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Paietta EN, Kraberger S, Regney M, Custer JM, Ehmke E, Yoder AD, Varsani A. Interspecies Papillomavirus Type Infection and a Novel Papillomavirus Type in Red Ruffed Lemurs ( Varecia rubra). Viruses 2023; 16:37. [PMID: 38257737 PMCID: PMC10818365 DOI: 10.3390/v16010037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 12/16/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
The Papillomaviridae are a family of vertebrate-infecting viruses of oncogenic potential generally thought to be host species- and tissue-specific. Despite their phylogenetic relatedness to humans, there is a scarcity of data on papillomaviruses (PVs) in speciose non-human primate lineages, particularly the lemuriform primates. Varecia variegata (black-and-white ruffed lemurs) and Varecia rubra (red ruffed lemurs), two closely related species comprising the Varecia genus, are critically endangered with large global captive populations. Varecia variegata papillomavirus (VavPV) types -1 and -2, the first PVs in lemurs with a fully identified genome, were previously characterized from captive V. variegata saliva. To build upon this discovery, saliva samples were collected from captive V. rubra with the following aims: (1) to identify PVs shared between V. variegata and V. rubra and (2) to characterize novel PVs in V. rubra to better understand PV diversity in the lemuriform primates. Three complete PV genomes were determined from V. rubra samples. Two of these PV genomes share 98% L1 nucleotide identity with VavPV2, denoting interspecies infection of V. rubra by VavPV2. This work represents the first reported case of interspecies PV infection amongst the strepsirrhine primates. The third PV genome shares <68% L1 nucleotide identity with that of all PVs. Thus, it represents a new PV species and has been named Varecia rubra papillomavirus 1 (VarPV1). VavPV1, VavPV2, and VarPV1 form a new clade within the Papillomaviridae family, likely representing a novel genus. Future work diversifying sample collection (i.e., lemur host species from multiple genera, sample type, geographic location, and wild populations) is likely to uncover a world of diverse lemur PVs.
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Affiliation(s)
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (S.K.); (M.R.); (J.M.C.)
| | - Melanie Regney
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (S.K.); (M.R.); (J.M.C.)
| | - Joy M. Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (S.K.); (M.R.); (J.M.C.)
| | - Erin Ehmke
- Duke Lemur Center, Durham, NC 27705, USA;
| | - Anne D. Yoder
- Department of Biology, Duke University, Durham, NC 27708, USA;
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (S.K.); (M.R.); (J.M.C.)
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7925, South Africa
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Shao Y, Zhou L, Li F, Zhao L, Zhang BL, Shao F, Chen JW, Chen CY, Bi X, Zhuang XL, Zhu HL, Hu J, Sun Z, Li X, Wang D, Rivas-González I, Wang S, Wang YM, Chen W, Li G, Lu HM, Liu Y, Kuderna LFK, Farh KKH, Fan PF, Yu L, Li M, Liu ZJ, Tiley GP, Yoder AD, Roos C, Hayakawa T, Marques-Bonet T, Rogers J, Stenson PD, Cooper DN, Schierup MH, Yao YG, Zhang YP, Wang W, Qi XG, Zhang G, Wu DD. Phylogenomic analyses provide insights into primate evolution. Science 2023; 380:913-924. [PMID: 37262173 DOI: 10.1126/science.abn6919] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/26/2023] [Indexed: 06/03/2023]
Abstract
Comparative analysis of primate genomes within a phylogenetic context is essential for understanding the evolution of human genetic architecture and primate diversity. We present such a study of 50 primate species spanning 38 genera and 14 families, including 27 genomes first reported here, with many from previously less well represented groups, the New World monkeys and the Strepsirrhini. Our analyses reveal heterogeneous rates of genomic rearrangement and gene evolution across primate lineages. Thousands of genes under positive selection in different lineages play roles in the nervous, skeletal, and digestive systems and may have contributed to primate innovations and adaptations. Our study reveals that many key genomic innovations occurred in the Simiiformes ancestral node and may have had an impact on the adaptive radiation of the Simiiformes and human evolution.
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Affiliation(s)
- Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Long Zhou
- Center of Evolutionary & Organismal Biology, and Women's Hospital at Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Fang Li
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Institute of Animal Sex and Development, ZhejiangWanli University, Ningbo 315100, China
| | - Lan Zhao
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China
| | | | - Chun-Yan Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Xupeng Bi
- Center of Evolutionary & Organismal Biology, and Women's Hospital at Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiao-Lin Zhuang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming 650204, China
| | | | - Jiang Hu
- Grandomics Biosciences, Beijing 102206, China
| | - Zongyi Sun
- Grandomics Biosciences, Beijing 102206, China
| | - Xin Li
- Grandomics Biosciences, Beijing 102206, China
| | - Depeng Wang
- Grandomics Biosciences, Beijing 102206, China
| | | | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Yun-Mei Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Wu Chen
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou 510070, China
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Hui-Meng Lu
- School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yang Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Lukas F K Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA 92122, USA
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA 92122, USA
| | - Peng-Fei Fan
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhi-Jin Liu
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - George P Tiley
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
- Japan Monkey Centre, Inuyama, Aichi 484-0081, Japan
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Peter D Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | | | - Yong-Gang Yao
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming 650204, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
| | - Xiao-Guang Qi
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Center of Evolutionary & Organismal Biology, and Women's Hospital at Zhejiang University School of Medicine, Hangzhou 310058, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650204, China
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Kaczanowska J, Ganglberger F, Chernomor O, Kargl D, Galik B, Hess A, Moodley Y, von Haeseler A, Bühler K, Haubensak W. Molecular archaeology of human cognitive traits. Cell Rep 2022; 40:111287. [PMID: 36044840 DOI: 10.1016/j.celrep.2022.111287] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 05/20/2022] [Accepted: 08/05/2022] [Indexed: 01/06/2023] Open
Abstract
The brains and minds of our human ancestors remain inaccessible for experimental exploration. Therefore, we reconstructed human cognitive evolution by projecting nonsynonymous/synonymous rate ratios (ω values) in mammalian phylogeny onto the anatomically modern human (AMH) brain. This atlas retraces human neurogenetic selection and allows imputation of ancestral evolution in task-related functional networks (FNs). Adaptive evolution (high ω values) is associated with excitatory neurons and synaptic function. It shifted from FNs for motor control in anthropoid ancestry (60-41 mya) to attention in ancient hominoids (26-19 mya) and hominids (19-7.4 mya). Selection in FNs for language emerged with an early hominin ancestor (7.4-1.7 mya) and was later accompanied by adaptive evolution in FNs for strategic thinking during recent (0.8 mya-present) speciation of AMHs. This pattern mirrors increasingly complex cognitive demands and suggests that co-selection for language alongside strategic thinking may have separated AMHs from their archaic Denisovan and Neanderthal relatives.
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Affiliation(s)
- Joanna Kaczanowska
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | | | - Olga Chernomor
- Center for Integrative Bioinformatics Vienna (CIBIV), Max Perutz Labs, University of Vienna, Medical University of Vienna, Dr. Bohr Gasse 9, 1030 Vienna, Austria
| | - Dominic Kargl
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; Department of Neuronal Cell Biology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Bence Galik
- Bioinformatics and Scientific Computing, Vienna Biocenter Core Facilities (VBCF), Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Andreas Hess
- Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander University Erlangen-Nuremberg, Fahrstrasse 17, 91054 Erlangen, Germany
| | - Yoshan Moodley
- Department of Zoology, University of Venda, Private Bag X5050, Thohoyandou, Republic of South Africa
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna (CIBIV), Max Perutz Labs, University of Vienna, Medical University of Vienna, Dr. Bohr Gasse 9, 1030 Vienna, Austria; Faculty of Computer Science, University of Vienna, Währinger Str. 29, 1090 Vienna, Austria
| | - Katja Bühler
- VRVis Research Center, Donau-City Strasse 11, 1220 Vienna, Austria
| | - Wulf Haubensak
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; Department of Neuronal Cell Biology, Center for Brain Research, Medical University of Vienna, Vienna, Austria.
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4
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Smith ML, Vanderpool D, Hahn MW. Using all gene families vastly expands data available for phylogenomic inference. Mol Biol Evol 2022; 39:6596367. [PMID: 35642314 PMCID: PMC9178227 DOI: 10.1093/molbev/msac112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Traditionally, single-copy orthologs have been the gold standard in phylogenomics. Most phylogenomic studies identify putative single-copy orthologs using clustering approaches and retain families with a single sequence per species. This limits the amount of data available by excluding larger families. Recent advances have suggested several ways to include data from larger families. For instance, tree-based decomposition methods facilitate the extraction of orthologs from large families. Additionally, several methods for species tree inference are robust to the inclusion of paralogs and could use all of the data from larger families. Here, we explore the effects of using all families for phylogenetic inference by examining relationships among 26 primate species in detail and by analyzing five additional data sets. We compare single-copy families, orthologs extracted using tree-based decomposition approaches, and all families with all data. We explore several species tree inference methods, finding that identical trees are returned across nearly all subsets of the data and methods for primates. The relationships among Platyrrhini remain contentious; however, the species tree inference method matters more than the subset of data used. Using data from larger gene families drastically increases the number of genes available and leads to consistent estimates of branch lengths, nodal certainty and concordance, and inferences of introgression in primates. For the other data sets, topological inferences are consistent whether single-copy families or orthologs extracted using decomposition approaches are analyzed. Using larger gene families is a promising approach to include more data in phylogenomics without sacrificing accuracy, at least when high-quality genomes are available.
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Affiliation(s)
- Megan L Smith
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, Indiana, USA
| | - Dan Vanderpool
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, Indiana, USA
| | - Matthew W Hahn
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, Indiana, USA
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5
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Pozzi L, Penna A. Rocks and clocks revised: New promises and challenges in dating the primate tree of life. Evol Anthropol 2022; 31:138-153. [PMID: 35102633 DOI: 10.1002/evan.21940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 10/04/2021] [Accepted: 01/12/2022] [Indexed: 01/14/2023]
Abstract
In recent years, multiple technological and methodological advances have increased our ability to estimate phylogenies, leading to more accurate dating of the primate tree of life. Here we provide an overview of the limitations and potentials of some of these advancements and discuss how dated phylogenies provide the crucial temporal scale required to understand primate evolution. First, we review new methods, such as the total-evidence dating approach, that promise a better integration between the fossil record and molecular data. We then explore how the ever-increasing availability of genomic-level data for more primate species can impact our ability to accurately estimate timetrees. Finally, we discuss more recent applications of mutation rates to date divergence times. We highlight example studies that have applied these approaches to estimate divergence dates within primates. Our goal is to provide a critical overview of these new developments and explore the promises and challenges of their application in evolutionary anthropology.
