Abstract
Population size information is critical for managing endangered or harvested populations. Population size can now be estimated from non-invasive genetic sampling. However, pitfalls remain such as genotyping errors (allele dropout and false alleles at microsatellite loci). To evaluate the feasibility of non-invasive sampling (e.g., for population size estimation), a pilot study is required. Here, we present a pilot study consisting of (i) a genetic step to test loci amplification and to estimate allele frequencies and genotyping error rates when using faecal DNA, and (ii) a simulation step to quantify and minimise the effects of errors on estimates of population size. The pilot study was conducted on a population of red deer in a fenced natural area of 5440 ha, in France. Twelve microsatellite loci were tested for amplification and genotyping errors. The genotyping error rates for microsatellite loci were 0–0.83 (mean=0.2) for allele dropout rates and 0–0.14 (mean=0.02) for false allele rates, comparable to rates encountered in other non-invasive studies. Simulation results suggest we must conduct 6 PCR amplifications per sample (per locus) to achieve approximately 97% correct genotypes. The 3% error rate appears to have little influence on the accuracy and precision of population size estimation. This paper illustrates the importance of conducting a pilot study (including genotyping and simulations) when using non-invasive sampling to study threatened or managed populations.
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Acknowledgements
The authors would thanks staff of Office National des Forêts (ONF) and Office National de la Chasse (ONCFS), Aurélie Cohas and Ondine Lucas for their help in the field. We also greatly thanks Francis Forget (ONF), Christian Gambier (ONF) and Dominique Odier (ONCFS) for their cooperation. We thanks E. Petit, Joe Niegel and two anonymous reviewers for their comments on previous version of this manuscript. Funding for this project was provided by the ONCFS (contract CNRS-ONCFS no 2002/08).
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Valière, N., Bonenfant, C., Toïgo, C. et al. Importance of a pilot study for non-invasive genetic sampling: genotyping errors and population size estimation in red deer. Conserv Genet 8, 69–78 (2007). https://doi.org/10.1007/s10592-006-9149-2
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DOI: https://doi.org/10.1007/s10592-006-9149-2