Shifting mammal communities and declining species richness along an elevational gradient on Mount Kenya.

Conservation areas encompassing elevation gradients are biodiversity hotspots because they contain a wide range of habitat types in a relatively small space. Studies of biodiversity patterns along elevation gradients, mostly on small mammal or bird species, have documented a peak in diversity at mid elevations. Here, we report on a field study of medium and large mammals to examine the impact of elevation, habitat type, and gross primary productivity on community structure. Species richness was observed using a camera trap transect with 219 sites situated across different habitat types from 2329 to 4657 m above the sea level on the western slope of Mt Kenya, the second highest mountain in Africa. We found that the lowest elevation natural habitats had the highest species richness and relative abundance and that both metrics decreased steadily as elevation increased, paralleling changes in gross primary productivity, and supporting the energy richness hypothesis. We found no evidence for the mid-domain effect on species diversity. The lowest elevation degraded Agro-Forestry lands adjacent to the National Park had high activity of domestic animals and reduced diversity and abundance of native species. The biggest difference in community structure was between protected and unprotected areas, followed by more subtle stepwise differences between habitats at different elevations. Large carnivore species remained relatively consistent but dominant herbivore species shifted along the elevation gradient. There was some habitat specialization and turnover in species, such that the elevation gradient predicts a high diversity of species, demonstrating the high conservation return for protecting mountain ecosystems for biodiversity conservation.

Rethinking atoll futures: local resilience to global challenges.

Atoll islands are often perceived as inevitably lost due to rising sea levels. However, unlike other islands, atoll islands are dynamic landforms that have evolved, at least historically, to vertically accrete at a pace commensurate with changing sea levels. Rather than atoll islands' low elevation per se, the impairment of natural accretion processes is jeopardising their persistence. While global marine impacts are deteriorating coral reefs, local impacts also significantly affect accretion, together potentially tipping the scales toward atoll island erosion. Maintaining atoll island accretion requires intact sediment generation on coral reefs, unobstructed sediment transport from reef to island, and available vegetated deposition sites on the island. Ensuring the persistence of atoll islands must include global greenhouse gas emission reduction and local restoration of accretion processes.

Differences in the behavior and diet between shoaling and solitary surgeonfish (Acanthurus triostegus).

Variation in behavior within marine and terrestrial species can influence the functioning of the ecosystems they inhabit. However, the contribution of social behavior to ecosystem function remains underexplored. Many coral reef fish species provide potentially insightful models for exploring how social behavior shapes ecological function because they exhibit radical intraspecific variation in sociality within a shared habitat. Here, we provide an empirical exploration on how the ecological function of a shoaling surgeonfish (Acanthurus triostegus) may differ from that of solitary conspecifics on two Pacific coral reefs combining insight from behavioral observations, stable isotope analysis, and macronutrient analysis of gut and fecal matter. We detected important differences in how the social mode of A. triostegus affected its spatial and feeding ecology, as well as that of other reef fish species. Specifically, we found increased distance traveled and area covered by shoaling fish relative to solitary A. triostegus. Additionally, shoaling A. triostegus primarily grazed within territories of other herbivorous fish and had piscivorous and nonpiscivorous heterospecific fish associated with the shoal, while solitary A. triostegus grazed largely grazed outside of any territories and did not have any such interactions with heterospecific fish. Results from stable isotope analysis show a difference in δ15N isotopes between shoaling and solitary fish, which suggests that these different social modes are persistent. Further, we found a strong interaction between social behavior and site and carbohydrate and protein percentages in the macronutrient analysis, indicating that these differences in sociality are associated with measurable differences in both the feeding ecology and nutrient excretion patterns. Our study suggests that the social behavior of individuals may play an important and underappreciated role in mediating their ecological function.

Changes in invertebrate food web structure between high- and low-productivity environments are driven by intermediate but not top-predator diet shifts.

Predator-prey interactions shape ecosystem stability and are influenced by changes in ecosystem productivity. However, because multiple biotic and abiotic drivers shape the trophic responses of predators to productivity, we often observe patterns, but not mechanisms, by which productivity drives food web structure. One way to capture mechanisms shaping trophic responses is to quantify trophic interactions among multiple trophic groups and by using complementary metrics of trophic ecology. In this study, we combine two diet-tracing methods: diet DNA and stable isotopes, for two trophic groups (top predators and intermediate predators) in both low- and high-productivity habitats to elucidate where in the food chain trophic structure shifts in response to changes in underlying ecosystem productivity. We demonstrate that while top predators show increases in isotopic trophic position (δ15N) with productivity, neither their isotopic niche size nor their DNA diet composition changes. Conversely, intermediate predators show clear turnover in DNA diet composition towards a more predatory prey base in high-productivity habitats. Taking this multi-trophic approach highlights how predator identity shapes responses in predator-prey interactions across environments with different underlying productivity, building predictive power for understanding the outcomes of ongoing anthropogenic change.

