Assessment of microsatellite and SNP markers for parentage assignment in ex situ African Penguin (Spheniscus demersus) populations

Christiaan Labuschagne, Lisa Jane Nupen, Antoinette Kotze, J. Paul Grobler, Desire Dalton

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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.
Original languageEnglish
Pages (from-to)4389-4399
Number of pages11
JournalEcology and Evolution
Issue number19
Publication statusPublished - 6 Oct 2015


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