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Affiliation(s)
- Luca Pozzi
- Department of Anthropology, The University of Texas at San Antonio, San Antonio, Texas, USA
| | - Anna Penna
- Department of Anthropology, The University of Texas at San Antonio, San Antonio, Texas, USA
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6
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Cornman RS, Cryan PM. Positively selected genes in the hoary bat ( Lasiurus cinereus) lineage: prominence of thymus expression, immune and metabolic function, and regions of ancient synteny. PeerJ 2022; 10:e13130. [PMID: 35317076 PMCID: PMC8934532 DOI: 10.7717/peerj.13130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 02/25/2022] [Indexed: 01/12/2023] Open
Abstract
Background Bats of the genus Lasiurus occur throughout the Americas and have diversified into at least 20 species among three subgenera. The hoary bat (Lasiurus cinereus) is highly migratory and ranges farther across North America than any other wild mammal. Despite the ecological importance of this species as a major insect predator, and the particular susceptibility of lasiurine bats to wind turbine strikes, our understanding of hoary bat ecology, physiology, and behavior remains poor. Methods To better understand adaptive evolution in this lineage, we used whole-genome sequencing to identify protein-coding sequence and explore signatures of positive selection. Gene models were predicted with Maker and compared to seven well-annotated and phylogenetically representative species. Evolutionary rate analysis was performed with PAML. Results Of 9,447 single-copy orthologous groups that met evaluation criteria, 150 genes had a significant excess of nonsynonymous substitutions along the L. cinereus branch (P < 0.001 after manual review of alignments). Selected genes as a group had biased expression, most strongly in thymus tissue. We identified 23 selected genes with reported immune functions as well as a divergent paralog of Steep1 within suborder Yangochiroptera. Seventeen genes had roles in lipid and glucose metabolic pathways, partially overlapping with 15 mitochondrion-associated genes; these adaptations may reflect the metabolic challenges of hibernation, long-distance migration, and seasonal variation in prey abundance. The genomic distribution of positively selected genes differed significantly from background expectation by discrete Kolmogorov-Smirnov test (P < 0.001). Remarkably, the top three physical clusters all coincided with islands of conserved synteny predating Mammalia, the largest of which shares synteny with the human cat-eye critical region (CECR) on 22q11. This observation coupled with the expansion of a novel Tbx1-like gene family may indicate evolutionary innovation during pharyngeal arch development: both the CECR and Tbx1 cause dosage-dependent congenital abnormalities in thymus, heart, and head, and craniodysmorphy is associated with human orthologs of other positively selected genes as well.
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Schön M, Nosanova A, Jacob C, Kraus JM, Kestler HAK, Mayer B, Feldengut S, Amunts K, Del Tredici K, Boeckers TM, Braak H. A comparative study of pre-alpha islands in the entorhinal cortex from selected primates and in lissencephaly. J Comp Neurol 2021; 530:683-704. [PMID: 34402535 DOI: 10.1002/cne.25233] [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: 05/20/2020] [Revised: 08/08/2021] [Accepted: 08/12/2021] [Indexed: 11/11/2022]
Abstract
The entorhinal cortex (EC) is the main interface between the sensory association areas of the neocortex and the hippocampus. It is crucial for the evaluation and processing of sensory data for long-term memory consolidation, and shows damage in many brain diseases, e.g., neurodegenerative diseases, such as Alzheimer's disease and developmental disorders. The pre-alpha layer of the EC in humans (layer II) displays a remarkable distribution of neurons in islands. These cellular islands give rise to a portion of the perforant path - the major reciprocal data stream for neocortical information into the hippocampal formation. However, the functional relevance of the morphological appearance of the pre-alpha layer in cellular islands and the precise timing of their initial appearance during primate evolution are largely unknown. Here, we conducted a comparative study of the EC from 38 non-human primates and Homo sapiens and found a strong relationship between gyrification index (GI) and the presence of the pre-alpha cellular islands. The formation of cellular islands also correlated wih brain and body weight as well as neopallial volume. In the two human lissencephalic cases, the cellular islands in the pre-alpha layer were lacking. These findings emphasize the relationship between cortical folding and island formation in the entorhinal cortex from an evolutionary perspective, and suggest a role in the pathomechanism of developmental brain disorders. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- M Schön
- Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany
| | - A Nosanova
- Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany
| | - C Jacob
- Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany
| | - J M Kraus
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - H A K Kestler
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - B Mayer
- Institute of Epidemiology and Medical Biometry, Ulm University, Ulm, Germany
| | - S Feldengut
- Clinical Neuroanatomy, Department of Neurology, Center for Clinical Research, Ulm University, Ulm, Germany
| | - K Amunts
- Institute of Neuroscience and Medicine (INM-1), Research Center Jülich, Jülich, Germany.,C. and O. Vogt Institute for Brain Research, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - K Del Tredici
- Clinical Neuroanatomy, Department of Neurology, Center for Clinical Research, Ulm University, Ulm, Germany
| | - T M Boeckers
- Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany.,DZNE, Ulm site, Ulm, Germany
| | - H Braak
- Clinical Neuroanatomy, Department of Neurology, Center for Clinical Research, Ulm University, Ulm, Germany
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New Insights on the Evolution of the Sweet Taste Receptor of Primates Adapted to Harsh Environments. Animals (Basel) 2020; 10:ani10122359. [PMID: 33321745 PMCID: PMC7764350 DOI: 10.3390/ani10122359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/01/2020] [Accepted: 12/04/2020] [Indexed: 11/16/2022] Open
Abstract
Simple Summary A sense of taste is vital to an animal’s fitness. It enables animals to select and ingest beneficial foods and avoid harmful substances in their daily lives. There have been relatively few studies regarding the evolution of the taste receptor gene for sweetness, particularly in regard to endemic Bornean primates. We constructed TAS1R2 gene phylogenies for 20 anthropoid primate species using four different methods as well as established the phylogenic time divergence. The phylogenetic analysis successfully separated the primates into their taxonomic groups and as per their dietary preferences. Of note, the estimated time of divergence for the primate speciation pattern in this study was more recent than the previously published estimates. This difference may have been due to environmental changes, such as food scarcity and climate change, during the late Miocene epoch, which likely forced primates to adapt their dietary preferences. These findings establish a foundation for further investigations. Abstract Taste perception is an essential function that provides valuable dietary and sensory information, which is crucial for the survival of animals. Studies into the evolution of the sweet taste receptor gene (TAS1R2) are scarce, especially for Bornean endemic primates such as Nasalis larvatus (proboscis monkey), Pongo pygmaeus (Bornean orangutan), and Hylobates muelleri (Muller’s Bornean gibbon). Primates are the perfect taxa to study as they are diverse dietary feeders, comprising specialist folivores, frugivores, gummivores, herbivores, and omnivores. We constructed phylogenetic trees of the TAS1R2 gene for 20 species of anthropoid primates using four different methods (neighbor-joining, maximum parsimony, maximum-likelihood, and Bayesian) and also established the time divergence of the phylogeny. The phylogeny successfully separated the primates into their taxonomic groups as well as by their dietary preferences. Of note, the reviewed time of divergence estimation for the primate speciation pattern in this study was more recent than the previously published estimates. It is believed that this difference may be due to environmental changes, such as food scarcity and climate change, during the late Miocene epoch, which forced primates to change their dietary preferences. These findings provide a starting point for further investigation.
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Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression. PLoS Biol 2020; 18:e3000954. [PMID: 33270638 PMCID: PMC7738166 DOI: 10.1371/journal.pbio.3000954] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 12/15/2020] [Accepted: 11/02/2020] [Indexed: 12/17/2022] Open
Abstract
Our understanding of the evolutionary history of primates is undergoing continual revision due to ongoing genome sequencing efforts. Bolstered by growing fossil evidence, these data have led to increased acceptance of once controversial hypotheses regarding phylogenetic relationships, hybridization and introgression, and the biogeographical history of primate groups. Among these findings is a pattern of recent introgression between species within all major primate groups examined to date, though little is known about introgression deeper in time. To address this and other phylogenetic questions, here, we present new reference genome assemblies for 3 Old World monkey (OWM) species: Colobus angolensis ssp. palliatus (the black and white colobus), Macaca nemestrina (southern pig-tailed macaque), and Mandrillus leucophaeus (the drill). We combine these data with 23 additional primate genomes to estimate both the species tree and individual gene trees using thousands of loci. While our species tree is largely consistent with previous phylogenetic hypotheses, the gene trees reveal high levels of genealogical discordance associated with multiple primate radiations. We use strongly asymmetric patterns of gene tree discordance around specific branches to identify multiple instances of introgression between ancestral primate lineages. In addition, we exploit recent fossil evidence to perform fossil-calibrated molecular dating analyses across the tree. Taken together, our genome-wide data help to resolve multiple contentious sets of relationships among primates, while also providing insight into the biological processes and technical artifacts that led to the disagreements in the first place. Combining three newly sequenced primate genomes with other published genomes, this study adapts a little-known method for detecting ancient introgression to genome-scale data, revealing multiple previously unknown examples of hybridization between primate species.
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10
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Mantovani V, Hauzman E, Corredor VH, Goulart PRK, Galvão O, Talebi M, Pessoa DMA, Soares JGM, Fiorani M, Gattass R, Fix Ventura D, Bonci DMO. Genetic variability of the sws1 cone opsin gene among New World monkeys. Am J Primatol 2020; 82:e23199. [PMID: 32990997 DOI: 10.1002/ajp.23199] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 09/03/2020] [Accepted: 09/07/2020] [Indexed: 02/05/2023]
Abstract
Vision is a major sense for Primates and the ability to perceive colors has great importance for the species ecology and behavior. Visual processing begins with the activation of the visual opsins in the retina, and the spectral absorption peaks are highly variable among species. In most Primates, LWS/MWS opsins are responsible for sensitivity to long/middle wavelengths within the visible light spectrum, and SWS1 opsins provide sensitivity to short wavelengths, in the violet region of the spectrum. In this study, we aimed to investigate the genetic variation on the sws1 opsin gene of New World monkeys (NWM) and search for amino acid substitutions that might be associated with the different color vision phenotypes described for a few species. We sequenced the exon 1 of the sws1 opsin gene of seven species from the families Callitrichidae, Cebidae, and Atelidae, and searched for variation at the spectral tuning sites 46, 49, 52, 86, 90, 93, 114, 116, and 118. Among the known spectral tuning sites, only residue 114 was variable. To investigate whether other residues have a functional role in the SWS1 absorption peak, we performed computational modeling of wild-type SWS1 and mutants A50I and A50V, found naturally among the species investigated. Although in silico analysis did not show any visible effect caused by these substitutions, it is possible that interactions of residue 50 with other sites might have some effect in the spectral shifts in the order of ~14 nm, found among the NWM. We also performed phylogenetic reconstruction of the sws1 gene, which partially recovered the species phylogeny. Further studies will be important to uncover the mutations responsible for the phenotypic variability of the SWS1 of NWM, and how spectral tuning may be associated with specific ecological features such as preferred food items and habitat use.
