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Bernegossi AM, Galindo DJ, Peres PHF, Vozdova M, Cernohorska H, Kubickova S, Kadlcikova D, Rubes J, Duarte JMB. Comparative karyotype analysis of the red brocket deer (M. americana sensu lato and M. rufa) complex: evidence of drastic chromosomal evolution and implications on speciation process. J Appl Genet 2024; 65:601-614. [PMID: 38662189 DOI: 10.1007/s13353-024-00861-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/14/2024] [Accepted: 03/21/2024] [Indexed: 04/26/2024]
Abstract
Chromosomal rearrangements are often associated with playing a role in the speciation process. However, the underlying mechanism that favors the genetic isolation associated with chromosomal changes remains elusive. In this sense, the genus Mazama is recognized by its high level of karyotype diversity among species with similar morphology. A cryptic species complex has been identified within the genus, with the red brocket deer (Mazama americana and Mazama rufa) being the most impressive example. The chromosome variation was clustered in cytotypes with diploid numbers ranging from 42 to 53 and was correlated with geographical location. We conducted an analysis of chromosome evolution of the red brocket deer complex using comparative chromosome painting and Bacterial Artificial Chromosome (BAC) clones among different cytotypes. The aim was to deepen our understanding of the karyotypic relationships within the red brocket, thereby elucidating the significant chromosome variation among closely related species. This underscores the significance of chromosome changes as a key evolutionary process shaping their genomes. The results revealed the presence of three distinct cytogenetic lineages characterized by significant karyotypic divergence, suggesting the existence of efficient post-zygotic barriers. Tandem fusions constitute the main mechanism driving karyotype evolution, following a few centric fusions, inversion X-autosomal fusions. The BAC mapping has improved our comprehension of the karyotypic relationships within the red brocket deer complex, prompting questions regarding the role of these changes in the speciation process. We propose the red brocket as a model group to investigate how chromosomal changes contribute to isolation and explore the implications of these changes in taxonomy and conservation.
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Affiliation(s)
- Agda Maria Bernegossi
- Deer Research and Conservation Center (NUPECCE), School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, Sao Paulo, 14884-900, Brazil
| | - David Javier Galindo
- Deer Research and Conservation Center (NUPECCE), School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, Sao Paulo, 14884-900, Brazil.
- Laboratory of Animal Reproduction, Faculty of Veterinary Medicine, National University of San Marcos, San Borja, 15021, Lima, Peru.
| | - Pedro Henrique Faria Peres
- Deer Research and Conservation Center (NUPECCE), School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, Sao Paulo, 14884-900, Brazil
| | - Miluse Vozdova
- Central European Institute of Technology-Veterinary Research Institute, 621 00, Brno, Czech Republic
| | - Halina Cernohorska
- Central European Institute of Technology-Veterinary Research Institute, 621 00, Brno, Czech Republic
| | - Svatava Kubickova
- Central European Institute of Technology-Veterinary Research Institute, 621 00, Brno, Czech Republic
| | - Dita Kadlcikova
- Central European Institute of Technology-Veterinary Research Institute, 621 00, Brno, Czech Republic
| | - Jiri Rubes
- Central European Institute of Technology-Veterinary Research Institute, 621 00, Brno, Czech Republic
| | - José Maurício Barbanti Duarte
- Deer Research and Conservation Center (NUPECCE), School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, Sao Paulo, 14884-900, Brazil.
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Ulloa GM, Greenwood AD, Cornejo OE, Monteiro FOB, Scofield A, Santolalla Robles ML, Lescano AG, Mayor P. Phylogenetic congruence of Plasmodium spp. and wild ungulate hosts in the Peruvian Amazon. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 118:105554. [PMID: 38246398 PMCID: PMC11331447 DOI: 10.1016/j.meegid.2024.105554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/11/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024]
Abstract
Malaria parasites are known to infect a variety of vertebrate hosts, including ungulates. However, ungulates of Amazonia have not been investigated. We report for the first time, the presence of parasite lineages closely related to Plasmodium odocoilei clade 1 and clade 2 in free-ranging South American red-brocket deer (Mazama americana; 44.4%, 4/9) and gray-brocket deer (Mazama nemorivaga; 50.0%, 1/2). We performed PCR-based analysis of blood samples from 47 ungulates of five different species collected during subsistence hunting by an indigenous community in the Peruvian Amazon. We detected Plasmodium malariae/brasilianum lineage in a sample from red-brocket deer. However, no parasite DNA was detected in collared peccary (Pecari tajacu; 0.0%, 0/10), white-lipped peccary (Tayassu pecari; 0.0%, 0/15), and tapir (Tapirus terrestris; 0.0%, 0/11). Concordant phylogenetic analyses suggested a possible co-evolutionary relationship between the Plasmodium lineages found in American deer and their hosts.
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Affiliation(s)
- Gabriela M Ulloa
- Departament de Sanitat i d'Anatomia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, Edifici V, Bellaterra-Barcelona E-08193, Spain; Programa de Pós-Graduação em Saúde e Produção Animal na Amazônia, Universidade Federal Rural da Amazônia (UFRA), Av. Presidente Tancredo Neves 2501, Terra Firme, Belém 66077-830, Pará, Brazil; Grupo de Enfermedades Infecciosas Re-Emergentes, Universidad Científica del Sur (UCSUR), Lima, Peru.
| | - Alex D Greenwood
- Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Strasse 17, Berlin 10315, Germany; School of Veterinary Medicine, Freie Universität Berlin, Oertzenweg 19b, 14163, Germany
| | - Omar E Cornejo
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States of America
| | - Frederico Ozanan Barros Monteiro
- Programa de Pós-Graduação em Saúde e Produção Animal na Amazônia, Universidade Federal Rural da Amazônia (UFRA), Av. Presidente Tancredo Neves 2501, Terra Firme, Belém 66077-830, Pará, Brazil
| | - Alessandra Scofield
- Laboratory of Animal Parasitology, Postgraduate Program in Animal Health in the Amazon, Institute of Veterinary Medicine, Federal University of Pará, Castanhal, Brazil
| | - Meddly L Santolalla Robles
- Emerge, Research Unit on Emerging Diseases and Climate Change, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Andres G Lescano
- Emerge, Research Unit on Emerging Diseases and Climate Change, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Pedro Mayor
- Departament de Sanitat i d'Anatomia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, Edifici V, Bellaterra-Barcelona E-08193, Spain; Programa de Pós-Graduação em Saúde e Produção Animal na Amazônia, Universidade Federal Rural da Amazônia (UFRA), Av. Presidente Tancredo Neves 2501, Terra Firme, Belém 66077-830, Pará, Brazil; Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica (COMFAUNA), 332 Malecon Tarapaca, Iquitos, Peru; Museo de Culturas Indígenas Amazónicas, Loreto, Iquitos, Peru.
