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Javier MCF, Noblezada AC, Sienes PMQ, Guino-o RS, Palomar-Abesamis N, Malay MCD, del Castillo CS, Ferriols VMEN. Draft genome of the endangered visayan spotted deer ( Rusa alfredi), a Philippine endemic species. GIGABYTE 2025; 2025:gigabyte150. [PMID: 40041424 PMCID: PMC11876970 DOI: 10.46471/gigabyte.150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2024] [Accepted: 02/18/2025] [Indexed: 03/06/2025] Open
Abstract
The Visayan Spotted Deer (VSD), or Rusa alfredi, is an endangered and endemic species in the Philippines. Despite its status, genomic information on R. alfredi, and the genus Rusa in general, is missing. This study presents the first draft genome assembly of the VSD using the Illumina short-read sequencing technology. The resulting RusAlf_1.1 assembly has a 2.52 Gb total length, with a contig N50 of 46 Kb and scaffold N50 size of 75 Mb. The assembly has a BUSCO complete score of 95.5%, demonstrating the genome's completeness, and includes the annotation of 24,531 genes. Our phylogenetic analysis based on single-copy orthologs revealed a close evolutionary relationship between R. alfredi and the genus Cervus. RusAlf_1.1 represents a significant advancement in our understanding of the VSD. It opens opportunities for further research in population genetics and evolutionary biology, potentially contributing to more effective conservation and management strategies for this endangered species.
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Affiliation(s)
- Ma. Carmel F. Javier
- Philippine Genome Center Visayas, University of the Philippines Visayas, Miagao Iloilo, Philippines
| | - Albert C. Noblezada
- Philippine Genome Center Visayas, University of the Philippines Visayas, Miagao Iloilo, Philippines
| | | | - Robert S. Guino-o
- Angelo King Center for Research and Environmental Management, Silliman University, Dumaguete, Philippines
| | | | - Maria Celia D. Malay
- Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines
| | - Carmelo S. del Castillo
- Institute of Aquaculture, College of Fisheries and Ocean Sciences, University of the Philippines Visayas, Miagao Iloilo, Philippines
- National Institute of Molecular Biology and Biotechnology, University of the Philippines Visayas, Miagao Iloilo, Philippines
| | - Victor Marco Emmanuel N. Ferriols
- Philippine Genome Center Visayas, University of the Philippines Visayas, Miagao Iloilo, Philippines
- Institute of Aquaculture, College of Fisheries and Ocean Sciences, University of the Philippines Visayas, Miagao Iloilo, Philippines
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2
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Proskuryakova AA, Ivanova ES, Makunin AI, Larkin DM, Ferguson-Smith MA, Yang F, Uphyrkina OV, Perelman PL, Graphodatsky AS. Comparative studies of X chromosomes in Cervidae family. Sci Rep 2023; 13:11992. [PMID: 37491593 PMCID: PMC10368622 DOI: 10.1038/s41598-023-39088-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 07/20/2023] [Indexed: 07/27/2023] Open
Abstract
The family Cervidae is the second most diverse in the infraorder Pecora and is characterized by variability in the diploid chromosome numbers among species. X chromosomes in Cervidae evolved through complex chromosomal rearrangements of conserved segments within the chromosome, changes in centromere position, heterochromatic variation, and X-autosomal translocations. The family Cervidae consists of two subfamilies: Cervinae and Capreolinae. Here we build a detailed X chromosome map with 29 cattle bacterial artificial chromosomes of representatives of both subfamilies: reindeer (Rangifer tarandus), gray brocket deer (Mazama gouazoubira), Chinese water deer (Hydropotes inermis) (Capreolinae); black muntjac (Muntiacus crinifrons), tufted deer (Elaphodus cephalophus), sika deer (Cervus nippon) and red deer (Cervus elaphus) (Cervinae). To track chromosomal rearrangements during Cervidae evolution, we summarized new data, and compared them with available X chromosomal maps and chromosome level assemblies of other species. We demonstrate the types of rearrangements that may have underlined the variability of Cervidae X chromosomes. We detected two types of cervine X chromosome-acrocentric and submetacentric. The acrocentric type is found in three independent deer lineages (subfamily Cervinae and in two Capreolinae tribes-Odocoileini and Capreolini). We show that chromosomal rearrangements on the X-chromosome in Cervidae occur at a higher frequency than in the entire Ruminantia lineage: the rate of rearrangements is 2 per 10 million years.
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Affiliation(s)
- Anastasia A Proskuryakova
- Institute of Molecular and Cellular Biology, SB RAS, Lavrentiev Ave 8/2, Novosibirsk, Russia, 630090.
| | - Ekaterina S Ivanova
- Institute of Molecular and Cellular Biology, SB RAS, Lavrentiev Ave 8/2, Novosibirsk, Russia, 630090
- Novosibirsk State University, Pirogova Str. 1, Novosibirsk, Russia, 630090
| | - Alexey I Makunin
- Institute of Molecular and Cellular Biology, SB RAS, Lavrentiev Ave 8/2, Novosibirsk, Russia, 630090
| | - Denis M Larkin
- The Royal Veterinary College, Royal College Street, University of London, London, NW1 0TU, UK
| | - Malcolm A Ferguson-Smith
- Department of Veterinary Medicine, Cambridge Resource Center for Comparative Genomics, University of Cambridge, Cambridge, UK
| | - Fengtang Yang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Olga V Uphyrkina
- Federal Research Center for Biodiversity of the Terrestrial Biota of East Asia, Vladivostok, Russia
| | - Polina L Perelman
- Institute of Molecular and Cellular Biology, SB RAS, Lavrentiev Ave 8/2, Novosibirsk, Russia, 630090
| | - Alexander S Graphodatsky
- Institute of Molecular and Cellular Biology, SB RAS, Lavrentiev Ave 8/2, Novosibirsk, Russia, 630090
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3
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Morales-Donoso JA, Vacari GQ, Bernegossi AM, Sandoval EDP, Peres PHF, Galindo DJ, de Thoisy B, Vozdova M, Kubickova S, Barbanti Duarte JM. Revalidation of Passalites Gloger, 1841 for the Amazon brown brocket deer P.nemorivagus (Cuvier, 1817) (Mammalia, Artiodactyla, Cervidae). Zookeys 2023; 1167:241-264. [PMID: 37388777 PMCID: PMC10300653 DOI: 10.3897/zookeys.1167.100577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 04/24/2023] [Indexed: 07/01/2023] Open
Abstract
Mazamanemorivaga (Cuvier, 1817) is a gray brocket deer that inhabits the Amazon region. An assessment of previous studies revealed inconsistencies in its current taxonomic classification, suggesting the need for an update in its genus classification. A taxonomic repositioning of this species is proposed through the collection of a specimen from its type locality (French Guiana) with subsequent morphological (coloring pattern, body measurements, and craniometry), cytogenetics (G Band, C Band, conventional Giemsa, Ag-NOR staining, and BAC probe mapping), and molecular phylogenetic analysis (mitochondrial genes Cyt B of 920 bp, COI I of 658 bp, D-loop 610 bp), and comparisons with other specimens of the same taxon, as well as other Neotropical deer species. The morphological and cytogenetic differences between this and other Neotropical Cervidae confirm the taxon as a unique and valid species. The phylogenetic analysis evidenced the basal position of the M.nemorivaga specimens within the Blastocerina clade. This shows early diversification and wide divergence from the other species, suggesting that the taxon should be transferred to a different genus. A taxonomic update of the genus name is proposed through the validation of Passalites Gloger, 1841, with Passalitesnemorivagus (Cuvier, 1817) as the type species. Future research should focus on evaluating the potential existence of other species within the genus Passalites, as suggested in the literature.
