Conservation Genetics

, Volume 8, Issue 1, pp 69–78

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

  • Nathaniel Valière
  • Christophe Bonenfant
  • Carole Toïgo
  • Gordon Luikart
  • Jean-Michel Gaillard
  • François Klein
Original Paper

DOI: 10.1007/s10592-006-9149-2

Cite this article as:
Valière, N., Bonenfant, C., Toïgo, C. et al. Conserv Genet (2007) 8: 69. doi:10.1007/s10592-006-9149-2

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.

Keywords

Non-invasive samplingMicrosatellitesGenotyping errorPilot studyCervus elaphusPopulation size

Copyright information

© Springer Science+Business Media B.V. 2006 2006

Authors and Affiliations

  • Nathaniel Valière
    • 1
  • Christophe Bonenfant
    • 1
    • 2
  • Carole Toïgo
    • 2
  • Gordon Luikart
    • 3
  • Jean-Michel Gaillard
    • 1
  • François Klein
    • 2
  1. 1.UMR CNRS 5558 Biométrie et Biologie, EvolutiveUniversité Claude Bernard Lyon IVilleurbanneFrance
  2. 2.Office National de la Chasse et de la Faune SauvageCentre National d’Etudes et de Recherches AppliquéesCervidés-Sanglier, ErsteinFrance
  3. 3.UMR CNRS 5553 Laboratoire d’Ecologie AlpineUniversité Joseph FourrierGrenobleFrance