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3
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Hrabina P, Pernerová L, Suchomel J, Robovský J. Utility of cytochrome c oxidase I for the deciphering of unstable phylogeny and taxonomy of gorals, genus Nemorhaedus Hamilton Smith, 1827 (Bovidae, Ovibovina). Zookeys 2023; 1181:81-110. [PMID: 38313159 PMCID: PMC10838175 DOI: 10.3897/zookeys.1181.108019] [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: 06/14/2023] [Accepted: 09/04/2023] [Indexed: 02/06/2024] Open
Abstract
Gorals represent ungulate mammals of the Palearctic and Indo-Malayan realms that face habitat destruction and intense hunting pressure. Their classification has been the subject of various (mainly genetic) assessments in the last decade, but some results are conflicting, hampering some conservation-based decisions. Genetic sampling of gorals has increased considerably in recent years, at least for mitochondrial (mt) DNA. Results based on two mt genes (cytochrome b and the D-loop) are currently available. Still, the utility of cytochrome oxidase subunit I remains unanalysed, even though it belongs among the gene markers that enable a correct species identification in mammals. This study examines phylogenetic relationships and species delimitation in gorals using all currently available cytochrome oxidase subunit I sequences, including the not yet analysed goral population from Pakistan. Our results of various phylogenetic approaches, such as maximum parsimony, likelihood and Bayesian inference, and exploration of species boundaries via species delimitation support the validity of six species of goral, namely N.baileyi, N.caudatus, N.cranbrooki, N.evansi, N.goral, and N.griseus. This result accords well with results based on other mt genes, especially the cytochrome b from the highly exhaustive data sampling. Our study also summarises common sources of errors in the assessment of goral phylogeny and taxonomy and highlights future priorities in understanding goral diversification.
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Affiliation(s)
- Petr Hrabina
- Department of Zoology, Fisheries, Hydrobiology and Apiculture, Mendel University in Brno, Zemědělská 1, Brno, 61300, Czech Republic Mendel University in Brno Brno Czech Republic
| | - Ludmila Pernerová
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, 37005, Czech Republic University of South Bohemia České Budějovice Czech Republic
| | - Josef Suchomel
- Department of Zoology, Fisheries, Hydrobiology and Apiculture, Mendel University in Brno, Zemědělská 1, Brno, 61300, Czech Republic Mendel University in Brno Brno Czech Republic
| | - Jan Robovský
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, 37005, Czech Republic University of South Bohemia České Budějovice Czech Republic
- Liberec Zoo, Lidové sady 425/1, Liberec, 46001, Czech Republic Liberec Zoo Liberec Czech Republic
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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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Sandoval EDP, Vacari GQ, Juliá JP, González S, Vozdova M, Cernohorska H, Kubickova S, Kalthoff DC, Duarte JMB. Assessing the Taxonomic Status of the Gray Brocket Mazama simplicicornis argentina Lönnberg, 1919 (Artiodactyla: Cervidae). Zool Stud 2023; 62:e30. [PMID: 37671175 PMCID: PMC10475465 DOI: 10.6620/zs.2023.62-30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 04/28/2023] [Indexed: 09/07/2023]
Abstract
Mazama simplicicornis argentina is the name that was given to describe a gray brocket collected by Lönberg in 1919 in the central Chaco region of Argentina. Subsequent authors, based on morphological similarities, considered this name to be a synonym for the species Subulo gouazoubira Fischer, 1814 from Paraguay. In the absence of genetic analyses to compare the Argentinian and Paraguayan gray brockets, we aimed to clarify the taxonomy of M. simplicicornis argentina through an integrative assessment using morphological, cytogenetical, and molecular data from its holotype and a current topotype. Qualitative skull features and cranio-morphometric results of M. simplicicornis argentina showed a great similarity with the S. gouazoubira neotype characters. The diploid chromosome number of M. simplicicornis argentina topotype corresponded with the karyotypical pattern of S. gouazoubira with 2n = 70 and FN = 70, showing a great similarity in all classic and molecular cytogenetic results and revealing the homologies between karyotypes. The phylogenetic analysis of mitochondrial genes used in this study (concatenated partial ND5 and Cytb gene) allocated the M. simplicicornis argentina specimens in the monophyletic clade of S. gouazoubira with a branch value of 100%. These results show that there is no discontinuity between the Argentinian and Paraguayan gray brockets. Therefore, the individuals originally described as M. simplicicornis argentina should be recognized as S. gouazoubira.
