Isolation and characterization of 13 microsatellite loci for the Neotropical otter, Lontra longicaudis, by next generation sequencing

  • María Camila Latorre-CardenasEmail author
  • Carla Gutiérrez-Rodríguez
  • Stacey L. Lance
Short Communication


The Neotropical otter, Lontra longicaudis, is an ecologically important species for freshwater ecosystems that is threatened due to habitat destruction and hunting. However, there is limited information regarding the population sizes, genetic diversity, genetic structure and gene flow of the species, which is crucial for the elaboration of conservation plans. The aim of this study was to isolate and characterize microsatellites for L. longicaudis, using Illumina paired-end-sequencing. Initial amplification tests were performed in 48 loci, out of which, 13 yielded high-quality PCR products and thus were further evaluated. Genetic diversity and discrimination power of the 13 microsatellite loci was assessed using 19 non-invasive samples collected in the Jamapa basin in Veracruz, Mexico and blood samples from six captive individuals. All loci were polymorphic, the number of alleles per locus ranged from 4 to 10, the observed heterozygosity from 0.21 to 0.69, and the expected heterozygosity from 0.55 to 0.82. The combined set of 13 microsatellites showed a high power for discriminating among individuals (probability of identity PID = 1.551 × 10−16) and among siblings (probability of identity of siblings PIDSIB = 3.349 × 10−06). A combination of nine loci are sufficient to discriminate among siblings with high confidence (PIDSIB < 0.0001). The new set of microsatellites for the Neotropical otter reported here will provide a useful genetic tool to assess population genetic patterns and ecological parameters of the species.


Discrimination power Genetic diversity Lontra longicaudis Microsatellites Freshwater ecosystems 



This work was partially supported by the National Geographic Society Early Career Grant (# WW-185ER-17), by research funds from the Instituto de Ecología, A.C. (20012-11-080) and by the U. S. Department of Energy under Award Number DOE #DE-EM0004391 to the University of Georgia Research Foundation. María Camila Latorre-Cárdenas was supported by a Doctoral scholarship (#414864) from the Consejo Nacional de Ciencia y Tecnología (CONACyT). The “Acuario de Veracruz, A.C.” donated blood from six individuals. Pablo C. Hernández-Romero, Tarcisio Solis and Luz Magali Sánchez Méndez provided field assistance; and Luz Magali Sánchez Méndez, Denisse Maldonado Sánchez and Cristina Bárcenas laboratory assistance.

Compliance with ethical standards

Conflict of interest

All authors declares that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

11033_2019_5165_MOESM1_ESM.docx (17 kb)
Supplementary material 1 (DOCX 16 kb)


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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Red de Biología Evolutiva, Instituto de Ecología A.CXalapaMéxico
  2. 2.Posgrado Ciencias Biológicas, Universidad Nacional Autónoma de MéxicoCiudad de MéxicoMéxico
  3. 3.Savannah River Ecology LaboratoryUniversity of GeorgiaAikenUSA

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