DROPOUT: A program to identify problem loci and samples for noninvasive genetic samples in a capture-mark-recapture framework

Molecular Ecology Notes (Impact Factor: 2.38). 09/2005; 5(3). DOI: 10.1111/j.1471-8286.2005.01038.x
Source: OAI


Genotyping error, often associated with low-quantity/quality DNA samples, is an important issue when using genetic tags to estimate abundance using capture-mark-recapture (CMR). dropout, an MS-Windows program, identifies both loci and samples that likely contain errors affecting CMR estimates. dropout uses a 'bimodal test', that enumerates the number of loci different between each pair of samples, and a 'difference in capture history test' (DCH) to determine those loci producing the most errors. Importantly, the DCH test allows one to determine that a data set is error-free. dropout has been evaluated in McKelvey & Schwartz (2004) and is now available online.

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Available from: Kevin S. McKelvey
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    • "When F ST was set to 0 (that simulates no divergence among samples), the proportion of false significances (α error of type I) was in all cases lower than the intended value of 5%. Finally, a bimodal test for each locus and sampling site was performed to detect possible genotyping errors due to preferential amplification of 1 of the 2 alleles, misreading of bands, or transcription errors, using the program droPout (McKelvey and Schwartz 2005). Additionally, Microchecker v2.23 (Van Oosterhout et al. 2004) was used to explore the existence of null alleles and to evaluate their impact on the estimation of genetic differentiation. "
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    • "For final individual identification results, we used the Difference in Capture History test (DCH) and the Examining-Bimodality test (EB) implemented in DROPOUT [49], using recommended values for PID and PID-sib [50] (see below). DCH examines if the rate of adding new individuals by adding more loci exceeds that expected just by increasing resolution, also a typical sign of a likely genotyping error. "
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    • "When available, photo-identification data were also used to identify duplicate samples from the same individual. The program DROPOUT (McKelvey and Schwartz 2005) was used to identify additional pairs of samples whose genotypes differed at 4 or fewer loci. These pairs could represent duplicate samples with genotyping errors. "
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