body size is hypothesized to have resulted in the third molar being crowded out of the jaws leading to its evolutionary loss in this family. To further explore this hypothesis, we measured the cranium and dentition of 142 individuals spanning all five platyrrhine families. These data reveal that callitrichids have a significantly smaller proportion of mandibular postcanine tooth row length relative to other platyrrhines, refuting the "crowding out" hypothesis. However, postcanine tooth row length is significantly correlated with mandibular length and cranial length (P < 0.01) across all platyrrhines providing evidence for a strong allometric association between postcanine tooth row length and body size more generally. The small body size that characterizes callitrichids results in part from slower prenatal growth rates. Given the allometric relationship between postcanine tooth row length and body size, reported here and in previous studies, we hypothesize that the evolutionary loss of the third molars in callitrichids results from the inhibition of third molar development as a consequence of the slower prenatal growth rates associated with small body size in this family. Anat Rec, 302:1419-1433, 2019. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Tesla A Monson
- Department of Integrative Biology, University of California, Berkeley, California.,Museum of Vertebrate Zoology, University of California, Berkeley, California.,Human Evolution Research Center, University of California, Berkeley, California
| | - Jeffrey L Coleman
- Department of Integrative Biology, University of California, Berkeley, California
| | - Leslea J Hlusko
- Department of Integrative Biology, University of California, Berkeley, California.,Museum of Vertebrate Zoology, University of California, Berkeley, California.,Human Evolution Research Center, University of California, Berkeley, California
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25
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Nishihara H, Stanyon R, Kusumi J, Hirai H, Koga A. Evolutionary Origin of OwlRep, a Megasatellite DNA Associated with Adaptation of Owl Monkeys to Nocturnal Lifestyle. Genome Biol Evol 2018; 10:157-165. [PMID: 29294004 PMCID: PMC5765563 DOI: 10.1093/gbe/evx281] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2017] [Indexed: 12/14/2022] Open
Abstract
Rod cells of many nocturnal mammals have a “non-standard” nuclear architecture, which is called the inverted nuclear architecture. Heterochromatin localizes to the central region of the nucleus. This leads to an efficient light transmission to the outer segments of photoreceptors. Rod cells of diurnal mammals have the conventional nuclear architecture. Owl monkeys (genus Aotus) are the only taxon of simian primates that has a nocturnal or cathemeral lifestyle, and this adaptation is widely thought to be secondary. Their rod cells were shown to exhibit an intermediate chromatin distribution: a spherical heterochromatin block was found in the central region of the nucleus although it was less complete than that of typical nocturnal mammals. We recently demonstrated that the primary DNA component of this heterochromatin block was OwlRep, a megasatellite DNA consisting of 187-bp-long repeat units. However, the origin of OwlRep was not known. Here we show that OwlRep was derived from HSAT6, a simple repeat sequence found in the centromere regions of human chromosomes. HSAT6 occurs widely in primates, suggesting that it was already present in the last common ancestor of extant primates. Notably, Strepsirrhini and Tarsiformes apparently carry a single HSAT6 copy, whereas many species of Simiiformes contain multiple copies. Comparison of nucleotide sequences of these copies revealed the entire process of the OwlRep formation. HSAT6, with or without flanking sequences, was segmentally duplicated in New World monkeys. Then, in the owl monkey linage after its divergence from other New World monkeys, a copy of HSAT6 was tandemly amplified, eventually forming a megasatellite DNA.
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Affiliation(s)
- Hidenori Nishihara
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | | | - Junko Kusumi
- Faculty of Social and Cultural Studies, Kyushu University, Fukuoka, Japan
| | - Hirohisa Hirai
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Akihiko Koga
- Primate Research Institute, Kyoto University, Inuyama, Japan
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26
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How Many Species, Taxa, or Lineages of Cebus albifrons (Platyrrhini, Primates) Inhabit Ecuador? Insights from Mitogenomics. INT J PRIMATOL 2018. [DOI: 10.1007/s10764-018-0062-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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27
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Martins-Junior AMG, Carneiro J, Sampaio I, Ferrari SF, Schneider H. Phylogenetic relationships among Capuchin (Cebidae, Platyrrhini) lineages: An old event of sympatry explains the current distribution of Cebus and Sapajus. Genet Mol Biol 2018; 41:699-712. [PMID: 30235394 PMCID: PMC6136366 DOI: 10.1590/1678-4685-gmb-2017-0012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 01/20/2018] [Indexed: 11/22/2022] Open
Abstract
Capuchin monkeys are currently represented by four species of Cebus and eight of Sapajus. This group is taxonomically complex and several questions still need to be clarified. In the current study, using mtDNA markers and a larger sample representation than in previous studies, we seek to understand the phylogenetic relationships among the capuchin lineages and their historical biogeography. All 12 species of capuchins were analyzed for the mitochondrial Control Region and Cytochrome b to test two biogeographical hypotheses: "Reinvasion of the Amazon (ROA)" and "Sympatric Evolution (SEV)". The phylogenetic relationships among distinct lineages within genera is consistent with an evolutionary diversification pattern probably resulting from an explosive process of diversification and dispersal between 2.0 Ma and 3.0 Ma. Also, the analyses show that the ancestral capuchins were distributed in a wide area encompassing the Amazon and Atlantic Forest. Our results support the SEV hypothesis, showing that the current syntopic distribution of Cebus and Sapajus can be explained by a sympatric speciation event in the Amazon. We also indicate that the recently proposed species taxonomy of Cebus is not supported, and that S. cay and S. macrocephalus are a junior synonym of S. apella.