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Affiliation(s)
- Jorge Alfonso Morales-Donoso
- Núcleo de Pesquisa e Conservação de Cervídeos (NUPECCE), Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal-SP, BrazilUniversidade Estadual Paulista (UNESP)JaboticabalBrazil
| | - Gabrielle Queiroz Vacari
- Núcleo de Pesquisa e Conservação de Cervídeos (NUPECCE), Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal-SP, BrazilUniversidade Estadual Paulista (UNESP)JaboticabalBrazil
| | - Agda Maria Bernegossi
- Núcleo de Pesquisa e Conservação de Cervídeos (NUPECCE), Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal-SP, BrazilUniversidade Estadual Paulista (UNESP)JaboticabalBrazil
| | - Eluzai Dinai Pinto Sandoval
- Núcleo de Pesquisa e Conservação de Cervídeos (NUPECCE), Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal-SP, BrazilUniversidade Estadual Paulista (UNESP)JaboticabalBrazil
| | - Pedro Henrique Faria Peres
- Núcleo de Pesquisa e Conservação de Cervídeos (NUPECCE), Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal-SP, BrazilUniversidade Estadual Paulista (UNESP)JaboticabalBrazil
| | - David Javier Galindo
- Laboratorio de Reproducción Animal, Departamento de Producción Animal, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marco, San Borja, Lima, PeruUniversidad Nacional Mayor de San MarcoLimaPeru
| | | | - Miluse Vozdova
- Central European Institute of Technology-Veterinary Research Institute, 621 00, Brno, Czech RepublicCentral European Institute of Technology-Veterinary Research InstituteBrnoCzech Republic
| | - Svatava Kubickova
- Central European Institute of Technology-Veterinary Research Institute, 621 00, Brno, Czech RepublicCentral European Institute of Technology-Veterinary Research InstituteBrnoCzech Republic
| | - José Mauricio Barbanti Duarte
- Núcleo de Pesquisa e Conservação de Cervídeos (NUPECCE), Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal-SP, BrazilUniversidade Estadual Paulista (UNESP)JaboticabalBrazil
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4
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Heckeberg NS, Zachos FE, Kierdorf U. Antler tine homologies and cervid systematics: A review of past and present controversies with special emphasis on Elaphurus davidianus. Anat Rec (Hoboken) 2023; 306:5-28. [PMID: 35578743 DOI: 10.1002/ar.24956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 01/29/2023]
Abstract
Antlers are the most conspicuous trait of cervids and have been used in the past to establish a classification of their fossil and living representatives. Since the availability of molecular data, morphological characters have generally become less important for phylogenetic reconstructions. In recent years, however, the appreciation of morphological characters has increased, and they are now more frequently used in addition to molecular data to reconstruct the evolutionary history of cervids. A persistent challenge when using antler traits in deer systematics is finding a consensus on the homology of structures. Here, we review early and recent attempts to homologize antler structures and objections to this approach, compare and evaluate recent advances on antler homologies, and critically discuss these different views in order to offer a basis for further scientific exchange on the topic. We further present some developmental aspects of antler branching patterns and discuss their potential for reconstructing cervid systematics. The use of heterogeneous data for reconstructing phylogenies has resulted in partly conflicting hypotheses on the systematic position of certain cervid species, on which we also elaborate here. We address current discussions on the use of different molecular markers in cervid systematics and the question whether antler morphology and molecular data can provide a consistent picture on the evolutionary history of cervids. In this context, special attention is given to the antler morphology and the systematic position of the enigmatic Pere David's deer (Elaphurus davidianus).
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Affiliation(s)
- Nicola S Heckeberg
- Staatliches Museum für Naturkunde Karlsruhe, Karlsruhe, Germany.,Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Frank E Zachos
- Natural History Museum Vienna, Vienna, Austria.,Department of Genetics, University of the Free State, Bloemfontein, South Africa.,Department of Evolutionary Biology, University of Vienna, Vienna, Austria
| | - Uwe Kierdorf
- Department of Biology, University of Hildesheim, Hildesheim, Germany
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5
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Mennecart B, Dziomber I, Aiglstorfer M, Bibi F, DeMiguel D, Fujita M, Kubo MO, Laurens F, Meng J, Métais G, Müller B, Ríos M, Rössner GE, Sánchez IM, Schulz G, Wang S, Costeur L. Ruminant inner ear shape records 35 million years of neutral evolution. Nat Commun 2022; 13:7222. [PMID: 36473836 PMCID: PMC9726890 DOI: 10.1038/s41467-022-34656-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 11/02/2022] [Indexed: 12/12/2022] Open
Abstract
Extrinsic and intrinsic factors impact diversity. On deep-time scales, the extrinsic impact of climate and geology are crucial, but poorly understood. Here, we use the inner ear morphology of ruminant artiodactyls to test for a deep-time correlation between a low adaptive anatomical structure and both extrinsic and intrinsic variables. We apply geometric morphometric analyses in a phylogenetic frame to X-ray computed tomographic data from 191 ruminant species. Contrasting results across ruminant clades show that neutral evolutionary processes over time may strongly influence the evolution of inner ear morphology. Extant, ecologically diversified clades increase their evolutionary rate with decreasing Cenozoic global temperatures. Evolutionary rate peaks with the colonization of new continents. Simultaneously, ecologically restricted clades show declining or unchanged rates. These results suggest that both climate and paleogeography produced heterogeneous environments, which likely facilitated Cervidae and Bovidae diversification and exemplifies the effect of extrinsic and intrinsic factors on evolution in ruminants.
