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Bonde, Robert K.; McGuire, Peter M.; Hunter, Margaret E.
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2012 |
A review of the key genetic tools to assist imperiled species conservation: analyzing West Indian manatee populations.
Jour. Marine Animals & Their Ecology 5(1): 8-19. 2 figs.
–ABSTRACT: Managers faced with decisions on threatened and endangered wildlife populations often are lacking detailed information about the species of concern. Integration of genetic applications will provide management teams with a better ability to assess and monitor recovery efforts on imperiled species. The field of molecular biology continues to progress rapidly and many tools are currently available. Presently, little guidance is available to assist researchers and managers with the appropriate selection of genetic tools to study the status of wild manatee populations. We discuss several genetic tools currently employed in the application of conservation genetics, and address the utility of using these tools to determine population status to aid in conservation efforts. As an example, special emphasis is focused on the endangered West Indian manatee (Order Sirenia). All four extant species of sirenians are imperiled throughout their range, predominately due to anthropogenic sources; therefore, the need for genetic information on their population status is direly needed.
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Hunter, Margaret E.; Mignucci-Giannoni, Antonio A.; Pause Tucker, Kimberly C.; King, Timothy L.; Bonde, Robert K.; Gray, Brian A.; McGuire, Peter M.
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2012 |
Puerto Rico and Florida manatees represent genetically distinct groups.
Conserv. Genet. 13(6): 1623-1635. 3 tabs. 4 figs. + online supplemental material. DOI 10.1007/s10592-012-0414-2 Dec. 2012 (publ. online Oct. 7, 2012).
–ABSTRACT: The West Indian manatee (Trichechus manatus) populations in Florida (T. m. latirostris) and Puerto Rico (T. m. manatus) are considered distinct subspecies and are listed together as endangered under the United States Endangered Species Act. Sustained management and conservation efforts for the Florida subspecies have led to the suggested reclassification of the species to a threatened or delisted status. However, the two populations are geographically distant, morphologically distinct, and habitat degradation and boat strikes continue to threaten the Puerto Rico population. Here, 15 microsatellite markers and mitochondrial control region sequences were used to determine the relatedness of the two populations and investigate the genetic diversity and phylogeographic organization of the Puerto Rico population. Highly divergent allele frequencies were identified between Florida and Puerto Rico using microsatellite (F ST = 0.16; R ST = 0.12 (P < 0.001)) and mitochondrial (F ST = 0.66; Ф ST = 0.50 (P < 0.001)) DNA. Microsatellite Bayesian cluster analyses detected two populations (K = 2) and no admixture or recent migrants between Florida (q = 0.99) and Puerto Rico (q = 0.98). The microsatellite genetic diversity values in Puerto Rico (HE = 0.45; NA = 3.9), were similar, but lower than those previously identified in Florida (HE = 0.48, NA = 4.8). Within Puerto Rico, the mitochondrial genetic diversity values (π = 0.001; h = 0.49) were slightly lower than those previously reported (π = 0.002; h = 0.54) and strong phylogeographic structure was identified (F ST global = 0.82; Ф ST global = 0.78 (P < 0.001)). The genetic division with Florida, low diversity, small population size (N = 250), and distinct threats and habitat emphasize the need for separate protections in Puerto Rico. Conservation efforts including threat mitigation, migration corridors, and protection of subpopulations could lead to improved genetic variation in the endangered Puerto Rico manatee population.
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Luna, Fábia de Oliveira; Bonde, Robert K.; Attademo, Fernanda L. N.; Saunders, Jonathan W.; Meigs-Friend, Gaia; Passavante, José Zanon O.; Hunter, Margaret E.
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2012 |
Phylogeographic implications for release of critically endangered manatee calves rescued in northeast Brazil.
Aquatic Conserv.: Mar. Freshw. Ecosyst. 22(5): 665–672. 2 tabs. 1 fig. DOI: 10.1002/aqc.2260 Publ. online July 4, 2012 in wileyonlinelibrary.com.
–ABSTRACT: 1. The Antillean manatee (Trichechus manatus manatus), a subspecies of the West Indian manatee, is a large-bodied marine mammal found in fresh, brackish, and marine habitats throughout the Caribbean Islands and Central and South America. Antillean manatees in Brazil are classified as critically endangered, with a census size of approximately 500 individuals. The population in the Northeast region of Brazil is suspected to have approximately 300 manatees and is threatened by habitat alteration and incidental entanglement in fishing gear.
