A metagenomic survey of the fecal microbiome of the African savanna elephant (Loxodonta africana).

The African savanna elephant (Loxodonta africana) is the largest terrestrial animal on Earth and is found primarily in Southern and Eastern Africa. It is a hindgut, colonic fermenter and subsists on a diet of raw plant materials found in its grazing area. In this study the bacterial, archaeal and fungal populations of seven African savanna elephant fecal metagenomes were first characterized using amplicon sequencing. On the genus level it was observed that the p-1088-a5 gut group in the bacteriome, Methanocorpusulum and Methanobrevibacter in the archaeome and Alternaria, Aurobasidium, Didymella and Preussia in the mycome, predominated. Subsequently, metagenomic shotgun sequencing was employed to identify possible functional pathways and carbohydrate-active enzymes (CAZymes). Carbohydrate catabolic pathways represented the main degradation pathways, and the fecal metagenome was enriched in the glycohydroside (GH) class of CAZymes. Additionally, the top GH families identified - GH43, GH2, GH13 and GH3 - are known to be associated with cellulytic, hemicellulytic and pectolytic activities. Finally, the CAZymes families identified in the African savanna elephant were compared with those found in the Asian elephant and it was demonstrated that there is a unique repository of CAZymes that could be leveraged in the biotechnological context such as the degradation of lignocellulose for the production of second-generation biofuels and energy.

The Elephant Evolved p53 Isoforms that Escape MDM2-Mediated Repression and Cancer.

The p53 tumor suppressor is a transcription factor with roles in cell development, apoptosis, oncogenesis, aging, and homeostasis in response to stresses and infections. p53 is tightly regulated by the MDM2 E3 ubiquitin ligase. The p53-MDM2 pathway has coevolved, with MDM2 remaining largely conserved, whereas the TP53 gene morphed into various isoforms. Studies on prevertebrate ancestral homologs revealed the transition from an environmentally induced mechanism activating p53 to a tightly regulated system involving cell signaling. The evolution of this mechanism depends on structural changes in the interacting protein motifs. Elephants such as Loxodonta africana constitute ideal models to investigate this coevolution as they are large and long-living as well as having 20 copies of TP53 isoformic sequences expressing a variety of BOX-I MDM2-binding motifs. Collectively, these isoforms would enhance sensitivity to cellular stresses, such as DNA damage, presumably accounting for strong cancer defenses and other adaptations favoring healthy aging. Here we investigate the molecular evolution of the p53-MDM2 system by combining in silico modeling and in vitro assays to explore structural and functional aspects of p53 isoforms retaining the MDM2 interaction, whereas forming distinct pools of cell signaling. The methodology used demonstrates, for the first time that in silico docking simulations can be used to explore functional aspects of elephant p53 isoforms. Our observations elucidate structural and mechanistic aspects of p53 regulation, facilitate understanding of complex cell signaling, and suggest testable hypotheses of p53 evolution referencing Peto's Paradox.

Understanding Mycobacterium tuberculosis complex in elephants through a One Health approach: a systematic review.

BACKGROUND: Mycobacterium tuberculosis complex (MTC) that causes the chronic infectious disease- tuberculosis (TB), often presents with a complicated epidemiological pattern where the transmission chain may include humans, domestic animals and wildlife, including elephants. TB has been reported globally in both captive and wild elephants. The One Health approach might be the most effective way of understanding the shared MTC infection dynamics in captive and wild animals like Asian elephants. This systematic review accumulates evidence on occurrence, transmission pathways, and preventive measures of TB in elephants from a One Health perspective. RESULTS: The prevalence of TB reported in elephant populations ranges from 0 to 23.33% and high prevalence's are reported for elephants that are in close proximity to infected humans. The risk of elephant to human infection transmission increased significantly with exposure duration and contact with infected elephants. Some studies described the plausible TB transmission to captive elephants from other animals (wild and domestic), suggesting inter- and intra-species transmission. The results of this systematic review based on 27 relevant published works, suggest three overarching interrelated transmission pathways for M. tuberculosis infections in Asian elephants- i) humans and elephants, ii) other animals (wild or domestic) and elephants and iii) unclear sources of infection. CONCLUSIONS: The progress made with new TB diagnostic tools provides multiple methods to choose from. However, lack of harmonization of TB testing in elephants and their human contacts remains a challenge to prevent TB in those animals. Routine TB screening among elephants and caretakers by setting up an occupational health program for early diagnosis of infection through combined efforts of public health, veterinary medicine, and occupational health experts is suggested. This implies the need for a One Health approach to elephant TB control. This review reveals the need for more research on Mycobacterium tuberculosis complex transmission pathways at the human-animal interface.

