Poaching forensics : animal victims in the courtroom

ERRATA : An online log of corrections to Annual Review of Animal Biosciences articles may be found at http://www.annualreviews.org/errata/animalPoaching 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.http://www.annualreviews.org/journal/animalam2024GeneticsSDG-15:Life on lan

Saving the Rhino : Veterinary Genetics Laboratory of the Faculty of Veterinary Science at the forefront of the fight against rhino poaching

The poaching of rhinos has reached alarming levels in 2010. With the specific aim of providing a tool to support the forensic investigation of the poaching cases, the Veterinary Genetics Laboratory of the Faculty at the Onderstepoort Campus established a method to successfully extract nuclear DNA from rhinoceros horn and genotype it using a set of DNA markers.Originally published as HTML file, converted to PDF with Adobe Acrobat 9 Pro Version 9.0.0

Cyclic neutropenia in a basset hound

A 6 month old, male basset hound was referred for intermittent malaise, and pyrexia that repeated every 10-11 days. Sequential blood counts and bone marrow aspirates demonstrated severe neutropaenia and increased myeloid precursor cells in the bone marrow from day two of each cycle. By day five the bone marrow had predominantly mature neutrophils and band cells, and by day 10 the myeloid precursors had decreased with a myeloid:erythroid of 0.4:1. During the same period the blood neutrophils had rebounded to normal counts by day five, and were declining by day 9 and 10. The monocytes and platelets were oscillating in an opposite phase to the neutrophils. The age of onset, regular cycle length, oscillation of neutrophil, platelet and monocyte counts and characteristic bone marrow cytology were diagnostic for cyclic neutropaenia. This syndrome has never before been described in any breed other than the grey collie. The grey collie gene mutation was not found in this dog. However, based on the clinical signs, and haematological and bone marrow results, it can be deduced that cyclic neutropaenia may develop as a result of other mutations in neutrophil elastase expression.http://vetrecordcasereports.bmj.comhb201

Prediction of the optimal time for insemination using frozen-thawed semen in a multi-sire insemination trial in bitches

The aims of the study were to determine which of Days 5, 6 or 7 after the blood plasma progesterone concentration (PPC) of bitches first reached 6–9 nmol/L (Day 0) yield the highest fertility and whether day of insemination affects the gender ratio of conceptuses. Six bitches were inseminated on Days 5 and 6 and 6 on Days 6 and 7. Ten million progressively motile frozen-thawed sperm from each of 5 dogs were pooled for the first insemination. The same number of sperm from 5 other dogs were pooled for the second insemination. Only one batch of semen from each dog was used on all bitches, which largely prevented any effect of male and semen. Twenty-three autosomal microsatellites and the amelogenin gene were used to determine the paternity and gender of the conceptuses. Pregnancy rate was 100%. Out of 103 ovulations 66 conceptuses were conceived (conception rate: 64%). The proportion of available oocytes fertilised was 0.11, 0.56, and 0.27 for Days 5, 6, and 7, respectively. The odds of fertilisation was 16.7 and 4.2 times higher from insemination on Day 6 compared to Day 5 (P < 0.001) and Day 7 (P = 0.013), respectively. The numbers of male- and female conceptuses were equal (33 each) and gender was independent of insemination day (P = 0.18). This study suggests that intrauterine insemination of bitches should best be done 6 days after PPC first reaches a value between 6 and 9 nmol/L with a second insemination one day later.http://www.elsevier.com/locate/anireproscihb2014ab201

Genetic diversity, relatedness and inbreeding of ranched and fragmented Cape buffalo populations in southern Africa

