De novo whole-genome assembly and resequencing resources for the roan (Hippotragus equinus), an iconic African antelope

Roan antelope (Hippotragus equinus) is the second-largest member of the Hippotraginae (Bovidae), and is widely distributed across sub-Saharan mesic woodlands. Despite being listed as "Least Concern" across its African range, population numbers are decreasing with many regional Red List statuses varying between Endangered and Locally Extinct. Although the roan antelope has become an economically-important game species in Southern Africa, the vast majority of wild populations are found only in fragmented protected areas, which is of conservation concern. Genomic information is crucial in devising optimal management plans. To this end, we report here the first de novo assembly and annotation of the whole-genome sequence of a male roan antelope from a captive-breeding program. Additionally, we uncover single-nucleotide variants (SNVs) through re-sequencing of five wild individuals representing five of the six described subspecies. We used 10X Genomics Chromium chemistry to produce a draft genome of 2.56 Gb consisting of 16,880 scaffolds with N50 = 8.42 Mb and a BUSCO completeness of 91.2%. The draft roan genome includes 1.1 Gbp (42.2%) repetitive sequences. De novo annotation identified 20,518 protein-coding genes. Genome synteny to the domestic cow showed an average identity of 92.7%. Re-sequencing of five wild individuals to an average sequencing depth of 9.8x resulted in the identification of a filtered set of 3.4x106 bi-allelic SNVs. The proportion of alternative homozygous SNVs for the individuals representing different subspecies, as well as differentiation as measured by PCA, were consistent with expected divergence from the reference genome and among samples. The roan antelope genome is a valuable resource for evolutionary and population genomic questions, as well as management and conservation actions.

Reproductive events and respective faecal androgen metabolite concentrations in captive male roan antelope (Hippotragus equinus)

Understanding the reproductive biology of the roan antelope (Hippotragus equinus) (É. Geoffroy Saint-Hilaire, 1803) is crucial to optimise breeding success in captive breeding programmes of this threatened species. In this study, the pattern of faecal androgen metabolite (fAM) production related to reproductive events (calving or birthing, mating, gestation, and lactation), sexual behaviours as well as environmental cues were studied in captive adult male roan antelope. Faecal sample collection and behavioural observations were carried out from August 2017 to July 2018 for three reproductive males participating in a conservation breeding programme at the Lapalala Wilderness Nature Reserve in South Africa. As a prerequisite, the enzyme immunoassay used in this study was biologically validated for the species by demonstrating a significant difference between fAM concentrations in non-breeding adults, breeding adults and juvenile males. Results revealed that in adults males, the overall mean fAM levels were 73% higher during the breeding period compared to the non-breeding periods, and 85% higher when exclusively compared to the lactation/gestation periods, but only 5.3% higher when compared to the birthing period. Simultaneously, fAM concentrations were lower during the wet season compared to the dry season, increasing with a reduction in photoperiod. With the exception of courtship, frequencies of sexual behaviours monitored changed in accordance with individual mean fAM concentrations in male roan antelope, the findings suggest that androgen production varies with the occurrence of mating activity and may be influenced by photoperiod but not with rainfall.

Human Use-Pressure and Sustainable Wildlife Management in Burkina Faso: A Case Study of Bushmeat Hunting in Bobo-Dioulasso

Hunting is an important activity for the survival of local communities. However, unregulated hunting threatens the sustainability of wildlife and subsequently affects the same populations. This study investigated bushmeat hunting practices and their implications in wildlife sustainable management in Bobo-Dioulasso (Burkina-Faso). A total of 226 hunters were interviewed, using a random sampling technique and a semi-structured questionnaire. It revealed four groups of hunters. Group 1 (32.57% of the sample) was young and commercial hunters from Bobo ethnic group with 42.15±6.01 as average age. Hunting is their main activity and they hunt all year round in groups using direct catch and hunting dogs. Group 2 (19.76%) prefers to hunt in the daytime and their products serve for diseases treatments through traditional medicine. Group 3 (29.06%) consists of the Mossi ethnic group with an average age of 58.92±3.69. They belong to the confederation of hunters called "Dozo". They are farmers with hunting as the secondary activity. They hunt at night with headlamps. Group 4 (18.60%), mainly Mossi with an average age of 63.06±7.19, hunts occasionally and respects the accredited hunting periods. The animals at the risk and most commonly used as bushmeat are Francolin, Porcupine, Cape hare, Buffalo, Nile monitor, Python, and Parrot. The locally threatened animals are respectively Ostrich, Roan antelope, Bat, Crocodile, and Striped hyena. Other animals are endangered and becoming increasingly rare (Lion, Elephant, Hippopotamus, and Warthog). Actions need to be taken by decision-makers and involve local communities for the sustainable management of wildlife in Bobo-Dioulasso.