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Alvarez-Aleman A, Hunter ME, Frazer TK, Powell JA, Alfonso EG, Austin JD. The first assessment of the genetic diversity and structure of the endangered West Indian manatee in Cuba. Genetica 2022; 150:327-341. [PMID: 36271978 DOI: 10.1007/s10709-022-00172-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 10/04/2022] [Indexed: 11/04/2022]
Abstract
The coastal waters of Cuba are home to a small, endangered population of West Indian manatee, which would benefit from a comprehensive characterization of the population's genetic variation. We conducted the first genetic assessment of Cuban manatees to determine the extent of the population's genetic structure and characterize the neutral genetic diversity among regions within the archipelago. We genotyped 49 manatees at 18 microsatellite loci, a subset of 27 samples on 1703 single nucleotide polymorphisms (SNPs), and sequenced 59 manatees at the mitochondrial control region. The Cuba manatee population had low nuclear (microsatellites HE = 0.44, and SNP HE = 0.29) and mitochondrial genetic diversity (h = 0.068 and π = 0.00025), and displayed moderate departures from random mating (microsatellite FIS = 0.12, SNP FIS = 0.10). Our results suggest that the western portion of the archipelago undergoes periodic exchange of alleles based on the evidence of shared ancestry and low but significant differentiation. The southeast Guantanamo Bay region and the western portion of the archipelago were more differentiated than southwest and northwest manatees. The genetic distinctiveness observed in the southeast supports its recognition as a demographically independent unit for natural resource management regardless of whether it is due to historical isolation or isolation by distance. Estimates of the regional effective population sizes, with the microsatellite and SNP datasets, were small (all Ne < 60). Subsequent analyses using additional samples could better examine how the observed structure is masking simple isolation by distance patterns or whether ecological or biogeographic forces shape genetic patterns.
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Affiliation(s)
- Anmari Alvarez-Aleman
- School of Natural Resources and Environment, University of Florida, 2035 McCarty hall D, Gainesville, FL, 32611, USA. .,Centro de Investigaciones Marinas, Universidad de La Habana, Calle 16 # 114 Entre 1ra y 3ra Plaza, Havana, Cuba. .,Clearwater Marine Aquarium Research Institute, Clearwater Marine Aquarium, Clearwater, FL, USA.
| | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, USA
| | - Thomas K Frazer
- School of Natural Resources and Environment, University of Florida, 2035 McCarty hall D, Gainesville, FL, 32611, USA.,College of Marine Science, University of South Florida, 140 Seventh Avenue South, KRC 3109, St. Petersburg, FL, 33701, USA
| | - James A Powell
- Clearwater Marine Aquarium Research Institute, Clearwater Marine Aquarium, Clearwater, FL, USA
| | - Eddy Garcia Alfonso
- Refugio de Fauna Lanzanillo-Pajonal-Fragoso, Empresa Provincial para la Protección de la Flora y la Fauna, Villa Clara, Cuba
| | - James D Austin
- School of Natural Resources and Environment, University of Florida, 2035 McCarty hall D, Gainesville, FL, 32611, USA.,Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, FL, 32611, USA
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Poommouang A, Piboon P, Buddhachat K, Brown JL, Kriangwanich W, Chomdej S, Kampuansai J, Mekchay S, Kaewmong P, Kittiwattanawong K, Nganvongpanit K. Microsatellite Polymorphism and the Population Structure of Dugongs (Dugong dugon) in Thailand. Animals (Basel) 2022; 12:ani12030235. [PMID: 35158560 PMCID: PMC8833502 DOI: 10.3390/ani12030235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary For this study, skin samples were analyzed from 77 individual stranded dugongs collected in Thai waters from 1994–2019 using six microsatellite markers to assess the genetic diversity and population structure. Dugongs in the Andaman Sea had higher genetic variation than those in the Gulf of Thailand. Populations in Trang, Satun and some areas of Krabi had highest diversity compared to other regions of Thailand. The analysis of Bayesian genetic clustering showed that dugongs in Thailand consist of five genetic groups. Furthermore, dugongs in the middle and lower Andaman Sea presented the greatest gene flow compared to other regions. Based on calculation of inbreeding coefficients, dugong populations in the Sea of Thailand are experiencing some levels of inbreeding, and so may warrant special protections. Results of this study provide important information on genetic diversity and genetic population structuring of dugongs in Thailand and for understanding the genetic status of dugongs that can lead to improved management and conservation of this endangered species. Abstract The dugong (Dugong dugon) is an endangered species of marine mammals, so knowledge of genetic diversity of these populations is important for conservation planning within different habitats. In this study, six microsatellite markers were used to assess the genetic diversity and population structure of 77 dugongs from skin samples of stranded animals collected from 1994–2019 (69 from Andaman Sea and 8 from the Gulf of Thailand). Our results found that dugongs in the Andaman Sea had higher genetic variation than those in the Gulf of Thailand. Populations in Trang, Satun, and some areas of Krabi had highest diversity compared to other regions of Thailand. Bayesian genetic clustering analysis revealed that dugongs in Thailand consist of five genetic groups. Moreover, dugongs in the middle and lower Andaman Sea presented the greatest gene flow compared to other regions. However, based on calculation of inbreeding coefficients (Fis value = 0.239), dugong populations in the Sea of Thailand are experiencing some levels of inbreeding, and so may warrant special protections. These results provide important information for understanding the genetic status of dugongs that can lead to improved management and conservation of this endangered species.