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Affiliation(s)
- Eluzai Dinai Pinto Sandoval
- Núcleo de Pesquisa e Conservação de Cervídeos (NUPECCE), Faculdade de Ciências Agrárias e Veterinárias da Universidade Estadual Paulista (UNESP), Jaboticabal-SP, Brazil. E-mail: (Duarte); (Sandoval); (Vacari)
| | - Gabrielle Queiroz Vacari
- Núcleo de Pesquisa e Conservação de Cervídeos (NUPECCE), Faculdade de Ciências Agrárias e Veterinárias da Universidade Estadual Paulista (UNESP), Jaboticabal-SP, Brazil. E-mail: (Duarte); (Sandoval); (Vacari)
| | - Juan Pablo Juliá
- Facultad de Ciencias Naturales. Universidad Nacional de Tucumán, Argentina. E-mail: (Juliá)
| | - Susana González
- Departamento de Biodiversidad y Genética, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay. E-mail: (González)
| | - Miluse Vozdova
- Veterinary Research Institute, Brno, Czech Republic. E-mail: (Vozdova); (Cernohorska); (Kubickova)
| | - Halina Cernohorska
- Veterinary Research Institute, Brno, Czech Republic. E-mail: (Vozdova); (Cernohorska); (Kubickova)
| | - Svatava Kubickova
- Veterinary Research Institute, Brno, Czech Republic. E-mail: (Vozdova); (Cernohorska); (Kubickova)
| | - Daniela C Kalthoff
- Swedish Museum of Natural History, Frescativägen 40, Stockholm, Sweden. E-mail: (Kalthoff)
| | - José Mauricio Barbanti Duarte
- Núcleo de Pesquisa e Conservação de Cervídeos (NUPECCE), Faculdade de Ciências Agrárias e Veterinárias da Universidade Estadual Paulista (UNESP), Jaboticabal-SP, Brazil. E-mail: (Duarte); (Sandoval); (Vacari)
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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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Filip E, Strzała T, Stępień E, Cembrowska-Lech D. Universal mtDNA fragment for Cervidae barcoding species identification using phylogeny and preliminary analysis of machine learning approach. Sci Rep 2023; 13:9133. [PMID: 37277428 DOI: 10.1038/s41598-023-35637-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/21/2023] [Indexed: 06/07/2023] Open
Abstract
The aim of the study was to use total DNA obtained from bone material to identify species of free-living animals based on the analysis of mtDNA fragments by molecular methods using accurate bioinformatics tools Bayesian approach and the machine learning approach. In our research, we present a case study of successful species identification based on degraded samples of bone, with the use of short mtDNA fragments. For better barcoding, we used molecular and bioinformatics methods. We obtained a partial sequence of the mitochondrial cytochrome b (Cytb) gene for Capreolus capreolus, Dama dama, and Cervus elaphus, that can be used for species affiliation. The new sequences have been deposited in GenBank, enriching the existing Cervidae mtDNA base. We have also analysed the effect of barcodes on species identification from the perspective of the machine learning approach. Machine learning approaches of BLOG and WEKA were compared with distance-based (TaxonDNA) and tree-based (NJ tree) methods based on the discrimination accuracy of the single barcodes. The results indicated that BLOG and WEKAs SMO classifier and NJ tree performed better than TaxonDNA in discriminating Cervidae species, with BLOG and WEKAs SMO classifier performing the best.
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Affiliation(s)
- Ewa Filip
- Institute of Biology, University of Szczecin, Wąska 13, 71-415, Szczecin, Poland.
- The Centre for Molecular Biology and Biotechnology, University of Szczecin, Szczecin, Poland.
| | - Tomasz Strzała
- Department of Genetics, Faculty of Biology and Animal Science, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Edyta Stępień
- Institute of Marine and Environmental Sciences, University of Szczecin, Adama Mickiewicza 16, 70-383, Szczecin, Poland
| | - Danuta Cembrowska-Lech
- Institute of Biology, University of Szczecin, Wąska 13, 71-415, Szczecin, Poland
- Sanprobi Sp. z o. o. Sp. k., Kurza Stopka 5C, 70-535, Szczecin, Poland
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Escobedo-Morales LA, Castañeda-Rico S, Mandujano S, León-Paniagua L, Maldonado JE. First description of the mitochondrial genomes of the Central American brocket deer Mazama temama (Kerr, 1792) and the Yucatán Peninsula brocket deer Odocoileus pandora Merriam, 1901. Mol Biol Rep 2023; 50:4851-4863. [PMID: 37039999 DOI: 10.1007/s11033-023-08407-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/24/2023] [Indexed: 04/12/2023]
Abstract
BACKGROUND The Central American (Mazama temama) and the Yucatán Peninsula brocket deer (Odocoileus pandora) are deer species with cryptic habits, and little is known about their biology. Odocoileus pandora is listed as Vulnerable on the 2015 IUCN Red List of Threatened Species, while M. temama is considered Data Deficient; however, it currently faces a decreasing population trend. METHODS AND RESULTS We assembled the complete mitochondrial genome for two M. temama specimens and one complete and one partial for O. pandora from Illumina 150 bp paired-end reads. The mitogenomes of M. temama and O. pandora have a length of 16,479-16,480 and 16,419 bp, respectively, AT-biased; they consist of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one non-coding control region, most of them follow a transcription direction in the heavy strand of the molecule. The mitochondrial genome of O. pandora shows some particularities compared to other deer species, like a shorter control region of 987-990 bp and a cytochrome b gene with a length of 1,143 bp. Our phylogenetic analyses confirm the close affinity of M. temama to South American M. americana and the nested position of the genus Odocoileus, including O. pandora, into the genus Mazama. CONCLUSIONS Here, we described for the first time the complete mitochondrial genome for these two species. While our study provides additional information about the taxonomic status of the northern neotropical brocket deer, further research is needed to solve the complicated taxonomy of neotropical deer.
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Affiliation(s)
- Luis A Escobedo-Morales
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Edificio D, Primer piso, Circuito de Posgrados, AP 70-153, Ciudad Universitaria, Mexico City, 04510, Mexico.
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, 3001 Connecticut Ave., NW, Washington, DC, 20008, USA.
