Noninvasive Fecal Sampling Research Articles

Assessing reliability of microsatellite genotypes from kit fox faecal samples using genetic and GIS analyses

Noninvasive faecal DNA sampling has the potential to provide a wealth of information necessary for monitoring and managing endangered species while eliminating the need to capture, handle or observe rare individuals. However, scoring problems, and subsequent genotyping errors, associated with this monitoring method remain a great concern as they can lead to misidentification of individuals and biased estimates. We examined a kit fox scat data set (353 scats; 80 genotypes) for genotyping errors using both genetic and GIS analyses, and evaluated the feasibility of combining both approaches to assess reliability of the faecal DNA results. We further checked the appropriateness of using faecal genotypes to study kit fox populations by describing information about foxes that we could deduce from the 'acceptable' scat genotypes, and comparing it to information gathered with traditional field techniques. Overall, genetic tests indicated that our data set had a low rate of genotyping error. Furthermore, examination of distributions of scat locations confirmed our data set was relatively error free. We found that analysing information on sex primer consistency and scat locations provided a useful assessment of scat genotype error, and greatly limited the amount of additional laboratory work that was needed to identify potentially 'false' scores. 'Acceptable' scat genotypes revealed information on sex ratio, relatedness, fox movement patterns, latrine use, and size of home range. Results from genetic and field data were consistent, supporting the conclusion that our data set had a very low rate of genotyping error and that this noninvasive method is a reliable approach for monitoring kit foxes.

Identification of hepatitis B virus genome in faecal sample from wild living chimpanzee ( Pan troglodytes troglodytes) in Gabon

Non-invasive faecal sampling in the equatorial forest in Gabon allowed the first identification of the hepatitis B virus (HBV-Ch RC170) genome in samples collected from wild chimpanzees ( Pan troglodytes troglodytes). The HBV-Ch RCl70sequence clustered with 100% bootstrap support with previous viral sequences obtained from Pan troglodytes subspecies. This is the first evidence of HBV infection in wild apes and confirms that the HBV-like strains thus far characterized in captive apes are directly related to those circulating in the wild.

Reproductive biology and conservation of muriquis


 
 
 
 This paper summarizes some of the major findings on the reproductive biology of one group of northern muriquis (Brachyteles hypoxanthus) at the RPPN Feliciano Miguel Abdala (previously known as the Estação Biológica de Caratinga). Long-term monitoring of individual members of the Matão group, combined with non-invasive fecal sampling to measure hormone levels, provide insights into ovarian function, reproductive seasonality, and factors that influence individual and population reproductive rates. All of these parameters have direct applications for assessing the long-term viability of this population, and for conservation of this critically endangered species. These findings were presented at the first meeting of the Committee for the Conservation and Management of the Muriqui (IBAMA), held in Teresópolis, Rio de Janeiro, in October 2002; more recent data have been added or are included in the references.
 
 
 

Phylogeography, genetic structure, and diversity in the dhole (Cuon alpinus)

The Asiatic wild dog or dhole was once very widely distributed across Asia but now has a very fragmented range. In this first genetic study of this little-known species, we obtained information on genetic diversity, phylogeography, and social structure using both mitochondrial control region sequencing and microsatellite genotyping of noninvasive faecal samples from wild populations, as well as from museum and captive samples. A pattern largely consistent with isolation by distance across the Asian mainland was observed, with no clear subspecies distinctions. However, two major phylogeographical groupings were found across the mainland, one extending from South, Central, and North India (south of the Ganges) into Myanmar, and the other extending from India north of the Ganges into northeastern India, Myanmar, Thailand and the Malaysian Peninsula. We propose a scenario involving glaciation events that could explain this pattern. The origin of the dhole populations in Sumatra and Java is enigmatic and requires further study. Very low levels of genetic diversity were observed among wild dholes from Baluran National Park in Java, Indonesia, but in contrast, high levels were observed in Mudumalai Wildlife Sanctuary in South India.

Factors Related to Fecal Corticosterone Levels in California Spotted Owls: Implications for Assessing Chronic Stress

Abstract: The California Spotted Owl (Strix occidentalis occidentalis) is under consideration for federal protection and has stimulated ecosystem‐level management efforts in Sierra Nevada national forests. Because some populations are declining, we used a noninvasive fecal sampling method to estimate stress hormone (i.e., corticosterone) levels within a local population from April to August 2001. Fecal corticosterone levels were similar to those recorded in a previous study of Northern Spotted Owls (S.o. caurina) ( x̄= 80.1 ng/g dry feces, SE = 75.8). We then used an information‐theoretic approach to identify factors that influence fecal corticosterone levels in Spotted Owls. Our best overall model indicated that nonbreeding owls had higher fecal corticosterone levels than breeding owls early in the breeding season and lower levels later in the breeding season. We collected few samples from breeding owls early in the breeding season, however, which may have influenced the results. Management‐related factors reflecting habitat condition and proximity to roads were not correlated with fecal corticosterone. However, factors such as field storage method and sample mass were correlated with the amount of measured fecal corticosterone and should be considered in future studies. Sample vials initially stored on ice had higher levels than those stored immediately in liquid N2 (βstorage= 0.269 ln[ng/g], 95% CI = 0.026, 0.512). Hormone metabolites were extracted from extremely small samples (0.01 g) by slightly modifying the assay protocol, but the amount of corticosterone detected increased as the sample mass decreased (βmass=−6.248 ln[ng/g], 95% CI =−8.877, −3.620). Corticosterone levels were significantly higher in 10 cecal samples collected simultaneously with fecal samples (paired difference = 74.7 ng/g, SE = 45.0, p = 0.001 for a paired t test), so care must be taken to avoid contaminating fecal samples with cecal material. Most of the variation was unexplained by our best model ( R2= 0.24), and additional factors influencing fecal corticosterone levels need to be identified. Therefore, we recommend that well‐designed experiments be conducted under controlled conditions to better determine the effect of factors such as sample handling, partial sampling, and diet on fecal corticosterone levels in owls and other birds.