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Affiliation(s)
- Bastien Mennecart
- Naturhistorisches Museum Basel, Augustinergasse 2, 4001, Basel, Switzerland.
| | - Ilya Dziomber
- Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland
- Oeschger Centre for Climate Change Research, University of Bern, 3012, Bern, Switzerland
| | - Manuela Aiglstorfer
- Naturhistorisches Museum Mainz / Landessammlung für Naturkunde Rheinland-Pfalz, Reichklarastraße 10, 55116, Mainz, Germany
| | - Faysal Bibi
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, 10115, Germany
| | - Daniel DeMiguel
- Fundación ARAID, Zaragoza, Spain
- Departamento de Ciencias de la Tierra, Área de Paleontología / Instituto Universitario de Investigación en Ciencias Ambientales de Aragón (IUCA). Universidad de Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain
- Institut Català de Palaeontologia Miquel Crusafont (ICP), Edifici Z, c/de les columnes s/n, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | - Masaki Fujita
- National Museum of Nature and Science, Tsukuba, Japan
| | - Mugino O Kubo
- Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Flavie Laurens
- Swiss National Data and Service Center for the Humanities, 4123, Allschwil, Switzerland
| | - Jin Meng
- American Museum of Natural History, 10024 New York; Earth and Environmental Sciences, Graduate Center, City University of New York, New York, NY, 10016, USA
| | - Grégoire Métais
- CR2P - Centre de Recherche en Paléontologie - Paris, UMR 7207, CNRS, MNHN, Sorbonne Université. Muséum national d'Histoire naturelle, CP38, 8 rue Buffon, 75005, Paris, France
| | - Bert Müller
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Gewerbestrasse 14, 4123, Allschwil, Switzerland
| | - María Ríos
- Department of Earth Sciences, GeoBioTec, Nova School of Science and Technology, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516, Caparica, Portugal
| | - Gertrud E Rössner
- Staatliche Naturwissenschaftliche Sammlungen Bayerns - Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Strasse 10, 80333, Munich, Germany
- Department für Geo- und Umweltwissenschaften, Paläontologie & Geobiologie, Ludwig-Maximilians-Universität München, Richard-Wagner-Strasse 10, 80333, Munich, Germany
| | - Israel M Sánchez
- Institut Català de Palaeontologia Miquel Crusafont (ICP), Edifici Z, c/de les columnes s/n, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | - Georg Schulz
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Gewerbestrasse 14, 4123, Allschwil, Switzerland
- Micro- and Nanotomography Core Facility, Department of Biomedical Engineering, University of Basel Gewerbestrasse 14, 4123, Allschwil, Switzerland
| | - Shiqi Wang
- Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, 142 Xizhimenwai Street, Beijing, 100044, China
| | - Loïc Costeur
- Naturhistorisches Museum Basel, Augustinergasse 2, 4001, Basel, Switzerland
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6
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Phylogeny and evolution of the genus Cervus (Cervidae, Mammalia) as revealed by complete mitochondrial genomes. Sci Rep 2022; 12:16381. [PMID: 36180508 PMCID: PMC9525267 DOI: 10.1038/s41598-022-20763-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 09/19/2022] [Indexed: 11/24/2022] Open
Abstract
Mitochondrial DNA (mtDNA) lineages are recognized as important components of intra- and interspecific biodiversity, and allow to reveal colonization routes and phylogeographic structure of many taxa. Among these is the genus Cervus that is widely distributed across the Holarctic. We obtained sequences of complete mitochondrial genomes from 13 Cervus taxa and included them in global phylogenetic analyses of 71 Cervinae mitogenomes. The well-resolved phylogenetic trees confirmed Cervus to be monophyletic. Molecular dating based on several fossil calibration points revealed that ca. 2.6 Mya two main mitochondrial lineages of Cervus separated in Central Asia, the Western (including C. hanglu and C. elaphus) and the Eastern (comprising C. albirostris, C. canadensis and C. nippon). We also observed convergent changes in the composition of some mitochondrial genes in C. hanglu of the Western lineage and representatives of the Eastern lineage. Several subspecies of C. nippon and C. hanglu have accumulated a large portion of deleterious substitutions in their mitochondrial protein-coding genes, probably due to drift in the wake of decreasing population size. In contrast to previous studies, we found that the relic haplogroup B of C. elaphus was sister to all other red deer lineages and that the Middle-Eastern haplogroup E shared a common ancestor with the Balkan haplogroup C. Comparison of the mtDNA phylogenetic tree with a published nuclear genome tree may imply ancient introgressions of mtDNA between different Cervus species as well as from the common ancestor of South Asian deer, Rusa timorensis and R. unicolor, to the Cervus clade.
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7
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Bernegossi AM, Borges CHDS, Sandoval EDP, Cartes JL, Cernohorska H, Kubickova S, Vozdova M, Caparroz R, González S, Duarte JMB. Resurrection of the genus Subulo Smith, 1827 for the gray brocket deer, with designation of a neotype. J Mammal 2022. [DOI: 10.1093/jmammal/gyac068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
The gray brocket deer, Mazama gouazoubiraG. Fischer, 1814, occurs in South America and presents an extensive degree of morphological and genetic variability. Previous phylogenetic research showed that the genus Mazama is polyphyletic and imposed the designation of a different genus-group name for M. gouazoubira. We aimed to review and clarify the taxonomy of M. gouazoubira through the proposal of updating the nomenclature for this taxon and by the characterization of specimens collected close to the original type locality (topotypes). The topotypes were characterized by morphological (general characterization and morphometry), cytogenetic (conventional staining, Ag-NOR, G- and C-banding, and fluorescence in situ hybridization), and phylogenetic (mitogenomes) approaches. We revealed chromosome homologies between cattle and M. gouazoubira using an entire set of cattle whole chromosome painting probes and propose an updated G-band idiogram for the species. The morphometric analysis did not discriminate the individuals of M. gouazoubira, including the topotypes, from other small brocket deer species. However, the phylogenetic analysis, based on a Bayesian inference tree of the mitogenomes, confirmed the polyphyly of the genus Mazama and supported the need to change the gray brocket deer genus-group name. Based on our revision, we validated the genus SubuloSmith, 1827, and fixed a type species for the genus. In the absence of the holotype, we denominated a neotype described by the collection of a male topotype in Paraguay. The nomenclature rearrangement presented here is a starting point that will assist in the taxonomic resolution of Neotropical deer.