2. A high incidence of dependent calf strandings have been identified near areas of altered critical manatee habitat. The majority of the calves are neonates, discovered alive, with no potential mothers nearby. These calves typically require human intervention to survive.
3. Since 1989 the calves have been rescued (N=67), rehabilitated, and released (N=25) to supplement the small wild manatee population. The rescued calves, and those born in captivity, are typically, not released to their rescue location, mainly for logistical reasons. Therefore, phylogeographic analyses can help to identify related populations and appropriate release sites.
4. Here, mitochondrial DNA analyses identified low haplotype (h=0.08) and nucleotide (p=0.0026) genetic diversity in three closely related haplotypes. All three haplotypes (M01, M03, and a previously unidentified haplotype, M04) were found in the northern portion of the region, while only a single haplotype (M01) was represented in the south. This suggests the presence of two genetic groups with a central mixing zone. Release of rehabilitated calves to unrelated populations may result in genetic swamping of locally adapted alleles or genotypes, limiting the evolutionary potential of the population.
5. The small population size coupled with low genetic diversity indicates that the Northeast Brazil manatee population is susceptible to inbreeding depression and possible local extinction. Further conservation measures incorporating genetic information could be beneficial to the critically endangered Brazilian manatee population.
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Pause Tucker, Kimberly C.; Hunter, Margaret E.; Bonde, Robert K.; Austin, James D.; Clark, Ann Marie; Beck, Cathy A.; McGuire, Peter M.; Oli, Madan K.
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2012 |
Low genetic diversity and minimal population substructure in the endangered Florida manatee: implications for conservation.
Jour. Mammalogy 93(6): 1504-1511. 3 tabs. 1 fig. + online supporting information. DOI: 10.1644/12-MAMM-A-048.1 Dec. 17, 2012.
–ABSTRACT: Species of management concern that have been affected by human activities typically are characterized by low genetic diversity, which can adversely affect their ability to adapt to environmental changes. We used 18 microsatellite markers to genotype 362 Florida manatees (Trichechus manatus latirostris), and investigated genetic diversity, population structure, and estimated genetically effective population size (Ne). The observed and expected heterozygosity and average number of alleles were 0.455 ± 0.04, 0.479 ± 0.04, and 4.77 ± 0.51, respectively. All measures of Florida manatee genetic diversity were less than averages reported for placental mammals, including fragmented or nonideal populations. Overall estimates of differentiation were low, though significantly greater than zero, and analysis of molecular variance revealed that over 95% of the total variance was among individuals within predefined management units or among individuals along the coastal subpopulations, with only minor portions of variance explained by between group variance. Although genetic issues, as inferred by neutral genetic markers, appear not to be critical at present, the Florida manatee continues to face demographic challenges due to anthropogenic activities and stochastic factors such as red tides, oil spills, and disease outbreaks; these can further reduce genetic diversity of the manatee population.
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Breaux, Breanna; Heard-Ganir, Ashley; Sena, Leonardo; Hunter, Margaret E.; Bonde, Robert K.; Criscitiello, Michael F.
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2015 |
Understanding manatee immunogenetics and the implications for conservation (VET1P.1121).
Journal of Immunology 194. Suppl. 1.
–-ABSTRACT: The completion of the genome draft of the Florida manatee (Trichechus manatus latirostris) in 2012 made immunogenetic exploration of the Sirenia order more feasible. The endangered manatees are sentinel species for coastal ecosystems and their evolutionary origins are complex. It is believed that they evolved from a wading terrestrial mammal that became fully aquatic, which suggests distinctive adaptations for transitioning to a new environment. Discovering the genetic details of their immune system will help understand manatee evolution and allow species-specific diagnostic tools to be developed. Due to bottleneck signatures at other loci, the genetic diversity of the major histocompatibility complex (MHC) is expected to be low. This could pose problems for conservation efforts because low diversity can increase the chance of extirpation. The primary focus of this project is to determine the immune robustness of manatees by looking at their antibody repertoire and MHC polymorphism. Two species will be compared: the West Indian manatee (T. manatus) and the Amazonian manatee (T. inunguis). Using next generation sequencing, we will robustly sample the IgH and IgL rearrangements contributing to the antibody repertoire, and identify dominant MHC alleles and estimate their frequencies. The allelic distribution between the species could reveal clues to their evolutionary relationship and aid conservation efforts to help this species become more stable in their environment.