Food webs for three burn severities after wildfire in the Eldorado National Forest, California.

Wildfire dynamics are changing around the world and understanding their effects on ecological communities and landscapes is urgent and important. We report detailed food webs for unburned, low-to-moderate and high severity burned habitats three years post-fire in the Eldorado National Forest, California. The cumulative cross-habitat food web contains 3,084 ontogenetic stages (nodes) or plant parts comprising 849 species (including 107 primary producers, 634 invertebrates, 94 vertebrates). There were 178,655 trophic interactions between these nodes. We provide information on taxonomy, body size, biomass density and trophic interactions under each of the three burn conditions. We detail 19 sampling methods deployed across 27 sites (nine in each burn condition) used to estimate the richness, body size, abundance and biomass density estimates in the node lists. We provide the R code and raw data to estimate summarized node densities and assign trophic links.

Small mammal responses to fire severity mediated by vegetation characteristics and species traits.

The frequency of large, high-severity "mega-fires" has increased in recent decades, with numerous consequences for forest ecosystems. In particular, small mammal communities are vulnerable to post-fire shifts in resource availability and play critical roles in forest ecosystems. Inconsistencies in previous observations of small mammal community responses to fire severity underscore the importance of examining mechanisms regulating the effects of fire severity on post-fire recovery of small mammal communities. We compared small mammal abundance, diversity, and community structure among habitats that burned at different severities, and used vegetation characteristics and small mammal functional traits to predict community responses to fire severity three years after one mega-fire in the Sierra Nevada, California. Using a model-based fourth-corner analysis, we examined how interactions between vegetation variables and small mammal traits associated with their resource use were associated with post-fire small mammal community structure among fire severity categories. Small mammal abundance was similar across fire severity categories, but diversity decreased and community structure shifted as fire severity increased. Differences in small mammal communities were large only between unburned and high-severity sites. Three highly correlated fire-dependent vegetation variables affected by fire and the volume of soft coarse woody debris were associated with small mammal community structures. Furthermore, we found that interactions between vegetation variables and three small mammal traits (feeding guild, primary foraging mode, and primary nesting habit) predicted community structure across fire severity categories. We concluded that resource use was important in regulating small mammal recovery after the fire because vegetation provided required resources to small mammals as determined by their functional traits. Given the mechanistic nature of our analyses, these results may be applicable to other fire-prone forest systems, although it will be important to conduct studies across large biogeographic regions and over long post-fire time periods to assess generality.

Large-herbivore nemabiomes: patterns of parasite diversity and sharing.

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.

Effects of consumer surface sterilization on diet DNA metabarcoding data of terrestrial invertebrates in natural environments and feeding trials.

DNA metabarcoding is an emerging tool used to quantify diet in environments and consumer groups where traditional approaches are unviable, including small-bodied invertebrate taxa. However, metabarcoding of small taxa often requires DNA extraction from full body parts (without dissection), and it is unclear whether surface contamination from body parts alters presumed diet presence or diversity.We examined four different measures of diet (presence, rarefied read abundance, richness, and species composition) for a terrestrial invertebrate consumer (the spider Heteropoda venatoria) both collected in its natural environment and fed an offered diet item in contained feeding trials using DNA metabarcoding of full body parts (opisthosomas). We compared diet from consumer individuals surface sterilized to remove contaminants in 10% commercial bleach solution followed by deionized water with a set of unsterilized individuals.We found that surface sterilization did not significantly alter any measure of diet for consumers in either a natural environment or feeding trials. The best-fitting model predicting diet detection in feeding trial consumers included surface sterilization, but this term was not statistically significant (ß = -2.3, p-value = .07).Our results suggest that surface contamination does not seem to be a significant concern in this DNA diet metabarcoding study for consumers in either a natural terrestrial environment or feeding trials. As the field of diet DNA metabarcoding continues to progress into new environmental contexts with various molecular approaches, we suggest ongoing context-specific consideration of the possibility of surface contamination.

Effects of host extinction and vector preferences on vector-borne disease risk in phylogenetically structured host-hector communities.