Analogous laterality in trunk movements in captive African elephants: A pilot study.

Lateralization of hand use in primates has been extensively studied in a variety of contexts, and starts to be investigated in other species and organs in order to understand the evolution of the laterality according to different tasks. In elephants, the orientation of the movements of the trunk has been observed mainly in feeding and social contexts, in free conditions. However, little is known about the influence of task complexity on trunk laterality. In this study, we compared the lateralization of the trunk in two conditions: standardized and free. We offered granules to six African elephants on each side of an opened trapdoor to create a constraining environment and reported the different behaviours employed and their orientation. In addition, we observed the same individuals in free conditions and noted the lateralization of the use of their trunk. We revealed a common right side preference in all our elephants, both in standardized and free conditions. This side bias was stronger in our constraining task, adding evidence for the task complexity theory. We finally described laterality in new behaviours in the literature on elephants, such as pinching, gathering or exploration with the trunk.

Mycobacterium bovis Infection in Free-Ranging African Elephants.

Mycobacterium bovis infection in wildlife species occurs worldwide. However, few cases of M. bovis infection in captive elephants have been reported. We describe 2 incidental cases of bovine tuberculosis in free-ranging African elephants (Loxodonta africana) from a tuberculosis-endemic national park in South Africa and the epidemiologic implications of these infections.

Noise matters: elephants show risk-avoidance behaviour in response to human-generated seismic cues.

African elephants (Loxodonta africana) use many sensory modes to gather information about their environment, including the detection of seismic, or ground-based, vibrations. Seismic information is known to include elephant-generated signals, but also potentially encompasses biotic cues that are commonly referred to as 'noise'. To investigate seismic information transfer in elephants beyond communication, here we tested the hypothesis that wild elephants detect and discriminate between seismic vibrations that differ in their noise types, whether elephant- or human-generated. We played three types of seismic vibrations to elephants: seismic recordings of elephants (elephant-generated), white noise (human-generated) and a combined track (elephant- and human-generated). We found evidence of both detection of seismic noise and discrimination between the two treatments containing human-generated noise. In particular, we found evidence of retreat behaviour, where seismic tracks with human-generated noise caused elephants to move further away from the trial location. We conclude that seismic noise are cues that contain biologically relevant information for elephants that they can associate with risk. This expands our understanding of how elephants use seismic information, with implications for elephant sensory ecology and conservation management.

Increasing browse and social complexity can improve zoo elephant welfare.

While recent work has assessed how environmental and managerial changes influence elephant welfare across multiple zoos, few studies have addressed the effects of management changes within a single institution. In this paper, we examine how management changes related to social structure and diet affect the behavior of a group of zoo elephants over a 23-month period while also considering underlying factors, such as time of day, hormonal cycle, and individual differences. We recorded individual behaviors using 2-min scan samples during 60-min sessions. We analyzed behavioral changes across several study variables using generalized linear mixed models. We found that increasing browse can improve opportunities for foraging throughout the day but may not be sufficient to reduce repetitive behaviors. We observed that increasing group size and integration of bulls with cows can lead to increased social interaction in African elephants. Our results highlight the importance of using multiple management alterations to address elephant welfare, and considering environmental factors, when making management decisions.

Understanding the drivers of mortality in African savannah elephants.

Populations of African savannah elephants (Loxodonta africana) have been declining due to poaching, human-elephant conflict, and habitat loss. Understanding the causes of these declines could aid in stabilizing elephant populations. We used data from the Great Elephant Census, a 19-country aerial survey of savannah elephants conducted in 2014 and 2015, to examine effects of a suite of variables on elephant mortality. Independent variables included spatially explicit measures of natural processes and human presence as well as country-level socioeconomic measures. Our dependent variable was the carcass ratio, the ratio of dead elephants to live plus dead elephants, which is an index of recent elephant mortality. Carcass ratios are inversely proportional to population growth rates of elephants over the 4 yr prior to a survey. At the scale of survey strata (n = 275, median area = 1,222 km2 ), we found strong negative associations for carcass ratios with vegetation greenness at the time of the survey, overseas development aid to the country, and distance to the nearest international border. At the scale of ecosystems (n = 42, median area = 12,085 km2 ), carcass ratios increased with drought frequency and decreased with human density and overseas development aid to the country. Both stratum- and ecosystem-scale models explained well under one-half of the variance in carcass ratios. The differences in results between scales suggest that the drivers of mortality may be scale-specific and that the corresponding solutions may vary by scale as well.

