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Differences in the bacterial communities inhabiting mammalian gut microbiomes tend to reflect the phylogenetic relatedness of their hosts, a pattern dubbed phylosymbiosis. Although most research on this pattern has compared the gut microbiomes of host species across biomes, understanding the evolutionary and ecological processes that generate phylosymbiosis requires comparisons across phylogenetic scales and under similar ecological conditions. We analysed the gut microbiomes of 14 sympatric small mammal species in a semi‐arid African savanna, hypothesizing that there would be a strong phylosymbiotic pattern associated with differences in their body sizes and diets. Consistent with phylosymbiosis, microbiome dissimilarity increased with phylogenetic distance among hosts, ranging from congeneric sets of mice and hares that did not differ significantly in microbiome composition to species from different taxonomic orders that had almost no gut bacteria in common. While phylosymbiosis was detected among just the 11 species of rodents, it was substantially weaker at this scale than in comparisons involving all 14 species together. In contrast, microbiome diversity and composition were generally more strongly correlated with body size, dietary breadth, and dietary overlap in comparisons restricted to rodents than in those including all lineages. The starkest divides in microbiome composition thus reflected the broad evolutionary divergence of hosts, regardless of body size or diet, while subtler microbiome differences reflected variation in ecologically important traits of closely related hosts. Strong phylosymbiotic patterns arose deep in the phylogeny, and ecological filters that promote functional differentiation of cooccurring host species may disrupt or obscure this pattern near the tips.

 

Many populations of consumers consist of relatively specialized individuals that eat only a subset of the foods consumed by the population at large. Although the ecological significance of individual‐level diet variation is recognized, such variation is difficult to document, and its underlying mechanisms are poorly understood. Optimal foraging theory provides a useful framework for predicting how individuals might select different diets, positing that animals balance the “opportunity cost” of stopping to eat an available food item against the cost of searching for something more nutritious; diet composition should be contingent on the distribution of food, and individual foragers should be more selective when they have greater energy reserves to invest in searching for high‐quality foods. We tested these predicted mechanisms of individual niche differentiation by quantifying environmental (resource heterogeneity) and organismal (nutritional condition) determinants of diet in a widespread browsing antelope (bushbuck,Tragelaphus sylvaticus) in an African floodplain‐savanna ecosystem. We quantified individuals' realized dietary niches (taxonomic richness and composition) using DNA metabarcoding of fecal samples collected repeatedly from 15 GPS‐collared animals (range 6–14 samples per individual, median 12). Bushbuck diets were structured by spatial heterogeneity and constrained by individual condition. We observed significant individual‐level partitioning of food plants by bushbuck both within and between two adjacent habitat types (floodplain and woodland). Individuals with home ranges that were closer together and/or had similar vegetation structure (measured using LiDAR) ate more similar diets, supporting the prediction that heterogeneous resource distribution promotes individual differentiation. Individuals in good nutritional condition had significantly narrower diets (fewer plant taxa), searched their home ranges more intensively (intensity‐of‐use index), and had higher‐quality diets (percent digestible protein) than those in poor condition, supporting the prediction that animals with greater endogenous reserves have narrower realized niches because they can invest more time in searching for nutritious foods. Our results support predictions from optimal foraging theory about the energetic basis of individual‐level dietary variation and provide a potentially generalizable framework for understanding how individuals' realized niche width is governed by animal behavior and physiology in heterogeneous landscapes.

 

Diet composition is among the most important yet least understood dimensions of animal ecology. Inspired by the study of species abundance distributions (SADs), we tested for generalities in the structure of vertebrate diets by characterising them as dietary abundance distributions (DADs). We compiled data on 1167 population‐level diets, representing >500 species from six vertebrate classes, spanning all continents and oceans. DADs near‐universally (92.5%) followed a hollow‐curve shape, with scant support for other plausible rank‐abundance‐distribution shapes. This strong generality is inherently related to, yet incompletely explained by, the SADs of available food taxa. By quantifying dietary generalisation as the half‐saturation point of the cumulative distribution of dietary abundance (sp50, minimum number of foods required to account for 50% of diet), we found that vertebrate populations are surprisingly specialised: in most populations, fewer than three foods accounted for at least half the diet. Variation insp50was strongly associated with consumer type, with carnivores being more specialised than herbivores or omnivores. Other methodological (sampling method and effort, taxonomic resolution), biological (body mass, frugivory) and biogeographic (latitude) factors influencedsp50to varying degrees. Future challenges include identifying the mechanisms underpinning the hollow‐curve DAD, its generality beyond vertebrates, and the biological determinants of dietary generalisation.

 

Camera traps (CTs) are a valuable tool in ecological research, amassing large quantities of information on the behaviour of diverse wildlife communities. CTs are predominantly used as passive data loggers to gather observational data for correlational analyses. Integrating CTs into experimental studies, however, can enable rigorous testing of key hypotheses in animal behaviour and conservation biology that are otherwise difficult or impossible to evaluate.