| | - Susette Castañeda-Rico
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, 3001 Connecticut Ave., NW, Washington, DC, 20008, USA
- Smithsonian-Mason School of Conservation, 1500 Remount Road, Front Royal, VA, 22630, USA
- Department of Biology, George Mason University, 4400 University Drive, Fairfax, VA, 22030, USA
| | - Salvador Mandujano
- Red de Biología y Conservación de Vertebrados, Instituto de Ecología, A.C., Carretera antigua a Coatepec 351, Xalapa, Veracruz, 91070, Mexico
| | - Livia León-Paniagua
- Museo de Zoología Alfonso L. Herrera, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Mexico City, 04510, Mexico
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, 3001 Connecticut Ave., NW, Washington, DC, 20008, USA
- Smithsonian-Mason School of Conservation, 1500 Remount Road, Front Royal, VA, 22630, USA
- Department of Biology, George Mason University, 4400 University Drive, Fairfax, VA, 22030, USA
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9
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Browsing into a Panamanian tropical rainforest: micro- and mesowear study of Central American red brocket deer. MAMMAL RES 2023. [DOI: 10.1007/s13364-023-00676-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
AbstractThe Mazama genus is one of the more diverse genera among deer (Cervidae); its classification is controversial because of its complex phylogenetic relationships. The Central American red brocket deer (Mazama temama) is distributed from Central America to the northwest of South America. Studying the diet of mammals gives us information about the environment in which they live, considering that animals select food according to the resources available in the surrounding environment. Mesowear and microwear provide complementary data because they present direct evidence of feeding behaviour on different time scales. The use of extant animals as control samples or baselines allows for the interpretation of the results of a study performed using the archaeological record. For this reason, the aim of this paper was to study the diet of extant M. temama from Darien and to compare it with our previous results on ancient deer from Pedro Gonzalez Island archaeological site (6060–5620 cal yr BP) and extant individuals from San Jose Island (Panama). Evidence from the meso- and microwear analyses of M. temama from Darien suggests that they were browse-dominated mixed feeders during the last years of their lives and during the days before their death. There was no evidence of seasonal variation in their diets and between sexes. This paper exemplifies the potential of studying extant materials housed in museum collections as a reference to compare them to archaeological remains. The use of the same methods allows to construct baselines to better understand the archaeological record in the Neotropics.
Graphical Abstract
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10
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Oliveira MLD, Peres PHDF, Grotta-Neto F, Vogliotti A, Passos FDC, Duarte JMB. Using niche modelling and human influence index to indicate conservation priorities for Atlantic forest deer species. J Nat Conserv 2022. [DOI: 10.1016/j.jnc.2022.126262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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11
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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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12
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Harding LE. Available names for Rangifer (Mammalia, Artiodactyla, Cervidae) species and subspecies. Zookeys 2022; 1119:117-151. [PMID: 36762356 PMCID: PMC9848878 DOI: 10.3897/zookeys.1119.80233] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 07/19/2022] [Indexed: 11/12/2022] Open
Abstract
Advancements in molecular and phylogenetic analysis have revealed the need for greater taxonomic resolution since Rangifer (Reindeer and caribou: Cervidae) was last revised in 1961. Recent literature shows that many of the subspecies and several species synonymised out of existence are, in fact, valid, some names have been misapplied, and new subspecies-level clades are in need of description. This paper reviews available names for recently defined ecotypes of reindeer and caribou in compliance with ICZN rules for zoological nomenclature.
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Affiliation(s)
- Lee E. Harding
- 2339 Sumpter Drive, Coquitlam, BC, V3J 6Y3, Coquitlam, CanadaunaffiliatedCoquitlamCanada
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13
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The phytogeography and genetic diversity of the weedy hydrophyte, Pistia stratiotes L. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02798-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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14
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Wright EA, Roberts EK, Platt RN, Bayouth JV, Conway WC, Bradley RD. Mitochondrial capture and subsequent genetic divergence generates a novel haplogroup: evidence from ancient and ongoing hybridization in mule and white-tailed deer. J Mammal 2022. [DOI: 10.1093/jmammal/gyab156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Odocoileus virginianus (white-tailed deer) and O. hemionus (mule deer) are sympatric across much of North America. Molecular evidence suggests that up to 24% of individuals in some populations are a product of hybrid ancestry. Several studies have alluded to ancient and recent introgression between Odocoileus spp.; however, no divergence dates were proposed. Herein, phylogenetic analyses of DNA sequences obtained from the mitochondrial Cytochrome b gene in 690 individuals identified three clades corresponding to black-tailed deer, white-tailed deer, or a unique combination of both white-tailed deer and mule deer. White-tailed deer and mule deer diverged from a common ancestor of approximately 3.13 mya followed by an ancient hybridization event of approximately 1.32 mya, in which the white-tailed deer mitochondrial genome was “captured” by mule deer. This hybridization event produced a novel haplogroup for white-tailed deer and mule deer located west of the Appalachian Mountains and east of the Cascade Range, south to Veracruz, Mexico, and north to the Yukon Territory, Canada. The ancestral mule deer-like mitochondrial genome appears to be restricted to black-tailed deer distributed along the western portion of the Cascade and Sierra Nevada Ranges of the United States and Canada, whereas the ancestral white-tailed deer-like mitochondrial genome is restricted to the eastern United States and portions of Latin America and Caribbean regions. The “captured mitochondrial genome” has continued on an independent evolutionary trajectory and represents a unique and broadly distributed haplogroup that is 7.25% and 2.84% different from the ancestral mule deer and ancestral white-tailed deer haplogroups, respectively.
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Affiliation(s)
- Emily A Wright
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas 79409, USA
| | - Emma K Roberts
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas 79409, USA
| | - Roy N Platt
- Host Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, Texas 78258, USA
| | - Jacob V Bayouth
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas 79409, USA
| | - Warren C Conway
- Department of Natural Resources Management, Texas Tech University, Lubbock, Texas 79410, USA
| | - Robert D Bradley
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas 79409, USA
- Natural Science Research Laboratory at the Museum of Texas Tech University, Lubbock, Texas 79415, USA
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15
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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: 2] [Impact Index Per Article: 1.0] [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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16
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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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17
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Mantellatto AMB, González S, Duarte JMB. Cytochrome b sequence of the Mazama americana jucunda Thomas, 1913 holotype reveals Mazama bororo Duarte, 1996 as its junior synonym. Genet Mol Biol 2021; 45:e20210093. [PMID: 34919117 PMCID: PMC8679242 DOI: 10.1590/1678-4685-gmb-2021-0093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 09/21/2021] [Indexed: 11/22/2022] Open
Abstract
The small red brocket deer, Mazama bororo Duarte, 1996 was described based on karyotypical and morphological characters. However, the original description of Mazama americana jucunda suggested that this subspecies could represent the same taxon as Mazama bororo. This assumption was based on the type locality of Mazama americana jucunda and on morphological similarities between Mazama americana jucunda and Mazama bororo. To solve this question, we obtained DNA sequences of the holotype of Mazama americana jucunda and compared it with other species of Mazama, including the holotype of M. bororo. A phylogenetic tree was obtained to verify the relationships among these taxa. The results clearly showed that M. americana jucunda and M. bororo represent the same biological entity. Therefore, the oldest name available for the small red brocket occurring in the Atlantic Forest of southern Brazil should be Mazama jucunda, remaining M. bororo as a junior synonym. We emphasise the importance of using DNA from museum specimens, especially from holotypes, in order to obtain a more accurate taxonomic identification. We also highlight the importance of application of valid names for labelling all aspects of biodiversity research, as well as for monitoring and conservation efforts.