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Affiliation(s)
- Antonio Marcio Gomes Martins-Junior
- Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança,
PA, Brazil
- Laboratório de Genética, Evolução e Bioinformática, Instituto Federal do
Pará, Tucurui, PA, Brazil
| | - Jeferson Carneiro
- Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança,
PA, Brazil
| | - Iracilda Sampaio
- Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança,
PA, Brazil
| | - Stephen F. Ferrari
- Departamento de Ecologia, Universidade Federal de Sergipe, São
Cristovão, SE, Brazil
- Department of Life Sciences, Roehampton University, London, UK
| | - Horacio Schneider
- Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança,
PA, Brazil
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28
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DNA Polymerase Sequences of New World Monkey Cytomegaloviruses: Another Molecular Marker with Which To Infer Platyrrhini Systematics. J Virol 2018; 92:JVI.00980-18. [PMID: 29976674 DOI: 10.1128/jvi.00980-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 06/27/2018] [Indexed: 01/22/2023] Open
Abstract
Over the past few decades, a large number of studies have identified herpesvirus sequences from many mammalian species around the world. Among the different nonhuman primate species tested so far for cytomegaloviruses (CMVs), only a few were from the New World. Seeking to identify CMV homologues in New World monkeys (NWMs), we carried out molecular screening of 244 blood DNA samples from 20 NWM species from Central and South America. Our aim was to reach a better understanding of their evolutionary processes within the Platyrrhini parvorder. Using PCR amplification with degenerate consensus primers targeting highly conserved amino acid motifs encoded by the herpesvirus DNA polymerase gene, we characterized novel viral sequences from 12 species belonging to seven genera representative of the three NWM families. BLAST searches, pairwise nucleotide and amino acid sequence comparisons, and phylogenetic analyses confirmed that they all belonged to the Cytomegalovirus genus. Previously determined host taxa allowed us to demonstrate a good correlation between the distinct monophyletic clades of viruses and those of the infected primates at the genus level. In addition, the evolutionary branching points that separate NWM CMVs were congruent with the divergence dates of their hosts at the genus level. These results significantly expand our knowledge of the host range of this viral genus and strongly support the occurrence of cospeciation between these viruses and their hosts. In this respect, we propose that NWM CMV DNA polymerase gene sequences may serve as reliable molecular markers with which to infer Platyrrhini phylogenetics.IMPORTANCE Investigating evolutionary processes between viruses and nonhuman primates has led to the discovery of a large number of herpesviruses. No study published so far on primate cytomegaloviruses has extensively studied New World monkeys (NWMs) at the subspecies, species, genus, and family levels. The present study sought to identify cytomegalovirus homologues in NWMs and to decipher their evolutionary relationships. This led us to characterize novel viruses from 12 of the 20 primate species tested, which are representative of the three NWM families. The identification of distinct viruses in these primates not only significantly expands our knowledge of the host range of this viral genus but also sheds light on its evolutionary history. Phylogenetic analyses and molecular dating of the sequences obtained support a virus-host coevolution.
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29
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Valencia LM, Martins A, Ortiz EM, Di Fiore A. A RAD-sequencing approach to genome-wide marker discovery, genotyping, and phylogenetic inference in a diverse radiation of primates. PLoS One 2018; 13:e0201254. [PMID: 30118481 PMCID: PMC6097672 DOI: 10.1371/journal.pone.0201254] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 07/11/2018] [Indexed: 01/08/2023] Open
Abstract
Until recently, most phylogenetic and population genetics studies of nonhuman primates have relied on mitochondrial DNA and/or a small number of nuclear DNA markers, which can limit our understanding of primate evolutionary and population history. Here, we describe a cost-effective reduced representation method (ddRAD-seq) for identifying and genotyping large numbers of SNP loci for taxa from across the New World monkeys, a diverse radiation of primates that shared a common ancestor ~20-26 mya. We also estimate, for the first time, the phylogenetic relationships among 15 of the 22 currently-recognized genera of New World monkeys using ddRAD-seq SNP data using both maximum likelihood and quartet-based coalescent methods. Our phylogenetic analyses robustly reconstructed three monophyletic clades corresponding to the three families of extant platyrrhines (Atelidae, Pitheciidae and Cebidae), with Pitheciidae as basal within the radiation. At the genus level, our results conformed well with previous phylogenetic studies and provide additional information relevant to the problematic position of the owl monkey (Aotus) within the family Cebidae, suggesting a need for further exploration of incomplete lineage sorting and other explanations for phylogenetic discordance, including introgression. Our study additionally provides one of the first applications of next-generation sequencing methods to the inference of phylogenetic history across an old, diverse radiation of mammals and highlights the broad promise and utility of ddRAD-seq data for molecular primatology.
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Affiliation(s)
- Lina M. Valencia
- Primate Molecular Ecology and Evolution Laboratory, Department of Anthropology, University of Texas at Austin, Austin, United States of America
| | - Amely Martins
- Primate Molecular Ecology and Evolution Laboratory, Department of Anthropology, University of Texas at Austin, Austin, United States of America
- Centro Nacional de Pesquisa de Conservação de Primatas Brasileiros, ICMBio/MMA, Brazil, Brazil
| | - Edgardo M. Ortiz
- Department of Integrative Biology, University of Texas at Austin, Austin, United States of America
| | - Anthony Di Fiore
- Primate Molecular Ecology and Evolution Laboratory, Department of Anthropology, University of Texas at Austin, Austin, United States of America
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30
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Sookdeo A, Ruiz-García M, Schneider H, Boissinot S. Contrasting Rates of LINE-1 Amplification among New World Primates of the Atelidae Family. Cytogenet Genome Res 2018; 154:217-228. [PMID: 29991050 DOI: 10.1159/000490481] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2018] [Indexed: 11/19/2022] Open
Abstract
LINE-1 (L1) retrotransposons constitute the dominant category of transposons in mammalian genomes. L1 elements are active in the vast majority of mammals, and only a few cases of L1 extinction have been documented. The only possible case of extinction in primates was suggested for South American spider monkeys. However, these previous studies were based on a single species. We revisited this question with a larger phylogenetic sample, covering all 4 genera of Atelidae and 3 species of spider monkeys. We used an enrichment method to clone recently inserted L1 elements and performed an evolutionary analysis of the sequences. We were able to identify young L1 elements in all taxa, suggesting that L1 is probably still active in all Atelidae examined. However, we also detected considerable variations in the proportion of recent elements indicating that the rate of L1 amplification varies among Atelidae by a 3-fold factor. The extent of L1 amplification in Atelidae remains overall lower than in other New World monkeys. Multiple factors can affect the amplification of L1, such as the demography of the host and the control of transposition. These factors are discussed in the context of host life history.
