Tree communities and functional traits determine herbivore compositional turnover.

There are many factors known to drive species turnover, although the mechanisms by which these operate are less clear. Based on comprehensive datasets from the largest tree diversity experiment worldwide (BEF-China), we used shared herbivore species (zeta diversity) and multi-site generalized dissimilarity modelling to investigate the patterns and determinants of species turnover of Lepidoptera herbivores among study plots across a gradient in tree species richness. We found that zeta diversity declined sharply with an increasing number of study plots, with complete changes in caterpillar species composition observed even at the fine spatial scale of our study. Plant community characteristics rather than abiotic factors were found to play key roles in driving caterpillar compositional turnover, although these effects varied with an increasing number of study plots considered, due to the varying contributions of rare and common species to compositional turnover. Our study reveals details of the impact of phylogeny- and trait-mediated processes of trees on herbivore compositional turnover, which has implications for forest management and conservation and shows potential avenues for maintenance of heterogeneity in herbivore communities.

Launching insectphylo.org; a new hub facilitating construction and use of synthesis molecular phylogenies of insects.

The Holy Grail of an Insect Tree of Life can only be 'discovered' through extensive collaboration among taxon specialists, phylogeneticists and centralized frameworks such as Open Tree of Life, but insufficient effort from stakeholders has so far hampered this promising approach. The resultant unavailability of synthesis phylogenies is an unfortunate situation given the numerous practical usages of phylogenies in the near term and against the backdrop of the ongoing biodiversity crisis. To resolve this issue, we establish a new online hub that centralizes the collation of relevant phylogenetic data and provides the resultant synthesis molecular phylogenies. This is achieved through key developments in a proposed pipeline for the construction of a species-level insect phylogeny. The functionality of the framework is demonstrated through the construction of a highly supported, species-comprehensive phylogeny of Diptera, built from integrated omics data, COI DNA barcodes, and a compiled database of over 100 standardized, published Diptera phylogenies. Machine-readable forms of the phylogeny (and subsets thereof) are publicly available at insectphylo.org, a new public repository for species-comprehensive phylogenies for biological research.

Phylogeny-based assignment of functional traits to DNA barcodes outperforms distance-based, in a comparison of approaches.

The full potential for using DNA barcodes for profiling functional trait diversity has yet to be determined in plants and animals; thus, we outline a general framework for quantifying functional trait diversity of insect community DNA and propose and assess the accuracy of three methods for achieving this. We built a novel dataset of traits and DNA barcodes for wild bees in China. An informatics framework was developed for phylogeny-based integration of these data and prediction of traits for any subject barcodes, which was compared with two distance-based methods. For Phylogenetic Assignment, we additionally conducted a species-level analysis of publically available bee trait data. Under the specimen-level dataset, the rate of trait assignment was negatively correlated with distance between the query and the nearest trait-known reference, for all methods. Phylogenetic Assignment was found to perform best under several criteria; particularly, it had the lowest false-positive rate (rarely returning a state prediction where success was unlikely; where the distance from query to the nearest reference was high). For a wider range of compiled traits, conservative life-history traits showed the highest rates of assignment; for example, sociality was predicted with confidence at 53%, parasitism at 44% and nest location at 33%. As outlined herein, automated trait assignment might be applied at scale to either barcodes or metabarcodes. With further compilation and databasing of DNA barcode and trait data, the rate and accuracy of trait assignment is expected to increase to the point of being a widely viable and informative approach.

Multitrophic arthropod diversity mediates tree diversity effects on primary productivity.

Forests sustain 80% of terrestrial biodiversity and provide essential ecosystem services. Biodiversity experiments have demonstrated that plant diversity correlates with both primary productivity and higher trophic diversity. However, whether higher trophic diversity can mediate the effects of plant diversity on productivity remains unclear. Here, using 5 years of data on aboveground herbivorous, predatory and parasitoid arthropods along with tree growth data within a large-scale forest biodiversity experiment in southeast China, we provide evidence of multidirectional enhancement among the diversity of trees and higher trophic groups and tree productivity. We show that the effects of experimentally increased tree species richness were consistently positive for species richness and abundance of herbivores, predators and parasitoids. Richness effects decreased as trophic levels increased for species richness and abundance of all trophic groups. Multitrophic species richness and abundance of arthropods were important mediators of plant diversity effects on tree productivity, suggesting that optimizing forest management for increased carbon capture can be more effective when the diversity of higher trophic groups is promoted in concert with that of trees.

