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.

Resource availability and heterogeneity shape the self-organisation of regular spatial patterning.

Explaining large-scale ordered patterns and their effects on ecosystem functioning is a fundamental and controversial challenge in ecology. Here, we coupled empirical and theoretical approaches to explore how competition and spatial heterogeneity govern the regularity of colony dispersion in fungus-farming termites. Individuals from different colonies fought fiercely, and inter-nest distances were greater when nests were large and resources scarce-as expected if competition is strong, large colonies require more resources and foraging area scales with resource availability. Building these principles into a model of inter-colony competition showed that highly ordered patterns emerged under high resource availability and low resource heterogeneity. Analysis of this dynamical model provided novel insights into the mechanisms that modulate pattern regularity and the emergent effects of these patterns on system-wide productivity. Our results show how environmental context shapes pattern formation by social-insect ecosystem engineers, which offers one explanation for the marked variability observed across ecosystems.

Spatial patterning of soil microbial communities created by fungus-farming termites.

Spatially overdispersed mounds of fungus-farming termites (Macrotermitinae) are hotspots of nutrient availability and primary productivity in tropical savannas, creating spatial heterogeneity in communities and ecosystem functions. These termites influence the local availability of nutrients in part by redistributing nutrients across the landscape, but the links between termite ecosystem engineering and the soil microbes that are the metabolic agents of nutrient cycling are little understood. We used DNA metabarcoding of soils from Odontotermes montanus mounds to examine the influence of termites on soil microbial communities in a semi-arid Kenyan savanna. We found that bacterial and fungal communities were compositionally distinct in termite-mound topsoils relative to the surrounding savanna, and that bacterial communities were more diverse on mounds. The higher microbial alpha and beta diversity associated with mounds created striking spatial patterning in microbial community composition, and boosted landscape-scale microbial richness and diversity. Selected enzyme assays revealed consistent differences in potential enzymatic activity, suggesting links between termite-induced heterogeneity in microbial community composition and the spatial distribution of ecosystem functions. We conducted a large-scale field experiment in which we attempted to simulate termites' effects on microbes by fertilizing mound-sized patches; this altered both bacterial and fungal communities, but in a different way than natural mounds. Elevated levels of inorganic nitrogen, phosphorus and potassium may help to explain the distinctive fungal communities in termite-mound soils, but cannot account for the distinctive bacterial communities associated with mounds.

Distinctive fungal communities in an obligate African ant-plant mutualism.

Three ant species nest obligately in the swollen-thorn domatia of the African ant-plant Vachellia (Acacia) drepanolobium, a model system for the study of ant-defence mutualisms and species coexistence. Here we report on the characteristic fungal communities generated by these ant species in their domatia. First, we describe behavioural differences between the ant species when presented with a cultured fungal isolate in the laboratory. Second, we use DNA metabarcoding to show that each ant species has a distinctive fungal community in its domatia, and that these communities remain characteristic of the ant species over two Kenyan sampling locations separated by 190 km. Third, we find that DNA extracted from female alates of Tetraponera penzigi and Crematogaster nigriceps contained matches for most of the fungal metabarcodes from those ant species' domatia, respectively. Fungal hyphae and other debris are also visible in sections of these alates' infrabuccal pockets. Collectively, our results indicate that domatium fungal communities are associated with the ant species occupying the tree. To the best of our knowledge, this is the first record of such ant-specific fungal community-level differences on the same myrmecophytic host species. These differences may be shaped by ant behaviour in the domatia, and by ants vectoring fungi when they disperse to establish new colonies. The roles of the fungi with respect to the ants and their host plant remain to be determined.

Rhizosphere microbial community structure differs between constant subzero and freeze-thaw temperature regimes in a subarctic soil.

In the Arctic and subarctic, climate change is causing reduced snowpack extent and earlier snowmelt. Shallower snowpack decreases the thermal insulation of underlying soil and results in more freeze-thaw conditions reflective of dynamic air temperatures. The aim of this study was to determine the effect of alternative temperature regimes on overall microbial community structure and rhizosphere recruitment across representatives of three subarctic plant functional groups. We hypothesized that temperature regime would influence rhizosphere community structure more than plant type. Planted microcosms were established using a tree, forb, grass, or no plant control and subjected to either freeze-thaw cycling or static subzero temperatures. Our results showed rhizosphere communities exhibited reduced diversity compared to bulk soils, and were influenced by temperature conditions and to a lesser extent plant type. We found that plants have a core microbiome that is persistent under different winter temperature scenarios but also have temperature regime-specific rhizosphere microbes. Freeze-thaw cycling resulted in greater community shifts from the pre-incubation soils when compared to constant subzero temperature. This finding suggests that wintertime snowpack conditions may be a significant factor for plant-microbe interactions upon spring thaw.