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Affiliation(s)
- Aline Meira Bonfim Mantellatto
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, Núcleo de Pesquisa e Conservação de Cervídeos, Jaboticabal, SP, Brazil
| | - Susana González
- Instituto de Investigaciones Biológicas Clemente Estable, Departamento de Biodiversidad y Genética, Montevideo, Uruguay
| | - José Maurício Barbanti Duarte
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, Núcleo de Pesquisa e Conservação de Cervídeos, Jaboticabal, SP, Brazil
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18
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Diaz EA, Donoso G, Saenz C, Aponte PM. Spermatogenesis in a vulnerable South American cervid, dwarf red brocket (Mazama rufina). Anat Histol Embryol 2021; 51:91-102. [PMID: 34820886 DOI: 10.1111/ahe.12766] [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: 08/23/2021] [Revised: 10/12/2021] [Accepted: 11/15/2021] [Indexed: 11/29/2022]
Abstract
The brocket deer (Genus Mazama) is a highly diverse cervid group distributed from Mexico to Argentina, with a downward population trend. However, literature on the basic reproductive biology of the genus is scarce. This work aimed to study biometric, histological and stereological aspects of the testes of Dwarf Red Brocket (Mazama rufina). Testes from free-ranging adult brockets (n = 3) were retrieved from necropsies. Testes were histologically processed. From histological images, several stereological parameters were estimated, and seminiferous epithelium cycle morphology was described. Testes volumes were between 8.2 and 18.4 ml and weights from 8.3 to 19.4 g. Gonadosomatic index (% paired-testes weight to body weight) went from 0.17 to 0.64. The tubular cross-sectional diameter was 179.8 ± 2.8 µm. Estimated volume densities for parenchyma and interstitium were 78.8% and 21.2% respectively. There were (in millions/ml) 96.0 ± 13.1 germ cells and 37.7 ± 6.0 somatic cells. Specific cell densities were (all expressed in millions/ml) as follows: spermatogonia 13.1 ± 4.2; primary spermatocytes 43.1 ± 5.0; round spermatids 36.8 ± 8.0 (lower density near the caudal pole, p < 0.01); sustentacular (Sertoli) cells 16.8 ± 4.1 and interstitial endocrine (Leydig) cells 17.4 ± 3.4. Sertoli cell index (germ cells per Sertoli cell) was 6.72. Eight stages of the cycle were described, and frequencies estimated, resembling those of goats. M. rufina adult testis anatomy is similar to that of other cervids and domestic ruminants, with an apparently lower spermatogenic efficiency. This work is a first approximation to the physiology of the testis of M. rufina. Basic knowledge of the reproductive physiology of vulnerable species may allow biotechnological approaches for the restitution of animal populations.
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Affiliation(s)
- Eduardo A Diaz
- Escuela de Medicina Veterinaria, Colegio de Ciencias de la Salud, Universidad San Francisco de Quito (USFQ), Quito, Ecuador.,Hospital de Fauna Silvestre Tueri, Instituto iBIOTROP, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Gustavo Donoso
- Hospital de Fauna Silvestre Tueri, Instituto iBIOTROP, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Carolina Saenz
- Hospital de Fauna Silvestre Tueri, Instituto iBIOTROP, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Pedro M Aponte
- Escuela de Medicina Veterinaria, Colegio de Ciencias de la Salud, Universidad San Francisco de Quito (USFQ), Quito, Ecuador.,Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito, Ecuador.,Instituto de Investigaciones en Biomedicina iBIOMED, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
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19
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Elusive deer occurrences at the Atlantic Forest: 20 years of surveys. MAMMAL RES 2021. [DOI: 10.1007/s13364-021-00604-4] [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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20
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Vozdova M, Kubickova S, Martínková N, Galindo DJ, Bernegossi AM, Cernohorska H, Kadlcikova D, Musilová P, Duarte JM, Rubes J. Satellite DNA in Neotropical Deer Species. Genes (Basel) 2021; 12:genes12010123. [PMID: 33478071 PMCID: PMC7835801 DOI: 10.3390/genes12010123] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 01/04/2023] Open
Abstract
The taxonomy and phylogenetics of Neotropical deer have been mostly based on morphological criteria and needs a critical revision on the basis of new molecular and cytogenetic markers. In this study, we used the variation in the sequence, copy number, and chromosome localization of satellite I-IV DNA to evaluate evolutionary relationships among eight Neotropical deer species. Using FISH with satI-IV probes derived from Mazama gouazoubira, we proved the presence of satellite DNA blocks in peri/centromeric regions of all analyzed deer. Satellite DNA was also detected in the interstitial chromosome regions of species of the genus Mazama with highly reduced chromosome numbers. In contrast to Blastocerus dichotomus, Ozotoceros bezoarticus, and Odocoileus virginianus, Mazama species showed high abundance of satIV DNA by FISH. The phylogenetic analysis of the satellite DNA showed close relationships between O. bezoarticus and B. dichotomus. Furthermore, the Neotropical and Nearctic populations of O. virginianus formed a single clade. However, the satellite DNA phylogeny did not allow resolving the relationships within the genus Mazama. The high abundance of the satellite DNA in centromeres probably contributes to the formation of chromosomal rearrangements, thus leading to a fast and ongoing speciation in this genus, which has not yet been reflected in the satellite DNA sequence diversification.
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Affiliation(s)
- Miluse Vozdova
- Department of Genetics and Reproductive Biotechnologies, Central European Institute of Technology—Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (S.K.); (H.C.); (D.K.); (P.M.); (J.R.)
