Assessing Genetic Diversity, Connectivity, and Demographic Parameters of Neotropical Otters (Lontra annectens) in Northern Costa Rica

The recent recognition of the Neotropical otter (Lontra annectens) as a distinct species highlights the need to evaluate its genetic status and connectivity across fragmented tropical habitats. We analyzed genetic diversity, population structure, and recent demographic patterns of L. annectens from two contrasting regions in northern Costa Rica—Tortuguero National Park (TNP) and the Sarapiquí River Basin (SRB). Non-invasive fecal and anal-gland secretion samples collected during 2021–2022 were genotyped at ten nuclear DNA microsatellite loci. Genetic diversity was moderate across regions (mean allelic richness [AR] = 3.98–4.03, observed heterozygosity [Ho] = 0.52–0.58), expected heterozygosity [He] = 0.62–0.65) with no significant inter-regional differences. Bayesian clustering, principal component analysis, and pairwise FST (0.002) supported a near-panmictic population. Kinship analyses detected localized clusters of related individuals, suggesting weak but non-random structuring, while contemporary migration estimates indicated low-frequency, asymmetric gene flow from SRB to TNP. Bottleneck tests revealed signatures of recent demographic contraction in both regions, particularly in TNP. These findings demonstrate limited yet ongoing connectivity among riverine subpopulations and emphasize that increasing habitat fragmentation could erode this exchange. Maintaining hydrological corridors and monitoring genetically vulnerable subpopulations should be conservation priorities to preserve gene flow and long-term viability of L. annectens in northern Costa Rica.