Functional and phylogenetic relationships link predators to plant diversity via trophic and non-trophic pathways.

Human-induced biodiversity loss negatively affects ecosystem function, but the interactive effects of biodiversity change across trophic levels remain insufficiently understood. We sampled arboreal spiders and lepidopteran larvae across seasons in 2 years in a subtropical tree diversity experiment, and then disentangled the links between tree diversity and arthropod predator diversity by deconstructing the pathways among multiple components of diversity (taxonomic, phylogenetic and functional) with structural equation models. We found that herbivores were major mediators of plant species richness effects on abundance, species richness, functional and phylogenetic diversity of predators, while phylogenetic, functional and structural diversity of trees were also important mediators of this process. However, the strength and direction differed between functional, structural and phylogenetic diversity effects, indicating different underlying mechanisms for predator community assembly. Abundance and multiple diversity components of predators were consistently affected by tree functional diversity, indicating that the variation in structure and environment caused by plant functional composition might play key roles in predator community assembly. Our study highlights the importance of an integrated approach based on multiple biodiversity components in understanding the consequences of biodiversity loss in multitrophic communities.

Tree dissimilarity determines multi-dimensional beta-diversity of herbivores and carnivores via bottom-up effects.

Global biodiversity decline and its cascading effects through trophic interactions pose a severe threat to human society. Establishing the impacts of biodiversity decline requires a more thorough understanding of multi-trophic interactions and, more specifically, the effects that loss of diversity in primary producers has on multi-trophic community assembly. Within a synthetic conceptual framework for multi-trophic beta-diversity, we tested a series of hypotheses on neutral and niche-based bottom-up processes in assembling herbivore and carnivore communities in a subtropical forest using linear models, hieratical variance partitioning based on linear mixed-effects models (LMMs) and simulation. We found that the observed taxonomic, phylogenetic and functional beta-diversity of both herbivorous caterpillars and carnivorous spiders were significantly and positively related to tree dissimilarity. Linear models and variance partitioning for LMMs jointly suggested that as a result of bottom-up effects, producer dissimilarities were predominant in structuring consumer dissimilarity, the strength of which highly depended on the trophic dependencies on producers, the diversity facet examined, and data quality. Importantly, linear models for standardized beta-diversities against producer dissimilarities implied a transition between niche-based processes such as environmental filtering and competitive exclusion, which supports the role of bottom-up effect in determining consumer community assembly. These findings enrich our mechanistic understanding of the 'Diversity Begets Diversity' hypothesis and the complexity of higher-trophic community assembly, which is fundamental for sustainable biodiversity conservation and ecosystem management.

An integrative bioinformatics pipeline shows that honeybee-associated microbiomes are driven primarily by pollen composition.

The microbiomes associated with bee nests influence colony health through various mechanisms, although it is not yet clear how honeybee congeners differ in microbiome assembly processes, in particular the degrees to which floral visitations and the environment contribute to different aspects of diversity. We used DNA metabarcoding to sequence bacterial 16S rRNA from honey and stored pollen from nests of 4 honeybee species (Apis cerana, A. dorsata, A. florea, and A. laboriosa) sampled throughout Yunnan, China, a global biodiversity hotspot. We developed a computational pipeline integrating multiple databases for quantifying key facets of diversity, including compositional, taxonomic, phylogenetic, and functional ones. Further, we assessed candidate drivers of observed microbiome dissimilarity, particularly differences in floral visitations, habitat disturbance, and other key environmental variables. Analyses revealed that microbiome alpha diversity was broadly equivalent across the study sites and between bee species, apart from functional diversity which was very low in nests of the reclusive A. laboriosa. Turnover in microbiome composition across Yunnan was driven predominantly by pollen composition. Human disturbance negatively impacted both compositional and phylogenetic alpha diversity of nest microbiomes, but did not correlate with microbial turnover. We herein make progress in understanding microbiome diversity associated with key pollinators in a biodiversity hotspot, and provide a model for the use of a comprehensive informatics framework in assessing pattern and drivers of diversity, which enables the inclusion of explanatory variables both subtly and fundamentally different and enables elucidation of emergent or unexpected drivers.

Leaf Nutritional Content, Tree Richness, and Season Shape the Caterpillar Functional Trait Composition Hosted by Trees.