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Foote, Andrew D.; Liu, Yue; Thomas, Gregg W. C.; Vinar, Tomas; Alfoeldi, Jessica; Deng, Jixin; Dugan, Shannon; van Elk, Cornelis E.; Hunter, Margaret E.; Joshi, Vandita; Khan, Ziad; Kovar, Christie; Lee, Sandra L.; Lindblad-Toh, Kerstin; Mancia, Annalaura; Nielsen, Rasmus; Qin, Xiang; Qu, Jiaxin; Raney, Brian J.; Vijay, Nagarjun; Wolf, Jochen B. W.; Hahn, Matthew W.; Muzny, Donna M.; Worley, Kim C.; Gilbert, M. Thomas P.; Gibbs, Richard A.
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2015 |
Convergent evolution of the genomes of marine mammals.
Nature Genetics 47(3): 272–275. 5 figs. DOI:10.1038/ng.3198. Mar. 2015.
–ABSTRACT: Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and therefore represent a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and performed de novo assembly of the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome and that a subset of these substitutions were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that, whereas convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare.
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Breaux, Breanna; Deiss, Thaddeus C.; Chen, Patricia L.; Cruz-Schneider, Maria Paula; Sena, Leonardo; Hunter, Margaret E.; Bonde, Robert K.; Criscitiello, Michael F.
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2017 |
The Florida manatee (Trichechus manatus latirostris) immunoglobulin heavy chain reveals the importance of clan III variable segments in repertoire diversity.
Developmental & Comparative Immunology 72: 57-68. 7 figs. + supplementary material. doi:/10.1016/j.dci.2017.01.022. Publ. online July 25, 2017.
–ABSTRACT: Manatees are a vulnerable, charismatic sentinel species from the evolutionarily divergent Afrotheria. Manatee health and resistance to infectious disease is of great concern to conservation groups, but little is known about their immune system. To develop manatee-specific tools for monitoring health, we first must have a general knowledge of how the immunoglobulin heavy (IgH) chain locus is organized and transcriptionally expressed. Using the genomic scaffolds of the Florida manatee (Trichechus manatus latirostris), we characterized the potential IgH segmental diversity and constant region isotypic diversity and performed the first Afrotherian repertoire analysis. The Florida manatee has low V(D)J combinatorial diversity (3744 potential combinations) and few constant region isotypes. They also lack clan III V segments, which may have caused reduced VH segment numbers. However, we found productive somatic hypermutation concentrated in the complementarity determining regions. In conclusion, manatees have limited IGHV clan and combinatorial diversity. This suggests that clan III V segments are essential for maintaining IgH locus diversity.
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Diaz-Ferguson, Edgardo; Hunter, Margaret E.; Guzmán, Héctor M.
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2017 |
Genetic composition and connectivity of the Antillean manatee (Trichechus manatus manatus) in Panama.
Aquatic Mammals 43(4): 378-386. 2 tabs. 2 figs. doi:10.1578/AM.43.4.2017.378. July 10, 2017.
–ABSTRACT: Genetic diversity and haplotype composition of the West Indian manatee (Trichechus manatus) population from the San San Pond Sak (SSPS) wetland in Bocas del Toro, Panama, was studied using a segment of the mitochondrial DNA (control region). No genetic information to date has been published for manatee populations in Panama. Due to the secretive behavior and small population size of the species in the area, DNA extraction was conducted from opportunistically collected fecal (N = 20), carcass tissue (N = 4), and bone (N = 4) samples. However, after DNA processing, only 10 samples provided enough quality DNA for sequencing -- three fecal, four tissue, and three bone samples. We identified three haplotypes in total: J01 was previously published (N = 3), while the other two haplotypes, J02 (N = 3) and J03 (N = 4), are reported for the first time. The genetic diversity was similar to previous analyses conducted in the Caribbean with moderate values of nucleotide (pi = 0.00152) and haplotypic (Hd = 0.57) diversity. Connectivity assessment between the SSPS population with published range-wide manatee haplotypes was based on sequence similarity, genetic distance, and genetic differentiation. The identified J01 haplotype is also found in populations to the north along the Central American and Gulf of Mexico coasts indicating reduced differentiation (Fst = 0.0094). In contrast, comparisons between SSPS sequences and South American populations (not including Colombia), the West Indies, and Florida showed fewer similarities (Fst = 0.049 and 0.058, respectively). These results corroborate previous phylogeographic patterns already established for manatee populations and situate the manatee population in Panama within the Belize/Mexico cluster. In addition, these findings provide a baseline for comparative studies of manatees in other areas of Panama and Central America. These results can assist with management decisions regarding conservation of genetic diversity, future introductions, connectivity, and effective population size of manatee populations along the Central American corridor.
