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Poaching and the international trade in wildlife are escalating problems driven by poverty and greed and coordinated by increasingly sophisticated criminal networks. Biodiversity loss, caused by habitat change, is exacerbated by poaching, and species globally are facing extinction. Forensic evidence underpins human and animal criminal investigations and is critical in criminal prosecution and conviction. The application of forensic tools, particularly forensic genetics, to animal case work continues to advance, providing the systems to confront the challenges of wildlife investigations. This article discusses some of these tools, their development, and implementations, as well as recent advances. Examples of cases are provided in which forensic evidence played a key role in obtaining convictions, thus laying the foundation for the future application of techniques to disrupt the criminal networks and safeguard biodiversity through species protection.

Wildlife ranching, although not considered a conventional conservation system, provides a sustainable model for wildlife utilization and could be a source of valuable genetic material. However, increased fragmentation and intensive management may threaten the evolutionary potential and conservation value of species. Disease-free Cape buffalo (Syncerus caffer caffer) in southern Africa exist in populations with a variety of histories and management practices. We compared the genetic diversity of buffalo in national parks to private ranches and found that, except for Addo Elephant National Park, genetic diversity was high and statistically equivalent. We found that relatedness and inbreeding levels were not substantially different between ranched populations and those in national parks, indicating that breeding practices likely did not yet influence genetic diversity of buffalo on private ranches in this study. High genetic differentiation between South African protected areas highlighted their fragmented nature. Structure analysis revealed private ranches comprised three gene pools, with origins from Addo Elephant National Park, Kruger National Park and a third, unsampled gene pool. Based on these results, we recommend the Addo population be supplemented with disease-free Graspan and Mokala buffalo (of Kruger origin). We highlight the need for more research to characterize the genetic diversity and composition of ranched wildlife species, in conjunction with wildlife ranchers and conservation authorities, in order to evaluate the implications for management and conservation of these species across different systems., Competing Interests: The authors have declared that no competing interests exist.

Disorders of sex development (DSD) have long been documented in domestic animal species including horses. However, there is only a single report of an androgen receptor (AR) mutation causative of such a DSD syndrome in a horse pedigree. Here, we present a new familial AR mutation in horses. A missense mutation (c.2042G>C) at AR exon 4 explains the segregation of the DSD in a Thoroughbred horse pedigree. The mutation, expected to affect the ligand-binding domain of the AR protein, led to complete androgen insensitivity of 64,XY SRY+, testicular DSD individuals. Additionally, the design of a PCR-RFLP technique provided an accurate molecular test for the identification of horses carrying the mutation., (© 2016 S. Karger AG, Basel.)

Population fragmentation is threatening biodiversity worldwide. Species that once roamed vast areas are increasingly being conserved in small, isolated areas. Modern management approaches must adapt to ensure the continued survival and conservation value of these populations. In South Africa, a managed metapopulation approach has been adopted for several large carnivore species, all protected in isolated, relatively small, reserves that are fenced. As far as possible these approaches are based on natural metapopulation structures. In this network, over the past 25 years, African lions (Panthera leo) were reintroduced into 44 fenced reserves with little attention given to maintaining genetic diversity. To examine the situation, we investigated the current genetic provenance and diversity of these lions. We found that overall genetic diversity was similar to that in a large national park, and included a mixture of four different southern African evolutionarily significant units (ESUs). This mixing of ESUs, while not ideal, provides a unique opportunity to study the impact of mixing ESUs over the long term. We propose a strategic managed metapopulation plan to ensure the maintenance of genetic diversity and improve the long-term conservation value of these lions. This managed metapopulation approach could be applied to other species under similar ecological constraints around the globe.

This is a report of the complete genome sequences of plaque-selected isolates of each of the four virus strains included in a South African commercial tetravalent African horse sickness attenuated live virus vaccine., (Copyright © 2015 Guthrie et al.)

Taylorella equigenitalis is the causative agent of contagious equine metritis (CEM), a sexually transmitted infection of horses. We report here the genome sequence of T. equigenitalis strain ERC_G2224, isolated in 2015 from a semen sample collected in 1996 from a Lipizzaner stallion in South Africa., (Copyright © 2015 May et al.)

This is a report of the complete genome sequences of plaque-selected isolates of each of the three virus strains included in a South African commercial trivalent African horse sickness attenuated live virus vaccine., (Copyright © 2015 Guthrie et al.)

