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.

Congenital and Neoplastic Cranial Deformities in Wild Giraffe (Giraffa spp.).

Congenital deformities and neoplasia are poorly documented in wildlife, owing to the difficulty of detection in wild populations. Congenital deformities may lead to premature mortality, thus reducing the chances of thorough documentation. Importantly, neoplasia diagnoses depend on either sampling suspicious lesions from living individuals or access to fresh, undisturbed carcasses, which can prove challenging. We describe five cases of suspected congenital cranial deformities (midfacial cleft, wry nose, and brachygnathia inferior) and two possible cases of cranial neoplasia (orbital bone mass and a soft tissue mass) opportunistically observed in wild giraffe (Giraffa spp.) across their range in Africa. Although cases are largely limited to subjective description because physical examination is often not possible, it is critical to document such observations to help identify and track potential health concerns in wild giraffe populations.

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.

Giraffe skin disease: Clinicopathologic characterization of cutaneous filariasis in the critically endangered Nubian giraffe (Giraffa camelopardalis camelopardalis).

Giraffe skin disease (GSD) is an emerging disease of free-ranging giraffe recognized in the last 25 years in several species, including the critically endangered Nubian giraffe (Giraffa camelopardalis camelopardalis) of Uganda. Identifying the cause of GSD and understanding its impact on health were deemed paramount to supporting these vulnerable populations. Sixty-four giraffes were immobilized in Murchison Falls National Park, Uganda, from 2017 to 2019, and GSD lesions were opportunistically biopsied. Fifty-five giraffes (86%) had GSD lesions on the neck, axilla, chest, and cranial trunk. Lesions were categorized into early, intermediary, and dormant stages based on gross and histological characteristics. Early lesions were smaller, crusted nodules with eosinophilic and pyogranulomatous dermatitis and furunculosis. Intermediary lesions were thick plaques of proliferative and fissured hyperkeratosis and acanthosis with dense dermal granulation tissue and severe eosinophilic and granulomatous dermatitis. Lesions appeared to resolve to dormancy, with dormant lesions consisting of hairless plaques of hyperkeratosis with dermal scarring and residual inflammation. The periphery of early and intermediary lesions included follicular granulomas containing adult filarid nematodes, with myriad encysted microfilariae in the superficial dermis. Stage L3 larvae were common in early and intermediary lesions, and dormant lesions had remnant encysted microfilariae with no adult or stage L3 larvae. Nematodes were morphologically and genetically novel with close identity to Stephanofilaria spp. and Brugia malayi, which cause infectious filariasis. Identification of potential insect vectors, long-term monitoring of GSD lesions, and evaluating response to therapy is ongoing in the efforts to help conserve the Nubian giraffe.

Camera settings and biome influence the accuracy of citizen science approaches to camera trap image classification.

Scientists are increasingly using volunteer efforts of citizen scientists to classify images captured by motion-activated trail cameras. The rising popularity of citizen science reflects its potential to engage the public in conservation science and accelerate processing of the large volume of images generated by trail cameras. While image classification accuracy by citizen scientists can vary across species, the influence of other factors on accuracy is poorly understood. Inaccuracy diminishes the value of citizen science derived data and prompts the need for specific best-practice protocols to decrease error. We compare the accuracy between three programs that use crowdsourced citizen scientists to process images online: Snapshot Serengeti, Wildwatch Kenya, and AmazonCam Tambopata. We hypothesized that habitat type and camera settings would influence accuracy. To evaluate these factors, each photograph was circulated to multiple volunteers. All volunteer classifications were aggregated to a single best answer for each photograph using a plurality algorithm. Subsequently, a subset of these images underwent expert review and were compared to the citizen scientist results. Classification errors were categorized by the nature of the error (e.g., false species or false empty), and reason for the false classification (e.g., misidentification). Our results show that Snapshot Serengeti had the highest accuracy (97.9%), followed by AmazonCam Tambopata (93.5%), then Wildwatch Kenya (83.4%). Error type was influenced by habitat, with false empty images more prevalent in open-grassy habitat (27%) compared to woodlands (10%). For medium to large animal surveys across all habitat types, our results suggest that to significantly improve accuracy in crowdsourced projects, researchers should use a trail camera set up protocol with a burst of three consecutive photographs, a short field of view, and determine camera sensitivity settings based on in situ testing. Accuracy level comparisons such as this study can improve reliability of future citizen science projects, and subsequently encourage the increased use of such data.

QUANTIFYING THE SEVERITY OF GIRAFFE SKIN DISEASE VIA PHOTOGRAMMETRY ANALYSIS OF CAMERA TRAP DATA.

Developing techniques to quantify the spread and severity of diseases afflicting wildlife populations is important for disease ecology, animal ecology, and conservation. Giraffes (Giraffa camelopardalis) are in the midst of a dramatic decline, but it is not known whether disease is playing an important role in the broad-scale population reductions. A skin disorder referred to as giraffe skin disease (GSD) was recorded in 1995 in one giraffe population in Uganda. Since then, GSD has been detected in 13 populations in seven African countries, but good descriptions of the severity of this disease are not available. We photogrammetrically analyzed camera trap images from both Ruaha and Serengeti National parks in Tanzania to quantify GSD severity. Giraffe skin disease afflicts the limbs of giraffes in Tanzania, and we quantified severity by measuring the vertical length of the GSD lesion in relation to the total leg length. Applying the Jenks natural breaks algorithm to the lesion proportions that we derived, we classified individual giraffes into disease categories (none, mild, moderate, and severe). Scaling up to the population level, we predicted the proportion of the Ruaha and Serengeti giraffe populations with mild, moderate, and severe GSD. This study serves to demonstrate that camera traps presented an informative platform for examinations of skin disease ecology.

The many faces of fear: a synthesis of the methodological variation in characterizing predation risk.

Predators affect prey by killing them directly (lethal effects) and by inducing costly antipredator behaviours in living prey (risk effects). Risk effects can strongly influence prey populations and cascade through trophic systems. A prerequisite for assessing risk effects is characterizing the spatiotemporal variation in predation risk. Risk effects research has experienced rapid growth in the last several decades. However, preliminary assessments of the resultant literature suggest that researchers characterize predation risk using a variety of techniques. The implications of this methodological variation for inference and comparability among studies have not been well recognized or formally synthesized. We couple a literature survey with a hierarchical framework, developed from established theory, to quantify the methodological variation in characterizing risk using carnivore-ungulate systems as a case study. Via this process, we documented 244 metrics of risk from 141 studies falling into at least 13 distinct subcategories within three broader categories. Both empirical and theoretical work suggest risk and its effects on prey constitute a complex, multi-dimensional process with expressions varying by spatiotemporal scale. Our survey suggests this multi-scale complexity is reflected in the literature as a whole but often underappreciated in any given study, which complicates comparability among studies and leads to an overemphasis on documenting the presence of risk effects rather than their mechanisms or scale of influence. We suggest risk metrics be placed in a more concrete conceptual framework to clarify inference surrounding risk effects and their cascading effects throughout ecosystems. We recommend studies (i) take a multi-scale approach to characterizing risk; (ii) explicitly consider 'true' predation risk (probability of predation per unit time); and (iii) use risk metrics that facilitate comparison among studies and the evaluation of multiple competing hypotheses. Addressing the pressing questions in risk effects research, including how, to what extent and on what scale they occur, requires leveraging the advantages of the many methods available to characterize risk while minimizing the confusion caused by variability in their application.