Christiaan Labuschagne

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.

Isolation and characterization of species-specific microsatellite loci in African penguin (Spheniscus demersus)

Eight microsatellite markers were developed via pyrosequencing of a microsatellite-enriched library for the African Penguin (Spheniscus demersus). These microsatellite loci displayed 2–6 alleles with expected heterozygosity values ranging between 0.316 and 0.782 and observed heterozygosity between 0.381 and 0.84. These loci may be suitable for assessing patterns of genetic variability in African penguin. This is the first development of species-specific markers for the African penguin.

Genetic Monitoring of ex situ African Penguin (Spheniscus demersus) Populations in South Africa

The African Penguin (Spheniscus demersus) has suffered population declines and is listed in the IUCN Red List as Endangered. The species is endemic to the coast of southern Africa, and breeding colonies are distributed on the south-western coast of Africa. Currently, African Penguins are being kept in zoo and aquarium facilities throughout South Africa. In this study, molecular genetic data based on 12 microsatellite markers from 1 119 African Penguin samples from four facilities were generated in order to determine the level of genetic variation, population structure and differentiation, and effective population size to assist in the development of an effective captive management plan. Expected heterozygosity ranged from 0.57 to 0.62, and allelic richness from 4.2 to 5.1. However, based on differences between first- and second-generation captive birds, we conclude that the ex situ population is at risk of losing genetic variability in the future and management programmes should include exchange of birds between captive facilities in order to induce gene flow and increase effective population size. Adding individuals from in situ populations should also be considered in the future in cases where these birds cannot be rehabilitated. Molecular genetic analyses of wild penguin populations should be carried out for comparison, and to ascertain to what degree ‘in situ genetic diversity’ is represented among ex situ populations. With regular resampling and analyses, the extent of the effect of processes such as genetic drift on diversity in the ex situ penguin populations will become evident.

A targeted gene approach to SNP discovery in the White Rhino ( Ceratotherium simum )

We report the characterization of 10 single nucleotide polymorphism (SNP) markers for the White Rhino (Ceratotherium simum), based on a targeted gene approach. The polymorphisms of these SNP loci were assessed using a captive population comprising 30 individuals. The minor allele frequency ranged from 0.256 to 0.413 and the observed and expected heterozygosity ranged from 0.05 to 0.37 and from 0.05 to 0.49, respectively. An understanding of genetic population structure is required to effectively formulate strategies for conservation and/or management. These SNP markers could be employed to provide estimates of parameters such as population structure, relatedness and current and historical gene flow.

Isolation and characterization of SNP markers for African Penguin (Spheniscus demersus)

We report the characterization of 30 new single nucleotide polymorphism (SNP) markers for an endangered species, the African Penguin (Spheniscus demersus), based on screening of a random genomic library. The polymorphisms of these SNP loci were assessed using a captive population comprising 34 individuals. The minor allele frequency ranged from 2.17 to 42.65 and the observed and expected heterozygosity ranged from 0.1 to 0.6897 and from 0.0435 to 0.4965, respectively. None of the loci deviated significantly from Hardy–Weinberg equilibrium. These SNP markers will provide a necessary addition to the genetic tools employed for understanding population structure and for developing a conservation management strategy for this endangered species.

Isolation and characterization of species-specific microsatellite loci in red-billed oxpeckers (Buphagus erythrorhynchus)

Ten microsatellite markers were developed via pyrosequencing for the red-billed oxpecker (Buphagus erythrorhynchus). These microsatellite loci displayed 3–15 alleles with expected heterozygosity values ranging between 0.580 and 0.907 and observed heterozygosity between 0.509 and 0.870. The high level of polymorphisms observed in the microsatellite markers supports future investigations to improve our knowledge of the genetic structure and relatedness of these birds. This is the first development of species specific markers for the red-billed oxpecker.