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Affiliation(s)
- Agda Maria Bernegossi
- Núcleo de Pesquisa e Conservação de Cervídeos (NUPECCE), Faculdade de Ciências Agrárias e Veterinárias da Universidade Estadual Paulista (UNESP) , Jaboticabal , São Paulo , Brazil
| | - Carolina Heloisa de Souza Borges
- Núcleo de Pesquisa e Conservação de Cervídeos (NUPECCE), Faculdade de Ciências Agrárias e Veterinárias da Universidade Estadual Paulista (UNESP) , Jaboticabal , São Paulo , Brazil
- Centro de Aquicultura da Unesp (CAUNESP) , Jaboticabal , São Paulo , Brazil
| | - Eluzai Dinai Pinto Sandoval
- Núcleo de Pesquisa e Conservação de Cervídeos (NUPECCE), Faculdade de Ciências Agrárias e Veterinárias da Universidade Estadual Paulista (UNESP) , Jaboticabal , São Paulo , Brazil
| | - José Luis Cartes
- Guyra Paraguay, Avda Cnel Bóveda , Parque del Río, Viñas Cue, Asunción , Paraguay
| | - Halina Cernohorska
- Department of Genetics and Reproductive Biotechnologies, Central European Institute of Technology—Veterinary Research Institute , Brno , Czech Republic
| | - Svatava Kubickova
- Department of Genetics and Reproductive Biotechnologies, Central European Institute of Technology—Veterinary Research Institute , Brno , Czech Republic
| | - Miluse Vozdova
- Department of Genetics and Reproductive Biotechnologies, Central European Institute of Technology—Veterinary Research Institute , Brno , Czech Republic
| | - Renato Caparroz
- Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília , Brasília , Brazil
| | - Susana González
- Departamento de Biodiversidad y Genética, Instituto de Investigaciones Biológicas Clemente Estable , Montevidéo , Uruguay
| | - José Maurício Barbanti Duarte
- Núcleo de Pesquisa e Conservação de Cervídeos (NUPECCE), Faculdade de Ciências Agrárias e Veterinárias da Universidade Estadual Paulista (UNESP) , Jaboticabal, São Paulo , Brazil
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8
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Peres PHF, Luduvério DJ, Bernegossi AM, Galindo DJ, Nascimento GB, Oliveira ML, Sandoval EDP, Vozdova M, Kubickova S, Cernohorska H, Duarte JMB. Revalidation of Mazama rufa (Illiger 1815) (Artiodactyla: Cervidae) as a Distinct Species out of the Complex Mazama americana (Erxleben 1777). Front Genet 2022; 12:742870. [PMID: 34970296 PMCID: PMC8712859 DOI: 10.3389/fgene.2021.742870] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
The red brocket deer Mazama americana Erxleben, 1777 is considered a polyphyletic complex of cryptic species with wide chromosomal divergence. Evidence indicates that the observed chromosomal divergences result in reproductive isolation. The description of a neotype for M. americana allowed its genetic characterization and represented a comparative basis to resolve the taxonomic uncertainties of the group. Thus, we designated a neotype for the synonym Mazama rufa Illiger, 1815 and tested its recognition as a distinct species from the M. americana complex with the analysis of morphological, cytogenetic and molecular data. We also evaluated its distribution by sampling fecal DNA in the wild. Morphological data from craniometry and body biometry indicated an overlap of quantitative measurements between M. rufa and the entire M. americana complex. The phylogenetic hypothesis obtained through mtDNA confirmed the reciprocal monophyly relationship between M. americana and M. rufa, and both were identified as distinct molecular operational taxonomic units by the General Mixed Yule Coalescent species delimitation analysis. Finally, classic cytogenetic data and fluorescence in situ hybridization with whole chromosome painting probes showed M. rufa with a karyotype of 2n = 52, FN = 56. Comparative analysis indicate that at least fifteen rearrangements separate M. rufa and M. americana (sensu stricto) karyotypes, which confirmed their substantial chromosomal divergence. This divergence should represent an important reproductive barrier and allow its characterization as a distinct and valid species. Genetic analysis of fecal samples demonstrated a wide distribution of M. rufa in the South American continent through the Atlantic Forest, Cerrado and south region of Amazon. Thus, we conclude for the revalidation of M. rufa as a distinct species under the concept of biological isolation, with its karyotype as the main diagnostic character. The present work serves as a basis for the taxonomic review of the M. americana complex, which should be mainly based on cytogenetic characterization and directed towards a better sampling of the Amazon region, the evaluation of available names in the species synonymy and a multi-locus phylogenetic analysis.
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Affiliation(s)
- Pedro H F Peres
- Deer Research and Conservation Center (NUPECCE), São Paulo State University (UNESP), Jaboticabal, Brazil
| | - Douglas J Luduvério
- Deer Research and Conservation Center (NUPECCE), São Paulo State University (UNESP), Jaboticabal, Brazil
| | - Agda Maria Bernegossi
- Deer Research and Conservation Center (NUPECCE), São Paulo State University (UNESP), Jaboticabal, Brazil
| | - David J Galindo
- Faculty of Veterinary Medicine, National University of San Marcos (UNMSM), Lima, Peru
| | | | - Márcio L Oliveira
- Deer Research and Conservation Center (NUPECCE), São Paulo State University (UNESP), Jaboticabal, Brazil
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9
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Feijó A, Brandão MV. Taxonomy as the first step towards conservation: an appraisal on the taxonomy of medium- and large-sized Neotropical mammals in the 21st century. ZOOLOGIA 2022. [DOI: 10.1590/s1984-4689.v39.e22007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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10
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Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer. Nat Commun 2021; 12:6858. [PMID: 34824214 PMCID: PMC8617201 DOI: 10.1038/s41467-021-27091-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 10/25/2021] [Indexed: 01/23/2023] Open
Abstract
Muntjac deer have experienced drastic karyotype changes during their speciation, making it an ideal model for studying mechanisms and functional consequences of mammalian chromosome evolution. Here we generated chromosome-level genomes for Hydropotes inermis (2n = 70), Muntiacus reevesi (2n = 46), female and male M. crinifrons (2n = 8/9) and a contig-level genome for M. gongshanensis (2n = 8/9). These high-quality genomes combined with Hi-C data allowed us to reveal the evolution of 3D chromatin architectures during mammalian chromosome evolution. We find that the chromosome fusion events of muntjac species did not alter the A/B compartment structure and topologically associated domains near the fusion sites, but new chromatin interactions were gradually established across the fusion sites. The recently borne neo-Y chromosome of M. crinifrons, which underwent male-specific inversions, has dramatically restructured chromatin compartments, recapitulating the early evolution of canonical mammalian Y chromosomes. We also reveal that a complex structure containing unique centromeric satellite, truncated telomeric and palindrome repeats might have mediated muntjacs' recurrent chromosome fusions. These results provide insights into the recurrent chromosome tandem fusion in muntjacs, early evolution of mammalian sex chromosomes, and reveal how chromosome rearrangements can reshape the 3D chromatin regulatory conformations during species evolution.
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Evolution of Transmissible Spongiform Encephalopathies and the Prion Protein Gene (PRNP) in Mammals. J MAMM EVOL 2021. [DOI: 10.1007/s10914-021-09557-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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13
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Fontoura E, Ferreira JD, Bubadué J, Ribeiro AM, Kerber L. Virtual brain endocast of Antifer (Mammalia: Cervidae), an extinct large cervid from South America. J Morphol 2020; 281:1223-1240. [PMID: 32815595 DOI: 10.1002/jmor.21243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/23/2020] [Accepted: 07/17/2020] [Indexed: 01/22/2023]
Abstract
A diverse fossil record of Cervidae (Mammalia) has been documented in the South American Pleistocene, when these animals arrived during the Great American Biotic Interchange. Using computed tomography-scanning techniques, it is possible to access the endocranial morphology of extinct species. Here, we studied the brain endocast of the extinct late Pleistocene cervid Antifer ensenadensis from southern Brazil, one of the largest forms that lived on this continent, using comparative morphology, geometric morphometrics, and encephalization quotients. The analyzed endocasts demonstrate that A. ensenadensis had a gyrencephalic brain, showing a prominent longitudinal sinus (=sagittal superior sinus), which is also observed in the large South American cervid Blastocerus dichotomus. The encephalization quotient is within the variation of extant cervids, suggesting maintenance of the pattern of encephalization from at least the late Pleistocene. Geometric morphometric analysis suggested a clear and linear allometric trend between brain endocast size and shape, and highlights A. ensenadensis as an extreme form within the analyzed cervids regarding brain morphology.