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Ferrante, J. A.; Hunter, Margaret E.; Wellehan, J. F. X.
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2018 |
Development and validation of quantitative PCR assays to measure cytokine transcript levels in the Florida manatee (Trichechus manatus latirostris).
Jour. Wildlife Diseases 54(2): 283-294. doi:10.7589/2017-06-139. April 2018.
–ABSTRACT: Cytokines have important roles in the mammalian response to viral and bacterial infections, trauma, and wound healing. Because of early cytokine production after physiologic stresses, the regulation of messenger RNA (mRNA) transcripts can be used to assess immunologic responses before changes in protein production. To detect and assess early immune changes in endangered Florida manatees (Trichechus manatus latirostris), we developed and validated a panel of quantitative PCR assays to measure mRNA transcription levels for the cytokines interferon (IFN)-?; interleukin (IL)-2, -6, and -10; tumor necrosis factor-?; and the housekeeping genes glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and ?-actin (reference genes). Assays were successfully validated using blood samples from free-ranging, apparently healthy manatees from the east and west coasts of central Florida, US. No cytokine or housekeeping gene transcription levels were significantly different among age classes or sexes. However, the transcription levels for GAPDH, IL-2, IL-6, and IFN-? were significantly higher (P<0.05) in manatees from the east coast of Florida than they were from those from the west coast. We found IL-10 and ?-actin to be consistent between sites and identified ?-actin as a good candidate for use as a reference gene in future studies. Our assays can aid in the investigation of manatee immune response to physical trauma and novel or ongoing environmental stressors.
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Hunter, Margaret E.; Meigs-Friend, Gaia; Ferrante, Jason A.; Takoukam Kamla, Aristide; Dorazio, Robert M.; Keith Diagne, Lucy; Luna, Fabia; Lanyon, Janet M.; Reid, James P.
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2018 |
Surveys of environmental DNA (eDNA): a new approach to estimate occurrence in Vulnerable manatee populations.
Endangered Species Research 35: 101-111. doi:10.3354/esr00880. Mar. 13, 2018.
–ABSTRACT: Environmental DNA (eDNA) detection is a technique used to non-invasively detect cryptic, low density, or logistically difficult-to-study species, such as imperiled manatees. For eDNA measurement, genetic material shed into the environment is concentrated from water samples and analyzed for the presence of target species. Cytochrome b quantitative PCR and droplet digital PCR eDNA assays were developed for the 3 Vulnerable manatee species: African, Amazonian, and both subspecies of the West Indian (Florida and Antillean) manatee. Environmental DNA assays can help to delineate manatee habitat ranges, high use areas, and seasonal population changes. To validate the assay, water was analyzed from Florida's east coast containing a high-density manatee population and produced 31564 DNA molecules l-1 on average and high occurrence (?) and detection (p) estimates (? = 0.84 [0.40-0.99]; p = 0.99 [0.95-1.00]; limit of detection 3 copies µl-1). Similar occupancy estimates were produced in the Florida Panhandle (? = 0.79 [0.54-0.97]) and Cuba (? = 0.89 [0.54-1.00]), while occupancy estimates in Cameroon were lower (? = 0.49 [0.09-0.95]). The eDNA-derived detection estimates were higher than those generated using aerial survey data on the west coast of Florida and may be effective for population monitoring. Subsequent eDNA studies could be particularly useful in locations where manatees are (1) difficult to identify visually (e.g. the Amazon River and Africa), (2) are present in patchy distributions or are on the verge of extinction (e.g. Jamaica, Haiti), and (3) where repatriation efforts are proposed (e.g. Brazil, Guadeloupe). Extension of these eDNA techniques could be applied to other imperiled marine mammal populations such as African and Asian dugongs.
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De María, Maite; Silva-Sanchez, Cecilia; Kroll, Kevin J.; Walsh, Michael T.; Nouria, Mohammad-Zaman; Hunter, Margaret E.; Ross, Monica; Clauss, Tonya M.; Denslow, Nancy D.
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2021 |
Chronic exposure to glyphosate in Florida manatee.
Environment International 152: 3 tabs. 3 figs. https://doi.org/10.1016/j.envint.2021.106493 July 2021.