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Affiliation(s)
- Viviani Mantovani
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Einat Hauzman
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil.,Hospital Israelita Albert Einstein, São Paulo, São Paulo, Brazil
| | - Vitor H Corredor
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Paulo R K Goulart
- Núcleo de Teoria de Pesquisa do Comportamento, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Olavo Galvão
- Núcleo de Teoria de Pesquisa do Comportamento, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Mauricio Talebi
- Departamento de Ciências Ambientais, Universidade Federal de São Paulo, Campus Diadema, São Paulo, São Paulo, Brazil
| | - Daniel M A Pessoa
- Departamento de Fisiologia e Comportamento, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Juliana G M Soares
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mario Fiorani
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ricardo Gattass
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Dora Fix Ventura
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil.,Hospital Israelita Albert Einstein, São Paulo, São Paulo, Brazil
| | - Daniela M O Bonci
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil.,Hospital Israelita Albert Einstein, São Paulo, São Paulo, Brazil
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11
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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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12
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D'arc M, Moreira FRR, Dias CA, Souza AR, Seuánez HN, Soares MA, Tavares MCH, Santos AFA. The characterization of two novel neotropical primate papillomaviruses supports the ancient within-species diversity model. Virus Evol 2020; 6:veaa036. [PMID: 32665860 PMCID: PMC7326299 DOI: 10.1093/ve/veaa036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Papillomaviruses (PVs) are non-enveloped icosahedral viruses with a circular double-stranded DNA genome of ∼8,000 base pairs (bp). More than 200 different PV types have been identified to date in humans, which are distributed in five genera, with several strains associated with cancer development. Although widely distributed in vertebrates, Neotropical Primates (NP) PV infection was described for the first time only in 2016. Currently, four complete genomes of NP PVs have been characterized, three from Saimiri sciureus (SscPV1 to SscPV3) and one from Alouatta guariba (AgPV1). In this work, we describe two novel PV strains infecting Callithrix penicillata (provisionally named CpenPV1 and CpenPV2), using anal swab samples from animals residing at the Brasilia Primatology Center and next generation sequencing. The genomes of CpenPV1 (7,288 bp; 41.5% guanine-cytosine content - GC) and CpenPV2 (7,250 bp; 40.7% GC) contain the characteristic open reading frames (ORFs) for the early (E6, E7, E1, E2, and E4) and late (L2 and L1) PV genes. The L1 ORFs, commonly used for phylogenetic identification, share 76 per cent similarity with each other and differ 32 per cent from any other known PV, indicating that these new strains meet the criteria for defining novel species. PV genes phylogenetic variance was analyzed and different degrees of saturation revealed similar levels of topological heterogeneity, ruling out saturation as primary etiological factor for this phenomenon. Interestingly, the two CpenPV strains form a monophyletic clade within the Gammapapillomavirus genus (provisionally named gammapapillomavirus 32). Unlike for other NP PV strains, which grouped into a new sister genus of Alphapapillomavirus, this is the first report of NP PV strains grouping into a genus previously considered to exclusively comprise Old World Primates (OWP) PVs, including human PVs. These findings confirm the existence of a common ancestor for Gammapapillomavirus already infecting primates before the split of OWP and NP at ∼40 million years ago. Finally, our findings are consistent with an ancient within-species diversity model and emphasize the importance of increasing sampling to help understanding the PV-primate codivergence dynamics and pathogenic potential.
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Affiliation(s)
- Mirela D'arc
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, Postal Code 21941-902, Rio de Janeiro, Brazil
| | - Filipe R R Moreira
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, Postal Code 21941-902, Rio de Janeiro, Brazil
| | - Cecilia A Dias
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, Postal Code 21941-902, Rio de Janeiro, Brazil
| | - Antonizete R Souza
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, Postal Code 21941-902, Rio de Janeiro, Brazil
| | - Héctor N Seuánez
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rua André Cavalcanti, Postal Code 20231-050, Rio de Janeiro, Brazil
| | - Marcelo A Soares
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, Postal Code 21941-902, Rio de Janeiro, Brazil.,Programa de Oncovirologia, Instituto Nacional de Câncer, Rua André Cavalcanti, Postal Code 20231-050, Rio de Janeiro, Brazil
| | - Maria C H Tavares
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, Postal Code 21941-902, Rio de Janeiro, Brazil
| | - André F A Santos
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, Postal Code 21941-902, Rio de Janeiro, Brazil
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13
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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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14
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Katsura Y, Nei M. The Reproducibility of an Inferred Tree and the Diploidization of Gene Segregation after Genome Duplication. Genome Biol Evol 2020; 12:3792-3796. [PMID: 31950994 PMCID: PMC7012300 DOI: 10.1093/gbe/evz272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2019] [Indexed: 12/03/2022] Open
Abstract
We previously introduced a numerical quantity called the stability (Ps) of an inferred tree and showed that for the tree to be reliable this stability as well as the reliability of the tree, which is usually computed as the bootstrap probability (Pb), must be high. However, if genome duplication occurs in a species, a gene family of the genome also duplicates, and for this reason alone some Ps values can be high in a tree of the duplicated gene families. In addition, the topology of the duplicated gene family can be similar to that of the original gene family if such gene families are identifiable. After genome duplication, however, the gene families are often partially deleted or partially duplicated, and the duplicated gene family may not show the same topology as that of the original family. It is therefore necessary to compute the similarity of the topologies of the duplicated and the original gene families. In this paper, we introduce another quantity called the reproducibility (Pr) for measuring the similarity of the two gene families. To show how to compute the Pr values, we first compute the Pb and Ps values for each of the MHC class II α and β chain gene families, which were apparently generated by genome duplication. We then compute the Pr values for the MHC class II α and β chain gene families. The Pr values for the α and β chain gene families are now low, and this suggests that the diploidization of gene segregation has occurred after the genome duplication. Currently higher animals, defined as animals with complex phenotypic characters, generally have a higher genome size, and this increase in genome size appears to have been caused by genome duplication and diploidization of gene segregation after genome duplication.
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Affiliation(s)
- Yukako Katsura
- Primate Research Institute, Kyoto University, Japan.,Department of Biology, Institute of Molecular Evolutionary Genetics, Pennsylvania State University.,Department of Biology, Institute for Genomics and Evolutionary Medicine, Temple University
| | - Masatoshi Nei
- Department of Biology, Institute of Molecular Evolutionary Genetics, Pennsylvania State University.,Department of Biology, Institute for Genomics and Evolutionary Medicine, Temple University
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15
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16
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Simian Foamy Viruses in Central and South America: A New World of Discovery. Viruses 2019; 11:v11100967. [PMID: 31635161 PMCID: PMC6832937 DOI: 10.3390/v11100967] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 12/16/2022] Open
Abstract
Foamy viruses (FVs) are the only exogenous retrovirus to date known to infect neotropical primates (NPs). In the last decade, an increasing number of strains have been completely or partially sequenced, and molecular evolution analyses have identified an ancient co-speciation with their hosts. In this review, the improvement of diagnostic techniques that allowed the determination of a more accurate prevalence of simian FVs (SFVs) in captive and free-living NPs is discussed. Determination of DNA viral load in American primates indicates that oral tissues are the viral replicative site and that buccal swab collection can be an alternative to diagnose SFV infection in NPs. Finally, the transmission potential of NP SFVs to primate workers in zoos and primate centers of the Americas is examined.
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17
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Chen Z, Long T, Wong PY, Ho WCS, Burk RD, Chan PKS. Non-human Primate Papillomaviruses Share Similar Evolutionary Histories and Niche Adaptation as the Human Counterparts. Front Microbiol 2019; 10:2093. [PMID: 31552003 PMCID: PMC6747053 DOI: 10.3389/fmicb.2019.02093] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 08/26/2019] [Indexed: 11/13/2022] Open
Abstract
Given high genetic diversity of papillomaviruses (PV) and complex scenario of virus-host interaction, the genetic basis underlying the mechanisms of HPV carcinogenicity is not well understood. In an effort to evaluate the origin and evolution of PV pathogenicity, we collected paired oral, perianal, and genital swabs from a wild macaque population. Of the 117 surveyed macaques, 88 (75.2%) were positive for PV DNA in one or more sites, mostly common from genital swabs, followed by oral and perianal sites. All putative macaque PV types phylogenetically clustered into the genera Alpha-, Beta-, and Gammapapillomavirus, with a strong phylogeny-tropism association as observed in HPVs. Using a Bayesian Markov Chain Monte Carlo framework, we demonstrated ancient intra-host divergence of primate PVs in which multiple ancestors had split and adapted to specific host ecosystems at least 41 million years ago, prior to the speciation events of primate host species. Following subsequent divergence and niche adaptation, distinct but phylogenetically related PV types were transmitted to similar host ecosystems by closely related host animals when host speciation occurred, which may explain in part the origin of carcinogenicity of HPV type 16 (HPV16) and Macaca fascicularis PV type 3 (MfPV3) that evolved from a most recent common ancestor containing the determinants for cervicovaginal colonization and cervical cancer. The findings identifying evolutionary and biological relatedness between human and non-human primate PVs lay a genetic foundation for research on parasite-host interactions and carcinogenic outcomes, which will prove useful in further study of viral pathogenesis and host specificity.