We developed the 'BoomBox', an open‐source Arduino‐compatible board that attaches to commercially available CTs to form an Automated Behavioural Response (ABR) system. The modular unit connects directly to the CT’s passive infrared (PIR) motion sensor, playing audio files over external speakers when the sensor is triggered. This creates a remote playback system that captures animal responses to specific cues, combining the benefits of camera trapping (e.g. continuous monitoring in remote locations, lack of human observers, large data volume) with the power of experimental manipulations (e.g. controlled perturbations for strong mechanistic inference).

Our system builds on previous ABR designs to provide a cheap (~100USD) and customizable field tool. We provide a practical guide detailing how to build and operate the BoomBox ABR system with suggestions for potential experimental designs that address a variety of questions in wildlife ecology. As proof‐of‐concept, we successfully field tested the BoomBox in two distinct field settings to study species interactions (predator–prey and predator–predator) and wildlife responses to conservation interventions.

This new tool allows researchers to conduct a unique suite of manipulative experiments on free‐living species in complex environments, enhancing the ability to identify mechanistic drivers of species' behaviours and interactions in natural systems.

 

Whether wild herbivores confer biotic resistance to invasion by exotic plants remains a key question in ecology. There is evidence that wild herbivores can impede invasion by exotic plants, but it is unclear whether and how this generalises across ecosystems with varying wild herbivore diversity and functional groups of plants, particularly over long‐term (decadal) time frames.

Using data from three long‐term (13‐ to 26‐year) exclosure experiments in central Kenya, we tested the effects of wild herbivores on the density of exotic invasive cacti,Opuntia strictaandO. ficus‐indica(collectively,Opuntia), which are among the worst invasive species globally. We also examined relationships between wild herbivore richness and elephant occurrence probability with the probability ofO. strictapresence at the landscape level (6150 km²).

Opuntiadensities were 74% to 99% lower in almost all plots accessible to wild herbivores compared to exclosure plots.Opuntiadensities also increased more rapidly across time in plots excluding wild herbivores. These effects were largely driven by megaherbivores (≥1000 kg), particularly elephants.

At the landscape level, modelledOpuntia strictaoccurrence probability was negatively correlated with estimated species richness of wild herbivores and elephant occurrence probability. On average,O. strictaoccurrence probability fell from ~0.56 to ~0.45 as wild herbivore richness increased from 6 to 10 species and fell from ~0.57 to ~0.40 as elephant occurrence probability increased from ~0.41 to ~0.84. These multi‐scale results suggest that any facilitative effects ofOpuntiaby wild herbivores (e.g. seed/vegetative dispersal) are overridden by suppression (e.g. consumption, uprooting, trampling).

Synthesis. Our experimental and observational findings that wild herbivores confer resistance to invasion by exotic cacti add to evidence that conserving and restoring native herbivore assemblages (particularly megaherbivores) can increase community resistance to plant invasions.

 

Major disturbances can temporarily remove factors that otherwise constrain population abundance and distribution. During such windows of relaxed top‐down and/or bottom‐up control, ungulate populations can grow rapidly, eventually leading to resource depletion and density‐dependent expansion into less‐preferred habitats. Although many studies have explored the demographic outcomes and ecological impacts of these processes, fewer have examined the individual‐level mechanisms by which they occur. We investigated these mechanisms in Gorongosa National Park, where the Mozambican Civil War devastated large‐mammal populations between 1977 and 1992. Gorongosa’s recovery has been marked by proliferation of waterbuck (Kobus ellipsiprymnus), an historically marginal 200‐kg antelope species, which is now roughly 20‐fold more abundant than before the war. We show that after years of unrestricted population growth, waterbuck have depleted food availability in their historically preferred floodplain habitat and have increasingly expanded into historically avoided savanna habitat. This expansion was demographically skewed: mixed‐sex groups of prime‐age individuals remained more common in the floodplain, while bachelors, loners, and subadults populated the savanna. By coupling DNA metabarcoding and forage analysis, we show that waterbuck in these two habitats ate radically different diets, which were more digestible and protein‐rich in the floodplain than in savanna; thus, although individuals in both habitats achieved positive net energy balance, energetic performance was higher in the floodplain. Analysis of daily activity patterns from high‐resolution GPS‐telemetry, accelerometry, and animal‐borne video revealed that savanna waterbuck spent less time eating, perhaps to accommodate their tougher, lower‐quality diets. Waterbuck in savanna also had more ectoparasites than those in the floodplain. Thus, plasticity in foraging behavior and diet selection enabled savanna waterbuck to tolerate the costs of density‐dependent spillover, at least in the short term; however, the already poorer energetic performance of these individuals implies that savanna occupancy may become prohibitively costly as heterospecific competitors and predators continue to recover in Gorongosa. Our results suggest that behavior can provide a leading indicator of the onset of density‐dependent limitation and the likelihood of subsequent population decline, but that reliable inference hinges on understanding the mechanistic basis of observed behavioral shifts.

 

Theory predicts that trophic specialization (i.e. low dietary diversity) should make consumer populations sensitive to environmental disturbances. Yet diagnosing specialization is complicated both by the difficulty of precisely quantifying diet composition and by definitional ambiguity: what makes a diet ‘diverse’?