Development of a multiplex, PCR-based genotyping assay for African and Asian elephants for forensic purposes.

Wildlife crimes and the threats they present to elephant populations raise the need to develop and implement DNA-based methodology as an aid for wildlife forensic investigations and conservation efforts. This study describes the development of a tetra-nucleotide repeat STR multiplex, genotyping assay that will identify Asian elephant (Elephas maximus) and African elephant (Loxodonta africana) DNA. The assay targets six tetra-nucleotide STRs and two sex-typing markers simultaneously in both genera of elephants, a first for elephant genotyping assays. The developed assay has potential application in wildlife investigations to associate a biological sample to a particular individual elephant and additionally in conservation science for population management.

Wildlife impacts and vulnerable livelihoods in a transfrontier conservation landscape.

Interactions between humans and wildlife resulting in negative impacts are among the most pressing conservation challenges globally. In regions of smallholder livestock and crop production, interactions with wildlife can compromise human well-being and motivate negative sentiment and retaliation toward wildlife, undermining conservation goals. Although impacts may be unavoidable when human and wildlife land use overlap, scant large-scale human data exist quantifying the direct costs of wildlife to livelihoods. In a landscape of global importance for wildlife conservation in southern Africa, we quantified costs for people living with wildlife through a fundamental measure of human well-being, food security, and we tested whether existing livelihood strategies buffer certain households against crop depredation by wildlife, predominantly elephants. To do this, we estimated Bayesian multilevel statistical models based on multicounty household data (n = 711) and interpreted model results in the context of spatial data from participatory land-use mapping. Reported crop depredation by wildlife was widespread. Over half of the sample households were affected and household food security was reduced significantly (odds ratio 0.37 [0.22, 0.63]). The most food insecure households relied on gathered food sources and welfare programs. In the event of crop depredation by wildlife, these 2 livelihood sources buffered or reduced harmful effects of depredation. The presence of buffering strategies suggests a targeted compensation strategy could benefit the region's most vulnerable people. Such strategies should be combined with dynamic and spatially explicit land-use planning that may reduce the frequency of negative human-wildlife impacts. Quantifying and mitigating the human costs from wildlife are necessary steps in working toward human-wildlife coexistence.

Impactos de la Fauna y Medios de Subsistencia Vulnerables en unkl Paisaje de Conservación Transfronteriza Resumen Las interacciones entre los humanos y la fauna que resultan en impactos negativos se encuentran entre los desafíos más apremiantes para la conservación a nivel mundial. En las regiones de ganaderos y agricultores minifundistas, las interacciones con la fauna pueden poner en peligro el bienestar humano y motivar sentimientos negativos y represalias hacia la fauna, lo que debilita los objetivos de conservación. Aunque los impactos pueden evitarse cuando el uso de suelo por humanos y fauna se traslapa, existen pocos datos humanos a gran escala que cuantifiquen el costo directo de la fauna para los medios de subsistencia. Cuantificamos el costo para las personas que conviven con animales silvestres en un paisaje de importancia global para la conservación de fauna en el sur de África. La cuantificación fue realizada por medio de una medida fundamental de bienestar humano y seguridad alimentaria, y probamos si las estrategias existentes de subsistencia amortiguan a ciertos hogares ante la depredación de cultivos realizada por animales silvestres, predominantemente los elefantes. Para realizar esto, estimamos algunos modelos estadísticos bayesianos de niveles múltiples basados en los datos de hogares ubicados en múltiples condados (n = 711) e interpretamos los resultados de los modelos en el contexto de los datos espaciales a partir de un mapeo participativo de uso de suelo. La depredación de cultivos por animales silvestres fue reportada de manera generalizada. Más de la mitad de los hogares en la muestra estuvieron afectados y la seguridad alimenticia de los hogares se redujo significativamente (proporción de probabilidades 0.37 [0.22, 0.63]). Los hogares con la menor seguridad alimentaria dependían de fuentes de recolección de alimentos y programas de bienestar. En el evento de la depredación por fauna de los cultivos, estas dos fuentes de subsistencia amortiguaron o redujeron los efectos dañinos de la depredación. La presencia de las estrategias de amortiguamiento sugiere que una estrategia de compensación enfocada podría beneficiar a las personas más vulnerables de la región. Dichas estrategias deberían estar combinadas con la planeación del uso de suelo dinámica y espacialmente explícita, la cual podría reducir la frecuencia de los impactos negativos entre los humanos y la fauna. La cuantificación y mitificación del costo humano a partir de la fauna son pasos necesarios en el camino hacia la coexistencia entre los humanos y la fauna.

