Delineating origins of cheetah cubs in the illegal wildlife trade: Improvements based on the use of hair δ18O measurements

All African felids are listed as vulnerable or endangered according to the IUCN (International Union for Conservation of Nature) Red List of Threatened Species. Cheetahs (Acinonyx jubatus) in particular have declined rapidly as a result of human impacts so that development of effective strategies and tools for conservation of this highly vulnerable species, as well as African felids in general, are essential for their survival in the wild. Here we use the oxygen stable isotopic compositions of cheetah hair to determine origins of cheetah cubs destined for the illegal exotic pet trade by associating individual cubs with predicted δ18O isoscape locations. We found that cheetah cubs most likely originated in East Africa, close to the corridors responsible for this aspect of the illegal wildlife trade to the Middle East. Further refinement of these assignments using a two isotope analysis (δ18O and δ13C values) indicate that these cubs were likely sourced in Southern Ethiopia or possibly as far as Tanzania. We also demonstrate that δ18O values in tissues can provide provenance information in cases where results of δ2H analyses may be obscured by the effects of metabolic routing of nutrients during nursing, starvation, or dehydration. This study demonstrates the utility of stable isotopic tools for conservation and forensic uses for endangered mammalian species

Parentage analysis in a managed free ranging population of southern white rhinoceros : genetic diversity, pedigrees and management

Small populations are vulnerable to the consequences of breeding within closed groups as the loss of genetic variability can lead to inbreeding depression. Here, we use microsatellite genotypes to assess variability and parentage within a small, managed population of southern white rhinoceros in northern Namibia. Tissue samples gathered from either a modified biopsy darting technique or ear notches allowed us to obtain genotypic data for all individuals in the population. As expected for this species, genetic variability in the population was relatively low (overall H obs 0.45). In combination with detailed management records for the period 1993–2009, we were able to assign both parents for all 23 offspring. Only one calf of seven in the F2 generation arose from father–daughter inbreeding within the population. Our analysis revealed that paternity was initially dominated by a single founder bull siring 10 of 13 calves over 9 years; paradoxically, the other founder bull was selected for removal based on observations suggesting he was behaviourally dominant and therefore the likely sire of most calves. We also found that young introduced bulls were breeding successfully within 6 months of their arrival, well before having established their home ranges. We argue that in order to optimally manage and conserve the southern African white rhinoceros meta-population it is essential to have accurate pedigree information and genetic data for all individuals in the numerous small populations that are key to the survival of the species.Ongava Research Centre is funded by charitable donations from the Namibian Wildlife Conservation Trust (UK), West Midlands Safari Park (UK) and the Directors of Ongava Game Reserve.http://link.springer.com/journal/10592hb201

Ultrasonographic and laparoscopic evaluation of the reproductive tract in older captive female cheetahs (Acinonyx jubatus)

The study uniquely described the clinical value of transabdominal ultrasonography for monitoring features characterizing the estrous cycle in female cheetahs (Acinonyx jubatus). The reproductive tracts of 21 female, nulliparous, and relatively aged (median: 11 and interquartile range: 9.25–14 years) captive cheetahs resident on two sites in Namibia were assessed by transabdominal ultrasound. Subsequently, the ovarian findings on ultrasound were compared with direct visualization while performing laparoscopic sterilization. A combination of these observations supported by concurrent sampling for vaginal cytology and serum progesterone concentrations defined the estrous status of individual animals. At one site, six cheetahs had been implanted with the GnRH agonist, deslorelin as a contraceptive at least once within the preceding 11 years. On ultrasound, 31 uterine horns and 35 ovaries with discernible structures on 28 (86%) were visualized in the 21 cheetahs. The uterine body was difficult to visualize because of its intrapelvic location. Eleven of 19 uteri (58%) visualized showed endometrial edema suggestive of estrogenization. The uteri of four cheetahs (19%) showed evidence of mild cystic endometrial hyperplasia. Paraovarian cysts were seen on ultrasound (n ¼ 21) and laparoscopy (n ¼ 26) in 16 (76.2%) and 18 (85.7%) cheetahs, respectively. Ovarian volumes obtained from ultrasonographically determined dimensions predicted cyclic activity. Laparoscopy showed that 19 ovaries had discernible follicular structures. In the study population, 10 (47.6%) cheetahswere in proestrus or estrus; none in the luteal phase; and 11 (52.4%) in anestrus. Transabdominal ultrasound, in combination with serum progesterone concentrations and vaginal cytology, was used with acceptable accuracy to assess cyclic ovarian activity in captive cheetahs. A considerable proportion of this aged population showed ovarian activity and the prevalence of paraovarian cysts was notable. A history of prior deslorelin treatment was not associated with either reproductive activity or uterine pathology.AfriCat Foundation and CCF in Namibia.http://www.theriojournal.com2016-12-31hb2015ab201