Anthropogenic disturbance impacts the phylogenetic composition and diversity of ecological communities. While changes in diversity are known to dramatically change species interactions and alter disease dynamics, the effects of phylogenetic changes in host and vector communities on disease have been relatively poorly studied. Using a theoretical model, we investigated how phylogeny and extinction influence network structural characteristics relevant to disease transmission in disturbed environments. We modelled a multi-host, multi-vector community as a bipartite ecological network, where nodes represent host and vector species and edges represent connections among them through vector feeding, and we simulated vector preferences and threat status on host and parasite phylogenies. We then simulated loss of hosts, including phylogenetically clustered losses, to investigate how extinction influences network structure. We compared effects of phylogeny and extinction to those of host specificity, which we predicted to strongly increase network modularity and reduce disease prevalence. The simulations revealed that extinction often increased modularity, with higher modularity as species loss increased, although not as much as increasing host specificity did. These results suggest that extinction itself, all else being equal, may reduce disease prevalence in disturbed communities. However, in real communities, systematic patterns in species loss (e.g. favoring high competence species) or changes in abundance may counteract these effects. Unexpectedly, we found that effects of phylogenetic signal in host and vector traits were relatively weak, and only important when phylogenetic signal of host and vector traits were similar, or when these traits both varied.

The effects of herbivore aggregations at water sources on savanna plants differ across soil and climate gradients.

Water sources in arid and semiarid ecosystems support humans, wildlife, and domestic animals, forming nodes of activity that sculpt surrounding plant communities and impact critical grazing and soil systems. However, global aridification and changing surface water supply threaten to disrupt these water resources, with strong implications for conservation and management of these ecosystems. To understand how effects of herbivore aggregation at water impact plant communities across contexts, we measured herbivore activity, plant height, cover (trees, grasses, forbs, and bare ground), diversity, and composition at 17 paired water sources and matrix sites across a range of abiotic factors in a semiarid savanna in Kenya. The effects of proximity to surface water and herbivore aggregation on plant communities varied substantially depending on soil and rainfall. In arid areas with nutrient-poor sandy soils, forb and tree cover were 50% lower at water sources compared to neighboring matrix sites, bare ground was 20% higher, species richness was 15% lower, and a single globally important grazing grass (Cynodon dactylon) dominated 60% of transects. However, in mesic areas with nutrient-rich finely textured soils, species richness was 25% higher, despite a 40% increase in bare ground, concurrent with the decline of a dominant tall grass (Themeda triandra) and increase in C. dactylon and other grass species near water sources. Recent rainfall was important for grasses; cover was higher relative to matrix sites only during wet periods, a potential indication of compensatory grazing. These findings suggest that effects of herbivore aggregation on vegetation diversity and composition will vary in magnitude, and in some cases direction, depending on other factors at the site. Where moisture and nutrient resources are high and promote the dominance of few plant species, herbivore aggregations may maintain diversity by promoting grazing lawns and increasing nondominant species cover. However, in arid conditions and sites with low nutrient availability, diversity can be substantially reduced by these aggregations. Our results highlight the importance of considering abiotic conditions when managing for effects of herbivore aggregations near water. This will be particularly important for future managers in light of growing global aridification and surface water changes.

The influence of vector-borne disease on human history: socio-ecological mechanisms.

Vector-borne diseases (VBDs) are embedded within complex socio-ecological systems. While research has traditionally focused on the direct effects of VBDs on human morbidity and mortality, it is increasingly clear that their impacts are much more pervasive. VBDs are dynamically linked to feedbacks between environmental conditions, vector ecology, disease burden, and societal responses that drive transmission. As a result, VBDs have had profound influence on human history. Mechanisms include: (1) killing or debilitating large numbers of people, with demographic and population-level impacts; (2) differentially affecting populations based on prior history of disease exposure, immunity, and resistance; (3) being weaponised to promote or justify hierarchies of power, colonialism, racism, classism and sexism; (4) catalysing changes in ideas, institutions, infrastructure, technologies and social practices in efforts to control disease outbreaks; and (5) changing human relationships with the land and environment. We use historical and archaeological evidence interpreted through an ecological lens to illustrate how VBDs have shaped society and culture, focusing on case studies from four pertinent VBDs: plague, malaria, yellow fever and trypanosomiasis. By comparing across diseases, time periods and geographies, we highlight the enormous scope and variety of mechanisms by which VBDs have influenced human history.

Soil fungal community composition and functional similarity shift across distinct climatic conditions.