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Next-Generation Sequencing of the Complete Mitochondrial Genome of the Endangered Species Black Lion Tamarin Leontopithecus chrysopygus (Primates) and Mitogenomic Phylogeny Focusing on the Callitrichidae Family. G3-GENES GENOMES GENETICS 2018; 8:1985-1991. [PMID: 29650540 PMCID: PMC5982826 DOI: 10.1534/g3.118.200153] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We describe the complete mitochondrial genome sequence of the Black Lion Tamarin, an endangered primate species endemic to the Atlantic Rainforest of Brazil. We assembled the Leontopithecus chrysopygus mitogenome, through analysis of 523M base pairs (bp) of short reads produced by next-generation sequencing (NGS) on the Illumina Platform, and investigated the presence of nuclear mitochondrial pseudogenes and heteroplasmic sites. Additionally, we conducted phylogenetic analyses using all complete mitogenomes available for primates until June 2017. The single circular mitogenome of BLT showed organization and arrangement that are typical for other vertebrate species, with a total of 16618 bp, containing 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 non-coding region (D-loop region). Our full phylogenetic tree is based on the most comprehensive mitogenomic dataset for Callitrichidae species to date, adding new data for the Leontopithecus genus, and discussing previous studies performed on primates. Moreover, the mitochondrial genome reported here consists of a robust mitogenome with 3000X coverage, which certainly will be useful for further phylogenetic and evolutionary analyses of Callitrichidae and higher taxa.
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Dagosto M, Gebo D, Ni X, Smith T. Estimating body size in early primates: The case of Archicebus and Teilhardina. J Hum Evol 2018; 115:8-19. [DOI: 10.1016/j.jhevol.2017.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 09/26/2016] [Accepted: 02/20/2017] [Indexed: 01/08/2023]
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Koga A, Tanabe H, Hirai Y, Imai H, Imamura M, Oishi T, Stanyon R, Hirai H. Co-Opted Megasatellite DNA Drives Evolution of Secondary Night Vision in Azara's Owl Monkey. Genome Biol Evol 2017; 9:1963-1970. [PMID: 28810713 PMCID: PMC5553404 DOI: 10.1093/gbe/evx142] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2017] [Indexed: 11/12/2022] Open
Abstract
Owl monkeys (genus Aotus) are the only taxon in simian primates that consists of nocturnal or otherwise cathemeral species. Their night vision is superior to that of other monkeys, apes, and humans but not as good as that of typical nocturnal mammals. This incomplete night vision has been used to conclude that these monkeys only secondarily adapted to a nocturnal lifestyle, or to their cathemeral lifestyle that involves high night-time activity. It is known that the rod cells of many nocturnal mammals possess a unique nuclear architecture in which heterochromatin is centrally located. This "inverted nuclear architecture", in contrast with "conventional nuclear architecture", provides elevated night vision by passing light efficiently to the outer segments of photoreceptors. Owl monkey rod cells exhibit an intermediate chromatin distribution, which may provide them with less efficient night vision than other nocturnal mammals. Recently, we identified three megasatellite DNAs in the genome of Azara's owl monkey (Aotus azarae). In the present study, we show that one of the three megasatellite DNAs, OwlRep, serves as the primary component of the heterochromatin block located in the central space of the rod nucleus in A. azarae. This satellite DNA is likely to have emerged in the Aotus lineage after its divergence from those of other platyrrhini taxa and underwent a rapid expansion in the genome. Our results indicate that the heterochromatin core in the A. azarae rod nucleus was newly formed in A. azarae or its recent ancestor, and supports the hypothesis that A. azarae, and with all probability other Aotus species, secondarily acquired night vision.
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Affiliation(s)
- Akihiko Koga
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Hideyuki Tanabe
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
| | - Yuriko Hirai
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Hiroo Imai
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | | | - Takao Oishi
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | | | - Hirohisa Hirai
- Primate Research Institute, Kyoto University, Inuyama, Japan
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Araújo NP, de Lima LG, Dias GB, Kuhn GCS, de Melo AL, Yonenaga-Yassuda Y, Stanyon R, Svartman M. Identification and characterization of a subtelomeric satellite DNA in Callitrichini monkeys. DNA Res 2017; 24:377-385. [PMID: 28854689 PMCID: PMC5737874 DOI: 10.1093/dnares/dsx010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 03/02/2017] [Indexed: 02/01/2023] Open
Abstract
Repetitive DNAs are abundant fast-evolving components of eukaryotic genomes, which often possess important structural and functional roles. Despite their ubiquity, repetitive DNAs are poorly studied when compared with the genic fraction of genomes. Here, we took advantage of the availability of the sequenced genome of the common marmoset Callithrix jacchus to assess its satellite DNAs (satDNAs) and their distribution in Callitrichini. After clustering analysis of all reads and comparisons by similarity, we identified a satDNA composed by 171 bp motifs, named MarmoSAT, which composes 1.09% of the C. jacchus genome. Fluorescent in situ hybridization on chromosomes of species from the genera Callithrix, Mico and Callimico showed that MarmoSAT had a subtelomeric location. In addition to the common monomeric, we found that MarmoSAT was also organized in higher-order repeats of 338 bp in Callimico goeldii. Our phylogenetic analyses showed that MarmoSAT repeats from C. jacchus lack chromosome-specific features, suggesting exchange events among subterminal regions of non-homologous chromosomes. MarmoSAT is transcribed in several tissues of C. jacchus, with the highest transcription levels in spleen, thymus and heart. The transcription profile and subtelomeric location suggest that MarmoSAT may be involved in the regulation of telomerase and modulation of telomeric chromatin.