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.S1 Appendix. Supplementary methods.S1 Fig. Estimated effective population size (Ne) of the buffalo population from each locality. Vertical lines indicate 95% confidence intervals. Numbers inserted for GNP and GNP-MNP indicate the value of the upper bound of the 95% CI. The dashed line indicates the lower 95% CI of GNP. Values are also shown in S3 Table. PVT: Private ranches combined.S2 Fig. Statistical support for K. The first column of graphs [L(K)] show the mean log likelihood of each value of K with its associated standard deviation, while the second column (DeltaK) shows the most likely value of K as determined by the Evanno method. Rows indicate the full data set (FDS) and the relatives removed (RR) data set. The graphs were generated using StructureHarvester and further organized in Inkscape v0.92 (https://inkscape.org/).S3 Fig. Individual assignment plots of the STRUCTURE analyses at K = 2 and K = 3. A–full data set, B–relatives removed. The plots were generated using the online version of Clumpak and further organized in Inkscape v0.92 (https://inkscape.org/).S4 Fig. Discriminant analysis of principal components (DAPC) of the full data set at K = 3. AENP Cluster: Addo Elephant National Park cluster, GNP-MNP Cluster: Graspan and Mokala National Park cluster, “Other” Cluster: Third, unknown origin cluster.S1 Table. Summary statistics of microsatellite loci used in this study. Calculated in Cervus v3.0.7.S2 Table. Mean and variance of the relatedness estimators available in COANCESTRY. TrioML (values in bold) had the lowest variance for each sampling locality and produces positive relatedness estimates between zero and one (as does DyadML).S3 Table. Population summary statistics for each sampling locality.S4 Table. Relatedness and individual inbreeding statistics.S5 Table. Mean relatedness within sexes.S6 Table. Pairwise DJOST and FST values with 95% confidence intervals.S7 Table. Hardy-Weinberg Equilibrium (HWE) probability tests of each sampling locality, with the full data set and relatives removed. Data sets from sampling localities conformed to HWE after relatives were removed.S8 Table. Original and Bonferroni-corrected linkage disequilibrium p-values of all pairs of loci in all sampling localities. Both the full data set (FDS) and relatives removed (RR) data set are shown.DdJ hereby acknowledges the financial contribution of the National Research Foundation (https://www.nrf.ac.za/), under the grant number SFH150630122321.http://www.plosone.orgam2021BiochemistryGeneticsMicrobiology and Plant Patholog

Single base-pair deletion in ASIP exon 3 associated with recessive black phenotype in impala (Aepyceros melampus)

No abstract is available.Wildlife Ranching South Africa (WRSA). Patent applications : ZA2014/05233, ZA2015/03778 and PCT/IB/2015/055391.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1365-20522017-08-31hb2016Equine Research CentreGenetic

Anthropogenic movement results in hybridisation in impala in southern Africa

Hybridisation caused by anthropogenic movements of animals is a conservation concern. Black-faced impala (Aepyceros melampus petersi) are endemic to north-western Namibia and south-western Angola and are geographically isolated from common impala (A. m. melampus). Common impala have been translocated into the black-faced impala range creating a hybridisation risk. We validated 13 microsatellite markers for the detection of recent hybridisation events. We used these markers to assess the genetic variation and differentiation among impala within Etosha National Park (NP), Southern Cross Private Game Reserve (SCPGR), Namibia, and private game ranches across South Africa. We confirmed that “black-nosed” impala in South Africa were A. m. melampus, thus providing more evidence that the black blaze on the face cannot be used to distinguish between the two subspecies. We detected four hybrids and one common impala on SCPGR. These five individuals were removed from SCPGR at time of sampling. We found two potential hybrids in southern Etosha NP. Further sampling of animals within Etosha NP is recommended to determine the extent of hybridisation within the park. The Namibian Ministry of the Environment & Tourism is developing a management plan for black-faced impala across Namibia that includes genetic testing for hybrids.A Postdoctoral Fellowship from the Faculty of Natural and Agricultural Sciences of the University of Pretoria and a Clancey Trust Postdoctoral Fellowship.http://link.springer.com/journal/105922021-04-28hj2020BiochemistryGeneticsMicrobiology and Plant Patholog

Poligame Nylkrokodille (Crocodylus niloticus) op ’n krokodilplaas : vrugvliese vertel die storie

