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Tavares FDS, Oliveira da Silva W, Ferguson-Smith MA, Klautau AGCDM, Oliveira JM, Rodrigues ALF, Melo-Santos G, Pieczarka JC, Nagamachi CY, Noronha RCR. Ancestral chromosomal signatures of Paenungulata (Afroteria) reveal the karyotype of Amazonian manatee (Trichechus inunguis, Sirenia: Trichechidae) as the oldest among American manatees. BMC Genomics 2023; 24:38. [PMID: 36694120 PMCID: PMC9872332 DOI: 10.1186/s12864-023-09129-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 01/11/2023] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Chromosomal painting in manatees has clarified questions about the rapid evolution of sirenians within the Paenungulata clade. Further cytogenetic studies in Afrotherian species may provide information about their evolutionary dynamics, revealing important insights into the ancestral karyotype in the clade representatives. The karyotype of Trichechus inunguis (TIN, Amazonian manatee) was investigated by chromosome painting, using probes from Trichechus manatus latirostris (TML, Florida manatee) to analyze the homeologies between these sirenians. RESULTS A high similarity was found between these species, with 31 homologous segments in TIN, nineteen of which are whole autosomes, besides the X and Y sex chromosomes. Four chromosomes from TML (4, 6, 8, and 9) resulted in two hybridization signals, totaling eight acrocentrics in the TIN karyotype. This study confirmed in TIN the chromosomal associations of Homo sapiens (HSA) shared in Afrotheria, such as the 5/21 synteny, and in the Paenungulata clade with the syntenies HSA 2/3, 8/22, and 18/19, in addition to the absence of HSA 4/8 common in eutherian ancestral karyotype (EAK). CONCLUSIONS TIN shares more conserved chromosomal signals with the Paenungulata Ancestral Karyotype (APK, 2n = 58) than Procavia capensis (Hyracoidea), Loxodonta africana (Proboscidea) and TML (Sirenia), where TML presents less conserved signals with APK, demonstrating that its karyotype is the most derived among the representatives of Paenungulata. The chromosomal changes that evolved from APK to the T. manatus and T. inunguis karyotypes (7 and 4 changes, respectively) are more substantial within the Trichechus genus compared to other paenungulates. Among these species, T. inunguis presents conserved traits of APK in the American manatee genus. Consequently, the karyotype of T. manatus is more derived than that of T. inunguis.
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Affiliation(s)
- Flávia Dos Santos Tavares
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal Do Pará (UFPA), Pará, Belém, Brazil
| | - Willam Oliveira da Silva
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal Do Pará (UFPA), Pará, Belém, Brazil
| | - Malcolm Andrew Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Jairo Moura Oliveira
- Zoological Park of Santarém - Universidade da Amazônia (ZOOUNAMA), Pará, Santarém, Brazil
| | - Angélica Lúcia Figueiredo Rodrigues
- Instituto de Biologia e Conservação de Mamíferos Aquáticos da Amazônia, Universidade Federal Rural da Amazônia (UFRA), Pará, Belém, Brazil
- Secretaria de Educação Do Estado Do Pará (SEDUC-PA), Belém, Brazil
| | - Gabriel Melo-Santos
- Instituto de Biologia e Conservação de Mamíferos Aquáticos da Amazônia, Universidade Federal Rural da Amazônia (UFRA), Pará, Belém, Brazil
- Laboratório de Ecologia Marinha e Conservação, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratório de Ecologia de Aves e Comportamento Animal, Universidade Estadual do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal Do Pará (UFPA), Pará, Belém, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal Do Pará (UFPA), Pará, Belém, Brazil
| | - Renata Coelho Rodrigues Noronha
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal Do Pará (UFPA), Pará, Belém, Brazil.