Nutritional content of host plants is expected to drive caterpillar species assemblages and their trait composition. These relationships are altered by tree richness-induced neighborhood variation and a seasonal decline in leaf quality. We tested how key functional traits related to the growth and defenses of the average caterpillar hosted by a tree species are shaped by nutritional host quality. We measured morphological traits and estimated plant community-level diet breadth based on occurrences from 1020 caterpillars representing 146 species in a subtropical tree diversity experiment from spring to autumn in one year. We focused on interspecific caterpillar trait variation by analyzing presence-only patterns of caterpillar species for each tree species. Our results show that tree richness positively affected caterpillar species-sharing among tree species, which resulted in lowered trait variation and led to higher caterpillar richness for each tree species. However, community-level diet breadth depended more on the nutritional content of host trees. Higher nutritional quality also supported species-poorer but more abundant communities of smaller and less well-defended caterpillars. This study demonstrates that the leaf nutritional quality of trees shapes caterpillar trait composition across diverse species assemblages at fine spatial scales in a way that can be predicted by ecological theory.

Tree diversity and functional leaf traits drive herbivore-associated microbiomes in subtropical China.

Herbivorous insects acquire microorganisms from host plants or soil, but it remains unclear how the diversity and functional composition of host plants contribute to structuring herbivore microbiomes. Within a controlled tree diversity setting, we used DNA metabarcoding of 16S rRNA to assess the contribution of Lepidoptera species and their local environment (particularly, tree diversity, host tree species, and leaf traits) to the composition of associated bacterial communities. In total, we obtained 7,909 bacterial OTUs from 634 caterpillar individuals comprising 146 species. Tree diversity was found to drive the diversity of caterpillar-associated bacteria both directly and indirectly via effects on caterpillar communities, and tree diversity was a stronger predictor of bacterial diversity than diversity of caterpillars. Leaf toughness and dry matter content were important traits of the host plant determining bacterial species composition, while leaf calcium and potassium concentration influenced bacterial richness. Our study reveals previously unknown linkages between trees and their characteristics, herbivore insects, and their associated microbes, which contributes to developing a more nuanced understanding of functional dependencies between herbivores and their environment, and has implications for the consequences of plant diversity loss for trophic interactions.

Global Patterns and Drivers of Bee Distribution.

Insects are the focus of many recent studies suggesting population declines, but even invaluable pollination service providers such as bees lack a modern distributional synthesis. Here, we combine a uniquely comprehensive checklist of bee species distributions and >5,800,000 public bee occurrence records to describe global patterns of bee biodiversity. Publicly accessible records are sparse, especially from developing countries, and are frequently inaccurate throughout much of the world, consequently suggesting different biodiversity patterns from checklist data. Global analyses reveal hotspots of species richness, together generating a rare bimodal latitudinal richness gradient, and further analyses suggest that xeric areas, solar radiation, and non-forest plant productivity are among the most important global drivers of bee biodiversity. Together, our results provide a new baseline and best practices for studies on bees and other understudied invertebrates.

Host functional and phylogenetic composition rather than host diversity structure plant-herbivore networks.

Declining plant diversity alters ecological networks, such as plant-herbivore interactions. However, our knowledge of the potential mechanisms underlying effects of plant species loss on plant-herbivore network structure is still limited. We used DNA barcoding to identify herbivore-host plant associations along declining levels of tree diversity in a large-scale, subtropical biodiversity experiment. We tested for effects of tree species richness, host functional and phylogenetic diversity, and host functional (leaf trait) and phylogenetic composition on species, phylogenetic and network composition of herbivore communities. We found that phylogenetic host composition and related palatability/defence traits but not tree species richness significantly affected herbivore communities and interaction network complexity at both the species and community levels. Our study indicates that evolutionary dependencies and functional traits of host plants determine the composition of higher trophic levels and corresponding interaction networks in species-rich ecosystems. Our findings highlight that characteristics of the species lost have effects on ecosystem structure and functioning across trophic levels that cannot be predicted from mere reductions in species richness.

Climatic and vegetational drivers of insect beta diversity at the continental scale.