Multiple paternity in crocodilian broods would increase effective population size and slow down the loss of genetic variation due to inbreeding and random genetic drift in real populations. Multiple paternity may also explain variation among offspring of the same brood with respect to characteristics of commercial interest to crocodile farmers. Foetal membranes may provide a non-invasive source of DNA from which to determine the genotypes of Nile crocodile (Crocodylus niloticus) hatchlings. The aims of this study were to determine the effectiveness of using the foetal membranes remaining inside the hatched eggs to determine the genotypes of Nile crocodile hatchlings, and to determine whether a brood (the hatchlings from a clutch of eggs) from a communal breeding pond on a commercial farm may have more than one sire. DNA profiles were determined on 4–6 (mean 4.4) foetal membrane specimens (FMSs) from each of 25 broods from the same breeding pond on a commercial Nile crocodile farm. Eleven microsatellite loci were used. DNA amplification occurred at all 11 loci in 95 of the 110 genotyped individuals, at 1–10 loci in 13 and at no locus in two. Three to 20 alleles were found per locus. Single-locus assessment showed that 13 broods had at least two sires. A multilocus programme (Colony) inferred that 19 broods had at least two sires, with polyandry and polygyny being common. Further research is necessary to determine the utility of foetal membranes as a source of DNA from nests in the wild and, using more FMSs per brood, to more precisely determine the extent of polyandry and polygyny in farmed and wild Nile crocodiles.Meer as een vaar in ’n krokodilbroeisel verhoog die effektiewe populasiegrootte en lei tot ’n stadiger verlies van genetiese variasie as gevolg van inteling en lukraak genetiese swerwing. Meer as een vaar kan ook die variasie met betrekking tot eienskappe wat van kommersiële belang is tussen krokodille uit dieselfde broeisel verklaar. Vrugvliese kan ’n nie-ingrypende bron van DNS verskaf waarmee die genotipe van Nylkrokodilbroeilinge (Crocodylus niloticus) bepaal kan word. Die doel van hierdie studie was om vas te stel hoe doeltreffend die genotipe van Nylkrokodilbroeilinge uit die vrugvliese wat in uitgebroeide eiers agterbly bepaal kan word en of ’n broeisel uit ’n kommunale teeldam op ’n kommersiële plaas meer as een vaar kan hê. Elf mikrosatellietloki is gebruik om die DNS-profiele van 4–6 (gemiddeld 4.4) vrugvliesmonsters (VVMe) van elk van 25 broeisels uit dieselfde teeldam op ’n kommersiële Nylkrokodilplaas te bepaal. DNS het op al 11 loki in 95 van die 110 individue vermeerder, op 1–10 loki in 13 en op geen lokus nie in twee. Drie tot 20 allele is per lokus gevind. Afsonderlike beoordeling van loki het getoon dat 13 broeisels minstens twee vaars gehad het. Met ’n multilokusprogram (Colony) is afgelei dat 19 broeisels minstens twee vaars gehad het, en dat poliandrie en poliginie algemeen was. Verdere navorsing is nodig om die nuttigheid van vrugvliese as ’n bron van DNS vir nesse uit die natuur te bepaal en om, deur meer VVMe per broeisel te gebruik, die mate van poliandrie en poliginie op Nylkrokodilplase en in die natuur meer presies te bepaal.The National Research Foundationhttp://www.satnt.ac.zaam2021GeneticsPhysicsProduction Animal Studie

Complete genome sequences of four African horse sickness virus strains from a commercial tetravalent live attenuated vaccine

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

Evaluation of microsatellite markers for populations studies and forensic identification of African lions (Panthera leo)

The South African lion (Panthera leo) population is highly fragmented. One third of its wild lions occur in small (<1000 km2) reserves. These lions were reintroduced from other areas of the species’ historical range. Management practices on these reserves have not prioritised 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 standardised, 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 one 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 x 10- 5 between siblings were identified for forensics. A further ten could be added for population genetics studies.Jesper Stagegaard and Frank Oberwemmer of the African Lion Interest Group in Europehttp://jhered.oxfordjournals.org2015-11-30hb201