A large part of ecosystem function in woodland systems depends on soil fungal communities. However, global climate change has the potential to fundamentally alter these communities as fungal species are filtered with changing environmental conditions. In this study, we examined the potential effects of climate on host-associated (i.e. tree-associated) soil fungal communities at climatically distinct sites in the Tehachapi Mountains in California, where more arid conditions represent likely regional climate futures. We found that soil fungal community composition changes strongly across sites, with species richness and diversity being highest at the most arid site. However, host association may buffer the effects of climate on community composition, as host-associated fungal communities are more similar to each other across climatically distinct sites than the whole fungal community. Lastly, an examination of functional traits for ectomycorrhizal fungi, a well-studied guild of fungal mutualist species, showed that stress-tolerant traits were more abundant at arid sites than mesic sites, providing a mechanistic understanding of these community patterns. Taken together, our results indicate that fungal community composition will likely shift with future climate change but that host association may buffer these effects, with shifts in functional traits having implications for future ecosystem function.

Effects of land-use change on community diversity and composition are highly variable among functional groups.

In order to understand how the effects of land-use change vary among taxa and environmental contexts, we investigate how three types of land-use change have influenced phylogenetic diversity (PD) and species composition of three functionally distinct communities: plants, small mammals, and large mammals. We found large mammal communities were by far the most heavily impacted by land-use change, with areas of attempted large wildlife exclusion and intense livestock grazing, respectively, containing 164 and 165 million fewer years of evolutionary history than conserved areas (~40% declines). The effects of land-use change on PD varied substantially across taxa, type of land-use change, and, for most groups, also across abiotic conditions. This highlights the need for taxa-specific or multi-taxa evaluations, for managers interested in conserving specific groups or whole communities, respectively. It also suggests that efforts to conserve and restore PD may be most successful if they focus on areas of particular land-use types and abiotic conditions. Importantly, we also describe the substantial species turnover and compositional changes that cannot be detected by alpha diversity metrics, emphasizing that neither PD nor other taxonomic diversity metrics are sufficient proxies for ecological integrity. Finally, our results provide further support for the emerging consensus that conserved landscapes are critical to support intact assemblages of some lineages such as large mammals, but that mosaics of disturbed land-uses, including both agricultural and pastoral land, do provide important habitats for a diverse array of plants and small mammals.

Microbial Ecology of the Western Gull (Larus occidentalis).

Avian species host diverse communities of microorganisms which have important roles in the life of birds, including increased metabolism, protection from disease, and immune system development. Along with high human populations and a diversity of human uses of coastal zones, anthropogenic food sources are becoming increasingly available to some species, including gulls. Anthropogenic associations increase the likelihood of encountering foreign or pathogenic bacteria. Diseases in birds caused by bacteria are a substantial source of avian mortality; therefore, it is essential to characterize the microbiome of seabirds. Here, we determined both core and environmentally derived microbial communities of breeding western gulls (Larus occidentalis) from six colonies in California and Oregon. Using DNA extracted from bacterial swabs of the bill, cloaca, and feet of gulls, 16S rRNA gene sequencing was performed targeting the V4 region. We identified a total of 8542 operational taxonomic units (OTUs) from 75 gulls. Sixty-eight OTUs were identified in gulls from all six colonies with the greatest representation from phyla's of Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. Overall, microbial richness based on Chao's Abundance-based Coverage Estimator (ACE) index was similar for all colonies (mean = 2347 OTUs) with the smallest coastal colonies having the highest richness (mean = 2626 OTUs) and the largest colonies, located farther off-shore, having the lowest (mean = 2068 OTUs). This survey represents the most in-depth assessment to date of microbes associated with western gulls, and the first study to identify both species-specific and environmentally derived bacteria across multiple populations.

Effects of road proximity on heavy metal concentrations in soils and common roadside plants in Southern California.

Concerns about motor vehicle emissions on human health are typically focused on aerial pollution and are regulated via controls on tailpipe emissions. However, vehicles also contribute heavy metal emissions through non-tailpipe pathways (e.g., brake wear, tire particulates). The metal pollutants produced via both tailpipe and non-tailpipe pathways pose threats to both human and ecosystem health long after they have settled from the atmosphere largely via contamination of soils and plants. In this study, we examined the effect of vehicular pollution on soils and plants in five paired sites in Gaviota, CA. In each site, we examined the effect of proximity to road on heavy metal concentrations (cadmium, nickel, lead, and zinc) in four of the most common roadside plant species-Melilotus indicus, Herschfeldia incana, Avena sativa, and Artemisia californica-as well as on soil metal concentrations. Then, to look at potential effects of road proximity and associated metal pollution on plants, we also examined the carbon and nitrogen ratios of all the plant samples. We found strong and significant effects of proximity to road on concentrations of all heavy metals in plants; plants in close proximity to roads had metal concentrations between 8 and 11 times higher than plants farther from roads. Plant C:N ratios also varied strongly among site types and were always higher in close proximity to roads as compared to farther off roads, potentially indicating broader effects of road proximity to plant ecology and leaf quality for consumers in the region.