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Affiliation(s)
- Naiara Pereira Araújo
- Universidade Federal de Minas Gerais, Laboratório de Citogenômica Evolutiva, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Avenida Presidente Antônio Carlos, 6627 - Pampulha, 31270-901, Belo Horizonte, Brazil
| | - Leonardo Gomes de Lima
- Universidade Federal de Minas Gerais, Laboratório de Citogenômica Evolutiva, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Avenida Presidente Antônio Carlos, 6627 - Pampulha, 31270-901, Belo Horizonte, Brazil
| | - Guilherme Borges Dias
- Universidade Federal de Minas Gerais, Laboratório de Citogenômica Evolutiva, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Avenida Presidente Antônio Carlos, 6627 - Pampulha, 31270-901, Belo Horizonte, Brazil
| | - Gustavo Campos Silva Kuhn
- Universidade Federal de Minas Gerais, Laboratório de Citogenômica Evolutiva, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Avenida Presidente Antônio Carlos, 6627 - Pampulha, 31270-901, Belo Horizonte, Brazil
| | - Alan Lane de Melo
- Universidade Federal de Minas Gerais, Laboratório de Taxonomia e Biologia de Invertebrados, Departamento de Parasitologia, Instituto de Ciências Biológicas, Belo Horizonte, Brazil
| | - Yatiyo Yonenaga-Yassuda
- Universidade de São Paulo, Laboratório de Citogenética de Vertebrados, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, São Paulo, Brazil
| | - Roscoe Stanyon
- University of Florence, Department of Biology, Florence, Italy
| | - Marta Svartman
- Universidade Federal de Minas Gerais, Laboratório de Citogenômica Evolutiva, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Avenida Presidente Antônio Carlos, 6627 - Pampulha, 31270-901, Belo Horizonte, Brazil
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Garbino GST, Martins-Junior AMG. Phenotypic evolution in marmoset and tamarin monkeys (Cebidae, Callitrichinae) and a revised genus-level classification. Mol Phylogenet Evol 2017; 118:156-171. [PMID: 28989098 DOI: 10.1016/j.ympev.2017.10.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/15/2017] [Accepted: 10/03/2017] [Indexed: 11/16/2022]
Abstract
Marmosets and tamarins (Cebidae, Callitrichinae) constitute the most species-rich subfamily of New World monkeys and one of the most diverse phenotypically. Despite the profusion of molecular phylogenies of the group, the evolution of phenotypic characters under the rapidly-emerging consensual phylogeny of the subfamily has been little studied, resulting in taxonomic proposals that have limited support from other datasets. We examined the evolution of 18 phenotypic traits (5 continuous and 13 discrete), including pelage, skull, dentition, postcrania, life-history and vocalization variables in a robust molecular phylogeny of marmoset and tamarin monkeys, quantifying their phylogenetic signal and correlations among some of the traits. At the family level, our resulting topology supports owl monkeys (Aotinae) as sister group of Callitrichinae. The topology of the callitrichine tree was congruent with previous studies except for the position of the midas group of Saguinus tamarins, which placement as sister of the bicolor group did not receive significant statistical support in both Maximum Parsimony and Bayesian Inference analyses. Our results showed that the highest value of phylogenetic signal among continuous traits was displayed by the long call character and the lowest was exhibited in the home range, intermediate values were found in characters related to osteology and skull size. Among discrete traits, pelage and osteology had similar phylogenetic signal. Based on genetic, osteological, pelage and vocalization data, we present an updated genus-level taxonomy of Callitrichinae, which recognizes six genera in the subfamily: Callimico, Callithrix, Cebuella, Mico, Leontopithecus and Saguinus. To reflect their phenotypic distinctiveness and to avoid the use of the informal "species group", we subdivided Saguinus in the subgenera Leontocebus, Saguinus and Tamarinus (revalidated here).
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Affiliation(s)
- Guilherme S T Garbino
- PPG-Zoologia, Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | - Antonio M G Martins-Junior
- Laboratório de Genética e Evolução, Instituto Federal do Pará, Campus de Tucuruí, Brazil; Centro de Genômica e Biologia de Sistemas, Universidade Federal do Pará, Belém, Brazil
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Baker JN, Walker JA, Vanchiere JA, Phillippe KR, St. Romain CP, Gonzalez-Quiroga P, Denham MW, Mierl JR, Konkel MK, Batzer MA. Evolution of Alu Subfamily Structure in the Saimiri Lineage of New World Monkeys. Genome Biol Evol 2017; 9:2365-2376. [PMID: 28957461 PMCID: PMC5622375 DOI: 10.1093/gbe/evx172] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2017] [Indexed: 12/22/2022] Open
Abstract
Squirrel monkeys, Saimiri, are commonly found in zoological parks and used in biomedical research. S. boliviensis is the most common species for research; however, there is little information about genome evolution within this primate lineage. Here, we reconstruct the Alu element sequence amplification and evolution in the genus Saimiri at the time of divergence within the family Cebidae lineage. Alu elements are the most successful SINE (Short Interspersed Element) in primates. Here, we report 46 Saimiri lineage specific Alu subfamilies. Retrotransposition activity involved subfamilies related to AluS, AluTa10, and AluTa15. Many subfamilies are simultaneously active within the Saimiri lineage, a finding which supports the stealth model of Alu amplification. We also report a high resolution analysis of Alu subfamilies within the S. boliviensis genome [saiBol1].