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Affiliation(s)
- Anocha Poommouang
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand; (A.P.); (P.P.); (W.K.)
| | - Promporn Piboon
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand; (A.P.); (P.P.); (W.K.)
| | - Kittisak Buddhachat
- Excellence Center in Veterinary Bioscience, Chiang Mai 50100, Thailand; (K.B.); (S.C.)
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Janine L. Brown
- Smithsonian Conservation Biology Institute, Center for Species Survival, 1500 Remount Road, Front Royal, VA 22630, USA;
| | - Wannapimol Kriangwanich
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand; (A.P.); (P.P.); (W.K.)
| | - Siriwadee Chomdej
- Excellence Center in Veterinary Bioscience, Chiang Mai 50100, Thailand; (K.B.); (S.C.)
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Jatupol Kampuansai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Supamit Mekchay
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand;
| | | | | | - Korakot Nganvongpanit
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand; (A.P.); (P.P.); (W.K.)
- Excellence Center in Veterinary Bioscience, Chiang Mai 50100, Thailand; (K.B.); (S.C.)
- Correspondence: ; Tel.: +66-53-948046
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Moreira S, Meirelles ACOD, Carvalho VL, Rêgo PSD, Araripe J. Molecular confirmation of twinning in the West Indian Manatee (Trichechus manatus). BIOTA NEOTROPICA 2022. [DOI: 10.1590/1676-0611-bn-2021-1241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract: Few twinning events have been recorded in the West Indian manatee (Trichechus manatus, Sirenia: Trichechidae) and no previous published study has provided confirmation of this phenomenon based in molecular tools. Here we investigate a possible case of twinning in an endangered Brazilian population of T. manatus using molecular tools. We analyzed two male neonates found stranded in Ceará State, on the northeastern coast of Brazil. The DNA of both individuals was isolated, and 10 microsatellite loci were amplified and genotyped. Following the identification of the alleles, the probabilities of identity by descent (∆7 and ∆8) and relatedness (rxy) were calculated using estimators that evaluate inbreeding. The two individuals shared most of the alleles, with differences in the genotypes being identified in only two loci. All the estimators identified a level of relatedness compatible with that found between siblings (selfed or outbred), indicating they were dizygotic twins. This is the first confirmed case of fraternal twins in free-ranging West Indian manatees in South America. The recognition of this type of twinning provides elements to improve actions for the rehabilitation of stranded animals and their subsequent release to the environment.
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Affiliation(s)
| | | | | | | | - Juliana Araripe
- Universidade Federal do Pará, Brasil; Universidade do Porto, Portugal
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Microsatellite Analysis for Identification of Individuals Using Bone from the Extinct Steller's Sea Cow (Hydrodamalis gigas). Methods Mol Biol 2017. [PMID: 28502003 DOI: 10.1007/978-1-4939-6990-6_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Microsatellite DNA can provide more detailed population genetic information than mitochondrial DNA which is normally used to research ancient bone. The methods detailed in this chapter can be utilized for any type of bone. However, for this example, four microsatellite loci were isolated from Steller's sea cow (Hydrodamalis gigas) using published primers for manatee and dugong microsatellites. The primers DduC05 (Broderick et al., Mol Ecol Notes 6:1275-1277, 2007), Tmakb60, TmaSC5 (Pause et al., Mol Ecol Notes 6: 1073-1076, 2007), and TmaE11 (Garcia-Rodriguez et al., Mol Ecol 12:2161-2163, 2000) all successfully amplified microsatellites from H. gigas. The DNA samples were from bone collected on Bering or St. Lawrence Islands. DNA was analyzed using primers with the fluorescent label FAM-6. Sequenced alleles were then used to indicate a difference in the number of repeats and thus a difference in individuals. This is the first time that H. gigas microsatellite loci have been isolated. These techniques for ancient bone microsatellite analysis allow an estimate of population size for a newly discovered St. Lawrence Island sea cow population.