We sought to characterize the relationship between taxonomic dietary diversity (TDD) and phylogenetic dietary diversity (PDD) in a species‐rich community of large mammalian herbivores in a semi‐arid East African savanna. We hypothesized that TDD and PDD would be positively correlated within and among species, because taxonomically diverse diets are likely to include plants from many lineages.

By using DNA metabarcoding to analyse 1,281 faecal samples collected across multiple seasons, we compiled high‐resolution diet profiles for 25 sympatric large‐herbivore species. For each of these populations, we calculated TDD and PDD with reference to a DNA reference library for local plants.

Contrary to our hypothesis, measures of TDD and PDD were either uncorrelated or negatively correlated with each other. Thus, these metrics reflect distinct dimensions of dietary specialization both within and among species. In general, grazers and ruminants exhibited greater TDD, but lower PDD, than did browsers and non‐ruminants. We found significant seasonal variation in TDD and/or PDD for all but four species (Grevy's zebra, buffalo, elephant, Grant's gazelle); however, the relationship between TDD and PDD was consistent across seasons for all but one of the 12 best‐sampled species (plains zebra).

Our results show that taxonomic generalists can be phylogenetic specialists, and vice versa. These two dimensions of dietary diversity suggest contrasting implications for efforts to predict how consumers will respond to climate change and other environmental perturbations. For example, populations with low TDD may be sensitive to phylogenetically ‘random’ losses of food species, whereas populations with low PDD may be comparatively more sensitive to environmental changes that disadvantage entire plant lineages—and populations with low dietary diversity in both taxonomic and phylogenetic dimensions may be most vulnerable of all.

 

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.

 

Megafauna assemblages have declined or disappeared throughout much of the world, and many efforts are underway to restore them. Understanding the trophic ecology of such reassembling systems is necessary for predicting recovery dynamics, guiding management, and testing general theory. Yet, there are few studies of recovering large‐mammal communities, and fewer still that have characterized food‐web structure with high taxonomic resolution.

In Gorongosa National Park, large herbivores have rebounded from near‐extirpation following the Mozambican Civil War (1977–1992). However, contemporary community structure differs radically from the prewar baseline: medium‐sized ungulates now outnumber larger bodied species, and several apex carnivores remain locally extinct.

We used DNA metabarcoding to quantify diet composition of Gorongosa’s 14 most abundant large‐mammal populations. We tested five hypotheses: (i) the most abundant populations exhibit greatest individual‐level dietary variability; (ii) these populations also have the greatest total niche width (dietary diversity); (iii) interspecific niche overlap is high, with the diets of less‐abundant species nested within those of more‐abundant species; (iv) partitioning of forage species is stronger in more structurally heterogeneous habitats; and (v) selectivity for plant taxa converges within guilds and digestive types, but diverges across them.

Abundant (and narrow‐mouthed) populations exhibited higher among‐individual dietary variation, but not necessarily the greatest dietary diversity. Interspecific dietary overlap was high, especially among grazers and in structurally homogenous habitat, whereas niche separation was more pronounced among browsers and in heterogeneous habitat. Patterns of selectivity were similar for ruminants—grazers and browsers alike—but differed between ruminants and non‐ruminants.

Synthesis. The structure of this recovering food web was consistent with several hypotheses predicated on competition, habitat complexity, and herbivore traits, but it differed from patterns observed in more intact assemblages. We propose that intraspecific competition in the fastest‐recovering populations has promoted individual variation and a more nested food web, wherein rare species use subsets of foods eaten by abundant species, and that this scenario is reinforced by weak predation pressure. Future work should test these conjectures and analyse how the taxonomic dietary niche axis studied here interacts with other mechanisms of diet partitioning to affect community reassembly following wildlife declines.

 

Extreme weather events perturb ecosystems and increasingly threaten biodiversity1. Ecologists emphasize the need to forecast and mitigate the impacts of these events, which requires knowledge of how risk is distributed among species and environments. However, the scale and unpredictability of extreme events complicate risk assessment1–4—especially for large animals (megafauna), which are ecologically important and disproportionately threatened but are wide-ranging and difficult to monitor5. Traits such as body size, dispersal ability and habitat affiliation are hypothesized to determine the vulnerability of animals to natural hazards1,6,7. Yet it has rarely been possible to test these hypotheses or, more generally, to link the short-term and long-term ecological effects of weather-related disturbance8,9. Here we show how large herbivores and carnivores in Mozambique responded to Intense Tropical Cyclone Idai, the deadliest storm on record in Africa, across scales ranging from individual decisions in the hours after landfall to changes in community composition nearly 2 years later. Animals responded behaviourally to rising floodwaters by moving upslope and shifting their diets. Body size and habitat association independently predicted population-level impacts: five of the smallest and most lowland-affiliated herbivore species declined by an average of 28% in the 20 months after landfall, while four of the largest and most upland-affiliated species increased by an average of 26%. We attribute the sensitivity of small-bodied species to their limited mobility and physiological constraints, which restricted their ability to avoid the flood and endure subsequent reductions in the quantity and quality of food. Our results identify general traits that govern animal responses to severe weather, which may help to inform wildlife conservation in a volatile climate.