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Affiliation(s)
- Emmanuelle Fontoura
- Programa de Pós-Graduação em Biodiversidade Animal, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, Brazil.,Centro de Apoio à Pesquisa Paleontológica da Quarta Colônia, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, São João do Polêsine, Brazil
| | - José Darival Ferreira
- Programa de Pós-Graduação em Biodiversidade Animal, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, Brazil.,Centro de Apoio à Pesquisa Paleontológica da Quarta Colônia, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, São João do Polêsine, Brazil
| | - Jamile Bubadué
- Programa de Pós-Graduação em Biodiversidade Animal, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, Brazil.,Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Brazil
| | - Ana Maria Ribeiro
- Seção de Paleontologia, Museu de Ciências Naturais, Secretaria do Meio Ambiente e Infraestrutura, Porto Alegre, Brazil
| | - Leonardo Kerber
- Programa de Pós-Graduação em Biodiversidade Animal, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, Brazil.,Centro de Apoio à Pesquisa Paleontológica da Quarta Colônia, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, São João do Polêsine, Brazil.,Museu Paraense Emílio Goeldi, Coordenação de Ciências da Terra e Ecologia, Belém, Brazil
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Garcia HA, Blanco PA, Rodrigues AC, Rodrigues CMF, Takata CSA, Campaner M, Camargo EP, Teixeira MMG. Pan-American Trypanosoma (Megatrypanum) trinaperronei n. sp. in the white-tailed deer Odocoileus virginianus Zimmermann and its deer ked Lipoptena mazamae Rondani, 1878: morphological, developmental and phylogeographical characterisation. Parasit Vectors 2020; 13:308. [PMID: 32532317 PMCID: PMC7291487 DOI: 10.1186/s13071-020-04169-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 06/04/2020] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The subgenus Megatrypanum Hoare, 1964 of Trypanosoma Gruby, 1843 comprises trypanosomes of cervids and bovids from around the world. Here, the white-tailed deer Odocoileus virginianus (Zimmermann) and its ectoparasite, the deer ked Lipoptena mazamae Rondani, 1878 (hippoboscid fly), were surveyed for trypanosomes in Venezuela. RESULTS Haemoculturing unveiled 20% infected WTD, while 47% (7/15) of blood samples and 38% (11/29) of ked guts tested positive for the Megatrypanum-specific TthCATL-PCR. CATL and SSU rRNA sequences uncovered a single species of trypanosome. Phylogeny based on SSU rRNA and gGAPDH sequences tightly cluster WTD trypanosomes from Venezuela and the USA, which were strongly supported as geographical variants of the herein described Trypanosoma (Megatrypanum) trinaperronei n. sp. In our analyses, the new species was closest to Trypanosoma sp. D30 from fallow deer (Germany), both nested into TthII alongside other trypanosomes from cervids (North American elk and European fallow, red and sika deer), and bovids (cattle, antelopes and sheep). Insights into the life-cycle of T. trinaperronei n. sp. were obtained from early haemocultures of deer blood and co-culture with mammalian and insect cells showing flagellates resembling Megatrypanum trypanosomes previously reported in deer blood, and deer ked guts. For the first time, a trypanosome from a cervid was cultured and phylogenetically and morphologically (light and electron microscopy) characterised. CONCLUSIONS In the analyses based on SSU rRNA, gGAPDH, CATL and ITS rDNA sequences, neither cervids nor bovids trypanosomes were monophyletic but intertwined within TthI and TthII major phylogenetic lineages. One host species can harbour more than one species/genotype of trypanosome, but each trypanosome species/genotype was found in a single host species or in phylogenetically closely related hosts. Molecular evidence that L. mazamae may transmit T. trinaperronei n. sp. suggests important evolutionary constraints making tight the tripartite T. trinaperronei-WTD-deer ked association. In a plausible evolutionary scenario, T. trinaperronei n. sp. entered South America with North American white-tailed deer at the Pliocene-Pleistocene boundary following the closure of the Panama Isthmus.
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Affiliation(s)
- Herakles A. Garcia
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP Brazil
- Department of Veterinary Pathology, Faculty of Veterinary Sciences, Central University of Venezuela, Maracay, Venezuela
| | - Pilar A. Blanco
- Department of Veterinary Pathology, Faculty of Veterinary Sciences, Central University of Venezuela, Maracay, Venezuela
- Fundación Esfera, Harpy Eagle Conservation Program in Venezuela, El Palmar, Bolívar Venezuela
- Earthmatters, Gainesville, FL USA
| | - Adriana C. Rodrigues
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP Brazil
| | - Carla M. F. Rodrigues
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP Brazil
- Instituto Nacional de Ciência e Tecnologia, INCT-EpiAmo, Porto Velho, Rondônia Brazil
| | - Carmen S. A. Takata
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP Brazil
| | - Marta Campaner
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP Brazil
| | - Erney P. Camargo
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP Brazil
- Instituto Nacional de Ciência e Tecnologia, INCT-EpiAmo, Porto Velho, Rondônia Brazil
| | - Marta M. G. Teixeira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP Brazil
- Instituto Nacional de Ciência e Tecnologia, INCT-EpiAmo, Porto Velho, Rondônia Brazil
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A new viewpoint on antlers reveals the evolutionary history of deer (Cervidae, Mammalia). Sci Rep 2020; 10:8910. [PMID: 32488122 PMCID: PMC7265483 DOI: 10.1038/s41598-020-64555-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/20/2020] [Indexed: 11/21/2022] Open
Abstract
Recent molecular phylogeny of deer revealed that the characters of antlers previously focused on are homoplasious, and antlers tend to be considered problematic for classification. However, we think antlers are important tools and reconsidered and analysed the characters and structures to use them for classification. This study developed a method to describe the branching structure of antlers by using antler grooves, which are formed on the antlers by growth, and then projecting the position of the branching directions of tines on the burr circumference. By making diagrams, comparing the branching structure interspecifically, homologous elements (tines, beams, and processes) of the antlers of 25 species of 16 genera were determined. Subsequently, ancestral state reconstruction was performed on the fixed molecular phylogenetic tree. It was revealed that Capreolinae and Cervini gained respective three-pointed antlers independently, and their subclades gained synapomorphous tines. We found new homologous and synapomorphous characters, as the antler of Eld’s deer, which has been classified in Rucervus, is structurally close to that of Elaphurus rather than that of Rucervus, consistent with molecular phylogeny. The methods of this study will contribute to the understanding of the branching structure and phylogeny of fossil species and uncover the evolutionary history of Cervidae.
