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

Abstract

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.

Maned wolves retain moderate levels of genetic diversity and gene flow despite drastic habitat fragmentation

“…Twelve microsatellite loci, originally designed for domestic dog, were selected on the basis of polymorphism level, reliable amplification and easy scorability in several canid species (Franco Berriel 2004, Smith et al 2006, Salim et al 2007, Fontoura-Rodrigues et al 2008, Lion et al 2011, Do Passo Ramalho et al 2014. Based on annealing temperature, fragment size and fluorochrome label, we designed 4 PCR multiplexes.…”

Impact of climatic factors on genetic diversity of Stipa breviflora populations in Inner Mongolia

“…In rice, the combination of hierarchical cluster analysis with GIS has been demonstrated as a useful tool for the accurate visualization of the spatial distribution of existing genetic diversity within a sample of the germplasm in a given geographic area (Parsons et al, 1999). Later studies have extended the approach to other species (Adams et al, 2003;Smith et al, 2006). In this study, we examined the genetic diversity of S. breviflora populations and the role of climatic factors in explaining this diversity at 8 sites in Inner Mongolia using GIS and RAPD-based fingerprinting techniques.…”

Non-invasive baseline genetic monitoring of the endangered San Joaquin kit fox on a photovoltaic solar facility

“…We also increased the number of PCR cycles for highly diluted samples and visualized all of our data on an automated sequencer, which allowed detection of small amounts of amplified DNA. Furthermore, we looked at sample locations for matching genotypes as described in Smith et al (2006b) to increase our confidence in assigning samples to individuals. We found an average of 5.3 scat samples individual −1 yr −1 overall, and samples from individuals were clumped throughout the survey area (see Figs.…”

“…After samples were positively identified as kit foxes, we genotyped them for individual identification using 6 microsatellite tetranucleotide repeat loci that were developed from domestic dogs (Francisco et al 1996) and proven to reliably work for individual identification of kit foxes in our lab (FH2137, FH2140, FH2226, FH2535, FH2561, Pez19;Smith et al 2006b). We assessed our ability to differentiate individuals by estimating the probability of a random match between unrelated individuals for all multilocus genotypes at 6 microsatellite loci (P ID unbiased) and the probability of a random match between siblings (P ID sibs) (Mills et al 2000, Waits et al 2001.…”

“…We used well-established methods for conducting non-invasive genetic surveys (Schwartz et al 2005, Cullingham et al 2010, De Barba et al 2010, Bozarth et al 2011, Dutta et al 2013, Lampa et al 2013) that were developed specifically for San Joaquin kit foxes (Smith et al 2003, 2006a. In brief, conservation detection doghandler teams searched transects for kit fox scats, and DNA from the fresh scats was subsequently analyzed using molecular genetic methods to identify species, sex, and unique genotypes of individuals (Ortega et al 2004, Smith et al 2006b, Bozarth et al 2010.…”