Strongylid infection varies with age, sex, movement and social factors in wild African elephants.

Comparing parasitic infection among individuals of wildlife populations can provide insight into factors that influence wildlife disease ecology. Strongylids are parasitic worms that infect the intestinal tract of vertebrates, and infection with strongylids can be approximated by counting strongylid eggs in dung samples. Here we tested for correlations between strongylid egg counts and 18 different individual characteristics, environmental and social factors in individually known wild African elephants. We counted more eggs in the dung samples of younger elephants and females relative to mature elephants and males. We also found that elephants spending more time outside reserves shed more strongylid eggs than elephants that were more often within reserves. Elephants that were less socially integrated, as measured by how much aggression they received from other elephants, shed fewer strongylid eggs; relatedly, socially isolated orphan elephants that had left their family shed fewer strongylid eggs than elephants that remained with their family. Our results suggest that landscapes altered by livestock grazing and social disruption caused by humans may impact parasitic infection in wildlife.

NONINVASIVE SAMPLING FOR DETECTION OF ELEPHANT ENDOTHELIOTROPIC HERPESVIRUS AND GENOMIC DNA IN ASIAN (ELEPHAS MAXIMUS) AND AFRICAN (LOXODONTA AFRICANA) ELEPHANTS.

Elephant endotheliotropic herpesvirus (EEHV) hemorrhagic disease (EEHV-HD) threatens Asian elephant (Elephas maximus) population sustainability in North America. Clusters of cases have also been reported in African elephants (Loxodonta africana). Risk to range country elephant populations is unknown. Currently, EEHV detection depends upon sampling elephants trained for invasive blood and trunk wash collection. To evaluate noninvasive sample collection options, paired invasively collected (blood, trunk wash and oral swabs), and noninvasively collected (chewed plant and fecal) samples were compared over 6 wk from 9 Asian elephants and 12 African elephants. EEHV shedding was detected simultaneously in a paired trunk wash and fecal sample from one African elephant. Elephant γ herpesvirus-1 shedding was identified in six chewed plant samples collected from four Asian elephants. Noninvasively collected samples can be used to detect elephant herpesvirus shedding. Longer sampling periods are needed to evaluate the clinical usefulness of noninvasive sampling for EEHV detection.

Leveraging multidimensional heterogeneity in resource selection to define movement tactics of animals.

Increasing interest in the complexity, variation and drivers of movement-related behaviours promise new insight into fundamental components of ecology. Resolving the multidimensionality of spatially explicit behaviour remains a challenge for investigating tactics and their relation to niche construction, but high-resolution movement data are providing unprecedented understanding of the diversity of spatially explicit behaviours. We introduce a framework for investigating individual variation in movement-defined resource selection that integrates the behavioural and ecological niche concepts. We apply it to long-term tracking data of 115 African elephants (Loxodonta africana), illustrating how a behavioural hypervolume can be defined based on differences between individuals and their ecological settings, and applied to explore population heterogeneity. While normative movement behaviour is frequently used to characterise population behaviour, we demonstrate the value of leveraging heterogeneity in the behaviour to gain greater insight into population structure and the mechanisms driving space-use tactics.

Mining morphometrics and age from past survey photographs.

