title: Assessment of microsatellite and SNP markers for parentage assignment in ex situ African Penguin (Spheniscus demersus) populations.
abstract: Captive management of ex situ populations of endangered species is traditionally based on pedigree information derived from studbook data. However, molecular methods could provide a powerful set of complementary tools to verify studbook records and also contribute to improving the understanding of the genetic status of captive populations. Here, we compare the utility of single nucleotide polymorphisms (SNPs) and microsatellites (MS) and two analytical methods for assigning parentage in ten families of captive African penguins held in South African facilities. We found that SNPs performed better than microsatellites under both analytical frameworks, but a combination of all markers was most informative. A subset of combined SNP (n = 14) and MS loci (n = 10) provided robust assessments of parentage. Captive or supportive breeding programs will play an important role in future African penguin conservation efforts as a source of individuals for reintroduction. Cooperation among these captive facilities is essential to facilitate this process and improve management. This study provided us with a useful set of SNP and MS markers for parentage and relatedness testing among these captive populations. Further assessment of the utility of these markers over multiple (>3) generations and the incorporation of a larger variety of relationships among individuals (e.g., half-siblings or cousins) is strongly suggested.
authors.affiliation: Department of Genetics University of the Free State P.O. Box 339 Bloemfontein 9300 South Africa; Inqaba Biotechnical Industries (Pty) Ltd P.O. Box 14356 Hatfield 0028 South Africa.
authors.forename: Christiaan
authors.initials: C
authors.lastname: Labuschagne
authors.affiliation: National Zoological Gardens of South Africa P.O. Box 754 Pretoria 0001 South Africa; Department of Biological Sciences Percy FitzPatrick Institute University of Cape Town Rondebosch Cape Town 7701 South Africa.
authors.forename: Lisa
authors.initials: L
authors.lastname: Nupen
authors.affiliation: Department of Genetics University of the Free State P.O. Box 339 Bloemfontein 9300 South Africa; National Zoological Gardens of South Africa P.O. Box 754 Pretoria 0001 South Africa.
authors.forename: Antoinette
authors.initials: A
authors.lastname: Kotzé
authors.affiliation: Department of Genetics University of the Free State P.O. Box 339 Bloemfontein 9300 South Africa.
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Grobler
authors.affiliation: Department of Genetics University of the Free State P.O. Box 339 Bloemfontein 9300 South Africa; National Zoological Gardens of South Africa P.O. Box 754 Pretoria 0001 South Africa.
authors.forename: Desiré L
authors.initials: DL
authors.lastname: Dalton
keywords: African penguin; ex situ populations; exclusion‐based paternity; pedigree
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