Isolation and characterization of microsatellite markers in the black rhinoceros (Diceros bicornis)

On-site genetic analysis for species identification using lab-on-a-chip

This paper presents a microfluidic device capable of performing genetic analysis on dung samples to identify White Rhinoceros (Ceratotherium simum). The development of a microfluidic device, which can be used in the field, offers a portable and cost-effective solution for DNA analysis and species identification to aid conservation efforts. Optimization of the DNA extraction processes produced equivalent yields compared to conventional kit-based methods within just 5 minutes. The use of a color-changing loop-mediated isothermal amplification reaction for simultaneous detection of the cytochrome B sequence of C. simum enabled positive results to be obtained within as little as 30 minutes. Field testing was performed at Knowsley Safari to demonstrate real-world applicability of the microfluidic device for testing of biological samples.

Mate choice, reproductive success and inbreeding in white rhinoceros: New insights for conservation management

Improving our sparse knowledge of the mating and reproductive behaviour of white rhinoceros (Ceratotherium simum Burchell, 1817) is essential for the effective conservation of this iconic species. By combining morphological, physiological and habitat data with paternity assignments of 104 known mother-offspring pairs collected over a period of 13 years, we provide the most comprehensive analysis of the mating system in this species. We show that while the overall mating system was promiscuous, and both males and females produced more offspring when mating with several partners, half of all females with multiple offspring were monogamous. Additionally, we find that mating and reproductive success varied significantly among territorial males in two independent sets of males. In females, however, variation in the mating and the reproductive success was not larger than expected by random demographic fluctuations. Horn size, testosterone metabolite concentration, territory size, habitat openness and the volume of preferred food within the territory did not seem to influence male mating or reproductive success. Moreover, there was no sign of inbreeding avoidance: females tended to mate more frequently with closely related males, and one daughter produced a progeny with her father. The lack of inbreeding avoidance, in combination with the skew in male reproductive success, the partial monogamy in females and the territorial-based mating system, jeopardizes the already low genetic variation in the species. Considering that the majority of populations are restricted to fenced reserves and private farms, we recommend taking preventive measures that aim to reduce inbreeding in white rhinoceros. A video abstract can be viewed here.

Lighting the Ivory Track: Are Near-Infrared and Chemometrics Up to the Job? A Proof of Concept

A rapid tool to discriminate rhino horn and ivory samples from different mammalian species based on the combination of near-infrared reflection (NIR) spectroscopy and chemometrics was evaluated. In this study, samples from the Australian Museum mammalogy collection were scanned between 950 nm and 1650 nm using a handheld spectrophotometer and analyzed using principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA). An overall correct classification rate of 73.5% was obtained for the classification of all samples. This study demonstrates the potential of NIR spectroscopy coupled with chemometrics as a means of a rapid, nondestructive classification technique of horn and ivory samples sourced from a museum. Near-infrared spectroscopy can be used as an alternative or complementary method in the detection of horn and ivory assisting in the combat of illegal trade and aiding the preservation of at-risk species.

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

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.

Sex-biased inbreeding effects on reproductive success and home range size of the critically endangered black rhinoceros

A central premise of conservation biology is that small populations suffer reduced viability through loss of genetic diversity and inbreeding. However, there is little evidence that variation in inbreeding impacts individual reproductive success within remnant populations of threatened taxa, largely due to problems associated with obtaining comprehensive pedigree information to estimate inbreeding. In the critically endangered black rhinoceros, a species that experienced severe demographic reductions, we used model selection to identify factors associated with variation in reproductive success (number of offspring). Factors examined as predictors of reproductive success were age, home range size, number of nearby mates, reserve location, and multilocus heterozygosity (a proxy for inbreeding). Multilocus heterozygosity predicted male reproductive success (p< 0.001, explained deviance >58%) and correlated with male home range size (p < 0.01, r(2) > 44%). Such effects were not apparent in females, where reproductive success was determined by age (p < 0.01, explained deviance 34%) as females raise calves alone and choose between, rather than compete for, mates. This first report of a 3-way association between an individual male's heterozygosity, reproductive output, and territory size in a large vertebrate is consistent with an asymmetry in the level of intrasexual competition and highlights the relevance of sex-biased inbreeding for the management of many conservation-priority species. Our results contrast with the idea that wild populations of threatened taxa may possess some inherent difference from most nonthreatened populations that necessitates the use of detailed pedigrees to study inbreeding effects. Despite substantial variance in male reproductive success, the increased fitness of more heterozygous males limits the loss of heterozygosity. Understanding how individual differences in genetic diversity mediate the outcome of intrasexual competition will be essential for effective management, particularly in enclosed populations, where individuals have restricted choice about home range location and where the reproductive impact of translocated animals will depend upon the background distribution in individual heterozygosity.