The South African lion (Panthera leo) population is highly fragmented. One-third of its wild lions occur in small (<1000 km(2)) reserves. These lions were reintroduced from other areas of the species' historical range. Management practices on these reserves have not prioritized genetic provenance or heterozygosity. These trends potentially constrain the conservation value of these lions. To ensure the best management and long-term survival of these subpopulations as a viable collective population, the provenance and current genetic diversity must be described. Concurrently, poaching of lions to supply a growing market for lion bones in Asia may become a serious conservation challenge in the future. Having a standardized, validated method for matching confiscated lion parts with carcasses will be a key tool in investigating these crimes. We evaluated 28 microsatellites in the African lion using samples from 18 small reserves and 1 captive facility in South Africa, two conservancies in Zimbabwe, and Kruger National and Kgalagadi Transfrontier Parks to determine the loci most suited for population management and forensic genetic applications. Twelve microsatellite loci with a match probability of 1.1×10(-5) between siblings were identified for forensics. A further 10 could be added for population genetics studies., (© The American Genetic Association 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Reasons for Performing Study: The carrier prevalence of severe combined immunodeficiency (SCID), lavender foal syndrome (LFS) and cerebellar abiotrophy (CA) in Arabian foals in South Africa was determined in order to quantify the potential impact of these conditions locally. Furthermore, the carrier prevalence of SCID prior to and following the introduction of a genetic test was compared to evaluate the effect of testing in the population., Objectives: To estimate the carrier prevalence of SCID, LFS and CA in registered purebred Arabians born in South Africa in the 2004/5 and 2009/10 foaling seasons and compare the changes in prevalence in these disorders between the 2 groups of foals., Study Design: Cross-sectional survey., Methods: Samples were collected from individuals randomly selected from 2 populations of purebred Arabian foals born during the 2004/5 and 2009/10 foaling seasons. Genetic testing for SCID, LFS and CA was performed on DNA extracts using specific polymerase chain reactions, with the products being analysed using fragment analysis on a genetic analyser., Results: The carrier prevalence of LFS and CA for the 2009/10 season was 11.7% (95% confidence interval [CI] 7.6-17.0%) and 5.1% (95% CI 2.5-9.1%), respectively, with no statistically significant change in prevalence between the 2004/5 and 2009/10 foaling seasons. However, the carrier prevalence of SCID was found to have decreased significantly from 6.4% (95% CI 4.8-8.3%) in the 2004/5 foals to 3.4% (95% CI 2.2-5.1%) in the 2009/10 foals (P = 0.009)., Conclusions: The results of this study indicate that genetic screening of Arabian horses for SCID may have played a role in significantly reducing the carrier prevalence within the breeding population and thereby reducing the birth of clinically affected individuals. This study provides an indication of the positive effect of genetic screening for specific conditions in horses., (© 2013 EVJ Ltd.)

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., (Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.)

Color markings among felid species display both a remarkable diversity and a common underlying periodicity. A similar range of patterns in domestic cats suggests a conserved mechanism whose appearance can be altered by selection. We identified the gene responsible for tabby pattern variation in domestic cats as Transmembrane aminopeptidase Q (Taqpep), which encodes a membrane-bound metalloprotease. Analyzing 31 other felid species, we identified Taqpep as the cause of the rare king cheetah phenotype, in which spots coalesce into blotches and stripes. Histologic, genomic expression, and transgenic mouse studies indicate that paracrine expression of Endothelin3 (Edn3) coordinates localized color differences. We propose a two-stage model in which Taqpep helps to establish a periodic pre-pattern during skin development that is later implemented by differential expression of Edn3.

Dermatosparaxis is a heritable collagen dysplasia causing skin extensibility and fragility. In Belgian Blue cattle this mutation has been described as a 3 base pair (bp) change followed by a 17bp deletion in the gene coding for procollagen 1 N-Proteinase (pNPI). An outbreak in a commercial Drakensberger herd in South Africa followed the introduction in late 2000 of a 3-year-old bull that developed skin lesions in 2001 and was culled in 2002. Some of his offspring were similarly affected, 1 of which was kept as a breeding bull after his sire's death. Two affected calves were referred to the Onderstepoort Veterinary Academic Hospital in October 2005. Detailed examination revealed only skin abnormalities limited to the lateral extremities of the thorax, abdomen and pelvis, viz. either acute lacerations of varying sizes, slow healing defects or thin scars in chronic cases. During a subsequent farm visit, 13 animals with similar wounds were seen in the herd of 146 animals. Electron microscopic examination of skin biopsies revealed haphazard arrangement and loose packing of dermal collagen fibrils within collagen fibres. The fibrils showed size variation and slightly irregular outlines on cross-section, consistent with mild dermatosparaxis. DNA samples of affected calves were analysed using primers designed to amplify the region of the pNPI gene that contained the mutation described in Belgian Blue cattle, but this mutation could not be demonstrated in any of the animals tested. It is concluded that a form of dermatosparaxis with a different gene mutation from that described in Belgian Blue cattle exists in Drakensberger cattle in South Africa. This possibly also explains the milder and more delayed clinical signs and the milder dermal collagen ultrastructural abnormalities.

A congenital myasthenic syndrome in Brahman cattle is caused by a homozygous 20 base pair deletion (470del20) in the gene coding for the epsilon subunit of the acetylcholine receptor at the neuromuscular junction. It causes a progressive muscle weakness starting either at birth or within the first month. A PCR-based DNA test, using blood or semen stored on FTA paper, was developed and validated; the test makes it possible to differentiate rapidly and accurately between homozygous wild-type, heterozygous and homozygous affected animals. Preliminary testing of Brahman cattle in South Africa has revealed several carrier animals, some of them influential animals in the breeding population.