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Herpesvirus and adenovirus surveillance in threatened wild West Indian (Trichechus manatus) and Amazonian manatees (Trichechus inunguis), Brazil. Acta Trop 2022; 237:106740. [DOI: 10.1016/j.actatropica.2022.106740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/26/2022] [Accepted: 10/31/2022] [Indexed: 11/07/2022]
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Caballero S, Ortiz-Giral MC, Bohorquez L, Lozano Mojica JD, Caicedo-Herrera D, Arévalo-González K, Mignucci-Giannoni AA. Mitochondrial Genetic Diversity, Population Structure and Detection of Antillean and Amazonian Manatees in Colombia: New Areas and New Techniques. Front Genet 2021; 12:726916. [PMID: 34899829 PMCID: PMC8662808 DOI: 10.3389/fgene.2021.726916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/08/2021] [Indexed: 11/26/2022] Open
Abstract
The Antillean manatee (Trichechus manatus) and the Amazonian manatee (Trichechus inunguis) are distributed in rivers in the Caribbean and Amazonian region of Colombia respectively. For 30 years, genetic information has been obtained from these populations in order to inform conservation programs for these endangered species and decide on the location to release them back to the wild. However, in previous studies, samples from rivers in some areas of the country were not included, given the difficulties to access these regions due to either logistic or safety issues. In this study, we analyzed mitochondrial DNA (mtDNA) control region (CR) sequences of from samples of T. manatus (n = 37) and T. inunguis (n = 4) (410 and 361 bp, respectively), obtained in new and previously unexplored rivers and bays in the country, including Santa Marta, Urabá Gulf, Ayapel Marsh (San Jorge River Basin), Meta River and Magdalena Medio and the low Magdalena River (Cesar Province and Canal del Dique) as well as additional samples from Puerto Nariño in the Colombian Amazon. Our results included the discovery of two newly described mtDNA CR haplotypes for T. manatus. In addition, we confirmed significant population differentiation at the mitochondrial level between the Magdalena and Sinú rivers and differentiation among areas of the same river, including the middle and low Magdalena River. This differentiation may be related to anthropic changes in the river since construction of the Canal del Dique in the XVI century. We also tested environmental DNA sampling and analyses techniques to evaluate its potential use for manatee detection and monitoring in bodies of water in Colombia, in order to evaluate new areas for future manatee conservation initiatives. We emphasize the need to continue using genetic information to provide evidence on the potential best locations to undertake animal release to prevent outbreeding depression.
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Affiliation(s)
- Susana Caballero
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos (LEMVA), Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
| | - Maria Camila Ortiz-Giral
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos (LEMVA), Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
| | - Laura Bohorquez
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos (LEMVA), Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
| | - Juan Diego Lozano Mojica
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos (LEMVA), Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
| | | | - Katherine Arévalo-González
- Cabildo Verde, Sabana de Torres, Colombia
- Fundación Internacional para La Defensa de La Naturaleza y La Sustentabilidad-FINS, Chetumal, Mexico
| | - Antonio A. Mignucci-Giannoni
- Centro de Conservación de Manatíes del Caribe, Universidad Interamericana de Puerto Rico, Bayamón, Puerto Rico
- Center for Conservation Medicine and Ecosystem Health, Ross University School of Veterinary Medicine, Basseterre, St. Kitts
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de Souza DA, Gonçalves ALS, von Muhlen EM, da Silva VMF. Estimating occupancy and detection probability of the Amazonian manatee (Trichechus inunguis), in Central Amazon, Brazil. Perspect Ecol Conserv 2021. [DOI: 10.1016/j.pecon.2021.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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The evolutionary history of manatees told by their mitogenomes. Sci Rep 2021; 11:3564. [PMID: 33574363 PMCID: PMC7878490 DOI: 10.1038/s41598-021-82390-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 01/18/2021] [Indexed: 12/24/2022] Open
Abstract
The manatee family encompasses three extant congeneric species: Trichechus senegalensis (African manatee), T. inunguis (Amazonian manatee), and T. manatus (West Indian manatee). The fossil record for manatees is scant, and few phylogenetic studies have focused on their evolutionary history. We use full mitogenomes of all extant manatee species to infer the divergence dates and biogeographical histories of these species and the effect of natural selection on their mitogenomes. The complete mitochondrial genomes of T. inunguis (16,851 bp), T. senegalensis (16,882 bp), and T. manatus (16,882 bp), comprise 13 protein-coding genes, 2 ribosomal RNA genes (rRNA - 12S and 16S), and 22 transfer RNA genes (tRNA), and (D-loop/CR). Our analyses show that the first split within Trichechus occurred during the Late Miocene (posterior mean 6.56 Ma and 95% HPD 3.81–10.66 Ma), followed by a diversification event in the Plio-Pleistocene (posterior mean 1.34 Ma, 95% HPD 0.1–4.23) in the clade composed by T. inunguis and T. manatus; T. senegalensis is the sister group of this clade with higher support values (pp > 0.90). The branch-site test identified positive selection on T. inunguis in the 181st position of the ND4 amino acid gene (LRT = 6.06, p = 0.0069, BEB posterior probability = 0.96). The ND4 gene encodes one subunit of the NADH dehydrogenase complex, part of the oxidative phosphorylation machinery. In conclusion, our results provide novel insight into the evolutionary history of the Trichechidae during the Late Miocene, which was influenced by geological events, such as Amazon Basin formation.