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Affiliation(s)
- Zigui Chen
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China.,Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Teng Long
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Po Yee Wong
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Wendy C S Ho
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Robert D Burk
- Department of Pediatrics, Microbiology and Immunology, Epidemiology and Population Health, and Obstetrics, Gynecology and Woman's Health, Albert Einstein College of Medicine, The Bronx, NY, United States
| | - Paul K S Chan
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China.,Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
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18
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Aristide L, Strauss A, Halenar-Price LB, Gilissen E, Cruz FW, Cartelle C, Rosenberger AL, Lopes RT, Dos Reis SF, Perez SI. Cranial and endocranial diversity in extant and fossil atelids (Platyrrhini: Atelidae): A geometric morphometric study. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 169:322-331. [PMID: 30972753 DOI: 10.1002/ajpa.23837] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 02/14/2019] [Accepted: 03/31/2019] [Indexed: 01/17/2023]
Abstract
OBJECTIVES Platyrrhines constitute a diverse clade, with the modern Atelidae exhibiting the most variation in cranial and endocast morphology. The processes responsible for this diversification are not well understood. Here, we present a geometric morphometric study describing variation in cranial and endocranial shape of 14 species of Alouatta, Ateles, Brachyteles, and Lagothrix and two extinct taxa, Cartelles and Caipora. METHODS We examined cranial and endocranial shape variation among species using images reconstructed from CT scans and geometric morphometric techniques based on three-dimensional landmarks and semilandmarks. Principal components analyses were used to explore variation, including the Procrustes shape coordinates, summing the logarithm of the Centroid Size, the common allometric component, and residual shape components. RESULTS Differences in endocranial shape are related to a relative increase or decrease in the volume of the neocortex region with respect to brainstem and cerebellum regions. The relative position of the brainstem varies from a posterior position in Alouatta to a more ventral position in Ateles. The shape of both the cranium and endocast of Caipora is within the observed variation of Brachyteles. Cartelles occupies the most differentiated position relative to the extant taxa, especially in regards to its endocranial shape. CONCLUSIONS The pattern of variation in the extant species in endocranial shape is similar to the variation observed in previous cranial studies, with Alouatta as an outlier. The similarities between Caipora and Brachyteles were unexpected and intriguing given the frugivorous adaptations inferred from the fossil's dentition. Our study shows the importance of considering both extant and fossil species when studying diversification of complex traits.
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Affiliation(s)
- Leandro Aristide
- División Antropología (FCNyM-UNLP), CONICET, La Plata, Argentina.,Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
| | - André Strauss
- Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo, Brazil.,Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.,Palaeoanthropology Senckenberg Centre for Human Evolution and Palaeoenvironment, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Lauren B Halenar-Price
- Department of Biology, Farmingdale State College (SUNY), New York, New York.,NYCEP Morphometrics Group, New York, NY
| | - Emmanuel Gilissen
- Department of African Zoology, Royal Museum for Central Africa, Tervuren, Belgium.,Laboratory of Histology and Neuropathology, Université Libre de Bruxelles, Brussels, Belgium
| | - Francisco W Cruz
- Instituto de Geociências, Universidade de São Paulo, São Paulo, Brazil
| | - Castor Cartelle
- Museu de Ciências Naturais, Pontificia Universidade Católica de Minas Gerais, Belo Horizonte, Brazil
| | - Alfred L Rosenberger
- NYCEP Morphometrics Group, New York, NY.,Department of Anthropology, City of New York Graduate Center, New York, New York
| | - Ricardo T Lopes
- Laboratório de Instrumentação Nuclear, Centro de Tecnologia (UFRJ), Río de Janeiro, Brazil
| | | | - S Ivan Perez
- División Antropología (FCNyM-UNLP), CONICET, La Plata, Argentina.,Instituto de Física 'Gleb Wataghin' (UNICAMP), Campinas, Brazil
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19
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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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20
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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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21
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Silvestro D, Tejedor MF, Serrano-Serrano ML, Loiseau O, Rossier V, Rolland J, Zizka A, Höhna S, Antonelli A, Salamin N. Early Arrival and Climatically-Linked Geographic Expansion of New World Monkeys from Tiny African Ancestors. Syst Biol 2018; 68:78-92. [PMID: 29931325 PMCID: PMC6292484 DOI: 10.1093/sysbio/syy046] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/06/2018] [Indexed: 12/16/2022] Open
Abstract
New World Monkeys (NWM) (platyrrhines) are one of the most diverse groups of primates, occupying today a wide range of ecosystems in the American tropics and exhibiting large variations in ecology, morphology, and behavior. Although the relationships among the almost 200 living species are relatively well understood, we lack robust estimates of the timing of origin, ancestral morphology, and geographic range evolution of the clade. Herein, we integrate paleontological and molecular evidence to assess the evolutionary dynamics of extinct and extant platyrrhines. We develop novel analytical frameworks to infer the evolution of body mass, changes in latitudinal ranges through time, and species diversification rates using a phylogenetic tree of living and fossil taxa. Our results show that platyrrhines originated 5–10 million years earlier than previously assumed, dating back to the Middle Eocene. The estimated ancestral platyrrhine was small—weighing 0.4 kg—and matched the size of their presumed African ancestors. As the three platyrrhine families diverged, we recover a rapid change in body mass range. During the Miocene Climatic Optimum, fossil diversity peaked and platyrrhines reached their widest latitudinal range, expanding as far South as Patagonia, favored by warm and humid climate and the lower elevation of the Andes. Finally, global cooling and aridification after the middle Miocene triggered a geographic contraction of NWM and increased their extinction rates. These results unveil the full evolutionary trajectory of an iconic and ecologically important radiation of monkeys and showcase the necessity of integrating fossil and molecular data for reliably estimating evolutionary rates and trends.
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Affiliation(s)
- Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden.,Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Gothenburg Global Biodiversity Center, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden.,Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland.,These authors contributed equally to this work
| | - Marcelo F Tejedor
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden.,Gothenburg Global Biodiversity Center, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden.,Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland.,Instituto Patagónico de Geología y Paleontología (CCT CONICET-CENPAT), Boulevard Almirante Brown 2915, 9120 Puerto Madryn, Chubut, Argentina.,Facultad de Ciencias Naturales, Sede Trelew, Universidad Nacional de la Patagonia 'San Juan Bosco', 9100 Trelew, Chubut, Argentina.,These authors contributed equally to this work
| | | | - Oriane Loiseau
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Victor Rossier
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Jonathan Rolland
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Department of Zoology, University of British Columbia, 2212 Main Mall, Vancouver, BC Canada
| | - Alexander Zizka
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden.,Gothenburg Global Biodiversity Center, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden
| | - Sebastian Höhna
- Division of Evolutionary Biology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2, 82152 Munich, Germany
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden.,Gothenburg Global Biodiversity Center, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden.,Gothenburg Botanical Garden, Carl Skottsbergs gata 22A, 413 19 Gothenburg, Sweden.,Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA 02138, USA.,These authors are severs as a co-last authorship
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland.,These authors are severs as a co-last authorship
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22
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Chen Z, DeSalle R, Schiffman M, Herrero R, Wood CE, Ruiz JC, Clifford GM, Chan PKS, Burk RD. Niche adaptation and viral transmission of human papillomaviruses from archaic hominins to modern humans. PLoS Pathog 2018; 14:e1007352. [PMID: 30383862 PMCID: PMC6211759 DOI: 10.1371/journal.ppat.1007352] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 09/22/2018] [Indexed: 02/07/2023] Open
Abstract
Recent discoveries on the origins of modern humans from multiple archaic hominin populations and the diversity of human papillomaviruses (HPVs) suggest a complex scenario of virus-host evolution. To evaluate the origin of HPV pathogenesis, we estimated the phylogeny, timing, and dispersal of HPV16 variants using a Bayesian Markov Chain Monte Carlo framework. To increase precision, we identified and characterized non-human primate papillomaviruses from New and Old World monkeys to set molecular clock models. We demonstrate specific host niche adaptation of primate papillomaviruses with subsequent coevolution with their primate hosts for at least 40 million years. Analyses of 212 HPV16 complete genomes and 3582 partial sequences estimated ancient divergence of HPV16 variants (between A and BCD lineages) from their most recent common ancestors around half a million years ago, roughly coinciding with the timing of the split between archaic Neanderthals and modern Homo sapiens, and nearly three times longer than divergence times of modern Homo sapiens. HPV16 A lineage variants were significantly underrepresented in present African populations, whereas the A sublineages were highly prevalent in European (A1-3) and Asian (A4) populations, indicative of viral sexual transmission from Neanderthals to modern non-African humans through multiple interbreeding events in the past 80 thousand years. Remarkably, the human leukocyte antigen B*07:02 and C*07:02 alleles associated with increased risk in cervix cancer represent introgressed regions from Neanderthals in present-day Eurasians. The archaic hominin-host-switch model was also supported by other HPV variants. Niche adaptation and virus-host codivergence appear to influence the pathogenesis of papillomaviruses.
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Affiliation(s)
- Zigui Chen
- Departments of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Rob DeSalle
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY, United States of America
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, United States of America
| | - Rolando Herrero
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- Proyecto Epidemiológico Guanacaste, Fundación INCIENSA, San José, Costa Rica
| | - Charles E. Wood
- Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC, United States of America
| | - Julio C. Ruiz
- Department of Veterinary Sciences, The University of Texas MD Anderson Cancer Center, Bastrop, Texas, United States of America
| | - Gary M. Clifford
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Paul K. S. Chan
- Departments of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Robert D. Burk
- Departments of Pediatrics, Microbiology and Immunology; Epidemiology and Population Health; Obstetrics, Gynecology and Woman’s Health, Albert Einstein College of Medicine, Bronx, NY, United States of America
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23
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Aristide L, Bastide P, Dos Reis SF, Pires Dos Santos TM, Lopes RT, Perez SI. Multiple factors behind early diversification of skull morphology in the continental radiation of New World monkeys. Evolution 2018; 72:2697-2711. [PMID: 30246282 DOI: 10.1111/evo.13609] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 09/03/2018] [Indexed: 01/24/2023]
Abstract
Understanding the origin of diversity is a fundamental problem in evolutionary biology. The null expectation for the evolutionary diversification is that all changes in biological diversity are the result of random processes. Adaptive radiations depart from this expectation as ecological factors and natural selection are supposed to play a central role in driving exceptional diversification. However, it is not well understood how large-scale continental radiations, given their characteristics, fit to these opposing theoretical models. Here, we used phylogenetic comparative methods and geometric morphometrics to study the evolutionary process of cranial diversification in the continental radiation of New World monkeys. Particularly, we tested several alternative evolutionary scenarios for morphological evolution in the clade. Results indicated that despite the platyrrhine radiation being old and geographically widespread, the formative patterns arising from the initial stages of diversification probably associated with an adaptive radiation can still be recognized today. We also show that no single explored factor (e.g., ecological or allometric) can be invoked as a complete explanation for the observed phenotypic diversity patterns in the clade and, moreover, that different cranial regions exhibit particular macroevolutionary patterns. Together, our results highlight the evident complexity behind large-scale evolutionary radiations.
