Abstract
Molecular tools provide critical insights into population processes by enabling the detection of genetic diversity, demographic history, and ecological interactions across landscapes. In this dissertation, I employed noninvasive DNA analyses to evaluate methodological improvements for river otters (Lontra canadensis and L. annectens) fecal sampling, characterize the genetic diversity, structure, and demography of Neotropical otters (L. annectens), and integrate kinship, and dietary assessments of Pampas cats (Leopardus garleppi). These studies illustrate how fine-scale genetic and ecological data inform conservation strategies for small and fragmented populations.In Chapter 1, I evaluate two noninvasive DNA collection and storage protocols for monitoring river otters (L. canadensis and L. annectens) in contrasting environments. I compared fecal material preserved in dimethyl sulfoxide saline solution (DETs buffer) with external fecal swabbing in sodium dodecyl sulfate (ATL buffer), predicting that swabbing would enhance PCR amplification and reduce microsatellite genotyping errors by targeting epithelial cells on the scat surface while avoiding inhibitors. Between 2021 and 2022, I collected fecal samples from the Big Sioux River, South Dakota (temperate environment), and Tortuguero National Park, Costa Rica (tropical environment). DNA was extracted from both fresh and aged scats stored using DETs and swab protocols. I assessed PCR amplification success, genotyping success, and mismatch rates. Swabbing outperformed DETs across both sites, yielding a 42% amplification rate compared to 18% for DETs, and 51% genotyping success versus 20%. Mismatch rates were 4% lower with swabbing, and jelly samples stored with swabs provided the highest success, particularly in tropical environments. These findings demonstrate that fecal swabbing improves DNA retrieval and reduces error, offering a robust tool for noninvasive genetic monitoring of otters and other elusive mammals.
In Chapter 2, I investigate the population genetics and demographic history of the Neotropical otter (L. annectens) across two ecologically distinct regions of northern Costa Rica: Tortuguero National Park (TNP) and the Sarapiquí River Basin (SRB). I genotyped 10 nuclear microsatellite loci from noninvasively collected fecal and anal-gland secretion samples obtained during 2021–2022. Genetic diversity was moderate and comparable across sites (observed [Ho = 0.52–0.58]; and expected heterozygosity [He = 0.62–0.65]). Bayesian clustering, principal component analysis, and pairwise FST (~0.002) all indicated a near-panmictic population, consistent with ongoing gene flow. Nevertheless, kinship analyses identified localized clusters of relatives, implying limited dispersal and fine-scale structure. Contemporary migration estimates showed low, asymmetric movement primarily from SRB to TNP, and bottleneck tests detected heterozygosity excess with reduced M-ratios, indicating recent demographic contractions. Overall, while connectivity persists, it appears increasingly constrained by fragmentation; these baseline data on diversity, kinship, and gene flow support targeted management to maintain corridor function and long-term viability of L. annectens in tropical freshwater systems.
In Chapter 3, I examine the genetic diversity, kin structure, and trophic ecology of the Pampas cat (L. garleppi) in the Mangroves San Pedro de Vice (MSPV), a Ramsar-listed wetland in northwestern Peru. Using noninvasive fecal DNA collected between 2019 and 2021, I genotyped eight microsatellite loci and characterized diet via DNA metabarcoding. From 68 genotyped scats, nine individuals were identified (six males, three females). Genetic diversity was moderate (allelic richness = 3.47; Ho = 0.69; He = 0.58), yet bottleneck signals, including heterozygosity excess and a low M-ratio, indicated recent demographic contraction. Relatedness analyses revealed several first-order kin pairs, suggesting a kin-structured population with limited immigration. Diet analyses detected eight vertebrate prey species dominated by the native rodent Aegialomys xanthaeolus, with no sex-based dietary differences. Together, these results reveal a small, closely related population with reduced allelic richness and constrained connectivity at the northwestern range edge. Overall, this chapter highlights the vulnerability of L. garleppi in degraded coastal wetlands and underscores the need for integrated genetic, demographic, and dietary monitoring to inform conservation actions.