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Oliveira JDA, Farias IP, Costa GC, Werneck FP. Model-based riverscape genetics: disentangling the roles of local and connectivity factors in shaping spatial genetic patterns of two Amazonian turtles with different dispersal abilities. Evol Ecol 2019. [DOI: 10.1007/s10682-019-09973-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Barros HMDDR, Meirelles ACO, Luna FO, Marmontel M, Cordeiro-Estrela P, Santos N, Astúa D. Cranial and chromosomal geographic variation in manatees (Mammalia: Sirenia: Trichechidae) with the description of the Antillean manatee karyotype in Brazil. J ZOOL SYST EVOL RES 2016. [DOI: 10.1111/jzs.12153] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Helen M. D. do R. Barros
- Laboratório de Mastozoologia; Departamento de Zoologia/CB; Universidade Federal de Pernambuco; Recife PE Brazil
- Laboratório de Genética e Citogenética Animal; Departamento de Genética/CB; Universidade Federal de Pernambuco; Recife PE Brazil
| | - Ana C. O. Meirelles
- Programa de Mamíferos Marinhos; Associação de Pesquisa e Preservação de Ecossistemas Aquáticos; Caucaia CE Brazil
| | - Fábia O. Luna
- Centro Nacional de Pesquisa e Conservação de Mamíferos Aquáticos; Instituto Chico Mendes de Conservação da Biodiversidade; Itamaracá PE Brazil
| | - Miriam Marmontel
- Grupo de Pesquisa em Mamíferos Aquáticos Amazônicos; Instituto de Desenvolvimento Sustentável Mamirauá; Tefé AM Brazil
| | - Pedro Cordeiro-Estrela
- Laboratório de Mamíferos/Coleção de Mamíferos; Departamento de Sistemática e Ecologia/CCEN; Universidade Federal da Paraíba; João Pessoa PB Brazil
| | - Neide Santos
- Laboratório de Genética e Citogenética Animal; Departamento de Genética/CB; Universidade Federal de Pernambuco; Recife PE Brazil
| | - Diego Astúa
- Laboratório de Mastozoologia; Departamento de Zoologia/CB; Universidade Federal de Pernambuco; Recife PE Brazil
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Satizábal P, Mignucci-Giannoni AA, Duchêne S, Caicedo-Herrera D, Perea-Sicchar CM, García-Dávila CR, Trujillo F, Caballero SJ. Phylogeography and sex-biased dispersal across riverine manatee populations (Trichechus inunguis and Trichechus manatus) in South America. PLoS One 2012; 7:e52468. [PMID: 23285054 PMCID: PMC3527500 DOI: 10.1371/journal.pone.0052468] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 11/13/2012] [Indexed: 11/23/2022] Open
Abstract
Phylogeographic patterns and sex-biased dispersal were studied in riverine populations of West Indian (Trichechus manatus) and Amazonian manatees (T. inunguis) in South America, using 410bp D-loop (Control Region, Mitochondrial DNA) sequences and 15 nuclear microsatellite loci. This multi-locus approach was key to disentangle complex patterns of gene flow among populations. D-loop analyses revealed population structuring among all Colombian rivers for T. manatus, while microsatellite data suggested no structure. Two main populations of T. inunguis separating the Colombian and Peruvian Amazon were supported by analysis of the D-loop and microsatellite data. Overall, we provide molecular evidence for differences in dispersal patterns between sexes, demonstrating male-biased gene flow dispersal in riverine manatees. These results are in contrast with previously reported levels of population structure shown by microsatellite data in marine manatee populations, revealing low habitat restrictions to gene flow in riverine habitats, and more significant dispersal limitations for males in marine environments.
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Affiliation(s)
- Paula Satizábal
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos-LEMVA, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia.