Rapid radiation of ant parasitic butterflies during the Miocene aridification of Africa.

Africa has undergone a progressive aridification during the last 20 My that presumably impacted organisms and fostered the evolution of life history adaptations. We test the hypothesis that shift to living in ant nests and feeding on ant brood by larvae of phyto-predaceous Lepidochrysops butterflies was an adaptive response to the aridification of Africa that facilitated the subsequent radiation of butterflies in this genus. Using anchored hybrid enrichment we constructed a time-calibrated phylogeny for Lepidochrysops and its closest, non-parasitic relatives in the Euchrysops section (Poloyommatini). We estimated ancestral areas across the phylogeny with process-based biogeographical models and diversification rates relying on time-variable and clade-heterogeneous birth-death models. The Euchrysops section originated with the emerging Miombo woodlands about 22 million years ago (Mya) and spread to drier biomes as they became available in the late Miocene. The diversification of the non-parasitic lineages decreased as aridification intensified around 10 Mya, culminating in diversity decline. In contrast, the diversification of the phyto-predaceous Lepidochrysops lineage proceeded rapidly from about 6.5 Mya when this unusual life history likely first evolved. The Miombo woodlands were the cradle for diversification of the Euchrysops section, and our findings are consistent with the hypothesis that aridification during the Miocene selected for a phyto-predaceous life history in species of Lepidochrysops, with ant nests likely providing caterpillars a safe refuge from fire and a source of food when vegetation was scarce.

Measuring protected-area effectiveness using vertebrate distributions from leech iDNA.

Protected areas are key to meeting biodiversity conservation goals, but direct measures of effectiveness have proven difficult to obtain. We address this challenge by using environmental DNA from leech-ingested bloodmeals to estimate spatially-resolved vertebrate occupancies across the 677 km2 Ailaoshan reserve in Yunnan, China. From 30,468 leeches collected by 163 park rangers across 172 patrol areas, we identify 86 vertebrate species, including amphibians, mammals, birds and squamates. Multi-species occupancy modelling shows that species richness increases with elevation and distance to reserve edge. Most large mammals (e.g. sambar, black bear, serow, tufted deer) follow this pattern; the exceptions are the three domestic mammal species (cows, sheep, goats) and muntjak deer, which are more common at lower elevations. Vertebrate occupancies are a direct measure of conservation outcomes that can help guide protected-area management and improve the contributions that protected areas make towards global biodiversity goals. Here, we show the feasibility of using invertebrate-derived DNA to estimate spatially-resolved vertebrate occupancies across entire protected areas.

Bacterial diversity across individual lichens.

Symbioses are unique habitats for bacteria. We surveyed the spatial diversity of bacterial communities across multiple individuals of closely related lichens using terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing. Centers of lichens house richer, more consistent assemblages than species-poor and compositionally disparate lichen edges, suggesting that ecological succession plays a role in structuring these communities.

Combining stable isotope analysis with DNA metabarcoding improves inferences of trophic ecology.

Knowing what animals eat is fundamental to our ability to understand and manage biodiversity and ecosystems, but researchers often must rely on indirect methods to infer trophic position and food intake. Using an approach that combines evidence from stable isotope analysis and DNA metabarcoding, we assessed the diet and trophic position of Anthene usamba butterflies, for which there are no known direct observations of larval feeding. An earlier study that analyzed adults rather than caterpillars of A. usamba inferred that this butterfly was aphytophagous, but we found that the larval guts of A. usamba and two known herbivorous lycaenid species contain chloroplast 16S sequences. Moreover, chloroplast barcoding revealed high sequence similarity between chloroplasts found in A. usamba guts and the chloroplasts of the Vachellia drepanolobium trees on which the caterpillars live. Stable isotope analysis provided further evidence that A. usamba caterpillars feed on V. drepanolobium, and the possibilities of strict herbivory versus limited omnivory in this species are discussed. These results highlight the importance of combining multiple approaches and considering ontogeny when using stable isotopes to infer trophic ecology where direct observations are difficult or impossible.