–ABSTRACT: Florida manatees depend on freshwater environments as a source of drinking water and as warm-water refuges. These freshwater environments are in direct contact with human activities where glyphosate-based herbicides are being used. Glyphosate is the most used herbicide worldwide and it is intensively used in Florida as a sugarcane ripener and to control invasive aquatic plants. The objective of the present study was to determine the concentration of glyphosate and its breakdown product, aminomethylphosphonic acid (AMPA), in Florida manatee plasma and assess their exposure to manatees seeking a warm-water refuge in Crystal River (west central Florida), and in South Florida. We analyzed glyphosate's and AMPA's concentrations in Florida manatee plasma (n = 105) collected during 2009–2019 using HPLC-MS/MS. We sampled eight Florida water bodies between 2019 and 2020, three times a year: before, during and after the sugarcane harvest using grab samples and molecular imprinted passive Polar Organic Chemical Integrative Samplers (MIP-POCIS). Glyphosate was present in 55.8% of the sampled Florida manatees' plasma. The concentration of glyphosate has significantly increased in Florida manatee samples from 2009 until 2019. Glyphosate and AMPA were ubiquitous in water bodies. The concentration of glyphosate and AMPA was higher in South Florida than in Crystal River, particularly before and during the sugarcane harvest when Florida manatees depend on warm water refuges. Based on our results, Florida manatees were chronically exposed to glyphosate and AMPA, during and beyond the glyphosate applications to sugarcane, possibly associated with multiple uses of glyphosate-based herbicides for other crops or to control aquatic weeds. This chronic exposure in Florida water bodies may have consequences for Florida manatees' immune and renal systems which may further be compounded by other environmental exposures such as red tide or cold stress.
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Luna, Fábia de Oliveira; Beaver, Caitlin E.; Nourisson, Coralie; Bonde, Robert K.; Attademo, Fernanda L. N.; Miranda, Adriana Vieira; Torres-Florez, Juan Pablo; Sousa, Glaucia Pereira de; Passavante, José Zanon; Hunter, Margaret E.
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2021 |
Genetic connectivity of the West Indian Manatee in the southern range and limited evidence of hybridization with Amazonian manatees.
Front. Mar. Sci. 7: 574455. 4 tabs. 4 figs. + online supplementary material. https://doi.org/10.3389/fmars.2020.574455 Jan. 6, 2021.
–ABSTRACT: The Antillean subspecies of the West Indian manatee is classified as endangered by the International Union for the Conservation of Nature (IUCN) Red List. In Brazil, the manatee population is listed as endangered with an estimated population size of 500–1,000. Historic hunting, recent habitat degradation, and fisheries bycatch have decreased the population size. The Amazonian manatee is listed as vulnerable by the IUCN with unknown population sizes within Brazil. The Antillean manatee occurs in sympatry with the Amazonian manatee in Brazil and hybridization has been previously indicated. To provide information on the genetic structure, diversity, and degree of hybridization in the sympatric zone near the Amazon River mouth, the mitochondrial DNA control region and 13 nuclear microsatellite markers were assessed on the two species. Samples were analyzed from the Antillean subspecies across its distribution in Brazil (n = 78) and from the Amazonian species (n = 17) at the Amazon River mouth and inland mainstem river. To assess the previously defined evolutionary significant units of Antillean manatees in the area, an additional 11 samples from Venezuela and Guyana were included. The Antillean manatee was found to be a single population in Brazil and had lower than average number of alleles (3.00), expected heterozygosity (0.34), and haplotype diversity (0.15) when compared to many other manatee populations. The low values may be influenced by the small population size and extended pressures from anthropogenic threats. Gene flow was identified with Venezuela/Guyana in admixed Antillean Brazil samples, although the two populations were found to be moderately divergent. The nuclear loci in Venezuela/Guyana Antillean manatee samples indicated high differentiation from the samples collected in the Amazon River (FST = 0.35 and RST = 0.18, p = 0.0001). No indication of nuclear hybridization was found except for a single sample, "Poque" that had been identified previously. The distribution of Antillean manatees in Brazil is extensive and the areas with unique habitat and threats would benefit from independent management and conservation actions. Gene flow, resulting in genetic diversity and long-term population stability, could be improved in the southern range through habitat restoration, and the establishments of travel corridors and protected areas, which are particularly important for successful parturition and neonatal calf survival.
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Alvarez-Aleman, Anmari; Hunter, Margaret E.; Frazer, Thomas K.; Powell, James A.; Garcia-Alfonso, Eddy; Austin, James D.
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2022 |
The first assessment of the genetic diversity and structure of the endangered West Indian manatee in Cuba.
Genetica 150: 327-341. Oct. 22, 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 pi=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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Bibliography and Index of the Sirenia and Desmostylia 