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Pineda-Catalan O, Mendez M, Gleizer A, García-Dávila C, Aguirre AA, Pinedo-Vasquez M, Amato G. Conservation genetics of harvested river turtles,Podocnemis expansaandPodocnemis unifilis, in the Peruvian Amazon: All roads lead to Iquitos. ACTA ACUST UNITED AC 2012; 23:230-8. [DOI: 10.3109/19401736.2012.674115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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10
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de OLIVEIRA LR, LOIZAGA DE CASTRO R, CÁRDENAS-ALAYZA S, BONATTO SL. Conservation genetics of South American aquatic mammals: an overview of gene diversity, population structure, phylogeography, non-invasive methods and forensics. Mamm Rev 2011. [DOI: 10.1111/j.1365-2907.2011.00201.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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Farias IP, Torrico JP, García-Dávila C, Santos MDCF, Hrbek T, Renno JF. Are rapids a barrier for floodplain fishes of the Amazon basin? A demographic study of the keystone floodplain species Colossoma macropomum (Teleostei: Characiformes). Mol Phylogenet Evol 2010; 56:1129-35. [DOI: 10.1016/j.ympev.2010.03.028] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2010] [Accepted: 03/25/2010] [Indexed: 11/17/2022]
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Arraut EM, Marmontel M, Mantovani JE, Novo EM, Macdonald DW, Kenward RE. The lesser of two evils: seasonal migrations of Amazonian manatees in the Western Amazon. J Zool (1987) 2009. [DOI: 10.1111/j.1469-7998.2009.00655.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Vasconcelos WR, Hrbek T, Da Silveira R, De Thoisy B, Ruffeil LAADS, Farias IP. Phylogeographic and conservation genetic analysis of the black caiman (Melanosuchus niger). ACTA ACUST UNITED AC 2008; 309:600-13. [DOI: 10.1002/jez.452] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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14
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Escalona T, Engstrom TN, Hernandez OE, Bock BC, Vogt RC, Valenzuela N. Population genetics of the endangered South American freshwater turtle, Podocnemis unifilis, inferred from microsatellite DNA data. CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9746-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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15
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Trinca CS, Waldemarin HF, Eizirik E. Genetic diversity of the Neotropical otter (Lontra longicaudis Olfers, 1818) in Southern and Southeastern Brazil. BRAZ J BIOL 2008; 67:813-8. [PMID: 18278347 DOI: 10.1590/s1519-69842007000500003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Accepted: 08/30/2007] [Indexed: 11/21/2022] Open
Abstract
The Neotropical otter is one of the least known otter species, and it is considered to be threatened to various degrees throughout its geographic range. Little information exists on the ecological characteristics of this species, and no genetic study has been published about it until now, hampering the design of adequate conservation strategies for its populations. To contribute with genetic information to comprehensive conservation efforts on behalf of L. longicaudis, we characterized the molecular diversity of the 5 portion of the mtDNA control region in samples from this species collected in Southern and Southeastern Brazil. The sequence analysis revealed a high level of haplotype diversity (h=0.819; SE=0.0052) and nucleotide variability ranging from 0.0039 to 0.0067. One of the sampled haplotypes was the most common in both regions and, from this sequence, several other (locally occurring) haplotypes could be derived by single point mutations. No significant genetic differentiation was observed between the Southern and Southeastern regions.
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Affiliation(s)
- C S Trinca
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 91501-970, Brazil
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Carter AM, Miglino MA, Ambrosio CE, Santos TC, Rosas FCW, Neto JAD, Lazzarini SM, Carvalho AF, da Silva VMF. Placentation in the Amazonian manatee (Trichechus inunguis). Reprod Fertil Dev 2008; 20:537-45. [DOI: 10.1071/rd08009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2008] [Accepted: 03/04/2008] [Indexed: 11/23/2022] Open
Abstract
Evidence from several sources supports a close phylogenetic relationship between elephants and sirenians. To explore whether this was reflected in similar placentation, we examined eight delivered placentae from the Amazonian manatee using light microscopy and immunohistochemistry. In addition, the fetal placental circulation was described by scanning electron microscopy of vessel casts. The manatee placenta was zonary and endotheliochorial, like that of the elephant. The interhaemal barrier comprised maternal endothelium, cytotrophoblasts and fetal endothelium. We found columnar trophoblast beneath the chorionic plate and lining lacunae in this region, but there was no trace in the term placenta of haemophagous activity. The gross anatomy of the cord and fetal membranes was consistent with previous descriptions and included a four-chambered allantoic sac, as also found in the elephant and other afrotherians. Connective tissue septae descended from the chorionic plate and carried blood vessels to the labyrinth, where they gave rise to a dense capillary network. This appeared to drain into shorter vessels near the chorionic plate. The maternal vasculature could not be examined in the same detail, but maternal capillaries ran rather straight and roughly parallel to the fetal ones. Overall, there is a close resemblance in placentation between the manatee and the elephant.