- Correspondence: ; Tel.: +4205-3333-1422
| | - Svatava Kubickova
- Department of Genetics and Reproductive Biotechnologies, Central European Institute of Technology—Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (S.K.); (H.C.); (D.K.); (P.M.); (J.R.)
| | - Natália Martínková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Kvetna 8, 603 65 Brno, Czech Republic;
| | - David Javier Galindo
- Deer Research and Conservation Center (NUPECCE), School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), 14884-900 Jaboticabal, Brazil; (D.J.G.); (A.M.B.); (J.M.D.)
| | - Agda Maria Bernegossi
- Deer Research and Conservation Center (NUPECCE), School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), 14884-900 Jaboticabal, Brazil; (D.J.G.); (A.M.B.); (J.M.D.)
| | - Halina Cernohorska
- Department of Genetics and Reproductive Biotechnologies, Central European Institute of Technology—Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (S.K.); (H.C.); (D.K.); (P.M.); (J.R.)
| | - Dita Kadlcikova
- Department of Genetics and Reproductive Biotechnologies, Central European Institute of Technology—Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (S.K.); (H.C.); (D.K.); (P.M.); (J.R.)
| | - Petra Musilová
- Department of Genetics and Reproductive Biotechnologies, Central European Institute of Technology—Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (S.K.); (H.C.); (D.K.); (P.M.); (J.R.)
| | - Jose Mauricio Duarte
- Deer Research and Conservation Center (NUPECCE), School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), 14884-900 Jaboticabal, Brazil; (D.J.G.); (A.M.B.); (J.M.D.)
| | - Jiri Rubes
- Department of Genetics and Reproductive Biotechnologies, Central European Institute of Technology—Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (S.K.); (H.C.); (D.K.); (P.M.); (J.R.)
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22
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Araujo Perini F, Quintaneiro Mota J. New records of Odocoileus virginianus Zimmermann 1780 (Artiodactyla: Cervidae) from northern Brazil. MAMMALOGY NOTES 2020. [DOI: 10.47603/mano.v6n2.168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We report new records of the White-Tailed Deer (Odocoileus virginianus) in Brazil based on specimens deposited in scientific collections. These new records expand the known geographic distribution of the species in Brazil southwards in the states of Roraima and Amapá, the latter the first record of the species below the equator line in Brazil, and register it for the first time in the state of Amazonas. These records contribute to increase the knowledge of the geographical distribution of O. virginianus in Brazil and highlights the importance of museum collections as a source of biogeographic and ecological data.
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23
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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: 0.3] [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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Cifuentes-Rincón A, Morales-Donoso JA, Sandoval EDP, Tomazella IM, Mantellatto AMB, de Thoisy B, Duarte JMB. Designation of a neotype for Mazama americana (Artiodactyla, Cervidae) reveals a cryptic new complex of brocket deer species. Zookeys 2020; 958:143-164. [PMID: 32863720 PMCID: PMC7434805 DOI: 10.3897/zookeys.958.50300] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 05/18/2020] [Indexed: 11/29/2022] Open
Abstract
Mazamaamericana (red brocket deer) is the genus-type species (first species described for this genus) and the basis for the identity of other Mazama species. Mazamaamericana is one of the most abundant and widely distributed deer species in the neotropical forest. However, recent studies suggest that this taxon belongs to a species complex. Our goal was to collect an animal at the type locality (topotype) in French Guiana with the aim of characterizing the morphological (biometric, craniometric), cytogenetic (Giemsa, C-banding, G-banding and NOR) and molecular (mitochondrial DNA) features. The comparisons showed that the collected specimen was very similar morphologically to specimens from other South American populations, but it was cytogenetically and molecularly very different from any of the cytotypes already described for this species, corroborating the existence of a complex of cryptic species. The data suggest that the M.americana topotype is a different species from all the cytotypes already described in the literature and which occupy the southern region of the Amazon River. The characterization and designation of the M.americana neotype is the first step toward a taxonomic reorganization of the genus Mazama, with the potential identification of new species.
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Affiliation(s)
- Analorena Cifuentes-Rincón
- Núcleo de Pesquisa e Conservação de Cervídeos (NUPECCE), Faculdade de Ciências Agrárias e Veterinárias da Universidade Estadual Paulista (UNESP), Via de Acesso Paulo Donato Castellane, s/n CEP: 14884-900, Jaboticabal-SP, Brazil Universidade Estadual Paulista Jaboticabal Brazil
| | - Jorge Alfonso Morales-Donoso
- Núcleo de Pesquisa e Conservação de Cervídeos (NUPECCE), Faculdade de Ciências Agrárias e Veterinárias da Universidade Estadual Paulista (UNESP), Via de Acesso Paulo Donato Castellane, s/n CEP: 14884-900, Jaboticabal-SP, Brazil Universidade Estadual Paulista Jaboticabal Brazil
| | - Eluzai Dinai Pinto Sandoval
- Núcleo de Pesquisa e Conservação de Cervídeos (NUPECCE), Faculdade de Ciências Agrárias e Veterinárias da Universidade Estadual Paulista (UNESP), Via de Acesso Paulo Donato Castellane, s/n CEP: 14884-900, Jaboticabal-SP, Brazil Universidade Estadual Paulista Jaboticabal Brazil
| | - Iara Maluf Tomazella
- Núcleo de Pesquisa e Conservação de Cervídeos (NUPECCE), Faculdade de Ciências Agrárias e Veterinárias da Universidade Estadual Paulista (UNESP), Via de Acesso Paulo Donato Castellane, s/n CEP: 14884-900, Jaboticabal-SP, Brazil Universidade Estadual Paulista Jaboticabal Brazil
| | - Aline Meira Bonfim Mantellatto
- Universidade Federal do Sul da Bahia, Campus Sosígenes Costa, Porto Seguro, BA, CEP: 45810-000, Brazil Universidade Federal do Sul da Bahia Porto Seguro Brazil
| | - Benoit de Thoisy
