Population genomics reveals mito-nuclear discordance and admixed populations in southern giraffe

Studying wildlife taxonomic diversity and identifying distinct populations has traditionally been largely based on morphology and geographic origin. More recently, this method has been supplemented by genetic data from the mitochondrial genome. However, this is limited as only maternally inherited and may not reflect the true nature of a population's genetics. Within the giraffe (Giraffa spp.), subspecies and unique populations were successfully characterized using both mitochondrial and genomic DNA studies, which led to new insights and, in some cases, unexpected results that required further verification. Here, we sequenced the genomes of 85 southern giraffe (G. giraffa) individuals from ten populations across southern Africa for a detailed investigation into the genetic diversity and history of its two subspecies, the Angolan (G. g. angolensis) and the South African (G. g. giraffa) giraffe. While the overall genotypes show low levels of runs of homozygosity compared to other mammals, the degree of heterozygosity is limited despite the large population size of South African giraffe. The nuclear genotype is largely congruent with the mitochondrial genotype. However, we have identified that the distribution of the Angolan giraffe is not as far east as indicated in an earlier mitochondrial DNA study. Botswana's Central Kalahari Game Reserve giraffe are unique, with a clear admixture of Angolan and South African giraffe populations. However, the enigmatic desert-dwelling giraffe of northwest Namibia is locally distinct from other Angolan giraffe yet exhibits intra-subspecies signs of admixture resulting from a recent introduction of individuals from Namibia's Etosha National Park. Whole genome sequencing is an invaluable and nearly indispensable tool for wildlife management to uncover genetic diversity that is undetectable through mitogenomic, geographical, and morphological means.

Saving the Last West African Giraffe Population: A Review of Its Conservation Status and Management

The West African giraffe (Giraffa camelopardalis peralta) was historically spread across much of the Sudano-Sahelian zone but is now restricted to Niger. Several factors resulted in their dramatic decline during the late 20th century. In 1996, only 49 individuals remained, concentrated in the 'Giraffe Zone'. Conservation activities implemented by the Government of Niger, supported by local communities and NGOs, facilitated their population numbers to increase. This review summarizes past and present conservation activities and evaluates their impact to advise and prioritize future conservation actions for the West African giraffe. The long-term conservation of the West African giraffe is highly dependent on the local communities who live alongside them, as well as supplementary support from local and international partners. Recent conservation initiatives range from community-based monitoring to the fitting of GPS satellite tags to better understand their habitat use, spatial movements to expansion areas, and environmental education to the establishment of the first satellite population of West African giraffe in Gadabedji Biosphere Reserve, the latter serving as a flagship for the future restoration of large mammal populations in West Africa. The integration of modern technologies and methods will hopefully provide better-quality data, improved spatial analyses, and greater understanding of giraffe ecology to inform the long-term management of West African giraffe.

Genomic analysis reveals limited hybridization among three giraffe species in Kenya

BACKGROUND

In the speciation continuum, the strength of reproductive isolation varies, and species boundaries are blurred by gene flow. Interbreeding among giraffe (Giraffa spp.) in captivity is known, and anecdotal reports of natural hybrids exist. In Kenya, Nubian (G. camelopardalis camelopardalis), reticulated (G. reticulata), and Masai giraffe sensu stricto (G. tippelskirchi tippelskirchi) are parapatric, and thus, the country might be a melting pot for these taxa. We analyzed 128 genomes of wild giraffe, 113 newly sequenced, representing these three taxa.

RESULTS

We found varying levels of Nubian ancestry in 13 reticulated giraffe sampled across the Laikipia Plateau most likely reflecting historical gene flow between these two lineages. Although comparatively weaker signs of ancestral gene flow and potential mitochondrial introgression from reticulated into Masai giraffe were also detected, estimated admixture levels between these two lineages are minimal. Importantly, contemporary gene flow between East African giraffe lineages was not statistically significant. Effective population sizes have declined since the Late Pleistocene, more severely for Nubian and reticulated giraffe.

CONCLUSIONS

Despite historically hybridizing, these three giraffe lineages have maintained their overall genomic integrity suggesting effective reproductive isolation, consistent with the previous classification of giraffe into four species.

Ranging behaviours across ecological and anthropogenic disturbance gradients: a pan-African perspective of giraffe (Giraffa spp.) space use

Animal movement behaviours are shaped by diverse factors, including resource availability and human impacts on the landscape. We generated home range estimates and daily movement rate estimates for 149 giraffe (Giraffa spp.) from all four species across Africa to evaluate the effects of environmental productivity and anthropogenic disturbance on space use. Using the continuous time movement modelling framework and a novel application of mixed effects meta-regression, we summarized overall giraffe space use and tested for the effects of resource availability and human impact on 95% autocorrelated kernel density estimate (AKDE) size and daily movement. The mean 95% AKDE was 359.9 km2 and the mean daily movement was 14.2 km, both with marginally significant differences across species. We found significant negative effects of resource availability, and significant positive effects of resource heterogeneity and protected area overlap on 95% AKDE size. There were significant negative effects of overall anthropogenic disturbance and positive effects of the heterogeneity of anthropogenic disturbance on daily movements and 95% AKDE size. Our results provide unique insights into the interactive effects of resource availability and anthropogenic development on the movements of a large-bodied browser and highlight the potential impacts of rapidly changing landscapes on animal space-use patterns.

