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Importance of a pilot study for non-invasive genetic sampling: genotyping errors and population size estimation in red deer

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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https://hal.archives-ouvertes.fr/halsde-00293178
Contributor : Kim Pla <>
Submitted on : Thursday, July 3, 2008 - 5:12:00 PM
Last modification on : Tuesday, July 20, 2021 - 5:20:06 PM

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N. Valiere, C. Bonenfant, C. Toigo, G. Luikart, J. M. Gaillard, et al.. Importance of a pilot study for non-invasive genetic sampling: genotyping errors and population size estimation in red deer. Conservation Genetics, Springer Verlag, 2007, 8 (1), pp.69-78. ⟨10.1007/s10592-006-9149-2⟩. ⟨halsde-00293178⟩

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