AIM: We construct a framework for mapping pattern and drivers of insect diversity at the continental scale and use it to test whether and which environmental gradients drive insect beta diversity. LOCATION: Global; North and Central America; Western Europe. TIME PERIOD: 21st century. MAJOR TAXA STUDIED: Insects. METHODS: An informatics system was developed to integrate terrestrial data on insects with environmental parameters. We mined repositories of data for distribution, climatic data were retrieved (WorldClim), and vegetation parameters inferred from remote sensing analysis (MODIS Vegetation Continuous Fields). Beta diversity between sites was calculated and then modeled with two methods, Mantel test with multiple regression and generalized dissimilarity modeling. RESULTS: Geographic distance was the main driver of insect beta diversity. Independent of geographic distance, bioclimate variables explained more variance in dissimilarity than vegetation variables, although the particular variables found to be significant were more consistent in the latter, particularly, tree cover. Tree cover gradients drove compositional dissimilarity at denser coverages, in both continental case studies. For climate, gradients in temperature parameters were significant in driving beta diversity more so than gradients in precipitation parameters. MAIN CONCLUSIONS: Although environmental gradients drive insect beta diversity independently of geography, the relative contribution of different climatic and vegetational parameters is not expected to be consistent in different study systems. With further incorporation of additional temporal information and variables, this approach will enable the development of a predictive framework for conserving insect biodiversity at the global scale.

Impacts of species richness on productivity in a large-scale subtropical forest experiment.

Biodiversity experiments have shown that species loss reduces ecosystem functioning in grassland. To test whether this result can be extrapolated to forests, the main contributors to terrestrial primary productivity, requires large-scale experiments. We manipulated tree species richness by planting more than 150,000 trees in plots with 1 to 16 species. Simulating multiple extinction scenarios, we found that richness strongly increased stand-level productivity. After 8 years, 16-species mixtures had accumulated over twice the amount of carbon found in average monocultures and similar amounts as those of two commercial monocultures. Species richness effects were strongly associated with functional and phylogenetic diversity. A shrub addition treatment reduced tree productivity, but this reduction was smaller at high shrub species richness. Our results encourage multispecies afforestation strategies to restore biodiversity and mitigate climate change.

Construction of a Species-Level Tree of Life for the Insects and Utility in Taxonomic Profiling.

Although comprehensive phylogenies have proven an invaluable tool in ecology and evolution, their construction is made increasingly challenging both by the scale and structure of publically available sequences. The distinct partition between gene-rich (genomic) and species-rich (DNA barcode) data is a feature of data that has been largely overlooked, yet presents a key obstacle to scaling supermatrix analysis. I present a phyloinformatics framework for draft construction of a species-level phylogeny of insects (Class Insecta). Matrix-building requires separately optimized pipelines for nuclear transcriptomic, mitochondrial genomic, and species-rich markers, whereas tree-building requires hierarchical inference in order to capture species-breadth while retaining deep-level resolution. The phylogeny of insects contains 49,358 species, 13,865 genera, 760 families. Deep-level splits largely reflected previous findings for sections of the tree that are data rich or unambiguous, such as inter-ordinal Endopterygota and Dictyoptera, the recently evolved and relatively homogeneous Lepidoptera, Hymenoptera, Brachycera (Diptera), and Cucujiformia (Coleoptera). However, analysis of bias, matrix construction and gene-tree variation suggests confidence in some relationships (such as in Polyneoptera) is less than has been indicated by the matrix bootstrap method. To assess the utility of the insect tree as a tool in query profiling several tree-based taxonomic assignment methods are compared. Using test data sets with existing taxonomic annotations, a tendency is observed for greater accuracy of species-level assignments where using a fixed comprehensive tree of life in contrast to methods generating smaller de novo reference trees. Described herein is a solution to the discrepancy in the way data are fit into supermatrices. The resulting tree facilitates wider studies of insect diversification and application of advanced descriptions of diversity in community studies, among other presumed applications. [Data integration; data mining; insects; phylogenomics; phyloinformatics; tree of life.].

Toward a methodical framework for comprehensively assessing forest multifunctionality.

Biodiversity-ecosystem functioning (BEF) research has extended its scope from communities that are short-lived or reshape their structure annually to structurally complex forest ecosystems. The establishment of tree diversity experiments poses specific methodological challenges for assessing the multiple functions provided by forest ecosystems. In particular, methodological inconsistencies and nonstandardized protocols impede the analysis of multifunctionality within, and comparability across the increasing number of tree diversity experiments. By providing an overview on key methods currently applied in one of the largest forest biodiversity experiments, we show how methods differing in scale and simplicity can be combined to retrieve consistent data allowing novel insights into forest ecosystem functioning. Furthermore, we discuss and develop recommendations for the integration and transferability of diverse methodical approaches to present and future forest biodiversity experiments. We identified four principles that should guide basic decisions concerning method selection for tree diversity experiments and forest BEF research: (1) method selection should be directed toward maximizing data density to increase the number of measured variables in each plot. (2) Methods should cover all relevant scales of the experiment to consider scale dependencies of biodiversity effects. (3) The same variable should be evaluated with the same method across space and time for adequate larger-scale and longer-time data analysis and to reduce errors due to changing measurement protocols. (4) Standardized, practical and rapid methods for assessing biodiversity and ecosystem functions should be promoted to increase comparability among forest BEF experiments. We demonstrate that currently available methods provide us with a sophisticated toolbox to improve a synergistic understanding of forest multifunctionality. However, these methods require further adjustment to the specific requirements of structurally complex and long-lived forest ecosystems. By applying methods connecting relevant scales, trophic levels, and above- and belowground ecosystem compartments, knowledge gain from large tree diversity experiments can be optimized.