- Kwata NGO, 16 Avenue Pasteur, 97300 Cayenne, French Guiana Kwata NGO Cayenne French Guyana
| | - José Maurício Barbanti Duarte
- Núcleo de Pesquisa e Conservação de Cervídeos (NUPECCE), Faculdade de Ciências Agrárias e Veterinárias da Universidade Estadual Paulista (UNESP), Via de Acesso Paulo Donato Castellane, s/n CEP: 14884-900, Jaboticabal-SP, Brazil Universidade Estadual Paulista Jaboticabal Brazil
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de Abreu-Jr EF, Pavan SE, Tsuchiya MTN, Wilson DE, Percequillo AR, Maldonado JE. Museomics of tree squirrels: a dense taxon sampling of mitogenomes reveals hidden diversity, phenotypic convergence, and the need of a taxonomic overhaul. BMC Evol Biol 2020; 20:77. [PMID: 32590930 PMCID: PMC7320592 DOI: 10.1186/s12862-020-01639-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 06/17/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Tree squirrels (Sciuridae, Sciurini), in particular the highly diverse Neotropical lineages, are amongst the most rapidly diversifying branches of the mammal tree of life but also some of the least known. Negligence of this group by systematists is likely a product of the difficulties in assessing morphological informative traits and of the scarcity or unavailability of fresh tissue samples for DNA sequencing. The highly discrepant taxonomic arrangements are a consequence of the lack of phylogenies and the exclusive phenotypic-based classifications, which can be misleading in a group with conservative morphology. Here we used high-throughput sequencing and an unprecedented sampling of museum specimens to provide the first comprehensive phylogeny of tree squirrels, with a special emphasis on Neotropical taxa. RESULTS We obtained complete or partial mitochondrial genomes from 232 historical and modern samples, representing 40 of the 43 currently recognized species of Sciurini. Our phylogenetic analyses-performed with datasets differing on levels of missing data and taxa under distinct analytical methods-strongly support the monophyly of Sciurini and consistently recovered 12 major clades within the tribe. We found evidence that the diversity of Neotropical tree squirrels is underestimated, with at least six lineages that represent taxa to be named or revalidated. Ancestral state reconstructions of number of upper premolars and number of mammae indicated that alternative conditions of both characters must have evolved multiple times throughout the evolutionary history of tree squirrels. CONCLUSIONS Complete mitogenomes were obtained from museum specimens as old as 120 years, reinforcing the potential of historical samples for phylogenetic inferences of elusive lineages of the tree of life. None of the taxonomic arrangements ever proposed for tree squirrels fully corresponded to our phylogenetic reconstruction, with only a few of the currently recognized genera recovered as monophyletic. By investigating the evolution of two morphological traits widely employed in the taxonomy of the group, we revealed that their homoplastic nature can help explain the incongruence between phylogenetic results and the classification schemes presented so far. Based on our phylogenetic results we suggest a tentative supraspecific taxonomic arrangement for Sciurini, employing 13 generic names used in previous taxonomic classifications.
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Affiliation(s)
- Edson Fiedler de Abreu-Jr
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, 13418900, Brazil.
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20013, USA.
| | - Silvia E Pavan
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20013, USA.
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Belém, PA, 66077530, Brazil.
| | - Mirian T N Tsuchiya
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20013, USA
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC, 20560, USA
| | - Don E Wilson
- Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA
| | - Alexandre R Percequillo
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, 13418900, Brazil
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20013, USA
- Department of Biology and Department of Environmental Science and Policy, George Mason University, Fairfax, VA, 22030, USA
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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: 1.0] [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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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: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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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: 41] [Impact Index Per Article: 10.3] [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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Morales-Martínez DM, Ramírez-Chaves HE, Colmenares-Pinzón JE, Gómez LG. The Koepcke’s spear-nosed bat, Gardnerycteris koepckeae (Gardner and Patton, 1972) (Chiroptera: Phyllostomidae), is not endemic to Peru: first record from the Amazon foothills of Colombia. MAMMALIA 2020. [DOI: 10.1515/mammalia-2019-0107] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
We report the first record of the rare Koepcke’s spear-nosed bat Gardnerycteris koepckeae collected outside of Peru, based on morphological and cytochrome b data. The species was found at the National Natural Park Alto Fragua Indi-Wasi, Department of Caquetá, Colombia. This record extended the species distribution 1400 km north from the northernmost known locality in Huanhuachayo, Ayacucho, Peru. This finding suggests that G. koepckeae is distributed over middle elevations along the eastern slope of the Andean-Amazonia foothills in Peru and Colombia, similar to other Phyllostomid bats, such as Vampyressa melissa and Lonchophylla handleyi. We reviewed the threatened category of G. koepckeae, currently categorized as Data Deficient (DD), according to the International Union for Conservation of Nature (IUCN), but considered as Endangered (EN) in recent papers. Based on this new record, we suggest that the species should be included in future assessments as Near Threatened (NT) or Vulnerable (VU) based on its wider distribution along the Andean-Amazonian foothills of Colombia, Ecuador and Peru, and probably the Orinoco slope of the Andes of Colombia and Venezuela.