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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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Tucker KP, Hunter ME, Bonde RK, Austin JD, Clark AM, Beck CA, McGuire PM, Oli MK. Low genetic diversity and minimal population substructure in the endangered Florida manatee: implications for conservation. J Mammal 2012. [DOI: 10.1644/12-mamm-a-048.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Hunter ME, Mignucci-Giannoni AA, Tucker KP, King TL, Bonde RK, Gray BA, McGuire PM. Puerto Rico and Florida manatees represent genetically distinct groups. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0414-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Nourisson C, Morales-Vela B, Padilla-Saldívar J, Tucker KP, Clark A, Olivera-Gómez LD, Bonde R, McGuire P. Evidence of two genetic clusters of manatees with low genetic diversity in Mexico and implications for their conservation. Genetica 2011; 139:833-42. [PMID: 21681472 DOI: 10.1007/s10709-011-9583-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 05/18/2011] [Indexed: 11/24/2022]
Abstract
The Antillean manatee (Trichechus manatus manatus) occupies the tropical coastal waters of the Greater Antilles and Caribbean, extending from Mexico along Central and South America to Brazil. Historically, manatees were abundant in Mexico, but hunting during the pre-Columbian period, the Spanish colonization and throughout the history of Mexico, has resulted in the significantly reduced population occupying Mexico today. The genetic structure, using microsatellites, shows the presence of two populations in Mexico: the Gulf of Mexico (GMx) and Chetumal Bay (ChB) on the Caribbean coast, with a zone of admixture in between. Both populations show low genetic diversity (GMx: N(A) = 2.69; H(E) = 0.41 and ChB: N(A) = 3.0; H(E) = 0.46). The lower genetic diversity found in the GMx, the largest manatee population in Mexico, is probably due to a combination of a founder effect, as this is the northern range of the sub-species of T. m. manatus, and a bottleneck event. The greater genetic diversity observed along the Caribbean coast, which also has the smallest estimated number of individuals, is possibly due to manatees that come from the GMx and Belize. There is evidence to support limited or unidirectional gene flow between these two important areas. The analyses presented here also suggest minimal evidence of a handful of individual migrants possibly between Florida and Mexico. To address management issues we suggest considering two distinct genetic populations in Mexico, one along the Caribbean coast and one in the riverine systems connected to the GMx.
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Affiliation(s)
- Coralie Nourisson
- El Colegio de la Frontera Sur, Av. Centenario Km 5.5, 77000 Chetumal, Quintana Roo, Mexico.
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Hunter ME, Auil-Gomez NE, Tucker KP, Bonde RK, Powell J, McGuire PM. Low genetic variation and evidence of limited dispersal in the regionally important Belize manatee. Anim Conserv 2010. [DOI: 10.1111/j.1469-1795.2010.00383.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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HUNTER MARGARETKELLOGG, BRODERICK DAMIEN, OVENDEN JENNIFERR, TUCKER KIMBERLYPAUSE, BONDE ROBERTK, MCGUIRE PETERM, LANYON JANETM. Characterization of highly informative cross‐species microsatellite panels for the Australian dugong (
Dugong dugon
) and Florida manatee (
Trichechus manatus latirostris
) including five novel primers. Mol Ecol Resour 2010; 10:368-77. [PMID: 21565032 DOI: 10.1111/j.1755-0998.2009.02761.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- MARGARET KELLOGG HUNTER
- Sirenia Project, Florida Integrated Science Center, U.S. Geological Survey, 2201 NW 40th Terrace, Gainesville, FL 32605, USA
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Box 100245 UFHSC, Gainesville, FL 32610, USA
| | - DAMIEN BRODERICK
- Molecular Fisheries Laboratory, Queensland Department of Primary Industries and Fisheries, Level 3 Ritchie Building, Research Lane, The University of Queensland, St. Lucia, Qld 4072, Australia
| | - JENNIFER R. OVENDEN
- Molecular Fisheries Laboratory, Queensland Department of Primary Industries and Fisheries, Level 3 Ritchie Building, Research Lane, The University of Queensland, St. Lucia, Qld 4072, Australia
| | - KIMBERLY PAUSE TUCKER
- College of Marine Science, University of South Florida, 140 7th Ave S. MSL 119, St. Petersburg, FL 33701, USA
| | - ROBERT K. BONDE
- Sirenia Project, Florida Integrated Science Center, U.S. Geological Survey, 2201 NW 40th Terrace, Gainesville, FL 32605, USA
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Box 100245 UFHSC, Gainesville, FL 32610, USA
| | - PETER M. MCGUIRE
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Box 100245 UFHSC, Gainesville, FL 32610, USA
| | - JANET M. LANYON
- School of Biological Sciences, The University of Queensland, St. Lucia, Qld 4072, Australia
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Tringali MD, Seyoum S, Carney SL, Davis MC, Rodriguez-Lopez MA, Reynolds Iii JE, Haubold E. PERMANENT GENETIC RESOURCES: Eighteen new polymorphic microsatellite markers for the endangered Florida manatee, Trichechus manatus latirostris. Mol Ecol Resour 2008; 8:328-31. [PMID: 21585782 DOI: 10.1111/j.1471-8286.2007.01944.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael D Tringali
- Florida Fish and Wildlife Research Institute, 100 Eighth Avenue S.E. Saint Petersburg, FL 33701-5095, USA, Mote Marine Laboratory, 1600 Thompson Parkway, Sarasota, FL 34236-1004, USA
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PAUSE KIMBERLYC, NOURISSON CORALIE, CLARK ANNMARIE, KELLOGG MARGARETE, BONDE ROBERTK, McGUIRE PETERM. Polymorphic microsatellite DNA markers for the Florida manatee (Trichechus manatus latirostris). ACTA ACUST UNITED AC 2007. [DOI: 10.1111/j.1471-8286.2007.01781.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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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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