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Affiliation(s)
- Leandro Aristide
- División Antropología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900 La Plata, Buenos Aires, Argentina.,École Normale Supérieure, Paris Sciences et Lettres (PSL) Research University, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France
| | - Paul Bastide
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Herestraat 49 box 1030 BE-3000, Leuven, Belgium
| | - Sergio Furtado Dos Reis
- Departamento de Biologia Animal, Universidade Estadual de Campinas, CEP 13.083-862 Campinas, São Paulo, Brazil
| | - Thaís M Pires Dos Santos
- Laboratório de Instrumentação Nuclear, Centro de Tecnologia, Universidade Federal do Rio de Janeiro, Ilha do Fundão, CEP 21949-900, Rio de Janeiro, Brazil
| | - Ricardo T Lopes
- Laboratório de Instrumentação Nuclear, Centro de Tecnologia, Universidade Federal do Rio de Janeiro, Ilha do Fundão, CEP 21949-900, Rio de Janeiro, Brazil
| | - S Ivan Perez
- División Antropología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900 La Plata, Buenos Aires, Argentina
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24
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Chen Z, Schiffman M, Herrero R, DeSalle R, Anastos K, Segondy M, Sahasrabuddhe VV, Gravitt PE, Hsing AW, Chan PKS, Burk RD. Classification and evolution of human papillomavirus genome variants: Alpha-5 (HPV26, 51, 69, 82), Alpha-6 (HPV30, 53, 56, 66), Alpha-11 (HPV34, 73), Alpha-13 (HPV54) and Alpha-3 (HPV61). Virology 2018; 516:86-101. [PMID: 29331867 PMCID: PMC6093212 DOI: 10.1016/j.virol.2018.01.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 12/25/2017] [Accepted: 01/02/2018] [Indexed: 11/17/2022]
Abstract
HPV variants from the same type can be classified into lineages and sublineages based on the complete genome differences and the phylogenetic topologies. We examined nucleotide variations of twelve HPV types within the species Alpha-5 (HPV26, 51, 69, 82), Alpha-6 (HPV30, 53, 56, 66), Alpha-11 (HPV34, 73), Alpha-13 (HPV54) and Alpha-3 (HPV61) by analyzing 1432 partial sequences and 181 complete genomes from multiple geographic populations. The inter-lineage and inter-sublineage mean differences of HPV variants ranged between 0.9-7.3% and 0.3-0.9%, respectively. The heterogeneity and phylogenies of HPV isolates indicate an independent evolutionary history for each type. The noncoding regions were the most variable regions whereas the capsid proteins were relatively conserved. Certain variant lineages and/or sublineages were geographically-associated. These data provide the basis to further classify HPV variants and should foster future studies on the evolution of HPV genomes and the associations of HPV variants with cancer risk.
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Affiliation(s)
- Zigui Chen
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States
| | - Rolando Herrero
- Proyecto Epidemiológico Guanacaste, Fundación INCIENSA, San José, Costa Rica; Prevention and Implementation Group, International Agency for Research on Cancer, World Health Organization, France
| | - Rob DeSalle
- Sackler Institute of Comparative Genomics, American Museum of Natural History, NY, United States
| | - Kathryn Anastos
- Department of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, United States; Departments of Epidemiology & Population Health and Obstetrics, Gynecology & Woman's Health, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Michel Segondy
- Department of Biology and Pathology, Montpellier University Hospital, Montpellier, France
| | | | - Patti E Gravitt
- Milken Institute School of Public Health, George Washington University, Washington, DC, United States
| | - Ann W Hsing
- Stanford Cancer Institute and Stanford Prevention Research Center, Stanford School of Medicine, Stanford University, CA, United States
| | - Paul K S Chan
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Robert D Burk
- Departments of Epidemiology & Population Health and Obstetrics, Gynecology & Woman's Health, Albert Einstein College of Medicine, Bronx, NY, United States; Departments of Pediatrics, and Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY, United States.
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25
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Rocatti G, Aristide L, Rosenberger AL, Perez SI. Early evolutionary diversification of mandible morphology in the New World monkeys (Primate, Platyrrhini). J Hum Evol 2017; 113:24-37. [PMID: 29054168 DOI: 10.1016/j.jhevol.2017.08.008] [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: 08/24/2016] [Revised: 08/02/2017] [Accepted: 08/03/2017] [Indexed: 10/18/2022]
Abstract
New World monkeys (order Primates) are an example of a major mammalian evolutionary radiation in the Americas, with a contentious fossil record. There is evidence of an early platyrrhine occupation of this continent by the Eocene-Oligocene transition, evolving in isolation from the Old World primates from then on, and developing extensive morphological and size variation. Previous studies postulated that the platyrrhine clade arose as a local version of the Simpsonian ecospace model, with an early phase involving a rapid increase in morphological and ecological diversity driven by selection and ecological opportunity, followed by a diversification rate that slowed due to niche-filling. Under this model, variation in extant platyrrhines, in particular anatomical complexes, may resemble patterns seen among middle-late Miocene (10-14 Ma) platyrrhines as a result of evolutionary stasis. Here we examine the mandible in this regard, which may be informative about the dietary and phylogenetic history of the New World monkeys. Specifically, we test the hypothesis that the Simpsonian ecospace model applies to the platyrrhine mandible through a geometric morphometric analysis of digital images of the jaws of extant and extinct species, and we compare these results to those obtained using a phylogenetic comparative approach based on extant species. The results show a marked phylogenetic structure in the mandibular morphology of platyrrhines. Principal component analyses highlight the morphological diversity among modern forms, and reveal a similar range of variation for the clade when fossil specimens are included. Disparity-Through-Time analysis shows that most of the shape variation between platyrrhines originated early in their evolution (between 20 and 15 Ma). Our results converge with previous studies of body mass, cranial shape, the brain and the basicranium to show that platyrrhine evolution might have been shaped by an early increase in morphological variation followed by a decelerated rate of diversification and evolutionary stasis.
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Affiliation(s)
- Guido Rocatti
- División Antropología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, CONICET. 122 y 60, 1900, La Plata, Argentina
| | - Leandro Aristide
- División Antropología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, CONICET. 122 y 60, 1900, La Plata, Argentina
| | - Alfred L Rosenberger
- Department of Anthropology and Archaeology, Brooklyn College, CUNY, 2900 Bedford Ave., Brooklyn, NY, USA
| | - S Ivan Perez
- División Antropología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, CONICET. 122 y 60, 1900, La Plata, Argentina.
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26
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Novo NM, Tejedor MF, Pérez ME, Krause JM. New primate locality from the early Miocene of Patagonia, Argentina. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 164:861-867. [PMID: 28895134 DOI: 10.1002/ajpa.23309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 08/19/2017] [Accepted: 08/23/2017] [Indexed: 11/07/2022]
Abstract
OBJECTIVES The purpose of this work is to present a new primate locality with evidence that increases the knowledge on the radiation of the extinct platyrrhine primates. MATERIALS AND METHODS We studied the new specimen and compared it to specimens identified as Mazzonicebus almendrae. RESULTS The new first and second molars were comparable to Mazzonicebus almendrae in all morphological details, allowing us to allocate the new specimen to M. almendrae and add comments on morphological variation in this species regarding the orientation of the labial cristae and development of the anterolingual cingulum. This new maxilla also present the first known M3 for the species. DISCUSSION The new specimen increases our knowledge of the extinct platyrrhines from Patagonia. Their age and geographical distribution ranges from early to middle Miocene in an area between 40° to 47° of southern latitude.
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Affiliation(s)
- Nelson M Novo
- Instituto Patagónico de Geología y Paleontología (IPGP, CCT CONICET-CENPAT), Boulevard Brown 2915, U91200, Puerto Madryn, Argentina.,Facultad de Ciencias Naturales, Sede Puerto Madryn. Universidad Nacional de la Patagonia "San Juan Bosco", Puerto Madryn, Argentina
| | - Marcelo F Tejedor
- Instituto Patagónico de Geología y Paleontología (IPGP, CCT CONICET-CENPAT), Boulevard Brown 2915, U91200, Puerto Madryn, Argentina.,Facultad de Ciencias Naturales, Sede Trelew. Universidad Nacional de la Patagonia "San Juan Bosco", Trelew, Argentina.,Gothenburg Global Biodiversity Centre, Box 461, 405-30 Göteborg, Sweden
| | - María E Pérez
- CONICET, Museo Paleontológico Egidio Feruglio, Av. Fontana 140, Trelew, U9100GYO, Chubut, Argentina.,Research Associate, Field Museum of Natural History, Chicago, IL, USA
| | - J Marcelo Krause
- CONICET, Museo Paleontológico Egidio Feruglio, Av. Fontana 140, Trelew, U9100GYO, Chubut, Argentina.,Departamento de Geología, Universidad Nacional de la Patagonia San Juan Bosco, Ruta Provincial 1 s/n, Comodoro Rivadavia, 9000, Chubut, Argentina
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27
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Fergnani PN, Ruggiero A. The latitudinal diversity gradient in South American mammals revisited using a regional analysis approach: The importance of climate at extra-tropical latitudes and history towards the tropics. PLoS One 2017; 12:e0184057. [PMID: 28873434 PMCID: PMC5584750 DOI: 10.1371/journal.pone.0184057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 08/17/2017] [Indexed: 11/18/2022] Open
Abstract
The latitudinal diversity gradient has been considered a consequence of a shift in the impact of abiotic and biotic factors that limit species distributions from the poles to the equator, thus influencing species richness variation. It has also been considered the outcome of evolutionary processes that vary over geographical space. We used six South American mammal groups to test the association of environmental and evolutionary factors and the ecological structuring of mammal assemblages with spatial variation in taxonomic richness (TR), at a spatial resolution of 110 km x 110 km, at tropical and extra-tropical latitudes. Based on attributes that represent what mammal species do in ecosystems, we estimated ecological diversity (ED) as a mean pairwise ecological distance between all co-occurring taxa. The mean pairwise phylogenetic distance between all co-occurring taxa (AvPD) was used as an estimation of phylogenetic diversity. Geographically Weighted Regression analyses performed separately for each mammal group identified tropical and extra-tropical high R2 areas where environmental and evolutionary factors strongly accounted for richness variation. Temperature was the most important predictor of TR in high R2 areas outside the tropics, as was AvPD within the tropics. The proportion of TR variation accounted for by environment (either independently or combined with AvPD) was higher in tropical areas of high richness and low ecological diversity than in tropical areas of high richness and high ecological diversity. In conclusion, we confirmed a shift in the impact of environmental factors, mainly temperature, that best account for mammal richness variation in extra-tropical regions, whereas phylogenetic diversity best accounts for richness variation within the tropics. Environment in combination with evolutionary history explained the coexistence of a high number of ecologically similar species within the tropics. Consideration of the influence of contemporary environmental variables and evolutionary history is crucial to understanding of the latitudinal diversity gradient.