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Hrbek T, Crossa M, Farias IP. Conservation strategies for Arapaima gigas (Schinz, 1822) and the Amazonian várzea ecosystem. BRAZ J BIOL 2007; 67:909-17. [DOI: 10.1590/s1519-69842007000500015] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2007] [Accepted: 09/12/2007] [Indexed: 11/22/2022] Open
Abstract
In the present study we report a spatial autocorrelation analysis of molecular data obtained for Arapaima gigas, and the implication of this study for conservation and management. Arapaima is an important, but critically over-exploited giant food fish of the Amazonian várzea. Analysis of 14 variable microsatellite loci and 2,347 bp of mtDNA from 126 individuals sampled in seven localities within the Amazon basin suggests that Arapaima forms a continuous population with extensive genetic exchange among localities. Weak effect of isolation-by-distance is observed in microsatellite data, but not in mtDNA data. Spatial autocorrelation analysis of genetic and geographic data suggests that genetic exchange is significantly restricted at distances greater than 2,500 km. We recommend implementing a source-sink metapopulation management and conservation model by proposing replicate high quality várzea reserves in the upper, central, and lower Amazon basin. This conservation strategy would: 1) preserve all of the current genetic diversity of Arapaima; 2) create a set of reserves to supply immigrants for locally depleted populations; 3) preserve core várzea areas in the Amazon basin on which many other species depend. We stress that conservation strategies should not only preserve current genetic diversity, but also the evolutionary processes which have generated the observed patterns.
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Affiliation(s)
- T. Hrbek
- Universidade Federal do Amazonas, Brazil; University of Puerto Rico, Puerto Rico
| | - M. Crossa
- Instituto de Pesquisa Ambiental da Amazônia, Brazil
| | - IP. Farias
- Universidade Federal do Amazonas, Brazil
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Pardini A, O'Brien P, Fu B, Bonde R, Elder F, Ferguson-Smith M, Yang F, Robinson T. Chromosome painting among Proboscidea, Hyracoidea and Sirenia: support for Paenungulata (Afrotheria, Mammalia) but not Tethytheria. Proc Biol Sci 2007; 274:1333-40. [PMID: 17374594 PMCID: PMC1914331 DOI: 10.1098/rspb.2007.0088] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Despite marked improvements in the interpretation of systematic relationships within Eutheria, particular nodes, including Paenungulata (Hyracoidea, Sirenia and Proboscidea), remain ambiguous. The combination of a rapid radiation, a deep divergence and an extensive morphological diversification has resulted in a limited phylogenetic signal confounding resolution within this clade both at the morphological and nucleotide levels. Cross-species chromosome painting was used to delineate regions of homology between Loxodonta africana (2n=56), Procavia capensis (2n=54), Trichechus manatus latirostris (2n=48) and an outgroup taxon, the aardvark (Orycteropus afer, 2n=20). Changes specific to each lineage were identified and although the presence of a minimum of 11 synapomorphies confirmed the monophyly of Paenungulata, no change characterizing intrapaenungulate relationships was evident. The reconstruction of an ancestral paenungulate karyotype and the estimation of rates of chromosomal evolution indicate a reduced rate of genomic repatterning following the paenungulate radiation. In comparison to data available for other mammalian taxa, the paenungulate rate of chromosomal evolution is slow to moderate. As a consequence, the absence of a chromosomal character uniting two paenungulates (at the level of resolution characterized in this study) may be due to a reduced rate of chromosomal change relative to the length of time separating successive divergence events.