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Mantellatto AMB, González S, Duarte JMB. Molecular identification of Mazama species (Cervidae: Artiodactyla) from natural history collections. Genet Mol Biol 2020; 43:e20190008. [PMID: 32215543 PMCID: PMC7197991 DOI: 10.1590/1678-4685-gmb-2019-0008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 08/02/2019] [Indexed: 11/21/2022] Open
Abstract
Natural history museum collections constitute an invaluable patrimony of
biological diversity for analysing the taxa distribution and evolution. However,
it is very common to discover taxonomic misidentification in museum collections
based on incorrect data. The aim of this research was to identify brocket deer
species (Mazama genus) using molecular markers. We collected
199 samples, performed DNA extraction and species identification using a
specific mitochondrial marker based on a fragment of cytochrome b
(Cytb) for Neotropical deer. We achieved the amplification
and sequencing of 77 specimens and verified that 26% of the skulls were wrongly
identified. Moreover, in the museum collections 57% of the specimens were only
identified as Mazama sp, and we were able to identify them by
molecular methods to the species level. Our findings clearly demonstrate the
importance of integrating molecular analyses to identify Mazama
species, since using only external morphology can result in a high probability
of errors. We recommend the selection of non-convergent morphological
characters, which together with the use of DNA collected from museum specimens
should contribute to more accurate taxonomic identifications.
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Affiliation(s)
- Aline Meira Bonfim Mantellatto
- Universidade Estadual Paulista "Júlio de Mesquota Filho" (UNESP), Faculdade de Ciências Agrárias e Veterinárias, Núcleo de Pesquisa e Conservação de Cervídeos, Jaboticabal, SP, Brazil.,Universidade Federal do Sul da Bahia, Centro de Formação em Ciências Ambientais, Laboratório de Ecologia e Conservação Marinha, Campus Sosígenes Costa, Porto Seguro, BA, Brazil
| | - Susana González
- Instituto de Investigaciones Biológicas Clemente Estable, Departamento de Biodiversidad y Genética, Montevideo, Uruguay
| | - José Maurício Barbanti Duarte
- Universidade Estadual Paulista "Júlio de Mesquota Filho" (UNESP), Faculdade de Ciências Agrárias e Veterinárias, Núcleo de Pesquisa e Conservação de Cervídeos, Jaboticabal, SP, Brazil
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Mawdsley JR. Phylogenetic Patterns Suggest Broad Susceptibility to Chronic Wasting Disease Across Cervidae. WILDLIFE SOC B 2020. [DOI: 10.1002/wsb.1059] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jonathan R. Mawdsley
- Association of Fish and Wildlife Agencies 1100 First Street NE Washington D.C. 20002 USA
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19
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de Oliveira ML, de Faria Peres PH, Gatti A, Morales-Donoso JA, Mangini PR, Duarte JMB. Faecal DNA and camera traps detect an evolutionarily significant unit of the Amazonian brocket deer in the Brazilian Atlantic Forest. EUR J WILDLIFE RES 2020. [DOI: 10.1007/s10344-020-1367-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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20
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Heckeberg NS. The systematics of the Cervidae: a total evidence approach. PeerJ 2020; 8:e8114. [PMID: 32110477 PMCID: PMC7034380 DOI: 10.7717/peerj.8114] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 10/28/2019] [Indexed: 11/22/2022] Open
Abstract
Systematic relationships of cervids have been controversial for decades. Despite new input from molecular systematics, consensus could only be partially reached. The initial, gross (sub) classification based on morphology and comparative anatomy was mostly supported by molecular data. The rich fossil record of cervids has never been extensively tested in phylogenetic frameworks concerning potential systematic relationships of fossil cervids to extant cervids. The aim of this work was to investigate the systematic relationships of extant and fossil cervids using molecular and morphological characters and make implications about their evolutionary history based on the phylogenetic reconstructions. To achieve these objectives, molecular data were compiled consisting of five nuclear markers and the complete mitochondrial genome of 50 extant and one fossil cervids. Several analyses using different data partitions, taxon sampling, partitioning schemes, and optimality criteria were undertaken. In addition, the most extensive morphological character matrix for such a broad cervid taxon sampling was compiled including 168 cranial and dental characters of 41 extant and 29 fossil cervids. The morphological and molecular data were analysed in a combined approach and other comprehensive phylogenetic reconstructions. The results showed that most Miocene cervids were more closely related to each other than to any other cervids. They were often positioned between the outgroup and all other cervids or as the sister taxon to Muntiacini. Two Miocene cervids were frequently placed within Muntiacini. Plio- and Pleistocene cervids could often be affiliated to Cervini, Odocoileini or Capreolini. The phylogenetic analyses provide new insights into the evolutionary history of cervids. Several fossil cervids could be successfully related to living representatives, confirming previously assumed affiliations based on comparative morphology and introducing new hypotheses. New systematic relationships were observed, some uncertainties persisted and resolving systematics within certain taxa remained challenging.
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Affiliation(s)
- Nicola S. Heckeberg
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
- SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Berlin, Germany
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Chen L, Qiu Q, Jiang Y, Wang K, Lin Z, Li Z, Bibi F, Yang Y, Wang J, Nie W, Su W, Liu G, Li Q, Fu W, Pan X, Liu C, Yang J, Zhang C, Yin Y, Wang Y, Zhao Y, Zhang C, Wang Z, Qin Y, Liu W, Wang B, Ren Y, Zhang R, Zeng Y, da Fonseca RR, Wei B, Li R, Wan W, Zhao R, Zhu W, Wang Y, Duan S, Gao Y, Zhang YE, Chen C, Hvilsom C, Epps CW, Chemnick LG, Dong Y, Mirarab S, Siegismund HR, Ryder OA, Gilbert MTP, Lewin HA, Zhang G, Heller R, Wang W. Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science 2019; 364:364/6446/eaav6202. [DOI: 10.1126/science.aav6202] [Citation(s) in RCA: 163] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 05/16/2019] [Indexed: 12/17/2022]
Abstract
The ruminants are one of the most successful mammalian lineages, exhibiting morphological and habitat diversity and containing several key livestock species. To better understand their evolution, we generated and analyzed de novo assembled genomes of 44 ruminant species, representing all six Ruminantia families. We used these genomes to create a time-calibrated phylogeny to resolve topological controversies, overcoming the challenges of incomplete lineage sorting. Population dynamic analyses show that population declines commenced between 100,000 and 50,000 years ago, which is concomitant with expansion in human populations. We also reveal genes and regulatory elements that possibly contribute to the evolution of the digestive system, cranial appendages, immune system, metabolism, body size, cursorial locomotion, and dentition of the ruminants.