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Affiliation(s)
- Jasmine N. Baker
- Department of Biological Sciences, Louisiana State University, Baton Rouge
| | - Jerilyn A. Walker
- Department of Biological Sciences, Louisiana State University, Baton Rouge
| | - John A. Vanchiere
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center, Shreveport
| | - Kacie R. Phillippe
- Department of Biological Sciences, Louisiana State University, Baton Rouge
| | | | | | - Michael W. Denham
- Department of Biological Sciences, Louisiana State University, Baton Rouge
| | - Jackson R. Mierl
- Department of Biological Sciences, Louisiana State University, Baton Rouge
| | - Miriam K. Konkel
- Department of Biological Sciences, Louisiana State University, Baton Rouge
- Department of Biological Sciences, Clemson University, South Carolina
| | - Mark A. Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge
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Novikova MA, Panyutina AA. Structural Diversity of the Extensor Digitorum Profundus Muscle Complex in Platyrrhini. Folia Primatol (Basel) 2017; 88:274-292. [PMID: 28854427 DOI: 10.1159/000478524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 06/11/2017] [Indexed: 11/19/2022]
Abstract
Separate extension of fingers in the hand of primates is performed by 3 muscles: m. extensor pollicis longus, m. extensor digiti secundi, and m. extensor digitorum lateralis. Here it is proposed to consider them as parts of the extensor digitorum profundus muscular complex. The diversity in structure of these muscles in primates is examined based both on original anatomical study of New World monkeys and analysis of extensive published data on primates from different taxonomic groups. It is shown that in these muscles there are 2 main types of structure variations - the division of the muscle belly into several heads which give rise to separate tendons, and the split of the single terminal tendon into several branches. The first type of modification ensures the possibility of a separate management of the fingers, and the second, on the contrary, ensures the coupled control of extension of fingers. A scheme of evolutionary transformations of muscles belonging to the complex of the deep extensors of fingers is proposed.
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Affiliation(s)
- Mellin A Novikova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
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Ramsier MA, Vinyard CJ, Dominy NJ. Auditory sensitivity of the tufted capuchin (Sapajus apella), a test of allometric predictions. THE JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA 2017; 141:4822. [PMID: 28679259 DOI: 10.1121/1.4986940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
New World monkeys are a diverse primate group and a model for understanding hearing in mammals. However, comparable audiograms do not exist for the larger monkeys, making it difficult to test the hypothesized relationship between interaural distance and high-frequency hearing limit (i.e., the allometric model). Here, the auditory brainstem response (ABR) method is used to assess auditory sensitivity in four tufted capuchins (Sapajus apella), a large monkey with a large interaural distance. A primate-typical four-peak pattern in the ABR waveforms was found with peak latencies from ca. 2 to 12 ms after stimulus onset. Response amplitude decreased linearly with decreasing stimulus level (mean r2 = 0.93, standard deviation 0.14). Individual variation in each threshold was moderate (mean ± 7 dB). The 10-dB bandwidth of enhanced sensitivity was 2-16 kHz-a range comparable to smaller monkeys and congruent with the bandwidth of their vocal repertoire. In accord with the general principles of the allometric model, the 60-dB high-frequency limit of S. apella (26 kHz) is lower than those of smaller-headed monkeys; however, it is substantially lower than 44.7 kHz, the value predicted by the allometric model. These findings and other exceptions to the allometric model warrant cautious application and further investigation of other potential selective factors.