Extraction of nuclear DNA from rhinoceros horn and characterization of DNA profiling systems for white (Ceratotherium simum) and black (Diceros bicornis) rhinoceros

Rhinoceros horn is now worth more, per unit weight, than gold, diamonds, or cocaine. Rhinoceros horn has been used in traditional Asian medicine as a presumed cure for a wide range of ailments. Rhinoceros poaching in South Africa has, on average, more than doubled each year over the past 5 years with the rapid economic growth in east and southeast Asia being assumed to be the primary factor driving the increased demand for horn. Here we report on the characterization of methods for genomic DNA extraction from rhinoceros horn and on DNA profiling systems for white (Ceratotherium simum) and black (Diceros bicornis) rhinoceros. The DNA profiling system described includes 22 short tandem repeat (STR), or microsatellite, markers and a gender marker (ZF1), which have been used previously in various studies on rhinoceros. Using a θ value of 0.1, a conservative estimate of random match probability in 5 white rhinoceros ranged from 1:7.3x10(6) to 1:3.0x10(8). Given that the total population of white rhinoceros is approximately 20,000 such random match probabilities indicate that the genotyping system described provides data which can be used for evidentiary purposes. Furthermore, the methods are appropriate for use in investigations involving trace amounts of rhinoceros horn and the matching of profiles obtained from seized rhinoceros horn with material collected from live animals or poached carcasses.

Genetic variation and population structure in remnant populations of black rhinoceros, Diceros bicornis, in Africa

Black rhinoceros (Diceros bicornis) are one of the most endangered mammal species in Africa, with a population decline of more than 96% by the end of the last century. Habitat destruction and encroachment has resulted in fragmentation of the remaining populations. To assist in conservation management, baseline information is provided here on relative genetic diversity and population differentiation among the four remaining recognized subspecies. Using microsatellite data from nine loci and 121 black rhinoceros individuals, and comparing the results with those of other African species affected in similar ways, Diceros bicornis michaeli retained the most genetic diversity (heterozygosity 0.675) compared with Diceros bicornis minor (0.459) and Diceros bicornis bicornis (0.505), suggesting that the duration of the known bottlenecks in these populations has only had a limited impact on diversity. Comparable and moderate degrees of population differentiation were found between D. b. minor, D. b. bicornis and D. b. michaeli. Results from the single sample available of the most endangered subspecies, Diceros bicornis longipes, showed the least diversity of all individuals examined. This information should assist conservation management decisions, especially those affecting population viability assessments and selection of individuals for translocations, and will also facilitate subspecies identification for ex situ individuals of uncertain origin.

Mating system and reproductive skew in the black rhinoceros

Only approximately 2600 black rhinoceros survive today, mainly in small, isolated populations of < 100 animals. The management of remaining black rhinoceros populations aims at preserving natural levels of genetic relatedness and optimizing breeding success, which requires an accurate knowledge of the mating system, reproductive skew and effective population size. DNA was extracted from faecal samples from a community of 35 wild black rhinoceros, and microsatellites were used to characterize patterns of paternity of 19 offspring born from eight females in this community. Paternity could be ascribed unequivocally for each offspring. Although our conclusions must be considered tentative, we present the first genetic evidence that black rhinoceros males are polygynous, with a high variance in reproductive success. We also describe a noninvasive management tool that can be used for the genetic management of this critically endangered species, both in the wild and in captivity.