Discovery of Four Novel Circular Single-Stranded DNA Viruses in Fungus-Farming Termites.

Here, we describe four novel circular single-stranded DNA viruses discovered in fungus-farming termites (Odontotermes sp.). The viruses, named termite-associated circular virus 1 (TaCV-1) through TaCV-4, are most similar to members of the family Genomoviridae and were widely detected in African termite mounds.

Virus discovery in all three major lineages of terrestrial arthropods highlights the diversity of single-stranded DNA viruses associated with invertebrates.

Viruses encoding a replication-associated protein (Rep) within a covalently closed, single-stranded (ss)DNA genome are among the smallest viruses known to infect eukaryotic organisms, including economically valuable agricultural crops and livestock. Although circular Rep-encoding ssDNA (CRESS DNA) viruses are a widespread group for which our knowledge is rapidly expanding, biased sampling toward vertebrates and land plants has limited our understanding of their diversity and evolution. Here, we screened terrestrial arthropods for CRESS DNA viruses and report the identification of 44 viral genomes and replicons associated with specimens representing all three major terrestrial arthropod lineages, namely Euchelicerata (spiders), Hexapoda (insects), and Myriapoda (millipedes). We identified virus genomes belonging to three established CRESS DNA viral families (Circoviridae, Genomoviridae, and Smacoviridae); however, over half of the arthropod-associated viral genomes are only distantly related to currently classified CRESS DNA viral sequences. Although members of viral and satellite families known to infect plants (Geminiviridae, Nanoviridae, Alphasatellitidae) were not identified in this study, these plant-infecting CRESS DNA viruses and replicons are transmitted by hemipterans. Therefore, members from six out of the seven established CRESS DNA viral families circulate among arthropods. Furthermore, a phylogenetic analysis of Reps, including endogenous viral sequences, reported to date from a wide array of organisms revealed that most of the known CRESS DNA viral diversity circulates among invertebrates. Our results highlight the vast and unexplored diversity of CRESS DNA viruses among invertebrates and parallel findings from RNA viral discovery efforts in undersampled taxa.

Dissecting host-associated communities with DNA barcodes.

DNA barcoding and metabarcoding methods have been invaluable in the study of interactions between host organisms and their symbiotic communities. Barcodes can help identify individual symbionts that are difficult to distinguish using morphological characters, and provide a way to classify undescribed species. Entire symbiont communities can be characterized rapidly using barcoding and especially metabarcoding methods, which is often crucial for isolating ecological signal from the substantial variation among individual hosts. Furthermore, barcodes allow the evolutionary histories of symbionts and their hosts to be assessed simultaneously and in reference to one another. Here, we describe three projects illustrating the utility of barcodes for studying symbiotic interactions: first, we consider communities of arthropods found in the ant-occupied domatia of the East African ant-plant Vachellia (Acacia) drepanolobium; second, we examine communities of arthropod and protozoan inquilines in three species of Nepenthes pitcher plant in South East Asia; third, we investigate communities of gut bacteria of South American ants in the genus Cephalotes Advances in sequencing and computation, and greater database connectivity, will continue to expand the utility of barcoding methods for the study of species interactions, especially if barcoding can be approached flexibly by making use of alternative genetic loci, metagenomes and whole-genome data.This article is part of the themed issue 'From DNA barcodes to biomes'.

Kin selection and the evolution of social information use in animal conflict.

Animals often use social information about conspecifics in making decisions about cooperation and conflict. While the importance of kin selection in the evolution of intraspecific cooperation and conflict is widely acknowledged, few studies have examined how relatedness influences the evolution of social information use. Here we specifically examine how relatedness affects the evolution of a stylised form of social information use known as eavesdropping. Eavesdropping involves individuals escalating conflicts with rivals observed to have lost their last encounter and avoiding fights with those seen to have won. We use a game theoretical model to examine how relatedness affects the evolution of eavesdropping, both when strategies are discrete and when they are continuous or mixed. We show that relatedness influences the evolution of eavesdropping, such that information use peaks at intermediate relatedness. Our study highlights the importance of considering kin selection when exploring the evolution of complex forms of information use.