BACKGROUND: Researchers often document wildlife surveys using images. These images contain data that can be used to understand alterative research objectives, even years after they were originally captured. We have developed a method to measure age and morphology (body size measurements and tusk size) from survey image databases and future surveys, without the availability of a known subject distance or a scale in each image. African savanna elephants (Loxodonta africana) serve as an ideal model species to develop a non-invasive, image-based morphometric methodology: as handling these animals is particularly invasive and expensive, involving anaesthesia and because of their IUCN 'vulnerable' status. We compare in situ measurements, taken during collaring events, to tusk-to-body-size ratios, measured from the images. RESULTS: We provide evidence that relative morphological measurements, musth timing, and age of male African savanna elephants can accurately be obtained from a survey image database of over 30,000 images, taken over an 18-year period. Of the 11 tusk to body size ratios calculated, we recommend the use of two in particular for future measurement in African elephants to determine size and age: 1) tusk length to tusk diameter and 2) tusk length to body height. CONCLUSIONS: We present a practical, non-invasive measure to estimate morphometrics, including both age and tusk size from photographs, which has conservation applications to the protection of elephants and is relevant to a range of other taxa.

Determinants of elephant foraging behaviour in a coupled human-natural system: Is brown the new green?

Crop raiding by wildlife poses major threats to both wildlife conservation and human well-being in agroecosystems worldwide. These threats are particularly acute in many parts of Africa, where crop raiders include globally threatened megafauna such as elephants, and where smallholder agriculture is a primary source of human livelihood. One framework for understanding herbivore feeding behaviour, the forage-maturation hypothesis, predicts that herbivores should align their movements with intermediate forage biomass (i.e., peak green-up); this phenomenon is known as "surfing the green wave." Crop-raiding elephants, however, often consume not just foliage, but also fruits and tubers (e.g., maize and potatoes), which generally mature after seasonal peaks in photosynthetic activity. Thus, although elephants have been reported to surf the green wave in natural habitats, they may utilize a different strategy in cultivated landscapes by selecting crops that are "browning down." We sought to understand the factors that underpin movement of elephants into agricultural landscapes. In Mozambique's Gorongosa National Park, we used movement data from GPS-collared elephants, together with precipitation records, remotely sensed estimates of landscape greenness (NDVI), DNA-based diet analysis, measurements of plant nutritional quality and survey-based metrics of crop availability to understand spatiotemporal variation in elephant crop-raiding behaviour. Elephants tracked peak NDVI while foraging inside the Park. During the dry season, however, when NDVI within the Park declined and availability of mature crops was high, crop raiding increased dramatically, and elephants consistently selected crop plants that were browning down while foraging in cultivated landscapes. Crops contained significantly higher digestible energy than wild food plants, but comparable (and sometimes lower) levels of digestible protein, suggesting that this foraging strategy maximized energy rather than protein intake. Our study is the first to combine GPS tracking data with high-resolution diet analysis and community-based reporting of crop availability to reveal fine-scale plasticity in foraging behaviour of elephants at the human-wildlife interface. Our results extend the forage-maturation hypothesis by showing that elephants surf waves of plant brown-down in cultivated landscapes. These findings can aid efforts to reduce human-elephant conflict by enabling wildlife managers to prioritize mitigation actions in time and space with limited resources.

ELEquant: a developmental framework and validation of forensic and conservation real-time PCR assays.

A framework for the development and validation of a qPCR assay for species identification and DNA quantification for conservation and forensic purposes is presented. Elephants are commonly poached for their ivory tusks, which is the primary driving force behind their endangered status. In addition to poaching and trade, habitat loss due to logging and mining has also resulted in loss of elephants. Crimes against animals can be deterred and/or further prosecution sought through testing with forensic genetic techniques. The creation of novel genetic assays can greatly impact wildlife forensic science investigations in identifying the species. Molecular genetic techniques can help enforce conservation efforts; however, they must be properly developed and validated to be of evidentiary quality for court systems. African and Asian elephant buccal cells were used as model in this work. The assay provides a method to differentiate biological fluids of both genera of elephants simultaneously. It can be used for identification of elephant derived products and presents valuable quantification for optimized further testing, such as microsatellite detection.

Megafaunal effects on vegetation structure throughout a densely wooded African landscape.