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Affiliation(s)
- Paula Nilda Fergnani
- Laboratorio Ecotono, Centro Regional Universitario Bariloche-Universidad Nacional del Comahue, INIBIOMA-CONICET, San Carlos de Bariloche, Argentina
- * E-mail:
| | - Adriana Ruggiero
- Laboratorio Ecotono, Centro Regional Universitario Bariloche-Universidad Nacional del Comahue, INIBIOMA-CONICET, San Carlos de Bariloche, Argentina
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28
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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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29
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Harrison SE, Harvey MS, Cooper SJB, Austin AD, Rix MG. Across the Indian Ocean: A remarkable example of trans-oceanic dispersal in an austral mygalomorph spider. PLoS One 2017; 12:e0180139. [PMID: 28767648 PMCID: PMC5540276 DOI: 10.1371/journal.pone.0180139] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 06/09/2017] [Indexed: 11/17/2022] Open
Abstract
The Migidae are a family of austral trapdoor spiders known to show a highly restricted and disjunct distribution pattern. Here, we aim to investigate the phylogeny and historical biogeography of the group, which was previously thought to be vicariant in origin, and examine the biogeographic origins of the genus Moggridgea using a dated multi-gene phylogeny. Moggridgea specimens were sampled from southern Australia and Africa, and Bertmainus was sampled from Western Australia. Sanger sequencing methods were used to generate a robust six marker molecular dataset consisting of the nuclear genes 18S rRNA, 28S rRNA, ITS rRNA, XPNPEP3 and H3 and the mitochondrial gene COI. Bayesian and Maximum Likelihood methods were used to analyse the dataset, and the key dispersal nodes were dated using BEAST. Based on our data, we demonstrate that Moggridgea rainbowi from Kangaroo Island, Australia is a valid member of the otherwise African genus Moggridgea. Molecular clock dating analyses show that the inter-specific divergence of M. rainbowi from African congeners is between 2.27-16.02 million years ago (Mya). This divergence date significantly post-dates the separation of Africa from Gondwana (95 Mya) and therefore does not support a vicariant origin for Australian Moggridgea. It also pre-dates human colonisation of Kangaroo Island, a result which is further supported by the intra-specific divergence date of 1.10-6.39 Mya between separate populations on Kangaroo Island. These analyses provide strong support for the hypothesis that Moggridgea colonised Australia via long-distance trans-Indian Ocean dispersal, representing the first such documented case in a mygalomorph spider.
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Affiliation(s)
- Sophie E Harrison
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Mark S Harvey
- Department of Terrestrial Zoology, Western Australian Museum, Welshpool DC, WA, Australia.,School of Biology, The University of Western Australia, Crawley, WA, Australia.,School of Natural Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Steve J B Cooper
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia.,Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, SA, Australia
| | - Andrew D Austin
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Michael G Rix
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia.,Department of Terrestrial Zoology, Western Australian Museum, Welshpool DC, WA, Australia.,Biodiversity and Geosciences Program, Queensland Museum, South Brisbane, QLD, Australia
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Dasmeh P, Kepp KP. Superoxide dismutase 1 is positively selected to minimize protein aggregation in great apes. Cell Mol Life Sci 2017; 74:3023-3037. [PMID: 28389720 PMCID: PMC11107616 DOI: 10.1007/s00018-017-2519-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 03/17/2017] [Accepted: 04/03/2017] [Indexed: 12/14/2022]
Abstract
Positive (adaptive) selection has recently been implied in human superoxide dismutase 1 (SOD1), a highly abundant antioxidant protein with energy signaling and antiaging functions, one of very few examples of direct selection on a human protein product (exon); the molecular drivers of this selection are unknown. We mapped 30 extant SOD1 sequences to the recently established mammalian species tree and inferred ancestors, key substitutions, and signatures of selection during the protein's evolution. We detected elevated substitution rates leading to great apes (Hominidae) at ~1 per 2 million years, significantly higher than in other primates and rodents, although these paradoxically generally evolve much faster. The high evolutionary rate was partly due to relaxation of some selection pressures and partly to distinct positive selection of SOD1 in great apes. We then show that higher stability and net charge and changes at the dimer interface were selectively introduced upon separation from old world monkeys and lesser apes (gibbons). Consequently, human, chimpanzee and gorilla SOD1s have a net charge of -6 at physiological pH, whereas the closely related gibbons and macaques have -3. These features consistently point towards selection against the malicious aggregation effects of elevated SOD1 levels in long-living great apes. The findings mirror the impact of human SOD1 mutations that reduce net charge and/or stability and cause ALS, a motor neuron disease characterized by oxidative stress and SOD1 aggregates and triggered by aging. Our study thus marks an example of direct selection for a particular chemical phenotype (high net charge and stability) in a single human protein with possible implications for the evolution of aging.
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Affiliation(s)
- Pouria Dasmeh
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Department of Biochemistry and Cedergren Center for Bioinformatics and Genomics, Faculty of Medicine, University of Montreal, 2900 Edouard-Montpetit, Montreal, QC, H3T 1J4, Canada
| | - Kasper P Kepp
- Technical University of Denmark, DTU Chemistry, 2800, Kongens Lyngby, Denmark.
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Nova Delgado M, Galbany J, Pérez-Pérez A. Molar shape variability in platyrrhine primates. J Hum Evol 2016; 99:79-92. [PMID: 27650581 DOI: 10.1016/j.jhevol.2016.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 07/18/2016] [Accepted: 07/22/2016] [Indexed: 11/26/2022]
Abstract
Recent phylogenetic analyses suggest that platyrrhines constitute a monophyletic group represented by three families: Cebidae, Atelidae, and Pitheciidae. Morphological variability between and within these three families, however, is widely discussed and debated. The aim of this study was to assess molar shape variability in platyrrhines, to explore patterns of interspecific variation among extant species, and to evaluate how molar shape can be used as a taxonomic indicator. The analyses were conducted using standard multivariate analyses of geometric morphometric data from 802 platyrrhine lower molars. The results indicated that the interspecific variation exhibited a highly homoplastic pattern related to functional adaptation of some taxa. However, phylogeny was also an important factor in shaping molar morphological traits, given that some phenotypic similarities were consistent with current phylogenetic positions. Our results show that the phylogenetic and functional signals of lower molar shape vary depending on the taxa and the tooth considered. Based on molar shape, Aotus showed closer similarities to Callicebus, as well as to some Cebidae and Ateles-Lagothrix, due to convergent evolutionary trends caused by similar dietary habits, or due to fast-evolving branches in the Aotus lineage, somewhat similar to the shape of Callicebus and Cebidae.
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Affiliation(s)
- Mónica Nova Delgado
- Secció de Zoologia i Antropologia Biològica, Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
| | - Jordi Galbany
- Secció de Zoologia i Antropologia Biològica, Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain; Center for the Advanced Study of Human Paleobiology, Department of Anthropology, George Washington University, 800 22nd Street NW, Ste 6000, Washington, D.C. 20052, USA
| | - Alejandro Pérez-Pérez
- Secció de Zoologia i Antropologia Biològica, Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain.
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32
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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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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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34
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Nova Delgado M, Galbany J, Pérez-Pérez A. Morphometric variation of extant platyrrhine molars: taxonomic implications for fossil platyrrhines. PeerJ 2016; 4:e1967. [PMID: 27190704 PMCID: PMC4867715 DOI: 10.7717/peerj.1967] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 04/04/2016] [Indexed: 12/25/2022] Open
Abstract
The phylogenetic position of many fossil platyrrhines with respect to extant ones is not yet clear. Two main hypotheses have been proposed: the layered or successive radiations hypothesis suggests that Patagonian fossils are Middle Miocene stem platyrrhines lacking modern descendants, whereas the long lineage hypothesis argues for an evolutionary continuity of all fossil platyrrhines with the extant ones. Our geometric morphometric analysis of a 15 landmark-based configuration of platyrrhines' first and second lower molars suggest that morphological stasis may explain the reduced molar shape variation observed. Platyrrhine lower molar shape might be a primitive retention of the ancestral state affected by strong ecological constraints throughout the radiation of the main platyrrhine families. The Patagonian fossil specimens showed two distinct morphological patterns of lower molars, Callicebus-like and Saguinus-like, which might be the precursors of the extant forms, whereas the Middle Miocene specimens, though showing morphological resemblances with the Patagonian fossils, also displayed new, derived molar patterns, Alouatta-like and Pitheciinae-like, thereby suggesting that despite the overall morphological stasis of molars, phenotypic diversification of molar shape was already settled during the Middle Miocene.
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Affiliation(s)
- Mónica Nova Delgado
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Zoology and Physical Anthropology Section, Universitat de Barcelona , Barcelona , Spain
| | - Jordi Galbany
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Zoology and Physical Anthropology Section, Universitat de Barcelona, Barcelona, Spain; Center for the Advanced Study of Human Paleobiology, Department of Anthropology, George Washington University, Washington DC, United States of America
| | - Alejandro Pérez-Pérez
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Zoology and Physical Anthropology Section, Universitat de Barcelona , Barcelona , Spain
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35
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Konkel MK, Ullmer B, Arceneaux EL, Sanampudi S, Brantley SA, Hubley R, Smit AFA, Batzer MA. Discovery of a new repeat family in the Callithrix jacchus genome. Genome Res 2016; 26:649-59. [PMID: 26916108 PMCID: PMC4864456 DOI: 10.1101/gr.199075.115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 02/23/2016] [Indexed: 11/24/2022]
Abstract
We identified a novel repeat family, termed Platy-1, in the Callithrix jacchus (common marmoset) genome that arose around the time of the divergence of platyrrhines and catarrhines and established itself as a repeat family in New World monkeys (NWMs). A full-length Platy-1 element is ∼100 bp in length, making it the shortest known short interspersed element (SINE) in primates, and harbors features characteristic of non-LTR retrotransposons. We identified 2268 full-length Platy-1 elements across 62 subfamilies in the common marmoset genome. Our subfamily reconstruction and phylogenetic analyses support Platy-1 propagation throughout the evolution of NWMs in the lineage leading to C. jacchus Platy-1 appears to have reached its amplification peak in the common ancestor of current day marmosets and has since moderately declined. However, identification of more than 200 Platy-1 elements identical to their respective consensus sequence, and the presence of polymorphic elements within common marmoset populations, suggests ongoing retrotransposition activity. Platy-1, a SINE, appears to have originated from an Alu element, and hence is likely derived from 7SL RNA. Our analyses illustrate the birth of a new repeat family and its propagation dynamics in the lineage leading to the common marmoset over the last 40 million years.