Reasons for Performing Study: West Nile virus (WNV) infection is endemic in southern Africa. With the recent emergence of WNV infection of horses in Europe and the USA the present study was performed to estimate the risk of seroconversion to WNV in a cohort of 488 young Thoroughbred (TB) horses., Objectives: To estimate the risk of seroconversion to WNV among a cohort of South African TB yearlings sold at the 2001 National Yearling Sales (NYS) and to determine whether the risk varied geographically. Two horses were also infected with a recent South African isolate of WNV to evaluate its virulence in horses., Methods: Serum samples were collected from the cohort of 488 TB yearlings at the 2001 NYS. Serum samples that were collected from the same horses at the time that they were identified were sourced from our serum bank. Sera from 243 of the dams that were collected at the time that the foals were identified were also sourced from our serum bank. These sera were subjected to serum neutralisation (SN) tests for antibody to WNV., Results: Approximately 11% of yearlings seroconverted to WNV on paired serum samples collected from each animal approximately 12 months apart. Studfarms with WNV-seropositive yearlings were widely distributed throughout South Africa and SN tests on sera from their dams indicated that exposure to WNV was even more prevalent (75%) in this population. Neurological disease was not described in any of the horses included in this study and 2 horses inoculated with a recent lineage 2 South African isolate of WNV showed no clinical signs of disease after infection and virus was not detected in their blood., Conclusions: Infection of horses with WNV is common in South Africa, but infection is not associated with neurological disease., Potential Relevance: In contrast to recent reports from Europe, North Africa, Asia and North America, the results of our field and experimental studies indicated that exposure of horses to the endemic southern African strains of WNV was not associated with neurological disease.

The aim of this study was to establish and validate a method to permit microsatellite analysis of DNA profiles obtained from frozen-thawed stallion sperm cells. This would provide reliable and accurate verification of the identification of a semen donor. Ejaculates from 5 pony stallions were collected, processed and frozen in 0.5 ml plastic straws. Aliquots of 100 microl of the frozen-thawed semen thus obtained were either placed directly, or diluted (1:10; 1:100; and 1:1000) and placed on slides of FTA paper. Similarly, blood samples obtained from each of the stallions were placed onto slides of FTA paper. A punch was removed from each sample after drying Each sample was mixed with FTA purification reagent, Dithiothreitol and Proteinase K before incubation and processing. All samples were processed with a set of 13 microsatellite markers. Further analysis permitted a comparison of the DNA profiles of the frozen-thawed semen and the blood samples. A full profile of markers was obtained from the 1:10 and 1:100 dilutions of the frozen-thawed semen samples as well as from the blood samples. The DNA profiles from the frozen-thawed semen and blood samples obtained from the stallions matched in all cases.

Background: A cataract is any opacity or partial loss of transparency of the lens, whether the absence of transparency is small or complete. Pupil dilation affords a view of a legion of internal variations and abnormalities of the human crystalline lens which often tell us about its events and insults, as well as when in the patient's life these might have occurred., Methods: In this article, we review the major non-age-related association of cataractogenesis with respect to metabolic, environmental, ocular-specific, infectious, dermatologic, retinal, and toxic etiologies. The data are presented from the clinical perspective of incidence for a given condition and cataract type., Results: Two simplified summary reference sheets are provided: (1) frequency of occurrence vs. etiology and (2) cataract type vs. etiology (color-coded). The busy clinician can refer to both tools chair-side., Conclusions: The human body has numerous methods of signaling insults and abnormalities. As the crystalline lens is an important gauge of overall health, an argument can be made for routine dilation of all patients. This information is also essential for future neutraceutical and pharmaceutical therapeutic intervention.

Occurrence and diversity of Eimeria species in two groups of indigenous South African goats kept under traditional management systems, as well as in a mixed herd of Saanen, indigenous and crossbred goats kept under an intensive management system were examined. Infection rates ranged from 88.7 to 100% in the various groups. Mean OPG of immature goats (< 1 year old) exceeded that of adult goats at all three sites. There was no consistent difference between adult OPG counts at the three sites. Under the intensive system, adult crossbred goats had significantly higher OPG counts than adult Saanen or indigenous goats. Overall, OPG counts of immature goats were significantly higher during the dry season (winter) than during the wet season (summer). Ten Eimeria species were identified, Eimeria arloingi being the most prevalent species at all three sites, followed by Eimeria hirci. Up to seven Eimeria species were recovered from individual specimens.

The seasonal occurrence of coccidial oocysts was determined in a mixed herd of indigenous goats and cross-bred sheep at Nebo, Northern Province, South Africa. The herd of c. 30 sheep was housed with c. 70 goats in 1 camp. Over a period of 14 months, 114 faecal specimens were collected from sheep and 369 from goats and the number of oocysts per gram of faeces (OPG) determined. The mean OPG value for the adult sheep (1187.9) was significantly (p = 0.035) lower than the mean OPG value for the adult goats (7042.9). The highest mean value was recorded in the adult sheep during March 1996 (3044.4) and in adult goats during June 1995 (51568.7).