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Affiliation(s)
- Darwin M. Morales-Martínez
- Grupo Biodiversidad y Conservación Genética, Instituto de Genética, Universidad Nacional de Colombia and Grupo de Fauna, Programa de Ecosistemas y Recursos Naturales, Instituto Amazónico de Investigaciones Científicas SINCHI , Calle 20 # 5-44, Bogota 111321 , Colombia
| | - Héctor E. Ramírez-Chaves
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, and Centro de Museos , Museo de Historia Natural, Universidad de Caldas , Calle 65 # 26-10 , Manizales , Colombia
| | - Javier E. Colmenares-Pinzón
- Grupo de Estudios en Biodiversidad, Universidad Industrial de Santander , Carrera 27 # 9 , Bucaramanga , Colombia
| | - Luis G. Gómez
- Departamento de Biología, Grupo GECO , Universidad del Cauca , Popayán , Colombia
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Geographic Distribution of Chronic Wasting Disease Resistant Alleles in Nebraska, with Comments on the Evolution of Resistance. JOURNAL OF FISH AND WILDLIFE MANAGEMENT 2019. [DOI: 10.3996/012019-jfwm-002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Abstract
Infectious diseases create major challenges for wildlife management. In particular, prion diseases are fatal and incurable, leaving managers with limited options. In cervids, chronic wasting disease (CWD) can decimate captive and wild populations by affecting neural tissue leading to body control loss, decay, and ultimately death resulting in ecological and economic consequences. Partial protection against CWD results from some genotypes at the prion (PRNP) locus encoding PrP proteins that are less likely to misfold and build up to fatal levels in the central nervous system. Although multiple studies have documented the association between CWD susceptibility and genotypes, little is known about the distribution of resistant genotypes across the natural landscape, and whether population pockets of protection in exist in particular regions. We surveyed the genetic variability and distribution of resistant alleles and genotypes of the PRNP locus across Nebraska in deer collected in 2017, where mule deer (Odocoileus hemionus) and white-tailed (O. virginianus) deer ranges meet on the North American Great Plains. We found that CWD-resistant alleles occur throughout the state in low frequencies, and our data suggest little evidence of geographic structure for the PRNP locus. In Nebraska, there is a lower frequency of the most common resistance allele (S96) compared with white-tailed deer in other parts of the Midwest. The frequency of resistant alleles (F225) was lower in mule deer. The low but widespread frequency of resistance alleles suggests that each species could be susceptible to CWD spread. Continued monitoring would be useful to determine if the frequency of resistant alleles increases in areas with increasing CWD rates. Three synonymous fixed genotypes at the PRNP locus allowed detection of hybrids between mule deer and white-tailed deer, although we found none, suggesting that CWD is not spread between species via hybridization. We also compare the PRNP genotypes of scrapie-resistant sheep with those of deer, and suggest that a single base-pair mutation at the PRNP locus could provide resistance in deer.
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Ruedas LA, Silva SM, French JH, Platt RN, Salazar-Bravo J, Mora JM, Thompson CW. Taxonomy of the Sylvilagus brasiliensis complex in Central and South America (Lagomorpha: Leporidae). J Mammal 2019. [DOI: 10.1093/jmammal/gyz126] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Abstract
A taxonomic framework for South American cottontail rabbits (Lagomorpha: Leporidae: Sylvilagus) was recently published by Diersing and Wilson (2017). Although we agree with some of its taxonomic conclusions (e.g., species status for S. apollinaris and S. fulvescens), we disagree with others. We provide herein evidence supporting S. andinus as a valid species based on morphological characters and novel molecular data. We also provide details of the morphological characters of S. apollinaris and S. fulvescens that support separating these from S. brasiliensis. We adduce data suggestive to the effect that—absent any type material—S. defilippi is at best a nomen dubium. Finally, we provide evidence in support of recognizing additional Neotropical species of Sylvilagus.
Un esquema taxonómico para los conejos sudamericanos (Lagomorpha: Leporidae: Sylvilagus) fue recientemente publicado por Diersing y Wilson (2017). Aunque estamos de acuerdo con algunas de sus conclusiones (por ejemplo: estatus de especie válida para S. apollinaris y S. fulvescens), no estamos de acuerdo con las restantes conclusiones taxonómicas. Aportamos aquí pruebas convincentes sobre la característica naturaleza de los caracteres morfológicos y moleculares de S. andinus, pruebas que esgrimimos en apoyo de la hipótesis que esta última es una especie válida, así confirmando su escisión de S. brasiliensis. Proporcionamos detalles de los caracteres morfológicos de S. apollinaris y S. fulvescens que confirman la decisión taxonómica de asimismo separarlos de S. brasiliensis. Proporcionamos datos en aditamento que indican que a falta de cualquier material tipo para S. defilippi, este nombre es en el mejor de los casos un nomen dubium. Finalmente, ofrecemos datos y evidencia apoyando nuestras decisiones de reconocer un mayor número de especies Neotropicales de Sylvilagus que previamente se conocían.
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Affiliation(s)
- Luis A Ruedas
- Department of Biology and Museum of Natural History, Portland State University, Portland, OR, USA
| | | | - Johnnie H French
- U.S. Fish and Wildlife Service, National Fish and Wildlife Forensics Laboratory, Ashland, OR, USA
| | - Roy Nelson Platt
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | | | - José M Mora
- Instituto Internacional en Conservación y Manejo de Vida Silvestre (ICOMVIS), Universidad Nacional de Costa Rica, Heredia, Costa Rica
| | - Cody W Thompson
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
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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: 7.4] [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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Gutiérrez EE, Garbino GST. Species delimitation based on diagnosis and monophyly, and its importance for advancing mammalian taxonomy. Zool Res 2018; 39:301-308. [PMID: 29551763 PMCID: PMC6102684 DOI: 10.24272/j.issn.2095-8137.2018.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/12/2018] [Indexed: 11/30/2022] Open
Abstract
A recently proposed taxonomic classification of extant ungulates sparked a series of publications that criticize the Phylogenetic Species Concept (PSC) claiming it to be a particularly poor species concept. These opinions reiteratively stated that (1) the two fundamental elements of the "PSC", i.e., monophyly and diagnosability, do not offer objective criteria as to where the line between species should be drawn; and (2) that extirpation of populations can lead to artificial diagnosability and spurious recognitions of species. This sudden eruption of criticism against the PSC is misleading. Problems attributed to the PSC are common to most approaches and concepts that modern systematists employ to establish species boundaries. The controversial taxonomic propositions that sparked criticism against the PSC are indeed highly problematic, not because of the species concept upon which they are based, but because no evidence (whatsoever) has become public to support a substantial portion of the proposed classification. We herein discuss these topics using examples from mammals. Numerous areas of biological research rest upon taxonomic accuracy (including conservation biology and biomedical research); hence, it is necessary to clarify what are (and what are not) the real sources of taxonomic inaccuracy.
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Affiliation(s)
- Eliécer E Gutiérrez
- Pós-Graduação em Biodiversidade Animal, Departamento de Ecologia e Evolução, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, RS 97105-900, Brazil; E-mail:
- Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington DC 20013-7012, USA
| | - Guilherme S T Garbino
- Pós-graduação, Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
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