A systematic study of Ichneumonosoma de Meijere, Pelmatops Enderlein, Pseudopelmatops Shiraki and Soita Walker (Diptera: Tephritidae).

Four fruit fly genera, Ichneumonosoma de Meijere, Pelmatops Enderlein, Pseudopelmatops Shiraki and Soita Walker, were studied and 19 species are recognized. Three new species, Soita infuscata Chen & Norrbom, Ichneumonosoma quadripunctata Chen & Freidberg, and I. triangularis Chen & Norrbom are described and illustrated. Ichneumonosoma and Soita are revised, and keys to all the species are provided. Ichneumonosoma imitans (de Meijere) is newly recorded from Thailand. One new synonym is established: Soita Walker = Xaniosternum Enderlein, and Xaniosternum ophioneum Enderlein is moved from Xaniosternum to Soita (n. comb.). In addition, new morphological, geographic and biological information for two stalk-eyed fruit fly genera, Pelmatops and Pseudopelmatops, are provided. Pelmatops fukienensis Zia & Chen is newly recorded from Burma, Pelmetops ichneumoneus (Westwood) is newly recorded from Thailand and Burma, Pseudopelmatops angustifasciatus Zia & Chen is newly recorded from Vietnam, and the male of P. angustifasciatus is described and illustrated for the first time. The morphology of the compound eye and occipital protuberance of Pelmatops and Pseudopelmatops is described and illustrated for the first time. A cladistic analysis based on morphological characters of adults, a partial molecular analysis using the nuclear 28S rDNA (28S) and the mitochondrial cytochrome c oxidase I (COI) genes and a combined dataset were conducted to reconstruct the phylogeny of the four genera and their species. The results showed good support for monophyly of each of the four genera and the clade of the stalk-eyed fruit flies (Pelmatops + Pseudopelmatops). However, relationships of the stalk-eyed fruit flies with Soita and Ichneumonosoma are not clearly resolved, with the morphological analysis indicating that Ichneumonosoma is the sister group of the stalk-eyed fruit flies, but the 28S analysis and the combined analysis group Soita closer to the stalk-eyed fruit flies. Regarding relationships amongst congeners, Pelmatops was well resolved; Ichneumonosoma and Soita were partly resolved, and Pseudopelmatops was unresolved. In addition, a hypothesis about the biology of Pseudopelmatops and its relationship with Sesiidae (Lepidoptera) is discussed.

Resolving the phylogeny of a speciose spider group, the family Linyphiidae (Araneae).

For high-level molecular phylogenies, a comprehensive sampling design is a key factor for not only improving inferential accuracy, but also for maximizing the explanatory power of the resulting phylogeny. Two standing problems in molecular phylogenies are the unstable placements of some deep and long branches, and the phylogenetic relationships shown by robust supported clades conflict with recognized knowledge. Empirical and theoretical studies suggest that increasing taxon sampling is expected to ameliorate, if not resolve, both problems; however, sometimes neither the current taxonomic system nor the established phylogeny can provide sufficient information to guide additional sampling design. We examined the phylogeny of the spider family Linyphiidae, and selected ingroup species based on epigynal morphology, which can be reconstructed in a phylogenetic context. Our analyses resulted in seven robustly supported clades within linyphiids. The placements of four deep and long branches are sensitive to variations in both outgroup and ingroup sampling, suggesting the possibility of long branch attraction artifacts. Results of ancestral state reconstruction indicate that successive state transformations of the epigynal plate are associated with early cladogenetic events in linyphiid diversification. Representatives of different subfamilies were mixed together within well supported clades and examination revealed that their defining characters, as per traditional taxonomy, are homoplastic. Furthermore, our results demonstrated that increasing taxon sampling produced a more informative framework, which in turn helps to study character evolution and interpret the relationships among linyphiid lineages. Additional defining characters are needed to revise the linyphiid taxonomic system based on our phylogenetic hypothesis.