Habitat deterioration and fragmentation increase the risk of wildlife extirpation as they have strong impacts on population size, genetic diversity and gene flow. Small populations are more susceptible to these factors because the loss of genetic diversity by drift and inbreeding occurs at faster rates. Therefore, estimates of genetic diversity and population sizes of threatened and small wildlife populations in deteriorated landscapes are critical for managing and conservation. Here, we used a non-invasive sampling approach in combination with eleven microsatellite loci to evaluate genetic diversity, genetic structure, and demographic parameters of the Neotropical otter (Lontra longicaudis) in three river basins (Actopan, La Antigua and Jamapa), which are priority conservation areas for Veracruz, Mexico. Our results revealed moderate genetic diversity and genetic structure among river basins. However, we detected first-generation migrants among basins, suggesting current gene flow. Effective population size for each basin was considerably lower than the value (N_e < 100) suggested to maintain genetic variation of populations in the short-term. Similarly, census population size was lower than estimates reported for L. longicaudis in a conserved region in Mexico. We did not find evidence of recent genetic bottlenecks for any basin. Our genetic and demographic results suggest that L. longicaudis in the three river basins could be experiencing genetic isolation and erosion, with La Antigua being the most vulnerable basin. Natural fragmentation and habitat deterioration seem to be shaping the observed patterns of genetic variation in the Neotropical otter.

栖息地的恶化和破碎化增加了野生动植物灭绝的风险，因为它们对种群数量，遗传多样性和基因流产生强烈影响。小种群更容易受到这些因素的影响，因为漂移和近交导致的遗传多样性丧失以更快的速度发生。因此，对退化景观中受威胁的野生动植物种群的遗传多样性和种群规模进行估算对于管理和保护至关重要。在这里，我们结合11个微卫星基因座使用了非侵入性采样方法来评估新热带水獭（Lontra longicaudis）的遗传多样性，遗传结构和人口统计学参数）位于三个流域（阿托邦，拉安提瓜和贾马帕），这是墨西哥韦拉克鲁斯的优先保护区。我们的研究结果揭示了流域之间适度的遗传多样性和遗传结构。但是，我们在盆地之间检测到第一代移民，这表明当前的基因流动。每个流域的有效种群规模大大低于 为维持短期种群遗传变异而建议的数值（N _e <100）。同样，人口普查的人口规模低于墨西哥一个自然保护区的L. longicaudis所报告的估计数。我们没有找到任何盆地最近的遗传瓶颈的证据。我们的遗传和人口统计学结果表明，L。longicaudis三个安提瓜流域可能正在遭受遗传隔离和侵蚀，拉安提瓜是最脆弱的流域。自然碎片和栖息地恶化似乎正在塑造新热带水獭的遗传变异模式。