Guidelines for MSAT and SNP panels that lead to high-quality data for genetic mark–recapture studies

Molecular markers with inadequate power to discriminate among individuals can lead to false recaptures (shadows), and inaccurate genotyping can lead to missed recaptures (ghosts), potentially biasing genetic mark–recapture estimates. We used simulations to examine the impact of microsatellite (MSAT)...

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Bibliographic Details
Published in:Canadian Journal of Zoology
Main Authors: Sethi, Suresh Andrew, Cook, Geoffrey M., Lemons, Patrick, Wenburg, John
Format: Article in Journal/Newspaper
Language:English
Published: Canadian Science Publishing 2014
Subjects:
Animal Science and Zoology
Ecology, Evolution, Behavior and Systematics
Pacific
Odobenus rosmarus
walrus*
Online Access:http://dx.doi.org/10.1139/cjz-2013-0302
http://www.nrcresearchpress.com/doi/full-xml/10.1139/cjz-2013-0302
http://www.nrcresearchpress.com/doi/pdf/10.1139/cjz-2013-0302
Description
Summary:Molecular markers with inadequate power to discriminate among individuals can lead to false recaptures (shadows), and inaccurate genotyping can lead to missed recaptures (ghosts), potentially biasing genetic mark–recapture estimates. We used simulations to examine the impact of microsatellite (MSAT) and single nucleotide polymorphism (SNP) marker-set size, allelic frequency, multitubes approaches, and sample matching protocols on shadow and ghost events in genetic mark–recapture studies, presenting guidance on the specifications for MSAT and SNP marker panels, and sample matching protocols necessary to produce high-quality data. Shadow events are controllable by increasing the number of markers or by selecting markers with high discriminatory power; reasonably sized marker sets (e.g., ≥9 MSATs or ≥32 SNPs) of moderate allelic diversity lead to low probabilities of shadow errors. Ghost events are more challenging to control and low allelic dropout or false-allele error rates produced high rates of erroneous mismatches in mark–recapture sampling. Fortunately, error-tolerant matching protocols, which use information from positively matching loci between comparisons of samples, and multitubes protocols to achieve consensus genotypes are effective at eliminating ghost events. We present a case study on Pacific walrus, Odobenus rosmarus divergens (Illiger, 1815), using simulation results to inform genetic marker choices.

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