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Affiliation(s)
- Marissa A Ramsier
- Department of Anthropology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, USA
| | - Christopher J Vinyard
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, Ohio 44272, USA
| | - Nathaniel J Dominy
- Department of Biological Sciences, Dartmouth College, 6047 Silsby Hall, Hanover, New Hampshire 03755-3537, USA
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Dumas F, Mazzoleni S. Neotropical primate evolution and phylogenetic reconstruction using chromosomal data. EUROPEAN ZOOLOGICAL JOURNAL 2017. [DOI: 10.1080/11250003.2016.1260655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- F. Dumas
- Department of “Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche”, University of Palermo, Italy
| | - S. Mazzoleni
- Department of “Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche”, University of Palermo, Italy
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
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41
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Garbino GST, de Aquino CC. Evolutionary Significance of the Entepicondylar Foramen of the Humerus in New World Monkeys (Platyrrhini). J MAMM EVOL 2016. [DOI: 10.1007/s10914-016-9366-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Bjarnason A, Soligo C, Elton S. Phylogeny, phylogenetic inference, and cranial evolution in pitheciids andAotus. Am J Primatol 2016; 79:1-11. [DOI: 10.1002/ajp.22621] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 10/21/2016] [Accepted: 11/03/2016] [Indexed: 11/08/2022]
Affiliation(s)
| | | | - Sarah Elton
- Department of Anthropology; Durham University; Durham DH1 3LE
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Tsutsui K, Otoh M, Sakurai K, Suzuki-Hashido N, Hayakawa T, Misaka T, Ishimaru Y, Aureli F, Melin AD, Kawamura S, Imai H. Variation in ligand responses of the bitter taste receptors TAS2R1 and TAS2R4 among New World monkeys. BMC Evol Biol 2016; 16:208. [PMID: 27733116 PMCID: PMC5062938 DOI: 10.1186/s12862-016-0783-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 09/30/2016] [Indexed: 12/02/2022] Open
Abstract
Background New World monkeys (NWMs) are unique in that they exhibit remarkable interspecific variation in color vision and feeding behavior, making them an excellent model for studying sensory ecology. However, it is largely unknown whether non-visual senses co-vary with feeding ecology, especially gustation, which is expected to be indispensable in food selection. Bitter taste, which is mediated by bitter taste receptors (TAS2Rs) in the tongue, helps organisms avoid ingesting potentially toxic substances in food. In this study, we compared the ligand sensitivities of the TAS2Rs of five species of NWMs by heterologous expression in HEK293T cells and calcium imaging. Results We found that TAS2R1 and TAS2R4 orthologs differ in sensitivity among the NWM species for colchicine and camphor, respectively. We then reconstructed the ancestral receptors of NWM TAS2R1 and TAS2R4, measured the evolutionary shift in ligand sensitivity, and identified the amino acid replacement at residue 62 as responsible for the high sensitivity of marmoset TAS2R4 to colchicine. Conclusions Our results provide a basis for understanding the differences in feeding ecology among NWMs with respect to bitter taste. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0783-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kei Tsutsui
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Masahiro Otoh
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Kodama Sakurai
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | | | - Takashi Hayakawa
- Primate Research Institute, Kyoto University, Inuyama, Japan.,Japan Monkey Centre, Inuyama, Japan
| | - Takumi Misaka
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yoshiro Ishimaru
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Filippo Aureli
- Research Centre in Evolutionary Anthropology and Palaeoecology, Liverpool John Moores University, Liverpool, UK.,Instituto de Neuroetologia, Universidad Veracruzana, Xalapa, Mexico
| | - Amanda D Melin
- Departments of Anthropology & Archaeology and Medical Genetics, University of Calgary, Calgary, Canada
| | - Shoji Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
| | - Hiroo Imai
- Primate Research Institute, Kyoto University, Inuyama, Japan.
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Vargas-Pinilla P, Babb P, Nunes L, Paré P, Rosa G, Felkl A, Longo D, Salzano FM, Paixão-Côrtes VR, Gonçalves GL, Bortolini MC. Progesterone Response Element Variation in the OXTR Promoter Region and Paternal Care in New World Monkeys. Behav Genet 2016; 47:77-87. [DOI: 10.1007/s10519-016-9806-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 08/10/2016] [Indexed: 01/25/2023]
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Marivaux L, Adnet S, Altamirano-Sierra AJ, Pujos F, Ramdarshan A, Salas-Gismondi R, Tejada-Lara JV, Antoine PO. Dental remains of cebid platyrrhines from the earliest late Miocene of Western Amazonia, Peru: Macroevolutionary implications on the extant capuchin and marmoset lineages. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 161:478-493. [DOI: 10.1002/ajpa.23052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 06/22/2016] [Accepted: 07/01/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Laurent Marivaux
- Laboratoire de Paléontologie, Institut des Sciences de l'Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE), c.c. 064, Université de Montpellier; F-34095 Montpellier, Cedex 05 France
| | - Sylvain Adnet
- Laboratoire de Paléontologie, Institut des Sciences de l'Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE), c.c. 064, Université de Montpellier; F-34095 Montpellier, Cedex 05 France
| | - Ali J. Altamirano-Sierra
- Departamento de Paleontología de Vertebrados; Museo de Historia Natural-Universidad Nacional Mayor San Marcos (MUSM); Lima 11 Peru
| | - François Pujos
- Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales (IANIGLA), CCT-CONICET-Mendoza; Mendoza 5500 Argentina
| | - Anusha Ramdarshan
- Laboratoire de Paléontologie, Institut des Sciences de l'Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE), c.c. 064, Université de Montpellier; F-34095 Montpellier, Cedex 05 France
| | - Rodolfo Salas-Gismondi
- Departamento de Paleontología de Vertebrados; Museo de Historia Natural-Universidad Nacional Mayor San Marcos (MUSM); Lima 11 Peru
| | - Julia V. Tejada-Lara
- Departamento de Paleontología de Vertebrados; Museo de Historia Natural-Universidad Nacional Mayor San Marcos (MUSM); Lima 11 Peru
- Columbia University in the City of New York and Division of Vertebrate Paleontology, American Museum of Natural History; New York NY 10024
| | - Pierre-Olivier Antoine