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22
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Schilling AM, Calderón-Capote MC, Rössner GE. Variability, morphometrics, and co-variation of the os lacrimale in Cervidae. J Morphol 2019; 280:1071-1090. [PMID: 31095779 DOI: 10.1002/jmor.21002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 04/15/2019] [Accepted: 04/24/2019] [Indexed: 11/06/2022]
Abstract
In Ruminantia, the lacrimal bone forms a considerable part of the facial skeleton, and the morphology of its facial facet is highly variable when compared to other mammals. In this study, we quantify the species-specific variability in size and shape of the lacrimal facial facet in species of Cervidae (deer) and relate it to systematics and various aspects of their ecology and behavior. We sampled 143 skull specimens from 10 genera; 12 Moschus and 3 Tragulus specimens were used as outgroups. We find that size and shape of the lacrimal facial facet allow differentiating most species analyzed here, except for Mazama gouazoubira and Capreolus capreolus. Size and shape of the lacrimal facial facet vary widely across Cervidae regardless of their systematic relationships, ecology or behavior. Thus, we could not detect a unique signature of adaptational criteria in lacrimal morphology. Our data indicate that the lacrimal facial facet scales allometrically with skull size, in particular, the lacrimojugal length scales positively and the lacrimomaxillar length scales negatively. However, correlation analyses did not reveal any differences in the integration of the lacrimal bone with any specific skull module in any of the species compared. Lastly, we could not ascertain any correlation between the size and position of the preorbital depression with the size and shape of the lacrimal facial facet. We conclude that the lacrimal facial facet is highly flexible and may rapidly adjust to its surrounding bones. Its allometric growth appears to be an example of exaptation: changes in size and shape in the context of the increase of the skull length provide lacrimal contacts, in particular, a lacrimojugal one, which may serve to reduce mechanical loads resulting from increasingly larger antlers in large cervids.
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Affiliation(s)
- Ann-Marie Schilling
- SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany.,Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Gertrud E Rössner
- SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany.,Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
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Hu P, Shao Y, Xu J, Wang T, Li Y, Liu H, Rong M, Su W, Chen B, Cui S, Cui X, Yang F, Tamate H, Xing X. Genome-wide study on genetic diversity and phylogeny of five species in the genus Cervus. BMC Genomics 2019; 20:384. [PMID: 31101010 PMCID: PMC6525406 DOI: 10.1186/s12864-019-5785-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 05/08/2019] [Indexed: 01/01/2023] Open
Abstract
Background Previous investigations of phylogeny in Cervus recovered many clades without whole genomic support. Methods In this study, the genetic diversity and phylogeny of 5 species (21 subspecies/populations from C. unicolor, C. albirostris, C. nippon, C. elaphus and C. eldii) in the genus Cervus were analyzed using reduced-representation genome sequencing. Results A total of 197,543 SNPs were identified with an average sequencing depth of 16 x. A total of 21 SNP matrices for each subspecies/population and 1 matrix for individual analysis were constructed, respectively. Nucleotide diversity and heterozygosity analysis showed that all 21 subspecies/populations had different degrees of genetic diversity. C. eldii, C. unicolor and C. albirostris showed relatively high expected and observed heterozygosity, while observed heterozygosity in C. nippon was the lowest, indicating there was a certain degree of inbreeding rate in these subspecies/populations. Phylogenetic ML tree of all Cervus based on the 21 SNP matrices showed 5 robustly supported clades that clearly separate C. eldii, C. unicolor, C. albirostris, C. elaphus and C. nippon. Within C. elaphus clade, 4 subclades were well differentiated and statistically highly supported: C. elaphus (New Zealand), C. e. yarkandensis, C. c. canadensis and the other grouping the rest of C. canadensis from China. In the C. nippon clade, 2 well-distinct subclades corresponding to C. n. aplodontus and other C. nippon populations were separated. Phylogenetic reconstruction indicated that the first evolutionary event of the genus Cervus occurred approximately 7.4 millions of years ago. The split between C. elaphus and C. nippon could be estimated at around 3.6 millions of years ago. Phylogenetic ML tree of all samples based on individual SNP matrices, together with geographic distribution, have shown that there were 3 major subclades of C. elaphus and C. canadensis in China, namely C. e. yarkandensis (distributed in Tarim Basin), C. c. macneilli/C. c. kansuensis/C. c. alashanicus (distributed in middle west of China), and C. c. songaricus/C. c. sibiricus (distributed in northwest of China). Among them, C. e. yarkandensis was molecularly the most primitive subclade, with a differentiation dating back to 0.8–2.2 Myr ago. D statistical analysis showed that there was high probability of interspecific gene exchange between C. albirostris and C. eldii, C. albirostris and C. unicolor, C. nippon and C. unicolor, and there might be 2 migration events among 5 species in the genus Cervus. Conclusions Our results provided new insight to the genetic diversity and phylogeny of Cervus deer. In view of the current status of these populations, their conservation category will need to be reassessed. Electronic supplementary material The online version of this article (10.1186/s12864-019-5785-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pengfei Hu
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Yuanchen Shao
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Jiaping Xu
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Tianjiao Wang
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Yiqing Li
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Huamiao Liu
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Min Rong
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Weilin Su
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Binxi Chen
- Animal Health Supervision Institute of Hainan Province, Haikou, China
| | - Songhuan Cui
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Xuezhe Cui
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Fuhe Yang
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | | | - Xiumei Xing
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China.
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Zurano JP, Magalhães FM, Asato AE, Silva G, Bidau CJ, Mesquita DO, Costa GC. Cetartiodactyla: Updating a time-calibrated molecular phylogeny. Mol Phylogenet Evol 2019; 133:256-262. [DOI: 10.1016/j.ympev.2018.12.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 10/27/2022]
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25
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Singh B, Kumar A, Uniyal VP, Gupta SK. Complete mitochondrial genome of northern Indian red muntjac (Muntiacus vaginalis) and its phylogenetic analysis. Mol Biol Rep 2018; 46:1327-1333. [PMID: 30456740 DOI: 10.1007/s11033-018-4486-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/08/2018] [Indexed: 10/27/2022]
Abstract
We report complete mitochondrial genome of Northern Indian red muntjac, Muntiacus vaginalis, and its phylogenetic inferences. Mitogenome composition was 16,352 bp in length and its overall base composition in the circular genome was A = 33.2%, T = 29.0%, C = 24.50% and G = 13.30%. It exhibited a typical mitogenome structure, including 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes and a major non-coding control region (D-loop region). All the genes except ND6 and eight tRNA's were encoded on the heavy strand. Phylogenetic analyses showed that M. vaginalis is closely related to M. muntjak and formed a sister relationship with Elaphodus cephalophus. In view of the unclear distribution range and escalating habitat loss, it is important to identify its population genetic status. The complete mitogenome described in this study can be used in further phylogenetics, identification of extant maternal lineage, evolutionary significance unit and its genetic conservation.