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Affiliation(s)
- Miriam K Konkel
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Brygg Ullmer
- School of Electrical Engineering and Computer Science, Center for Computation and Technology, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Erika L Arceneaux
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Sreeja Sanampudi
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Sarah A Brantley
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Robert Hubley
- Institute for Systems Biology, Seattle, Washington 98109-5263, USA
| | - Arian F A Smit
- Institute for Systems Biology, Seattle, Washington 98109-5263, USA
| | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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Muniz CP, Jia H, Shankar A, Troncoso LL, Augusto AM, Farias E, Pissinatti A, Fedullo LP, Santos AF, Soares MA, Switzer WM. An expanded search for simian foamy viruses (SFV) in Brazilian New World primates identifies novel SFV lineages and host age-related infections. Retrovirology 2015; 12:94. [PMID: 26576961 PMCID: PMC4650395 DOI: 10.1186/s12977-015-0217-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 10/20/2015] [Indexed: 11/19/2022] Open
Abstract
Background While simian foamy viruses have co-evolved with their primate hosts for millennia, most scientific studies have focused on understanding infection in Old World primates with little knowledge available on the epidemiology and natural history of SFV infection in New World primates (NWPs). To better understand the geographic and species distribution and evolutionary history of SFV in NWPs we extend our previous studies in Brazil by screening 15 genera consisting of 29 NWP species (140 monkeys total), including five genera (Brachyteles, Cacajao, Callimico, Mico, and Pithecia) not previously analyzed. Monkey blood specimens were tested using a combination of both serology and PCR to more accurately estimate prevalence and investigate transmission patterns. Sequences were phylogenetically analyzed to infer SFV and host evolutionary histories. Results The overall serologic and molecular prevalences were 42.8 and 33.6 %, respectively, with a combined assay prevalence of 55.8 %. Discordant serology and PCR results were observed for 28.5 % of the samples, indicating that both methods are currently necessary for estimating NWP SFV prevalence. SFV prevalence in sexually mature NWPs with a positive result in any of the WB or PCR assays was 51/107 (47.7 %) compared to 20/33 (61 %) for immature animals. Epidemiological analyses revealed an increase in SFV prevalence with age in captive Cebus monkeys. Phylogenetic analysis identified novel SFVs in Cacajao,Leontopithecus, and Chiropotes species that had 6–37 % nucleotide divergence to other NWP SFV. Comparison of host and SFV phylogenies showed an overall cospeciation evolutionary history with rare ancient and contemporaneous host-switching for Saimiri and Leontopithecus and Cebus xanthosternos, respectively. Conclusions We identified novel SFV in four neotropical monkey genera in Brazil and demonstrate that SFV prevalence increases with age in Cebus monkeys. Importantly, our test results suggest that both molecular and serological screening are currently required to accurately determine infection with NWP SFV. Our study significantly expands knowledge of the epidemiology and natural history of NWP SFVs. The tools and information provided in our study will facilitate further investigation of SFV in NWPs and the potential for zoonotic infection with these viruses.
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Affiliation(s)
- Cláudia P Muniz
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil. .,Laboratory Branch, Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd., MS G45, Atlanta, 30329, USA.
| | - Hongwei Jia
- Laboratory Branch, Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd., MS G45, Atlanta, 30329, USA.
| | - Anupama Shankar
- Laboratory Branch, Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd., MS G45, Atlanta, 30329, USA.
| | - Lian L Troncoso
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | | | - Elisabete Farias
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | | | | | - André F Santos
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Marcelo A Soares
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil. .,Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Brazil.
| | - William M Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd., MS G45, Atlanta, 30329, USA.
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Fergnani PN, Ruggiero A. Ecological Diversity in South American Mammals: Their Geographical Distribution Shows Variable Associations with Phylogenetic Diversity and Does Not Follow the Latitudinal Richness Gradient. PLoS One 2015; 10:e0128264. [PMID: 26053742 PMCID: PMC4460121 DOI: 10.1371/journal.pone.0128264] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 04/24/2015] [Indexed: 11/19/2022] Open
Abstract
The extent to which the latitudinal gradient in species richness may be paralleled by a similar gradient of increasing functional or phylogenetic diversity is a matter of controversy. We evaluated whether taxonomic richness (TR) is informative in terms of ecological diversity (ED, an approximation to functional diversity) and phylogenetic diversity (AvPD) using data on 531 mammal species representing South American old autochthonous (marsupials, xenarthrans), mid-Cenozoic immigrants (hystricognaths, primates) and newcomers (carnivorans, artiodactyls). If closely related species are ecologically more similar than distantly related species, AvPD will be a strong predictor of ED; however, lower ED than predicted from AvPD may be due to species retaining most of their ancestral characters, suggesting niche conservatism. This pattern could occur in tropical rainforests for taxa of tropical affinity (old autochthonous and mid-Cenozoic immigrants) and in open and arid habitats for newcomers. In contrast, higher ED than expected from AvPD could occur, possibly in association with niche evolution, in arid and open habitats for taxa of tropical affinity and in forested habitats for newcomers. We found that TR was a poor predictor of ED and AvPD. After controlling for TR, there was considerable variability in the extent to which AvPD accounted for ED. Taxa of tropical affinity did not support the prediction of ED deficit within tropical rainforests, rather, they showed a mosaic of regions with an excess of ED interspersed with zones of ED deficit within the tropics; newcomers showed ED deficit in arid and open regions. Some taxa of tropical affinity showed excess of ED in tropical desert areas (hystricognaths) or temperate semideserts (xenarthrans); newcomers showed excess of ED at cold-temperate latitudes in the Northern Hemisphere. This result suggests that extreme climatic conditions at both temperate and tropical latitudes may have promoted niche evolution in mammals.
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Affiliation(s)
- Paula Nilda Fergnani
- Laboratorio Ecotono, Centro Regional Universitario Bariloche-Universidad Nacional del Comahue, INIBIOMA-CONICET, San Carlos de Bariloche, Argentina
- * E-mail:
| | - Adriana Ruggiero
- Laboratorio Ecotono, Centro Regional Universitario Bariloche-Universidad Nacional del Comahue, INIBIOMA-CONICET, San Carlos de Bariloche, Argentina
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38
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Encephalization and diversification of the cranial base in platyrrhine primates. J Hum Evol 2015; 81:29-40. [DOI: 10.1016/j.jhevol.2015.02.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 02/02/2015] [Accepted: 02/03/2015] [Indexed: 11/19/2022]
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39
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Schrago CG, Menezes AN, Furtado C, Bonvicino CR, Seuanez HN. Multispecies coalescent analysis of the early diversification of neotropical primates: phylogenetic inference under strong gene trees/species tree conflict. Genome Biol Evol 2014; 6:3105-14. [PMID: 25377940 PMCID: PMC4255775 DOI: 10.1093/gbe/evu244] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Neotropical primates (NP) are presently distributed in the New World from Mexico to northern Argentina, comprising three large families, Cebidae, Atelidae, and Pitheciidae, consequently to their diversification following their separation from Old World anthropoids near the Eocene/Oligocene boundary, some 40 Ma. The evolution of NP has been intensively investigated in the last decade by studies focusing on their phylogeny and timescale. However, despite major efforts, the phylogenetic relationship between these three major clades and the age of their last common ancestor are still controversial because these inferences were based on limited numbers of loci and dating analyses that did not consider the evolutionary variation associated with the distribution of gene trees within the proposed phylogenies. We show, by multispecies coalescent analyses of selected genome segments, spanning along 92,496,904 bp that the early diversification of extant NP was marked by a 2-fold increase of their effective population size and that Atelids and Cebids are more closely related respective to Pitheciids. The molecular phylogeny of NP has been difficult to solve because of population-level phenomena at the early evolution of the lineage. The association of evolutionary variation with the distribution of gene trees within proposed phylogenies is crucial for distinguishing the mean genetic divergence between species (the mean coalescent time between loci) from speciation time. This approach, based on extensive genomic data provided by new generation DNA sequencing, provides more accurate reconstructions of phylogenies and timescales for all organisms.
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Affiliation(s)
- Carlos G Schrago
- Department of Genetics, Federal University of Rio de Janeiro, Brazil
| | - Albert N Menezes
- Division of Genetics, National Cancer Institute, Rio de Janeiro, Brazil
| | - Carolina Furtado
- Division of Genetics, National Cancer Institute, Rio de Janeiro, Brazil
| | - Cibele R Bonvicino
- Division of Genetics, National Cancer Institute, Rio de Janeiro, Brazil Laboratory of Biology and Parasitology of Wild Mammal Reservoirs, Instituto Oswaldo Cruz, Fiocruz, Brazil
| | - Hector N Seuanez
- Department of Genetics, Federal University of Rio de Janeiro, Brazil Division of Genetics, National Cancer Institute, Rio de Janeiro, Brazil
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Perez SI, Rosenberger AL. The status of platyrrhine phylogeny: A meta-analysis and quantitative appraisal of topological hypotheses. J Hum Evol 2014; 76:177-87. [DOI: 10.1016/j.jhevol.2014.08.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 08/16/2014] [Accepted: 08/17/2014] [Indexed: 11/27/2022]
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Significance of the evolutionary α1,3-galactosyltransferase (GGTA1) gene inactivation in preventing extinction of apes and old world monkeys. J Mol Evol 2014; 80:1-9. [PMID: 25315716 DOI: 10.1007/s00239-014-9652-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Accepted: 10/06/2014] [Indexed: 10/24/2022]
Abstract
The α1,3-galactosyltransferase (α1,3GT or GGTA1) gene displays unique evolutionary characteristics. This gene appeared early in mammalian evolution and is absent in other vertebrates. The α1,3GT gene is active in marsupials, nonprimate placental mammals, lemurs (prosimians) and New World monkeys, encoding the α1,3GT enzyme that synthesizes a carbohydrate antigen called "α-gal epitope." The α-gal epitope is present in large numbers on cell membrane glycolipids and glycoproteins. The α1,3GT gene was inactivated in ancestral Old World monkeys and apes by frameshift single-base deletions forming premature stop codons. Because of this gene inactivation, humans, apes, and Old World monkeys lack α-gal epitopes and naturally produce an antibody called the "anti-Gal antibody" which binds specifically to α-gal epitopes and which is the most abundant antibody in humans. The evolutionary event that resulted in the inactivation of the α1,3GT gene in ancestral Old World primates could have been mediated by a pathogen endemic to Eurasia-Africa landmass that exerted pressure for selection of primate populations lacking the α-gal epitope. Once the α-gal epitope was eliminated, primates could produce the anti-Gal antibody, possibly as means of defense against pathogens expressing this epitope. This assumption is supported by the fossil record demonstrating an almost complete extinction of apes in the late Miocene and failure of Old World monkeys to radiate into multiple species before that period. A present outcome of this evolutionary event is the anti-Gal-mediated rejection of mammalian xenografts expressing α-gal epitopes in humans, apes, and Old World monkeys.
