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) 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. Resume : Les marqueurs moleculaires pas assez puissants pour discriminer differents individus peuvent mener ade fausses recaptures (ombres), alors que le genotypage inexact peut mener ades recaptures manquees (fantomes), biaisant potentielle- ment les estimations genetiques basees sur le marquage-recapture. Nous nous sommes servi de simulations pour examiner l'incidence de la taille d'ensembles de marqueurs microsatellites (MSAT) et de polymorphisme mononucleotidique (SNP), de la frequence allelique, d'approches multieprouvettes et de protocoles d'appariement d'echantillons sur les evenements d'ombre et de fantome dans les etudes genetiques de marquage-recapture, et presentons des directives sur les specifications pour les panels de marqueurs MSAT et SNP et des protocoles d'appariement d'echantillons necessaires pour produire des donnees de grande qualite. Les ombres peuvent etre controles en augmentant le nombre de marqueurs ou en selectionnant des marqueurs dotes d'un grand pouvoir de discrimination; des ensembles de marqueurs de taille raisonnable (p. ex., ≥9 MSAT ou ≥32 SNP) de diversite allelique moderee entrainent de faibles probabilites d'erreurs decoulant d'ombres. Les evenements fantomes sont plus difficiles acontroler, et de faibles taux de perte allelique ou d'erreur de faux allele ont produit des taux eleves de mesapparie- ments errones dans l'echantillonnage de marquage-recapture. Heureusement, des protocoles d'appariement avec une bonne tolerance al'erreur qui utilisent de l'information issue de l'appariement positif de sites entre comparaisons d'echantillons et des protocoles multieprouvettes pour obtenir des genotypes consensuels sont efficaces pour eliminer les evenements fantomes. Nous presentons une etude de cas sur le morse du Pacifique, Odobenus rosmarus divergens (Illiger, 1815), qui fait appel aux resultats de simulations pour eclairer la selection de marqueurs genetiques. (Traduit par la Redaction) Mots-cles : etude genetique de marquage-recapture, microsatellite, polymorphisme mononucleotidique, erreur de genotypage, probabilite d'identite.

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