Assessment of CHD-specific primers for gender determination in red-billed oxpeckers (buphagus erythrorhynchus)

Red-billed Oxpeckers Buphagus erythrorhynchus are morphologically similar and do not display distinctive phenotypic difference between males and females. The development of DNA-based gender determination techniques constituted a breakthrough in reliable sex determination in birds. Two DNA-based methods of gender determination were evaluated to determine the preferred method for the Red-billed Oxpeckers. DNA-based gender determination of the Red-billed Oxpeckers was conducted so that specific sexes could be relocated  to new release sites within South Africa. The two primer sets used were 2550F/2718R and P2/P8. When comparing the results of the two primer sets, it was determined that 17% (n = 25) of individuals that were identified as having one sex by the 2550F/2718R primer set changed their DNA gender determination when the P2/P8 primer set was used. Based on molecular evidence and the pathology results for three recorded mortalities at the National Zoological Gardens of South Africa, it was determined that the P2/P8 primer set would be preferable to the 2550F/2718R primer set for DNA gender determination of Red-billed Oxpeckers. OSTRICH 2010, 81(3): 251–25

Diversity in the Toll-Like Receptor Genes of the African Penguin (Spheniscus demersus)

The African penguin, Spheniscus demersus, is listed as Endangered by the IUCN Red List of Threatened Species due to the drastic reduction in population numbers over the last 20 years. To date, the only studies on immunogenetic variation in penguins have been conducted on the major histocompatibility complex (MHC) genes. It was shown in humans that up to half of the genetic variability in immune responses to pathogens are located in non-MHC genes. Toll-like receptors (TLRs) are now increasingly being studied in a variety of taxa as a broader approach to determine functional genetic diversity. In this study, we confirm low genetic diversity in the innate immune region of African penguins similar to that observed in New Zealand robin that has undergone several severe population bottlenecks. Single nucleotide polymorphism (SNP) diversity across TLRs varied between ex situ and in situ penguins with the number of non-synonymous alterations in ex situ populations (n = 14) being reduced in comparison to in situ populations (n = 16). Maintaining adaptive diversity is of vital importance in the assurance populations as these animals may potentially be used in the future for re-introductions. Therefore, this study provides essential data on immune gene diversity in penguins and will assist in providing an additional monitoring tool for African penguin in the wild, as well as to monitor diversity in ex situ populations and to ensure that diversity found in the in situ populations are captured in the assurance populations

SNP discovery and characterisation in White Rhino (Ceratotherium simum) with application to parentage assignment

Abstract The white rhino is one of the great success stories of modern wildlife conservation, growing from as few as 50-100 animals in the 1880s, to approximately 20,000 white rhinoceros remaining today. However, illegal trade in conservational rhinoceros horns is adding constant pressure on remaining populations. Captive management of ex situ populations of endangered species using molecular methods can contribute to improving the management of the species. Here we compare for the first time the utility of 33 Single Nucleotide Polymorphisms (SNPs) and nine microsatellites (MS) in isolation and in combination for assigning parentage in captive White Rhinoceros. We found that a combined dataset of SNPs and microsatellites was most informative with the highest confidence level. This study thus provided us with a useful set of SNP and MS markers for parentage and relatedness testing. Further assessment of the utility of these markers over multiple (> three) generations and the incorporation of a larger variety of relationships among individuals (e.g. half-siblings or cousins) is strongly suggested

Survival and population dynamics of the Marabou Stork in an isolated population, Swaziland

Investigating the ecology of long lived birds is particularly challenging owing to the time scales involved. Here an analysis is presented of a long term study of the survival and population dynamics of the marabou stork (Leptoptilos crumeniferus), a wide ranging scavenging bird from Sub-Saharan Africa. Using resightings data of tagged nestlings and free flying birds we show that the stork population can be divided into three general life stages with unique survival probabilities and fecundities. Fecundity of the storks is inversely related to rainfall during their breeding season. Corroborative evidence for a metapopulation structure is discussed highlighting the impact of the Swaziland birds on the ecology of the species in the broader region. The importance of tag loss or illegibility over time is highlighted. Clearly, any attempt at conserving a species will require a detailed understanding of its population structure, of the sort examined here

Lack of diversity at innate immunity Toll-like receptor genes in the Critically Endangered White winged Flufftail (Sarothrura ayresi)

The White-winged Flufftail (Sarothrura ayresi) population is listed as globally Critically Endangered. White-winged Flufftails are only known to occur, with any regularity, in the high-altitude wetlands of South Africa and Ethiopia. Threats to the species include the limited number of suitable breeding sites in Ethiopia and severe habitat degradation and loss both in Ethiopia and South Africa. Toll-like receptors (TLRs) are increasingly being studied in a variety of taxa as a broader approach to determine functional genetic diversity. In this study, we confirm low genetic diversity in the innate immune regions of the White-winged Flufftail similar to that observed in other bird species that have undergone population bottlenecks. Low TLR diversity in White-winged Flufftail indicates that this species is more likely to be threatened by changes to the environment that would potentially expose the species to new diseases. Thus, conservation efforts should be directed towards maintaining pristine habitat for White-winged Flufftail in its current distribution range. To date, no studies on immunogenetic variation in White-winged Flufftail have been conducted and to our knowledge, this is the first study of TLR genetic diversity in a critically endangered species

Complete mitochondrial genomes of the African clawless (Aonyx capensis) and spotted necked (Hydrictis maculicollis) otter: structure, annotation, and interspecies variation

Otters are flagship species for pristine habitats and their southernmost distribution in Africa includes two species; Aonyx capensis and Hydrictis maculicollis. Here, we present novel full mitochondrial genomes of these otter species. The comparable mitogenomes consist of 36 genes including 13 protein-coding genes, 2 ribosomal RNAs, and 22 tRNAs including a hypervariable region. Only 19 out of the 36 genes showed some level of variation between species with the smallest being trnV (68 bp difference) and the biggest being nad5 (1830 bp difference). Such variations may provide guidance in selecting gene regions during marker development for phylogenetic assessments