- Laboratoire de Paléontologie, Institut des Sciences de l'Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE), c.c. 064, Université de Montpellier; F-34095 Montpellier, Cedex 05 France
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Marivaux L, Adnet S, Altamirano-Sierra AJ, Boivin M, Pujos F, Ramdarshan A, Salas-Gismondi R, Tejada-Lara JV, Antoine PO. Neotropics provide insights into the emergence of New World monkeys: New dental evidence from the late Oligocene of Peruvian Amazonia. J Hum Evol 2016; 97:159-75. [PMID: 27457552 DOI: 10.1016/j.jhevol.2016.05.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 05/17/2016] [Accepted: 05/20/2016] [Indexed: 10/21/2022]
Abstract
Recent field efforts in Peruvian Amazonia (Contamana area, Loreto Department) have resulted in the discovery of a late Oligocene (ca. 26.5 Ma; Chambira Formation) fossil primate-bearing locality (CTA-61). In this paper, we analyze the primate material consisting of two isolated upper molars, the peculiar morphology of which allows us to describe a new medium-sized platyrrhine monkey: Canaanimico amazonensis gen. et sp. nov. In addition to the recent discovery of Perupithecus ucayaliensis, a primitive anthropoid taxon of African affinities from the alleged latest Eocene Santa Rosa locality (Peruvian Amazonia), the discovery of Canaanimico adds to the evidence that primates were well-established in the Amazonian Basin during the Paleogene. Our phylogenetic results based on dental evidence show that none of the early Miocene Patagonian taxa (Homunculus, Carlocebus, Soriacebus, Mazzonicebus, Dolichocebus, Tremacebus, and Chilecebus), the late Oligocene Bolivian Branisella, or the Peruvian Canaanimico, is nested within a crown platyrrhine clade. All these early taxa are closely related and considered here as stem Platyrrhini. Canaanimico is nested within the Patagonian Soriacebinae, and closely related to Soriacebus, thereby extending back the soriacebine lineage to 26.5 Ma. Given the limited dental evidence, it is difficult to assess if Canaanimico was engaged in a form of pitheciine-like seed predation as is observed in Soriacebus and Mazzonicebus, but dental microwear patterns recorded on one upper molar indicate that Canaanimico was possibly a fruit and hard-object eater. If Panamacebus, a recently discovered stem cebine from the early Miocene of Panama, indicates that the crown platyrrhine radiation was already well underway by the earliest Miocene, Canaanimico indicates in turn that the "homunculid" radiation (as a part of the stem radiation) was well underway by the late Oligocene. These new data suggest that the stem radiation likely occurred in the Neotropics during the Oligocene, and that several stem lineages independently reached Patagonia during the early Miocene. Finally, we are still faced with a "layered" pattern of platyrrhine evolution, but modified in terms of timing of cladogeneses. If the crown platyrrhine radiation occurred in the Neotropics around the Oligocene-Miocene transition (or at least during the earliest Miocene), it was apparently concomitant with the diversification of the latest stem forms in Patagonia.
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Affiliation(s)
- Laurent Marivaux
- Laboratoire de Paléontologie, Institut des Sciences de l'Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE), c.c. 064, Université de Montpellier, place Eugène Bataillon, F-34095 Montpellier Cedex 05, France.
| | - Sylvain Adnet
- Laboratoire de Paléontologie, Institut des Sciences de l'Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE), c.c. 064, Université de Montpellier, place Eugène Bataillon, F-34095 Montpellier Cedex 05, France
| | - Ali J Altamirano-Sierra
- Departamento de Paleontología de Vertebrados, Museo de Historia Natural - Universidad Nacional Mayor San Marcos (MUSM), Av. Arenales 1256, Lima 11, Peru
| | - Myriam Boivin
- Laboratoire de Paléontologie, Institut des Sciences de l'Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE), c.c. 064, Université de Montpellier, place Eugène Bataillon, F-34095 Montpellier Cedex 05, France
| | - François Pujos
- Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales (IANIGLA), CCT-CONICET-Mendoza, Av. Ruiz Leal s/n, Parque Gral. San Martín, 5500 Mendoza, Argentina
| | - Anusha Ramdarshan
- Laboratoire de Paléontologie, Institut des Sciences de l'Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE), c.c. 064, Université de Montpellier, place Eugène Bataillon, F-34095 Montpellier Cedex 05, France
| | - Rodolfo Salas-Gismondi
- Laboratoire de Paléontologie, Institut des Sciences de l'Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE), c.c. 064, Université de Montpellier, place Eugène Bataillon, F-34095 Montpellier Cedex 05, France; Departamento de Paleontología de Vertebrados, Museo de Historia Natural - Universidad Nacional Mayor San Marcos (MUSM), Av. Arenales 1256, Lima 11, Peru
| | - Julia V Tejada-Lara
- Departamento de Paleontología de Vertebrados, Museo de Historia Natural - Universidad Nacional Mayor San Marcos (MUSM), Av. Arenales 1256, Lima 11, Peru; Columbia University in the City of New York and Division of Vertebrate Paleontology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Pierre-Olivier Antoine
- Laboratoire de Paléontologie, Institut des Sciences de l'Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE), c.c. 064, Université de Montpellier, place Eugène Bataillon, F-34095 Montpellier Cedex 05, France.
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French JA, Taylor JH, Mustoe AC, Cavanaugh J. Neuropeptide diversity and the regulation of social behavior in New World primates. Front Neuroendocrinol 2016; 42:18-39. [PMID: 27020799 PMCID: PMC5030117 DOI: 10.1016/j.yfrne.2016.03.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 02/27/2016] [Accepted: 03/24/2016] [Indexed: 01/09/2023]
Abstract
Oxytocin (OT) and vasopressin (AVP) are important hypothalamic neuropeptides that regulate peripheral physiology, and have emerged as important modulators of brain function, particularly in the social realm. OT structure and the genes that ultimately determine structure are highly conserved among diverse eutherian mammals, but recent discoveries have identified surprising variability in OT and peptide structure in New World monkeys (NWM), with five new OT variants identified to date. This review explores these new findings in light of comparative OT/AVP ligand evolution, documents coevolutionary changes in the oxytocin and vasopressin receptors (OTR and V1aR), and highlights the distribution of neuropeptidergic neurons and receptors in the primate brain. Finally, the behavioral consequences of OT and AVP in regulating NWM sociality are summarized, demonstrating important neuromodulatory effects of these compounds and OT ligand-specific influences in certain social domains.