Evaluating the effects of giraffe skin disease and wire snare wounds on the gaits of free-ranging Nubian giraffe

Giraffe skin disease (GSD), a condition that results in superficial lesions in certain giraffe (Giraffa spp.) populations, has emerged as a potential conservation threat. Preliminary findings suggested that individuals with GSD lesions move with greater difficulty which may in turn reduce their foraging efficiency or make them more vulnerable to predation. A current known threat to some giraffe populations is their mortality associated with entrapment in wire snares, and the morbidity and potential locomotor deficiencies associated with wounds acquired from snares. The goal of our study was to quantify the locomotor kinematics of free-ranging Nubian giraffe (G. camelopardalis camelopardalis) in Murchison Falls National Park (MFNP), Uganda, and compare spatiotemporal limb and neck angle kinematics of healthy giraffe to those of giraffe with GSD lesions, snare wounds, and both GSD lesions and snare wounds. The presence of GSD lesions did not significantly affect spatiotemporal limb kinematic parameters. This finding is potentially because lesions were located primarily on the necks of Nubian giraffe in MFNP. The kinematic parameters of individuals with snare wounds differed from those of healthy individuals, resulting in significantly shorter stride lengths, reduced speed, lower limb phase values, and increased gait asymmetry. Neck angle kinematic parameters did not differ among giraffe categories, which suggests that GSD neck lesions do not impair normal neck movements and range of motion during walking. Overall, MFNP giraffe locomotor patterns are largely conservative between healthy individuals and those with GSD, while individuals with snare wounds showed more discernible kinematic adjustments consistent with unilateral limb injuries. Additional studies are recommended to assess spatiotemporal limb kinematics of giraffe at sites where lesions are found predominantly on the limbs to better assess the potential significance of GSD on their locomotion.

Foot shape and radiographs of free-ranging Nubian giraffe in Uganda

Foot health in zoo giraffe has been a topic of recent research, although little is known about the foot health of free-ranging giraffe. This study describes the foot shape and radiographic pathological changes in 27 young adult Nubian giraffe (Giraffa camelopardalis camelopardalis) from a translocation in Uganda (August 2017). Giraffe feet were observed to have a concave sole, the hoof wall was longest by the toe tip, and the weight-bearing surface of the foot was primarily along the periphery of the foot including hoof wall, parts of the heel, and the edge of the sole. Radiographs showed that pedal osteitis and sesamoid bone cysts were relatively uncommon (3/24 giraffe with osteitis, 1/24 giraffe with sesamoid cysts), and that no giraffe in the study had P3 joint osteoarthritis, P3 rotation, or P3 fractures. Radiographs consistently demonstrated a positive palmar/plantar angle with the sole of the hoof thicker at the heel than by the toe tip, with the non weight-bearing palmar/plantar angle measuring 1.6°- 4.3°. This is the first systematic review of foot shape and radiographs in free-ranging giraffe and demonstrates a low prevalence of foot pathologies. This study suggests qualitative differences in foot shape, foot health, radiographic anatomy, and foot pathologies when comparing free-ranging and zoo giraffe. Further research is needed to identify why these differences occur and whether husbandry modifications could help improve zoo giraffe foot health and prevent associated lameness.

Behaviour Classification on Giraffes (Giraffa camelopardalis) Using Machine Learning Algorithms on Triaxial Acceleration Data of Two Commonly Used GPS Devices and Its Possible Application for Their Management and Conservation

Averting today's loss of biodiversity and ecosystem services can be achieved through conservation efforts, especially of keystone species. Giraffes (Giraffa camelopardalis) play an important role in sustaining Africa's ecosystems, but are 'vulnerable' according to the IUCN Red List since 2016. Monitoring an animal's behavior in the wild helps to develop and assess their conservation management. One mechanism for remote tracking of wildlife behavior is to attach accelerometers to animals to record their body movement. We tested two different commercially available high-resolution accelerometers, e-obs and Africa Wildlife Tracking (AWT), attached to the top of the heads of three captive giraffes and analyzed the accuracy of automatic behavior classifications, focused on the Random Forests algorithm. For both accelerometers, behaviors of lower variety in head and neck movements could be better predicted (i.e., feeding above eye level, mean prediction accuracy e-obs/AWT: 97.6%/99.7%; drinking: 96.7%/97.0%) than those with a higher variety of body postures (such as standing: 90.7-91.0%/75.2-76.7%; rumination: 89.6-91.6%/53.5-86.5%). Nonetheless both devices come with limitations and especially the AWT needs technological adaptations before applying it on animals in the wild. Nevertheless, looking at the prediction results, both are promising accelerometers for behavioral classification of giraffes. Therefore, these devices when applied to free-ranging animals, in combination with GPS tracking, can contribute greatly to the conservation of giraffes.

Skeletal dysplasia-like syndromes in wild giraffe

Objective

Skeletal dysplasias, cartilaginous or skeletal disorders that sometimes result in abnormal bone development, are seldom reported in free-ranging wild animals. Here, we use photogrammetry and comparative morphometric analyses to describe cases of abnormal appendicular skeletal proportions of free-ranging giraffe in two geographically distinct taxa: a Nubian giraffe (Giraffa camelopardalis camelopardalis) in Murchison Falls National Park, Uganda and an Angolan giraffe (Giraffa giraffa angolensis) on a private farm in central Namibia.

Results

These giraffe exhibited extremely shortened radius and metacarpal bones relative to other similarly aged giraffe. Both giraffe survived to at least subadult life stage. This report documents rare occurrences of these apparent skeletal dysplasias in free-ranging wild animals and the first records in giraffe.