Invasive rat eradication strongly impacts plant recruitment on a tropical atoll.

Rat eradication has become a common conservation intervention in island ecosystems and its effectiveness in protecting native vertebrates is increasingly well documented. Yet, the impacts of rat eradication on plant communities remain poorly understood. Here we compare native and non-native tree and palm seedling abundance before and after eradication of invasive rats (Rattus rattus) from Palmyra Atoll, Line Islands, Central Pacific Ocean. Overall, seedling recruitment increased for five of the six native trees species examined. While pre-eradication monitoring found no seedlings of Pisonia grandis, a dominant tree species that is important throughout the Pacific region, post-eradication monitoring documented a notable recruitment event immediately following eradication, with up to 688 individual P. grandis seedlings per 100m2 recorded one month post-eradication. Two other locally rare native trees with no observed recruitment in pre-eradication surveys had recruitment post-rat eradication. However, we also found, by five years post-eradication, a 13-fold increase in recruitment of the naturalized and range-expanding coconut palm Cocos nucifera. Our results emphasize the strong effects that a rat eradication can have on tree recruitment with expected long-term effects on canopy composition. Rat eradication released non-native C. nucifera, likely with long-term implications for community composition, potentially necessitating future management interventions. Eradication, nevertheless, greatly benefitted recruitment of native tree species. If this pattern persists over time, we expect long-term benefits for flora and fauna dependent on these native species.

Conservation lessons from large-mammal manipulations in East African savannas: the KLEE, UHURU, and GLADE experiments.

African savannas support an iconic fauna, but they are undergoing large-scale population declines and extinctions of large (>5 kg) mammals. Long-term, controlled, replicated experiments that explore the consequences of this defaunation (and its replacement with livestock) are rare. The Mpala Research Centre in Laikipia County, Kenya, hosts three such experiments, spanning two adjacent ecosystems and environmental gradients within them: the Kenya Long-Term Exclosure Experiment (KLEE; since 1995), the Glade Legacies and Defaunation Experiment (GLADE; since 1999), and the Ungulate Herbivory Under Rainfall Uncertainty experiment (UHURU; since 2008). Common themes unifying these experiments are (1) evidence of profound effects of large mammalian herbivores on herbaceous and woody plant communities; (2) competition and compensation across herbivore guilds, including rodents; and (3) trophic cascades and other indirect effects. We synthesize findings from the past two decades to highlight generalities and idiosyncrasies among these experiments, and highlight six lessons that we believe are pertinent for conservation. The removal of large mammalian herbivores has dramatic effects on the ecology of these ecosystems; their ability to rebound from these changes (after possible refaunation) remains unexplored.

Migration in the Anthropocene: how collective navigation, environmental system and taxonomy shape the vulnerability of migratory species.

Recent increases in human disturbance pose significant threats to migratory species using collective movement strategies. Key threats to migrants may differ depending on behavioural traits (e.g. collective navigation), taxonomy and the environmental system (i.e. freshwater, marine or terrestrial) associated with migration. We quantitatively assess how collective navigation, taxonomic membership and environmental system impact species' vulnerability by (i) evaluating population change in migratory and non-migratory bird, mammal and fish species using the Living Planet Database (LPD), (ii) analysing the role of collective navigation and environmental system on migrant extinction risk using International Union for Conservation of Nature (IUCN) classifications and (iii) compiling literature on geographical range change of migratory species. Likelihood of population decrease differed by taxonomic group: migratory birds were more likely to experience annual declines than non-migrants, while mammals displayed the opposite pattern. Within migratory species in IUCN, we observed that collective navigation and environmental system were important predictors of extinction risk for fishes and birds, but not for mammals, which had overall higher extinction risk than other taxa. We found high phylogenetic relatedness among collectively navigating species, which could have obscured its importance in determining extinction risk. Overall, outputs from these analyses can help guide strategic interventions to conserve the most vulnerable migrations.This article is part of the theme issue 'Collective movement ecology'.