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Affiliation(s)
- Jeffrey A French
- Program in Neuroscience and Behavior, University of Nebraska at Omaha, Omaha, NE 68182, USA.
| | - Jack H Taylor
- Program in Neuroscience and Behavior, University of Nebraska at Omaha, Omaha, NE 68182, USA
| | - Aaryn C Mustoe
- Program in Neuroscience and Behavior, University of Nebraska at Omaha, Omaha, NE 68182, USA
| | - Jon Cavanaugh
- Program in Neuroscience and Behavior, University of Nebraska at Omaha, Omaha, NE 68182, USA
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Kugou K, Hirai H, Masumoto H, Koga A. Formation of functional CENP-B boxes at diverse locations in repeat units of centromeric DNA in New World monkeys. Sci Rep 2016; 6:27833. [PMID: 27292628 PMCID: PMC4904201 DOI: 10.1038/srep27833] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 05/25/2016] [Indexed: 12/17/2022] Open
Abstract
Centromere protein B, which is involved in centromere formation, binds to centromeric repetitive DNA by recognizing a nucleotide motif called the CENP-B box. Humans have large numbers of CENP-B boxes in the centromeric repetitive DNA of their autosomes and X chromosome. The current understanding is that these CENP-B boxes are located at identical positions in the repeat units of centromeric DNA. Great apes also have CENP-B boxes in locations that are identical to humans. The purpose of the present study was to examine the location of CENP-B box in New World monkeys. We recently identified CENP-B box in one species of New World monkeys (marmosets). In this study, we found functional CENP-B boxes in CENP-A-assembled repeat units of centromeric DNA in 2 additional New World monkeys (squirrel monkeys and tamarins) by immunostaining and ChIP-qPCR analyses. The locations of the 3 CENP-B boxes in the repeat units differed from one another. The repeat unit size of centromeric DNA of New World monkeys (340–350 bp) is approximately twice that of humans and great apes (171 bp). This might be, associated with higher-order repeat structures of centromeric DNA, a factor for the observed variation in the CENP-B box location in New World monkeys.
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Affiliation(s)
- Kazuto Kugou
- Department of Frontier Research, Kazusa DNA Research Institute, Kisarazu 292-0818, Japan
| | - Hirohisa Hirai
- Primate Research Institute, Kyoto University, Inuyama 484-8506, Japan
| | - Hiroshi Masumoto
- Department of Frontier Research, Kazusa DNA Research Institute, Kisarazu 292-0818, Japan
| | - Akihiko Koga
- Primate Research Institute, Kyoto University, Inuyama 484-8506, Japan
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Hoyos M, Bloor P, Defler T, Vermeer J, Röhe F, Farias I. Phylogenetic relationships within the Callicebus cupreus species group (Pitheciidae: Primates): Biogeographic and taxonomic implications. Mol Phylogenet Evol 2016; 102:208-19. [PMID: 27235549 DOI: 10.1016/j.ympev.2016.05.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Revised: 05/10/2016] [Accepted: 05/24/2016] [Indexed: 10/21/2022]
Abstract
The genus Callicebus (Thomas, 1903) is one of the most diverse of Neotropical primate genera and the only extant member of the Callicebinae subfamily. It has a widespread distribution from Colombia to Brazil, Bolivia, Peru and northern Paraguay. Coat colouring and colour pattern vary substantially within the genus, and this has led to the description of numerous species and subspecies, as well as numerous species groups. However, a lack of molecular phylogenetic analyses on the genus means that phylogenetic relationships and biogeographic history of species are poorly understood. Here, we examined phylogenetic relationships and patterns of diversification within the Callicebus cupreus species Group (sensu Kobayashi, 1995) using complete mitochondrial DNA cytochrome b gene sequence. Analyses indicate that the Callicebus cupreus Group underwent recent and extensive diversification. The common ancestor appears to have emerged some 2.3 million years ago (Ma) from a centre of origin in the western Amazon region, followed by diversification of the group between about 1.5 and 1.2Ma. Phylogenetic analyses were able to recover most previously described species (including the recently described Colombian endemic Callicebus caquetensis). However, there are some notable inconsistences between the obtained phylogeny and current taxonomy. Some previously recognized taxa were not separated by our data (e.g., Callicebus caligatus and Callicebus dubius), while currently unrecognized species diversity was uncovered within C. cupreus in the form of two divergent lineages: one of which exhibited greater phylogenetic similarity to species from the C. moloch Group. Based on the present study, we challenge current taxonomic arrangements for the C. cupreus species Group and call for a thorough taxonomic revision within the genus Callicebus.
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Affiliation(s)
- Manuel Hoyos
- Instituto de Genética, Universidad Nacional de Colombia, Edificio 426, Bogotá D.C., Colombia.
| | - Paul Bloor
- Instituto de Genética, Universidad Nacional de Colombia, Edificio 426, Bogotá D.C., Colombia
| | - Thomas Defler
- Departamento de Biología, Universidad Nacional de Colombia, Edificio 421, Bogotá D.C., Colombia
| | - Jan Vermeer
- Le Conservatoire pour la Protection des Primates. La Vallée des Singes, 86700 Romagne, France
| | - Fabio Röhe
- Wildlife Conservation Society, Manaus, Brazil
| | - Izeni Farias
- Universidade Federal do Amazonas UFAM, Manaus, AM, Brazil
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50
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Delezene LK, Teaford MF, Ungar PS. Canine and incisor microwear in pitheciids andAtelesreflects documented patterns of tooth use. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 161:6-25. [DOI: 10.1002/ajpa.23002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 03/14/2016] [Accepted: 04/13/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Lucas K. Delezene
- Department of Anthropology; University of Arkansas; Fayetteville AR 72701
| | - Mark F. Teaford
- Department of Basic Sciences; Touro University California; Vallejo CA 94592
| | - Peter S. Ungar
- Department of Anthropology; University of Arkansas; Fayetteville AR 72701
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