Single-incision laparoscopic sterilization of the cheetah (Acinonyx jubatus)

OBJECTIVE : To describe laparoscopic ovariectomy and salpingectomy in the cheetah (Acinonyx jubatus) using single-incision laparoscopic surgery (SILS). STUDY DESIGN : Prospective cohort. ANIMALS : Female cheetahs (Acinonyx jubatus) ( n ¼ 21). METHODS : Cheetahs were randomly divided to receive either ovariectomy (n ¼ 11) or salpingectomy (n ¼ 10). The use and complications of a SILS port was evaluated in all of cheetahs. Surgery duration and insufflation volumes of carbon dioxide (CO2) were recorded and compared across procedures. RESULTS : Laparoscopic ovariectomy and salpingectomy were performed without complications using a SILS port. The poorly-developed mesosalpinx and ovarian bursa facilitated access to the uterine tube for salpingectomy in the cheetah. The median surgery duration for ovariectomy was 24 minutes (interquartile range 3) and for salpingectomy was 19.5 minutes (interquartile range 3) (P ¼.005). The median volume of CO2 used for ovariectomy was 11.25 L (interquartile range 3.08) and for salpingectomy was 4.90 L (interquartile range 2.52), (P ¼.001) CONCLUSIONS : Laparoscopic ovariectomy and salpingectomy can be performed in the cheetah using SILS without perioperative complications. Salpingectomy is faster than ovariectomy and requires less total CO2 for insufflation.NRF grants, AfriCat. Department of Companion Animal Clinical Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa and the Arabella Dean fund of the South African Veterinary Foundation.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1532-950X2016-07-30hb2015ab201

Digital gene expression for non-model organisms

Next-generation sequencing technologies offer new approaches for global measurements of gene expression but are mostly limited to organisms for which a high-quality assembled reference genome sequence is available. We present a method for gene expression profiling called EDGE, or EcoP15I-tagged Digital Gene Expression, based on ultra-high-throughput sequencing of 27-bp cDNA fragments that uniquely tag the corresponding gene, thereby allowing direct quantification of transcript abundance. We show that EDGE is capable of assaying for expression in >99% of genes in the genome and achieves saturation after 6–8 million reads. EDGE exhibits very little technical noise, reveals a large (106) dynamic range of gene expression, and is particularly suited for quantification of transcript abundance in non-model organisms where a high-quality annotated genome is not available. In a direct comparison with RNA-seq, both methods provide similar assessments of relative transcript abundance, but EDGE does better at detecting gene expression differences for poorly expressed genes and does not exhibit transcript length bias. Applying EDGE to laboratory mice, we show that a loss-of-function mutation in the melanocortin 1 receptor (Mc1r), recognized as a Mendelian determinant of yellow hair color in many different mammals, also causes reduced expression of genes involved in the interferon response. To illustrate the application of EDGE to a non-model organism, we examine skin biopsy samples from a cheetah (Acinonyx jubatus) and identify genes likely to control differences in the color of spotted versus non-spotted regions