Megafauna strongly affect vegetation structure and composition, often leading to management concern. However, the extent of their influence across large scales and varying ecosystems remains largely unknown. Using high resolution airborne Light Detection and Ranging (LiDAR), we investigated landscape-scale changes in vegetation height and three-dimensional (3D) structure across landscapes of varying elephant densities and presence over time, and in response to surface water distribution and terrain variability in the heavily managed thicket biome of the Addo Elephant National Park, South Africa. Elephants caused up to a fourfold reduction in vegetation height and altered the vertical profile, but increased vegetation height variability. Vegetation height also increased with elevation and distance from water, particularly in areas that elephants had long occupied at high densities. Slope had opposing effects on vegetation height, with height increasing with slope in areas long exposed to elephants, but decreasing where elephants had only recently been granted access. Our results suggest that elephants are the primary agents of vegetation change in this ecosystem, but that the strength of their effects varies across the landscape, enabling management to use water and terrain as mitigation tools. We further highlight the necessity of landscape-level experimental studies on megafaunal effects to untangle mechanisms and establish causality.

The impact of competition on elephant musth strategies: A game-theoretic model.

Mature male African Savannah elephants are known to periodically enter a temporary state of heightened aggression called "musth", often linked with increased androgens, particularly testosterone. Sexually mature males are capable of entering musth at any time of year, and will often travel long distances to find estrous females. When two musth bulls or two non-musth bulls encounter one another, the agonistic interaction is usually won by the larger male. However, when a smaller musth bull encounters a larger non-musth bull, the smaller musth male can win. The relative mating success of musth males is due partly to this fighting advantage, and partly to estrous females' general preference for musth males. Though musth behavior has long been observed and documented, the evolutionary advantages of musth remain poorly understood. Here we develop a game-theoretic model of male musth behavior which assumes musth duration as a parameter, and distributions of small, medium and large musth males are predicted in both time and space. The predicted results are similar to the musth timing behavior observed in the Amboseli National Park elephant population, and further results are generated with relevance to Samburu National Park. We discuss small male musth behavior, the effects of estrous female spatial heterogeneity on musth timing, conservation applications, and the assumptions underpinning the model.

USE OF COMPOSITE MATERIALS AS A COMPONENT OF TUSK FRACTURE MANAGEMENT IN AN ASIAN ELEPHANT (ELEPHAS MAXIMUS) AND AN AFRICAN ELEPHANT (LOXODONTA AFRICANA).

Tusk fractures in Asian (Elephas maximus) and African elephants (Loxodonta africana) can result in damage to the distal end or to longitudinal cracks, potentially progressing to pulpitis. With pulp exposure, endodontic therapy is the treatment of choice, but conservative therapy has sufficed for some elephants. This manuscript describes the use of composite materials as a component of tusk fracture management. A 7-yr-old male Asian elephant fractured the distal end of both tusks with pulp exposure in one. Capping of each tusk with a Kevlar/fiberglass composite prevented further damage, and a modification allowed care of the exposed pulp tissue. A 34-yr-old male African elephant with a longitudinal crack received a carbon fiber/fiberglass composite circumferential wrap to potentially stabilize the crack. Compression of the crack was achieved, but follow-up was truncated due to bacterial pulpitis. Both cases show that composite material allows for lightweight, durable management of tusk fractures with continued radiographic monitoring.

SUCCESSFUL TREATMENT OF DIGITAL OSTEITIS BY INTRAVENOUS REGIONAL PERFUSION OF CEFTIOFUR IN AN AFRICAN ELEPHANT (LOXODONTA AFRICANA).

A 41-yr-old African elephant ( Loxodonta africana ) presented with a swollen third digit of the left forelimb and a 2-cm hole in the pad. Corrective trimming, topical treatments, and an oral antibiotic resulted in apparent resolution; however, it reoccurred after 4 mo. Radiographs suggested bone lysis in the third phalanx, with the primary differential diagnosis being septic osteitis. Flushing with metronidazole solution and intravenous regional perfusion (IVRP) of the foot were commenced. A tourniquet was applied just above the carpus, an interdigital vein was identified by ultrasound, and into this vein 2 g (20 ml) of ceftiofur sodium solution, followed by 60 ml of heparinized saline, was administered. The foot was kept raised for 25 min and then the tourniquet was removed. IVRP was repeated every other day for 70 treatments over 6 mo. Healing occurred, which was confirmed radiographically. IVRP offers an excellent treatment modality in a well-trained elephant.