Noninvasive genetic sampling of two flying fox species provides a high rate of genotyping success and a low error rate during amplification

Noninvasive genetic sampling techniques are useful tools for providing genetic data that are crucially needed for determining suitable conservation actions. Yet these methods may be highly unreliable in certain situations for instance, when working with faecal samples of frugivorous species in tropical areas. In this study, we tested the applicability of noninvasive genetic sampling on two Comoro Islands flying fox species: Pteropus livingstonii and P.seychellensis comorensis in order to optimize the sampling and laboratory process. Both mitochondrial (mtDNA) and microsatellite markers were tested using two common faeces conservation protocols (ethanol and silica gel), and the polymerase chain reaction (PCR) success and genotyping error rates were assessed. The average proportion of mtDNA PCRs positive results was 55% for P.livingstonii and 38% for P.s.comorensis, and higher amplification success was obtained for samples preserved in ethanol as compared to silica gel. The average genotyping success rate was high (74% for P.livingstonii and 95% for P.s.comorensis) and the genotyping error rate was low for both species. Despite our results confirm the effectiveness of using noninvasive genetic sampling methods to study flying fox species, the protocol we used can be optimized to provide higher efficiency. Some recommendations related to field sampling protocols and laboratory methods are proposed in order to optimize amplification rate and minimize genotyping errors.

Genetic Diversity and Prediction Analysis of Small Isolated Giant Panda Populations After Release of Individuals

Release of individuals is an effective conservation approach to protect endangered species. To save this small isolated giant panda population in Liziping Nature Reserve, a few giant pandas have been released to this population. Here we assess genetic diversity and future changes in the population using noninvasive genetic sampling after releasing giant pandas. In this study, a total of 28 giant pandas (including 4 released individuals) were identified in the Liziping, China. Compared with other giant panda populations, this population has medium-level genetic diversity; however, a Bayesian-coalescent method clearly detected, quantified, and dated a recent decrease in population size. The predictions for genetic diversity and survival of the population in the next 100 years indicate that this population has a high risk of extinction. We show that released giant pandas can preserve genetic diversity and improve the probability of survival in this small isolated giant panda population. To promote the recovery of this population, we suggest that panda release should be continued and this population will need to release 10 males and 20 females in the future.

Estimating densities for sympatric kit foxes (Vulpes macrotis) and coyotes (Canis latrans) using noninvasive genetic sampling

Kit fox (Vulpes macrotis Merriam, 1888) populations in the Great Basin Desert have declined and are of increasing concern for managers. Increasing coyote (Canis latrans Say, 1823) abundance and subsequent intraguild interactions may be one cause for this decline. Concurrent monitoring of carnivores is challenging and therefore rarely conducted. One possible solution for monitoring elusive carnivores is using noninvasive genetic sampling. We used noninvasive genetic sampling to collect fecal DNA from kit foxes and coyotes and estimate their densities from 2013–2014 in Utah, USA. We identified individuals based on microsatellite genotypes and estimated density with multisession spatially explicit capture–recapture models. Mean kit fox density was 0.02 foxes·km−2, while coyote densities were up to four times greater (0.07–0.08 coyotes·km−2). Kit fox densities were significantly lower than densities in the 1950s but were comparable with estimates from the late 1990s, suggesting that populations may be stabilizing after a precipitous decline. Our kit fox density estimates were among the lowest documented for the species. Our coyote density estimate was the first reported in our region and revealed that despite seemingly high abundance, densities are low compared with other regions. Our results suggested that kit foxes may be able to coexist with coyotes.