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Springer SA, Diaz SL, Gagneux P. Parallel evolution of a self-signal: humans and new world monkeys independently lost the cell surface sugar Neu5Gc. Immunogenetics 2014; 66:671-4. [PMID: 25124893 DOI: 10.1007/s00251-014-0795-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 08/05/2014] [Indexed: 12/20/2022]
Abstract
Human sialic acid biology is unusual and thought to be unique among mammals. Humans lack a functional cytidine monophosphate-N-acetylneuraminic acid hydroxylase (CMAH) protein and cannot synthesize the sugar Neu5Gc, an innate mammalian signal of self. Losing this sugar changed how humans interact with some of our deadliest pathogens: malaria, influenza, and streptococcus among others. We show that the New World monkeys, comprising the third of all primate species, have human-like sialic acid biology. They have lost Neu5Gc because of an independent CMAH inactivation ~30 million years ago (mya) (compared to ~3 mya in hominids). This parallel loss of Neu5Gc opens sialic acid biology to comparative phylogenetic analysis and reveals an unexpected conservation priority. New World monkeys risk infection by human pathogens that can recognize cells in the absence of Neu5Gc. This striking molecular convergence provides a mechanism that could explain the long-standing observation that New World monkeys are susceptible to some human diseases that cannot be transmitted to other primates.
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Affiliation(s)
- Stevan A Springer
- Glycobiology Research and Training Center, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
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43
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Kim DS, Wang Y, Oh HJ, Lee K, Hahn Y. Frequent loss and alteration of the MOXD2 gene in catarrhines and whales: a possible connection with the evolution of olfaction. PLoS One 2014; 9:e104085. [PMID: 25102179 PMCID: PMC4125168 DOI: 10.1371/journal.pone.0104085] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 07/08/2014] [Indexed: 11/18/2022] Open
Abstract
The MOXD2 gene encodes a membrane-bound monooxygenase similar to dopamine-β-hydroxylase, and has been proposed to be associated with olfaction. In this study, we analyzed MOXD2 genes from 64 mammalian species, and identified loss-of-function mutations in apes (humans, Sumatran and Bornean orangutans, and five gibbon species from the four major gibbon genera), toothed whales (killer whales, bottlenose dolphins, finless porpoises, baijis, and sperm whales), and baleen whales (minke whales and fin whales). We also identified a shared 13-nt deletion in the last exon of Old World cercopithecine monkeys that results in conversion of a membrane-bound protein to a soluble form. We hypothesize that the frequent inactivation and alteration of MOXD2 genes in catarrhines and whales may be associated with the evolution of olfaction in these clades.
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Affiliation(s)
- Dong Seon Kim
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Korea
| | - Yao Wang
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Korea
| | - Hye Ji Oh
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Korea
| | - Kangseok Lee
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Korea
| | - Yoonsoo Hahn
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Korea
- * E-mail:
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Di Fiore A, Chaves PB, Cornejo FM, Schmitt CA, Shanee S, Cortés-Ortiz L, Fagundes V, Roos C, Pacheco V. The rise and fall of a genus: Complete mtDNA genomes shed light on the phylogenetic position of yellow-tailed woolly monkeys, Lagothrix flavicauda, and on the evolutionary history of the family Atelidae (Primates: Platyrrhini). Mol Phylogenet Evol 2014; 82 Pt B:495-510. [PMID: 24751996 DOI: 10.1016/j.ympev.2014.03.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 02/27/2014] [Accepted: 03/24/2014] [Indexed: 11/25/2022]
Abstract
Using complete mitochondrial genome sequences, we provide the first molecular analysis of the phylogenetic position of the yellow-tailed woolly monkey, Lagothrix flavicauda (a.k.a. Oreonax flavicauda), a critically endangered neotropical primate endemic to northern Perú. The taxonomic status and phylogenetic position of yellow-tailed woolly monkeys have been debated for many years, but in this study both Bayesian and maximum likelihood phylogenetic reconstructions unequivocally support a monophyletic woolly monkey clade that includes L. flavicauda as the basal taxon within the radiation. Bayesian dating analyses using several alternative calibrations suggest that the divergence of yellow-tailed woolly monkeys from other Lagothrix occurred in the Pleistocene, ∼2.1Ma, roughly 6.5 my after the divergence of woolly monkeys from their sister genus, Brachyteles. Additionally, comparative analysis of the cytochrome oxidase subunit 2 (COX2) gene shows that genetic distances between yellow-tailed woolly monkeys and other Lagothrix from across the genus' geographic distribution fall well within the range of between-species divergences seen in a large number of other platyrrhine primate genera at the same locus and outside the range of between-genus divergences. Our results thus confirm a position within Lagothrix for the yellow-tailed woolly monkey and strongly suggest that the name Oreonax be formally considered a synonym for this genus. This revision in taxonomic status does not change the dire conservation threats facing the yellow-tailed woolly monkey in Perú, where the remaining wild population is estimated at only ∼10,000 individuals living in a highly fragmented landscape.
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Affiliation(s)
- Anthony Di Fiore
- Department of Anthropology, New York University, USA; Primate Molecular Ecology and Evolution Laboratory, Department of Anthropology, University of Texas at Austin, USA.
| | - Paulo B Chaves
- Department of Anthropology, New York University, USA; Primate Molecular Ecology and Evolution Laboratory, Department of Anthropology, University of Texas at Austin, USA; New York Consortium in Evolutionary Primatology (NYCEP), USA
| | - Fanny M Cornejo
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, USA; Fundación Yunkawasi, Perú
| | - Christopher A Schmitt
- Department of Anthropology, New York University, USA; Center for Neurobehavioral Genetics, University of California, Los Angeles, USA; Department of Anthropology, University of Southern California, USA
| | | | | | - Valéria Fagundes
- Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo, Brazil
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Göttingen, Germany
| | - Víctor Pacheco
- Museo de Historia Natural, Departamento de Mastozoologia, Universidad Nacional Mayor de San Marcos, Perú
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Kay RF. Biogeography in deep time - What do phylogenetics, geology, and paleoclimate tell us about early platyrrhine evolution? Mol Phylogenet Evol 2013; 82 Pt B:358-74. [PMID: 24333920 DOI: 10.1016/j.ympev.2013.12.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Revised: 11/19/2013] [Accepted: 12/02/2013] [Indexed: 11/29/2022]
Abstract
Molecular data have converged on a consensus about the genus-level phylogeny of extant platyrrhine monkeys, but for most extinct taxa and certainly for those older than the Pleistocene we must rely upon morphological evidence from fossils. This raises the question as to how well anatomical data mirror molecular phylogenies and how best to deal with discrepancies between the molecular and morphological data as we seek to extend our phylogenies to the placement of fossil taxa. Here I present parsimony-based phylogenetic analyses of extant and fossil platyrrhines based on an anatomical dataset of 399 dental characters and osteological features of the cranium and postcranium. I sample 16 extant taxa (one from each platyrrhine genus) and 20 extinct taxa of platyrrhines. The tree structure is constrained with a "molecular scaffold" of extant species as implemented in maximum parsimony using PAUP with the molecular-based 'backbone' approach. The data set encompasses most of the known extinct species of platyrrhines, ranging in age from latest Oligocene (∼26 Ma) to the Recent. The tree is rooted with extant catarrhines, and Late Eocene and Early Oligocene African anthropoids. Among the more interesting patterns to emerge are: (1) known early platyrrhines from the Late Oligocene through Early Miocene (26-16.5Ma) represent only stem platyrrhine taxa; (2) representatives of the three living platyrrhine families first occur between 15.7 Ma and 13.5 Ma; and (3) recently extinct primates from the Greater Antilles (Cuba, Jamaica, Hispaniola) are sister to the clade of extant platyrrhines and may have diverged in the Early Miocene. It is probable that the crown platyrrhine clade did not originate before about 20-24 Ma, a conclusion consistent with the phylogenetic analysis of fossil taxa presented here and with recent molecular clock estimates. The following biogeographic scenario is consistent with the phylogenetic findings and climatic and geologic evidence: Tropical South America has been a center for platyrrhine diversification since platyrrhines arrived on the continent in the middle Cenozoic. Platyrrhines dispersed from tropical South America to Patagonia at ∼25-24 Ma via a "Paraná Portal" through eastern South America across a retreating Paranense Sea. Phylogenetic bracketing suggests Antillean primates arrived via a sweepstakes route or island chain from northern South America in the Early Miocene, not via a proposed land bridge or island chain (GAARlandia) in the Early Oligocene (∼34 Ma). Patagonian and Antillean platyrrhines went extinct without leaving living descendants, the former at the end of the Early Miocene and the latter within the past six thousand years. Molecular evidence suggests crown platyrrhines arrived in Central America by crossing an intermittent connection through the Isthmus of Panama at or after 3.5Ma. Any more ancient Central American primates, should they be discovered, are unlikely to have given rise to the extant Central American taxa in situ.
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Affiliation(s)
- Richard F Kay
- Department of Evolutionary Anthropology & Division of Earth and Ocean Sciences, Duke University, Box 90383, Durham, NC 27708, United States.
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Modeling lineage and phenotypic diversification in the New World monkey (Platyrrhini, Primates) radiation. Mol Phylogenet Evol 2013; 82 Pt B:375-85. [PMID: 24287474 DOI: 10.1016/j.ympev.2013.11.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 10/24/2013] [Accepted: 11/15/2013] [Indexed: 11/19/2022]
Abstract
Adaptive radiations that have taken place in the distant past can now be more thoroughly studied with the availability of large molecular phylogenies and comparative data drawn from extant and fossil species. Platyrrhines are a good example of a major mammalian evolutionary radiation confined to a single continent, involving a relatively large temporal scale and documented by a relatively small but informative fossil record. Here, we present comparative evidence using data on extant and fossil species to explore alternative evolutionary models in an effort to better understand the process of platyrrhine lineage and phenotypic diversification. Specifically, we compare the likelihood of null models of lineage and phenotypic diversification versus various models of adaptive evolution. Moreover, we statistically explore the main ecological dimension behind the platyrrhine diversification. Contrary to the previous proposals, our study did not find evidence of a rapid lineage accumulation in the phylogenetic tree of extant platyrrhine species. However, the fossil-based diversity curve seems to show a slowdown in diversification rates toward present times. This also suggests an early high rate of extinction among lineages within crown Platyrrhini. Finally, our analyses support the hypothesis that the platyrrhine phenotypic diversification appears to be characterized by an early and profound differentiation in body size related to a multidimensional niche model, followed by little subsequent change (i.e., stasis).
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