Data from: Serum amyloid A protein concentration in blood is influenced by genetic differences in the cheetah (Acinonyx jubatus)

Systemic amyloid A (AA) amyloidosis is a major cause of morbidity and mortality among captive cheetahs. The self-aggregating AA protein responsible for this disease is a byproduct of serum amyloid A (SAA) protein degradation. Transcriptional induction of the SAA1 gene is dependent on both C/EBPβ and NF-κB cis-acting elements within the promoter region. In cheetahs, 2 alleles exist for a single guanine nucleotide deletion in the putative NF-κB binding site. In this study, a novel genotyping assay was developed to screen for the alleles. The results show that the SAA1A −97delG allele is associated with decreased SAA protein concentrations in the serum of captive cheetahs (n = 58), suggesting genetic differences at this locus may be affecting AA amyloidosis prevalence. However, there was no significant difference in the frequency of the SAA1A −97delG allele between individuals confirmed AA amyloidosis positive versus AA amyloidosis negative at the time of necropsy (n = 48). Thus, even though there is evidence that having more copies of the SAA1A −97delG allele results in a potentially protective decrease in serum concentrations of SAA protein in captive cheetahs, genotype is not associated with this disease within the North American population. These results suggest that other factors are playing a more significant role in the pathogenesis of AA amyloidosis among captive cheetahs

SAA and Genotype Data

This excel file contains the genotypic data for the SAA1A SNP for cheetahs. Fixed factors and individual SAA concentrations are also provided

Categorising cheetah behaviour using tri-axial accelerometer data loggers: a comparison of model resolution and data logger performance

BACKGROUND: Extinction is one of the greatest threats to the living world, endangering organisms globally, advancing conservation to the forefront of species research. To maximise the efficacy of conservation efforts, understanding the ecological, physiological, and behavioural requirements of vulnerable species is vital. Technological advances, particularly in remote sensing, enable researchers to continuously monitor movement and behaviours of multiple individuals simultaneously with minimal human intervention. Cheetahs, Acinonyx jubatus, constitute a “vulnerable” species for which only coarse behaviours have been elucidated. The aims of this study were to use animal-attached accelerometers to (1) determine fine-scale behaviours in cheetahs, (2) compare the performances of different devices in behaviour categorisation, and (3) provide a behavioural categorisation framework. METHODS: Two different accelerometer devices (CEFAS, frequency: 30 Hz, maximum capacity: ~ 2 g; GCDC, frequency: 50 Hz, maximum capacity: ~ 8 g) were mounted onto collars, fitted to five individual captive cheetahs. The cheetahs chased a lure around a track, during which time their behaviours were videoed. Accelerometer data were temporally aligned with corresponding video footage and labelled with one of 17 behaviours. Six separate random forest models were run (three per device type) to determine the categorisation accuracy for behaviours at a fine, medium, and coarse resolution. RESULTS: Fine- and medium-scale models had an overall categorisation accuracy of 83–86% and 84–88% respectively. Non-locomotory behaviours were best categorised on both loggers with GCDC outperforming CEFAS devices overall. On a coarse scale, both devices performed well when categorising activity (86.9% (CEFAS) vs. 89.3% (GCDC) accuracy) and inactivity (95.5% (CEFAS) vs. 95.0% (GCDC) accuracy). This study defined cheetah behaviour beyond three categories and accurately determined stalking behaviours by remote sensing. We also show that device specification and configuration may affect categorisation accuracy, so we recommend deploying several different loggers simultaneously on the same individual. CONCLUSION: The results of this study will be useful in determining wild cheetah behaviour. The methods used here allowed broad-scale (active/inactive) as well as fine-scale (e.g. stalking) behaviours to be categorised remotely. These findings and methodological approaches will be useful in monitoring the behaviour of wild cheetahs and other species of conservation interest. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40462-022-00305-w