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Affiliation(s)
- Bhim Singh
- Wildlife Institute of India, Dehradun, India
| | - Ajit Kumar
- Wildlife Institute of India, Dehradun, India
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Carranza J, Roldán M, Duarte JMB. Lack of mate selectivity for genetic compatibility within the red brocket deer Mazama americana complex. Mamm Biol 2018. [DOI: 10.1016/j.mambio.2017.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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27
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Mennecart B, DeMiguel D, Bibi F, Rössner GE, Métais G, Neenan JM, Wang S, Schulz G, Müller B, Costeur L. Bony labyrinth morphology clarifies the origin and evolution of deer. Sci Rep 2017; 7:13176. [PMID: 29030580 PMCID: PMC5640792 DOI: 10.1038/s41598-017-12848-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 09/14/2017] [Indexed: 11/08/2022] Open
Abstract
Deer are an iconic group of large mammals that originated in the Early Miocene of Eurasia (ca. 19 Ma). While there is some consensus on key relationships among their members, on the basis of molecular- or morphology-based analyses, or combined approaches, many questions remain, and the bony labyrinth has shown considerable potential for the phylogenetics of this and other groups. Here we examine its shape in 29 species of living and fossil deer using 3D geometric morphometrics and cladistics. We clarify several issues of the origin and evolution of cervids. Our results give new age estimates at different nodes of the tree and provide for the first time a clear distinction of stem and crown Cervidae. We unambiguously attribute the fossil Euprox furcatus (13.8 Ma) to crown Cervidae, pushing back the origin of crown deer to (at least) 4 Ma. Furthermore, we show that Capreolinae are more variable in bony labyrinth shape than Cervinae and confirm for the first time the monophyly of the Old World Capreolinae (including the Chinese water deer Hydropotes) based on morphological characters only. Finally, we provide evidence to support the sister group relationship of Megaloceros giganteus with the fallow deer Dama.
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Affiliation(s)
- Bastien Mennecart
- Nathurhistorisches Museum Basel, Augustinergasse 2, 4001, Basel, Switzerland.
| | - Daniel DeMiguel
- ICTA-ICP, Edifici Z, c/de les columnes s/n, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Barcelona, Spain
- Departamento de Ciencias de la Tierra, Área de Paleontología.Universidad de Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain
- Fundación ARAID, Zaragoza, Spain
| | - Faysal Bibi
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science Invalidenstraße 43, 10115, Berlin, Germany
| | - Gertrud E Rössner
- Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Strasse 10, 80333, Munich, Germany
| | - Grégoire Métais
- CR2P - Centre de Recherches sur la Paléobiodiversité et les Paléoenvironnements, UMR 7207, Muséum National d'Histoire Naturelle, CNRS, UPMC, Sorbonne Universités. MNHN, CP38, 8 rue Buffon, 75005, Paris, France
| | - James M Neenan
- Oxford University Museum of Natural History, Parks Road, Oxford, OX1 3PW, United Kingdom
| | - Shiqi Wang
- Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, 142 Xizhimenwai Street, Beijing, 100044, China
| | - Georg Schulz
- University of Basel, Biomaterials Science Center, Department of Biomedical Engineering, Gewerbestrasse 14, 4123, Allschwil, Switzerland
| | - Bert Müller
- University of Basel, Biomaterials Science Center, Department of Biomedical Engineering, Gewerbestrasse 14, 4123, Allschwil, Switzerland
| | - Loïc Costeur
- Nathurhistorisches Museum Basel, Augustinergasse 2, 4001, Basel, Switzerland
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Gutiérrez EE, Helgen KM, McDonough MM, Bauer F, Hawkins MTR, Escobedo-Morales LA, Patterson BD, Maldonado JE. A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling. Zookeys 2017; 697:87-131. [PMID: 29134018 PMCID: PMC5673856 DOI: 10.3897/zookeys.697.15124] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 08/30/2017] [Indexed: 11/12/2022] Open
Abstract
The taxonomy of American deer has been established almost entirely on the basis of morphological data and without the use of explicit phylogenetic methods; hence, phylogenetic analyses including data for all of the currently recognized species, even if based on a single gene, might improve current understanding of their taxonomy. We tested the monophyly of the morphology-defined genera and species of New World deer (Odocoileini) with phylogenetic analyses of mitochondrial DNA sequences. This is the first such test conducted using extensive geographic and taxonomic sampling. Our results do not support the monophyly of Mazama, Odocoileus, Pudu, M. americana, M. nemorivaga, Od. hemionus, and Od. virginianus. Mazama contains species that belong to other genera. We found a novel sister-taxon relationship between "Mazama" pandora and a clade formed by Od. hemionus columbianus and Od. h. sitkensis, and transfer pandora to Odocoileus. The clade formed by Od. h. columbianus and Od. h. sitkensis may represent a valid species, whereas the remaining subspecies of Od. hemionus appear closer to Od. virginianus. Pudu (Pudu) puda was not found sister to Pudu (Pudella) mephistophiles. If confirmed, this result will prompt the recognition of the monotypic Pudella as a distinct genus. We provide evidence for the existence of an undescribed species now confused with Mazama americana, and identify other instances of cryptic, taxonomically unrecognized species-level diversity among populations here regarded as Mazama temama, "Mazama" nemorivaga, and Hippocamelus antisensis. Noteworthy records that substantially extend the known distributions of M. temama and "M." gouazoubira are provided, and we unveil a surprising ambiguity regarding the distribution of "M." nemorivaga, as it is described in the literature. The study of deer of the tribe Odocoileini has been hampered by the paucity of information regarding voucher specimens and the provenance of sequences deposited in GenBank. We pinpoint priorities for future systematic research on the tribe Odocoileini.
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Affiliation(s)
- Eliécer E. Gutiérrez
- PPG Biodiversidade Animal, Centro de Ciências Naturais e Exatas, Av. Roraima n. 1000, Prédio 17, sala 1140-D, Universidade Federal de Santa Maria, Santa Maria, RS 97105-900, Brazil
- Departamento de Zoologia, Universidade de Brasília, 70910-900 Brasília, DF, Brazil
- Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington DC, USA
- Center for Conservation Genomics, National Zoological Park, Smithsonian Institution, Washington DC, USA
| | - Kristofer M. Helgen
- School of Biological Sciences and Environment Institute, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Molly M. McDonough
- Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington DC, USA
- Center for Conservation Genomics, National Zoological Park, Smithsonian Institution, Washington DC, USA
| | - Franziska Bauer
- Museum of Zoology, Senckenberg Natural History Collections, Dresden, Germany
| | - Melissa T. R. Hawkins
- Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington DC, USA
- Center for Conservation Genomics, National Zoological Park, Smithsonian Institution, Washington DC, USA
| | - Luis A. Escobedo-Morales
- Instituto de Biología, Universidad Nacional Autónoma de México, circuito exterior s/n, Ciudad Universitaria, Coyoacán, CP04510, Mexico City, Mexico
| | - Bruce D. Patterson
- Integrative Research Center, Field Museum of Natural History, Chicago, IL60605, USA
| | - Jesús E. Maldonado
- Center for Conservation Genomics, National Zoological Park, Smithsonian Institution, Washington DC, USA
- Environmental Science & Policy, George Mason University, 4400 University Dr., Fairfax, VA 22030, USA
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