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Current understanding of the distribution of vegetation and large mammalian herbivores (LMH) is based on a combination of biogeographic studies and highly controlled field experiments, but a more complete understanding of these patterns requires study of their natural co‐occurrence patterns at intermediate spatial scales. The study was conducted in the 120‐ha Mpala Forest Global Earth Observatory (ForestGEO) plot, Kenya. We examined differences in herbaceous plant communities and habitat use by LMH among three topographic habitats with distinct soil types, namely steep slopes, valley and plateau. Each pair of habitats differed in plant and animal composition. The steep slopes and plateau respectively had ≥1‐fold higher percentage herbaceous cover than the valley, whereas the steep slopes and valley had >1.5‐fold greater grass species richness and diversity than the plateau. The activity of LMH was ≥1.7‐fold higher in the valley than the steep slopes and plateau, reflecting a positive relationship between LMH activity index and richness and diversity of grass species. Results indicate that fine‐scale variation in topography and soil are associated with both the distribution of herbaceous vegetation and LMH, suggesting a need to account for local habitat characteristics when examining the distributions of plants, animals, and plant‐herbivore interactions in natural systems.

 

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.

 

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.

 

Alkenones are biomarkers produced solely by algae in the order Isochrysidales that have been used to reconstruct sea surface temperature (SST) since the 1980s. However, alkenone-based SST reconstructions in the northern high latitude oceans show significant bias towards warmer temperatures in core-tops, diverge from other SST proxies in down core records, and are often accompanied by anomalously high relative abundance of the C₃₇tetra-unsaturated methyl alkenone (%C_37:4). Elevated %C_37:4is widely interpreted as an indicator of low sea surface salinity from polar water masses, but its biological source has thus far remained elusive. Here we identify a lineage of Isochrysidales that is responsible for elevated C_37:4methyl alkenone in the northern high latitude oceans through next-generation sequencing and lab-culture experiments. This Isochrysidales lineage co-occurs widely with sea ice in marine environments and is distinct from other known marine alkenone-producers, namelyEmiliania huxleyiandGephyrocapsa oceanica. More importantly, the %C_37:4in seawater filtered particulate organic matter and surface sediments is significantly correlated with annual mean sea ice concentrations. In sediment cores from the Svalbard region, the %C_37:4concentration aligns with the Greenland temperature record and other qualitative regional sea ice records spanning the past 14 kyrs, reflecting sea ice concentrations quantitatively. Our findings imply that %C_37:4is a powerful proxy for reconstructing sea ice conditions in the high latitude oceans on thousand- and, potentially, on million-year timescales.

 

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.

 

Individual animals should adjust diets according to food availability. We used DNA metabarcoding to construct individual-level dietary timeseries for elephants from two family groups in Kenya varying in habitat use, social position and reproductive status. We detected at least 367 dietary plant taxa, with up to 137 unique plant sequences in one fecal sample. Results matched well-established trends: elephants tended to eat more grass when it rained and other plants when dry. Nested within these switches from ‘grazing’ to ‘browsing’ strategies, dietary DNA revealed seasonal shifts in food richness, composition and overlap between individuals. Elephants of both families converged on relatively cohesive diets in dry seasons but varied in their maintenance of cohesion during wet seasons. Dietary cohesion throughout the timeseries of the subdominant ‘Artists’ family was stronger and more consistently positive compared to the dominant ‘Royals’ family. The greater degree of individuality within the dominant family's timeseries could reflect more divergent nutritional requirements associated with calf dependency and/or priority access to preferred habitats. Whereas theory predicts that individuals should specialize on different foods under resource scarcity, our data suggest family bonds may promote cohesion and foster the emergence of diverse feeding cultures reflecting links between social behaviour and nutrition. 

Ecological niche differences are necessary for stable species coexistence but are often difficult to discern. Models of dietary niche differentiation in large mammalian herbivores invoke the quality, quantity, and spatiotemporal distribution of plant tissues and growth forms but are agnostic toward food plant species identity. Empirical support for these models is variable, suggesting that additional mechanisms of resource partitioning may be important in sustaining large-herbivore diversity in African savannas. We used DNA metabarcoding to conduct a taxonomically explicit analysis of large-herbivore diets across southeastern Africa, analyzing ∼4,000 fecal samples of 30 species from 10 sites in seven countries over 6 y. We detected 893 food plant taxa from 124 families, but just two families—grasses and legumes—accounted for the majority of herbivore diets. Nonetheless, herbivore species almost invariably partitioned food plant taxa; diet composition differed significantly in 97% of pairwise comparisons between sympatric species, and dissimilarity was pronounced even between the strictest grazers (grass eaters), strictest browsers (nongrass eaters), and closest relatives at each site. Niche differentiation was weakest in an ecosystem recovering from catastrophic defaunation, indicating that food plant partitioning is driven by species interactions, and was stronger at low rainfall, as expected if interspecific competition is a predominant driver. Diets differed more between browsers than grazers, which predictably shaped community organization: Grazer-dominated trophic networks had higher nestedness and lower modularity. That dietary differentiation is structured along taxonomic lines complements prior work on how herbivores partition plant parts and patches and suggests that common mechanisms govern herbivore coexistence and community assembly in savannas. 

Amidst global shifts in the distribution and abundance of wildlife and livestock, we have only a rudimentary understanding of ungulate parasite communities and parasite-sharing patterns. We used qPCR and DNA metabarcoding of fecal samples to characterize gastrointestinal nematode (Strongylida) community composition and sharing among 17 sympatric species of wild and domestic large mammalian herbivore in central Kenya. We tested a suite of hypothesis-driven predictions about the role of host traits and phylogenetic relatedness in describing parasite infections. Host species identity explained 27–53% of individual variation in parasite prevalence, richness, community composition and phylogenetic diversity. Host and parasite phylogenies were congruent, host gut morphology predicted parasite community composition and prevalence, and hosts with low evolutionary distinctiveness were centrally positioned in the parasite-sharing network. We found no evidence that host body size, social-group size or feeding height were correlated with parasite composition. Our results highlight the interwoven evolutionary and ecological histories of large herbivores and their gastrointestinal nematodes and suggest that host identity, phylogeny and gut architecture—a phylogenetically conserved trait related to parasite habitat—are the overriding influences on parasite communities. These findings have implications for wildlife management and conservation as wild herbivores are increasingly replaced by livestock. 

Do hotspots of plant biodiversity translate into hotspots in the abundance and diversity of large mammalian herbivores? A common expectation in community ecology is that the diversity of plants and animals should be positively correlated in space, as with the latitudinal diversity gradient and the geographic mosaic of biodiversity. Whether this pattern ‘scales down’ to landscape-level linkages between the diversity of plants or the activities of highly mobile megafauna has received less attention. We investigated spatial associations between plants and large herbivores by integrating data from a plant-DNA-barcode phylogeny, camera traps, and a comprehensive map of woody plants across the 1.2-km2 Mpala Forest Global Earth Observatory (ForestGEO) plot, Kenya. Plant and large herbivore communities were strongly associated with an underlying soil gradient, but the richness of large herbivore species was negatively correlated with the richness of woody plants. Results suggest thickets and steep terrain create associational refuges for plants by deterring megaherbivores from browsing on otherwise palatable species. Recent work using dietary DNA metabarcoding has demonstrated that large herbivores often directly control populations of the plant species they prefer to eat, and our results reinforce the important role of megaherbivores in shaping vegetation across landscapes.