A new method for quantifying genotyping errors for noninvasive genetic studies

More and more noninvasive genetic data are being produced but a general methodology to quantify genotyping error rates from non-pilot data remains lacking. Here we propose a mathematical approach to estimate genotyping error rates by exploring the relationship between errors and PCR replicates. This method can be used to quantify the error rates for either the multi-tubes approach designed by Taberlet et al. (Nucleic Acids Res 24: 3189–3194, 1996) or the pilot method by Prugh et al. (Mol Ecol 14: 1585–1596, 2005).

[1]  Jane Goodall,et al.  Noninvasive paternity assignment in Gombe chimpanzees , 2001, Molecular ecology.

[2]  E. Petit,et al.  Quantifying genotyping errors in noninvasive population genetics , 2004, Molecular ecology.

[3]  Nathaniel Valière.  gimlet: a computer program for analysing genetic individual identification data , 2002 .

[4]  L. Waits,et al.  Noninvasive genetic tracking of the endangered Pyrenean brown bear population , 1997, Molecular ecology.

[5]  E. Petit,et al.  Noninvasive population genetics: a review of sample source, diet, fragment length and microsatellite motif effects on amplification success and genotyping error rates , 2006, Conservation Genetics.

[6]  KEVIN S. MCKELVEY,et al.  GENETIC ERRORS ASSOCIATED WITH POPULATION ESTIMATION USING NON-INVASIVE MOLECULAR TAGGING: PROBLEMS AND NEW SOLUTIONS , 2004 .

[7]  H. Ellegren,et al.  Colonization history and non-invasive monitoring of a re-established wolverine (Gulo gulo) population. , 2004 .

[8]  Henrik Brøseth,et al.  Colonization History and Noninvasive Monitoring of a Reestablished Wolverine Population , 2004 .

[9]  B. Goossens,et al.  Molecular analysis of dispersal in giant pandas , 2007, Molecular ecology.

[10]  W. McShea,et al.  Do Revised Giant Panda Population Estimates Aid in Their Conservation , 2008 .

[11]  Pierre Taberlet,et al.  An evaluation of field and non-invasive genetic methods to estimate brown bear (Ursus arctos) population size , 2006 .

[12]  P. Taberlet,et al.  Genotyping errors: causes, consequences and solutions , 2005, Nature Reviews Genetics.

[13]  Ming Li,et al.  Molecular censusing doubles giant panda population estimate in a key nature reserve , 2006, Current Biology.

[14]  P Taberlet,et al.  Reliable genotyping of samples with very low DNA quantities using PCR. , 1996, Nucleic acids research.

[15]  C. Krebs,et al.  Monitoring coyote population dynamics by genotyping faeces , 2005, Molecular ecology.

[16]  S. Creel,et al.  Population size estimation in Yellowstone wolves with error‐prone noninvasive microsatellite genotypes , 2003, Molecular ecology.

[17]  J. Altmann,et al.  Cross‐species amplification, non‐invasive genotyping, and non‐Mendelian inheritance of human STRPs in Savannah baboons , 2000, American journal of primatology.

[18]  D. Haydon,et al.  Maximum-Likelihood Estimation of Allelic Dropout and False Allele Error Rates From Microsatellite Genotypes in the Absence of Reference Data , 2007, Genetics.

[19]  Pierre Berthier,et al.  gemini: software for testing the effects of genotyping errors and multitubes approach for individual identification , 2002 .