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The first assessment of the genetic diversity and structure of the endangered West Indian manatee in Cuba

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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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Acknowledgements

Manatee captures in Cuba were coordinated and implemented by the Center for Marine Research at the University of Havana, the United State Geological Survey, and the Clearwater Marine Aquarium Research Institute. All the required national and international permits were obtained for the manatee capture, sample collection, and export to the United States. We thank the University of Havana, the National Center of Protected Areas, and the National Enterprise of Flora and Fauna for supporting this research. This work resulted from a partnership among colleagues and volunteers across Cuba, and we thank D. Cobian, Y. Forneiro, Z. Hernandez, L. Rodriguez, A. Hurtado, J. A. Tamayo, F. Pina, L. Garcia, D. Cruz, N. Hernandez, J. Izquierdo, A. Ruiz, M. E Ibarra-Martin (RIP), J. A. Santos (RIP), A. Arias, R. Fernandez, F. Hernández, N Vina, and R. Volta. Thanks to Dr. Jessy Castellanos-Gell and Courtney Pylant for their help with the initial optimization steps of the microsatellite protocol, sequencing, PCR, and lab work in general. Thanks to different colleagues for their input in this work, Gaia Meigs-Friend, Aristide Kamla, Lucy Keith, Sarah Duncan, Andrew Marx, and Paula Satizabal. J. Angulo and R. Bonde provided valuable advice and support. Thanks to Tracy Caledine for her input on the figures production. We thank two anonymous reviewers for helpful comments that greatly improved the manuscript. The content of this manuscript was part of the first author’s dissertation at the University of Florida. Any trade, firm, or product name is for descriptive purposes only and does not imply endorsement by the United States Government.

Funding

This work was supported by Sea to Shore Alliance, the John T and Catherine D MacArthur Foundation, the Eppley Foundation, the Waitt Foundation, the Marine Mammal Commission (Grant MMC17-222), the Society for Marine Mammalogy Grants in Aid of Research, the Ron Magill Conservation Scholarship, Operation Wallacea and the GEF-UNDP-CNAP project “Regional approach to the management of the South Archipelagos of Cuba, 2009–2014,” and the National Institute of Food and Agriculture, U.S. Department of Agriculture Hatch project (FLA-WEC-005797).

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Authors and Affiliations

  1. School of Natural Resources and Environment, University of Florida, 2035 McCarty hall D, Gainesville, FL, 32611, USA

    Anmari Alvarez-Aleman, Thomas K. Frazer & James D. Austin

  2. Centro de Investigaciones Marinas, Universidad de La Habana, Calle 16 # 114 Entre 1ra y 3ra Plaza, Havana, Cuba

    Anmari Alvarez-Aleman

  3. Clearwater Marine Aquarium Research Institute, Clearwater Marine Aquarium, Clearwater, FL, USA

    Anmari Alvarez-Aleman & James A. Powell

  4. U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, USA

    Margaret E. Hunter

  5. Refugio de Fauna Lanzanillo-Pajonal-Fragoso, Empresa Provincial para la Protección de la Flora y la Fauna, Villa Clara, Cuba

    Eddy Garcia Alfonso

  6. Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, FL, 32611, USA

    James D. Austin

  7. College of Marine Science, University of South Florida, 140 Seventh Avenue South, KRC 3109, St. Petersburg, FL, 33701, USA

    Thomas K. Frazer

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  1. Anmari Alvarez-Aleman
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Contributions

All authors contributed to the study conception and design. Data collection performed by AA-A, MH and EG. AA-A and JA implemented analysis. The first draft of the manuscript was written by AA-A and JA and all authors reviewed and commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Correspondence to Anmari Alvarez-Aleman.

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Alvarez-Aleman, A., Hunter, M.E., Frazer, T.K. et al. The first assessment of the genetic diversity and structure of the endangered West Indian manatee in Cuba. Genetica 150, 327–341 (2022). https://doi.org/10.1007/s10709-022-00172-8

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