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Affiliation(s)
- A.T Pardini
- Evolutionary Genomics Group, Department of Botany and Zoology, University of StellenboschPrivate Bag X1, Matieland, 7602 Stellenbosch, South Africa
| | - P.C.M O'Brien
- Centre for Veterinary Science, University of CambridgeCambridge CB3 0ES, UK
| | - B Fu
- Centre for Veterinary Science, University of CambridgeCambridge CB3 0ES, UK
| | - R.K Bonde
- U.S. Geological Survey, Florida Integrated Science CentreGainesville, FL 32605-3574, USA
| | - F.F.B Elder
- Department of Pathology, Cytogenetics LaboratoryUT Southwestern Medical Centre, Dallas, TX 75235, USA
| | - M.A Ferguson-Smith
- Centre for Veterinary Science, University of CambridgeCambridge CB3 0ES, UK
| | - F Yang
- Centre for Veterinary Science, University of CambridgeCambridge CB3 0ES, UK
| | - T.J Robinson
- Evolutionary Genomics Group, Department of Botany and Zoology, University of StellenboschPrivate Bag X1, Matieland, 7602 Stellenbosch, South Africa
- Author for correspondence ()
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Mora MS, Lessa EP, Kittlein MJ, Vassallo AI. PHYLOGEOGRAPHY OF THE SUBTERRANEAN RODENT CTENOMYS AUSTRALIS IN SAND-DUNE HABITATS: EVIDENCE OF POPULATION EXPANSION. J Mammal 2006. [DOI: 10.1644/05-mamm-a-399r1.1] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Wang XM, Cao LR, Liu ZS, Fang SG. Mitochondrial DNA variation and matrilineal structure in blue sheep populations of Helan Mountain, China. CAN J ZOOL 2006. [DOI: 10.1139/z06-137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mitochondrial DNA (mtDNA) control region (5′ hypervariable region, 554 bp) sequences from 71 samples of blue sheep ( Pseudois nayaur Hodgson, 1833) collected from six study localities throughout Helan Mountain Nature Reserve in Ningxia province of China were investigated to analyse distribution patterns of genetic variability, elucidate matrilineal structure, and investigate population history. Haplotype diversity (h) among the 71 samples was estimated to be 0.792 ± 0.037, and nucleotide diversity (Π) was relatively low (0.00392 ± 0.00046). A χ2contingency analysis of all mtDNA haplotype frequencies revealed that these haplotypes were distributed in a nonrandom fashion among study localities (χ2= 86.205, P = 0.092). Additional evidence of matrilineal structure was provided by the finding that a significant amount (9.02%; P < 0.01) of mtDNA variation was partitioned among different localities in the study area. We conclude that blue sheep of Helan Mountain Nature Reserve are structured spatially along matrilines. Pairwise computations of Φstand an AMOVA indicated that some sampling localities are differentiated relative to a random collection of genotypes and reflected differences in the spatial distribution of genetic variation. Isolation-by-distance (IBD) models (Mantel tests) revealed no obvious association between genetic differentiation and geographical distance. These results could be a basis for the development of suitable management strategies for conservation purposes. This work represents the first analysis of blue sheep mitochondrial control region DNA to be performed from a population genetics perspective.
