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,
    • "Null alleles and error rates were calculated using MICRO-CHEKER (Van Oosterhout et al. 2004), GIMLET 1.3.3 (Valière 2002) and DROPOUT (McKelvey and Schwartz 2005). We amplified a fragment of approximately 400 bp of the mtDNA control region using primers PHDL (Fumihito et al. 1995) and PH-H521 (Randi and Lucchini 1998), as described elsewhere (Rodriguez-Muñoz et al. 2007). "
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    ABSTRACT: Demographic models accounting for operational sex ratio (OSR) show that male numbers can have a substantial influence on the dynamics of wild populations. We used the Cantabrian capercaillie, a forest bird, as a model to assess the effects of the reduction in the number of breeding males (increased OSR) associated to male-biased hunting, on the genetics of the population. We based our assessment in the comparison of the dynamics of neutral markers transmitted by both parents (microsatellites) versus markers transmitted only by females (mitochondrial DNA—mtDNA). Parallel to the analysis of field data, we ran computer simulations to explore how different levels of OSR and two other important demographic factors, population size and connectivity, might influence the dynamics of genetic variation of microsatellites and mtDNA. We found evidence of a genetic bottleneck and low genetic variability affecting microsatellites but not mtDNA early in our study period, when male-biased hunting was more intense. This was followed by a decline in mtDNA variation around 10–20 years later. Simulations suggested that changes in genetic variation associated with high OSR had the closest similarity to those observed at the beginning of our study, whereas a combination of reduced size and migration rate better resembled the patterns found later on. Our findings indicate that male-biased hunting might have triggered the ongoing decline of the Cantabrian capercaillie, on its own or in combination with habitat configuration, and support the need to incorporate OSR into decision making for the management and conservation of exploited populations.
    Conservation Genetics 06/2015; DOI:10.1007/s10592-015-0747-8 · 2.19 Impact Factor
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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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    ABSTRACT: The secondary freshwater fish fauna of the western-Iberian Peninsula basin is primarily restricted to local coastal streams, and man-made salt evaporation ponds, etc., which are susceptible to periodical flood and drought events. Despite its uniqueness in ecological adaptation to high saltwater tolerance, very little is known about this fauna’s population dynamics and evolutionary history. The killifish, Aphanius baeticus (Cyprinodontidae) is an endemic species restricted to river basins on Spain’s southern Atlantic coastline, considered as “Endangered.” In this study, the genetic structure, diversity and historical demography of A. baeticus were analyzed using mitochondrial (cytochrome b, N = 131) and nuclear (4 out of 19 microsatellites tested, N = 288) markers across its distribution range. The phylogenetic and networking reconstruction revealed subtle phylogeographic structuring. A scattered expansion at the beginning of the interglacial periods, coupled with posterior events of extinction and colonization caused by periodical cycles of flooding, could explain the absence of well-defined phylogenetic relationships among populations. Moreover, very low genetic diversity values and a weak population differentiation were detected. We proposed that dispersals allowed by periodic floods connecting river drainages may have promoted a wide genetic exchange among populations and could have contributed to the current genetic relatedness of these populations.
    Journal of Heredity 06/2014; 105(5). DOI:10.1093/jhered/esu034 · 2.09 Impact Factor
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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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    ABSTRACT: Counting rare and elusive animals and evaluating their demographic status, are fundamental yet challenging aspects of population ecology and conservation biology. We set out to estimate population size (Nc), genetic effective population size (Ne gen), sex ratio, and movements based on genetic tagging for the threatened Cantabrian capercaillie. We used 9 microsatellite loci to genotype 134 droppings collected at 34 display areas during the breeding season. Using genetic capture-mark-recapture, we estimated 93 individuals (Nc, 95% CI: 70-116) in an area of about 500 km2, with sex ratio biased towards males (1∶1.6). Estimated Ne gen (35.5) was 38% of Nc, notably higher than the published average in wild populations. This capercaillie population is small and well within concern in terms of population viability. By genetic tagging, we detected mostly short movements; just a few males were recaptured between contiguous display areas. Non-invasive surveys of endangered populations have a great potential, yet adequate sample size and location are key to obtain reliable information on conservation status.
    PLoS ONE 06/2014; 9(6):e99799. DOI:10.1371/journal.pone.0099799 · 3.23 Impact Factor
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