Pygmy Rabbit Monitoring in Washington

Evaluating noninvasive genetic monitoring for endangered pygmy rabbit recovery efforts

Student: Steph DeMay

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Genetic monitoring of reintroduced pygmy rabbits (Brachylagus idahoensis) is crucial for assessing the success of recovery efforts for an endangered population in central Washington. Noninvasive genetic sampling of faecal pellets could be a valuable method. We evaluated the effect of sample age on DNA degradation in faecal pellets under summer field conditions. We placed 275 samples from known individuals in natural field conditions for 1 to 60 days before DNA analysis. We assessed DNA quality by amplifying a species-specific mitochondrial DNA (mtDNA) locus and 5 nuclear DNA (nDNA) microsatellite loci. Both mtDNA and nDNA exhibited high PCR success rates (94.%) in samples <1 day old. Success rates for microsatellite loci declined rapidly from 80.0% to 42.7% between days 5 and 7, likely due to increased environmental temperature. Success rates for mtDNA amplification were higher, with moderate success (66.7%) at 21 days. Logistic regression modelling indicated that DNA degradation was influenced by sample age, DNA type, locus length, and rabbit sex. Allelic dropout rates were relatively high (17.6% at < 1 day) and increased to 100% over time. False allele rates ranged from 0 to 30.0% and increased over time. We recommend collecting samples as fresh as possible for individual identification, ideally within 5 days. Our study suggests that this method can be useful for future monitoring efforts, including occupancy surveys, individual identification, population estimation, parentage analysis, and monitoring of demographic trends.