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Affiliation(s)
- Xiao-Ming Wang
- School of Life Science, East China Normal University, 3663 Zhongshan Road N, Shanghai 200062, China
- Key Laboratory of Conservation Genetics and Reproductive Biology for Endangered Wildlife of Ministry of Education, Zhejiang University, Hangzhou 310029, China
- The State Conservation Center for Gene Resources of Endangered Wildlife, Hangzhou 310029, China
| | - Li-Rong Cao
- School of Life Science, East China Normal University, 3663 Zhongshan Road N, Shanghai 200062, China
- Key Laboratory of Conservation Genetics and Reproductive Biology for Endangered Wildlife of Ministry of Education, Zhejiang University, Hangzhou 310029, China
- The State Conservation Center for Gene Resources of Endangered Wildlife, Hangzhou 310029, China
| | - Zhen-Sheng Liu
- School of Life Science, East China Normal University, 3663 Zhongshan Road N, Shanghai 200062, China
- Key Laboratory of Conservation Genetics and Reproductive Biology for Endangered Wildlife of Ministry of Education, Zhejiang University, Hangzhou 310029, China
- The State Conservation Center for Gene Resources of Endangered Wildlife, Hangzhou 310029, China
| | - Sheng-Guo Fang
- School of Life Science, East China Normal University, 3663 Zhongshan Road N, Shanghai 200062, China
- Key Laboratory of Conservation Genetics and Reproductive Biology for Endangered Wildlife of Ministry of Education, Zhejiang University, Hangzhou 310029, China
- The State Conservation Center for Gene Resources of Endangered Wildlife, Hangzhou 310029, China
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Pearse DE, Arndt AD, Valenzuela N, Miller BA, Cantarelli V, Sites JW. Estimating population structure under nonequilibrium conditions in a conservation context: continent-wide population genetics of the giant Amazon river turtle, Podocnemis expansa (Chelonia; Podocnemididae). Mol Ecol 2006; 15:985-1006. [PMID: 16599962 DOI: 10.1111/j.1365-294x.2006.02869.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Giant Amazon river turtles, Podocnemis expansa, are indigenous to the Amazon, Orinoco, and Essequibo River basins, and are distributed across nearly the entire width of the South American continent. Although once common, their large size, high fecundity, and gregarious nesting, made P. expansa especially vulnerable to over-harvesting for eggs and meat. Populations have been severely reduced or extirpated in many areas throughout its range, and the species is now regulated under Appendix II of the Convention on International Trade in Endangered Species. Here, we analyse data from mitochondrial DNA sequence and multiple nuclear microsatellite markers with an array of complementary analytical methods. Results show that concordance from multiple data sets and analyses can provide a strong signal of population genetic structure that can be used to guide management. The general lack of phylogeographic structure but large differences in allele and haplotype frequencies among river basins is consistent with fragmented populations and female natal-river homing. Overall, the DNA data show that P. expansa populations lack a long history of genetic differentiation, but that each major tributary currently forms a semi-isolated reproductive population and should be managed accordingly.
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Affiliation(s)
- Devon E Pearse
- Department of Integrative Biology, Brigham Young University, Provo, UT 84602, USA.
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Vianna JA, Bonde RK, Caballero S, Giraldo JP, Lima RP, Clark A, Marmontel M, Morales-Vela B, De Souza MJ, Parr L, Rodríguez-Lopez MA, Mignucci-Giannoni AA, Powell JA, Santos FR. Phylogeography, phylogeny and hybridization in trichechid sirenians: implications for manatee conservation. Mol Ecol 2006; 15:433-47. [PMID: 16448411 DOI: 10.1111/j.1365-294x.2005.02771.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Abstract The three living species of manatees, West Indian (Trichechus manatus), Amazonian (Trichechus inunguis) and West African (Trichechus senegalensis), are distributed across the shallow tropical and subtropical waters of America and the western coast of Africa. We have sequenced the mitochondrial DNA control region in 330 Trichechus to compare their phylogeographic patterns. In T. manatus we observed a marked population structure with the identification of three haplotype clusters showing a distinct spatial distribution. A geographic barrier represented by the continuity of the Lesser Antilles to Trinidad Island, near the mouth of the Orinoco River in Venezuela, appears to have restricted the gene flow historically in T. manatus. However, for T. inunguis we observed a single expanding population cluster, with a high diversity of very closely related haplotypes. A marked geographic population structure is likely present in T. senegalensis with at least two distinct clusters. Phylogenetic analyses with the mtDNA cytochrome b gene suggest a clade of the marine Trichechus species, with T. inunguis as the most basal trichechid. This is in agreement with previous morphological analyses. Mitochondrial DNA, autosomal microsatellites and cytogenetic analyses revealed the presence of hybrids between the T. manatus and T. inunguis species at the mouth of the Amazon River in Brazil, extending to the Guyanas and probably as far as the mouth of the Orinoco River. Future conservation strategies should consider the distinct population structure of manatee species, as well as the historical barriers to gene flow and the likely occurrence of interspecific hybridization.
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Affiliation(s)
- Juliana A Vianna
- Laboratory of Biodiversity and Molecular Evolution (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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23
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Vasconcelos WR, Hrbek T, Silveira RD, Thoisy BD, Marioni B, Farias IP. Population genetic analysis of Caiman crocodilus (Linnaeus, 1758) from South America. Genet Mol Biol 2006. [DOI: 10.1590/s1415-47572006000200006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Affiliation(s)
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Brazil; University of Puerto Rico, Puerto Rico
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