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.

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.

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.

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.

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.

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.

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.

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.

Integrative Profiling of Bee Communities from Habitats of Tropical Southern Yunnan (China)

Understanding and managing pollination service is hindered by taxonomic impediments and paucity of data, particularly in the tropics. Herein we apply integrative species delineation and taxonomy to test impacts of land use on the diversity of bee communities within Xishuangbanna (Yunnan, south China), a highly biodiverse tropical region which has undergone extensive land conversion to rubber plantation. 128 Operational Taxonomic Units (OTU) were inferred by an iterative and integrative approach. Bee activity differed significantly across land use samples, although community composition corresponded more to level of vegetation density, when accounting for spatial structure. Species diversity was high in young rubber plantations, although composition overlapped with other species-rich habitats (natural forest edge and river banks), and older plantations (>8 years) showed very low diversity under all measures. Community structures were similar between the natural forest interior and edge, although analysis indicated contrasting drivers of diversity, with clustering in the interior and overdispersion in the forest edge. Further, phylogenetic diversity and derived indices were underestimated when reference data were omitted from analysis. The description of bee communities herein permits more informed choices in land management with respect to ensuring continuation of essential services by bees.

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.

A protocol for species delineation of public DNA databases, applied to the Insecta

Public DNA databases are composed of data from many different taxa, although the taxonomic annotation on sequences is not always complete, which impedes the utilization of mined data for species-level applications. There is much ongoing work on species identification and delineation based on the molecular data itself, although applying species clustering to whole databases requires consolidation of results from numerous undefined gene regions, and introduces significant obstacles in data organization and computational load. In the current paper, we demonstrate an approach for species delineation of a sequence database. All DNA sequences for the insects were obtained and processed. After filtration of duplicated data, delineation of the database into species or molecular operational taxonomic units (MOTUs) followed a three-step process in which (i) the genetic loci L are partitioned, (ii) the species S are delineated within each locus, then (iii) species units are matched across loci to form the matrix L × S, a set of global (multilocus) species units. Partitioning the database into a set of homologous gene fragments was achieved by Markov clustering using edge weights calculated from the amount of overlap between pairs of sequences, then delineation of species units and assignment of species names were performed for the set of genes necessary to capture most of the species diversity. The complexity of computing pairwise similarities for species clustering was substantial at the cytochrome oxidase subunit I locus in particular, but made feasible through the development of software that performs pairwise alignments within the taxonomic framework, while accounting for the different ranks at which sequences are labeled with taxonomic information. Over 24 different homologs, the unidentified sequences numbered approximately 194,000, containing 41,525 species IDs (98.7% of all found in the insect database), and were grouped into 59,173 single-locus MOTUs by hierarchical clustering under parameters optimized independently for each locus. Species units from different loci were matched using a multipartite matching algorithm to form multilocus species units with minimal incongruence between loci. After matching, the insect database as represented by these 24 loci was found to be composed of 78,091 species units in total. 38,574 of these units contained only species labeled data, 34,891 contained only unlabeled data, leaving 4,626 units composed both of labeled and unlabeled sequences. In addition to giving estimates of species diversity of sequence repositories, the protocol developed here will facilitate species-level applications of modern-day sequence data sets. In particular, the L × S matrix represents a post-taxonomic framework that can be used for species-level organization of metagenomic data, and incorporation of these methods into phylogenetic pipelines will yield matrices more representative of species diversity.

Automated DNA-based plant identification for large-scale biodiversity assessment

Rapid degradation of tropical forests urges to improve our efficiency in large-scale biodiversity assessment. DNA barcoding can assist greatly in this task, but commonly used phenetic approaches for DNA-based identifications rely on the existence of comprehensive reference databases, which are infeasible for hyperdiverse tropical ecosystems. Alternatively, phylogenetic methods are more robust to sparse taxon sampling but time-consuming, while multiple alignment of species-diagnostic, typically length-variable, markers can be problematic across divergent taxa. We advocate the combination of phylogenetic and phenetic methods for taxonomic assignment of DNA-barcode sequences against incomplete reference databases such as GenBank, and we developed a pipeline to implement this approach on large-scale plant diversity projects. The pipeline workflow includes several steps: database construction and curation, query sequence clustering, sequence retrieval, distance calculation, multiple alignment and phylogenetic inference. We describe the strategies used to establish these steps and the optimization of parameters to fit the selected psbA-trnH marker. We tested the pipeline using infertile plant samples and herbivore diet sequences from the highly threatened Nicaraguan seasonally dry forest and exploiting a valuable purpose-built resource: a partial local reference database of plant psbA-trnH. The selected methodology proved efficient and reliable for high-throughput taxonomic assignment, and our results corroborate the advantage of applying 'strict' tree-based criteria to avoid false positives. The pipeline tools are distributed as the scripts suite 'BAGpipe' (pipeline for Biodiversity Assessment using GenBank data), which can be readily adjusted to the purposes of other projects and applied to sequence-based identification for any marker or taxon.

Phylogeography of Poorly Dispersing Net-Winged Beetles: A Role of Drifting India in the Origin of Afrotropical and Oriental Fauna

Ancient dispersal history may be obscured by subsequent dispersal events. Therefore, we intend to investigate the biogeography of metriorrhynchine net-winged beetles, a group characterized by limited dispersal propensity. We used DNA data to construct phylogenies and the BayesTraits and RASP programs to identify putative ancestral areas. Further, we inferred ultrametric trees to estimate the ages of selected nodes. The time frame is inferred from tectonic calibrations and the general mutation rate of the mitochondrial genes. Metriorrhynchini consists of two lineages with Afro/Oriental and Australian distributions. The basal lineages originated in Eastern Gondwana after the split of Australia, India and Madagascar; the Afrotropical and Madagascar Metriorrhynchini separated from the Oriental clades 65 and 62 mya. Several already diversified lineages colonized continental Asia 55-35 mya. A few genera of the Australian clade dispersed to the Oriental region 5-15 mya and reached Eastern India and Southern China. Only Xylobanus crossed the Makassar Strait to Sulawesi and does not occur further to the east. The current distribution of Metriorrhynchini is a result of drifting on continental fragments and over-sea dispersal events limited to a few hundreds of kilometers. We conclude that: (1) Afrotropical and Madagascar lineages originated independently from dispersal events during India's drift to the north and the Mozambique Channel completely isolates the respective faunas since then; (2) Oriental fauna is a recently established mixture of the Indian and Australian lineages, with predominance of the older Indian clades; (3) The fauna of islands located north of Australia colonized Sulawesi after collision with the Sundaland margin and the species rich Australian lineages did not reach Western Wallacea or the Philippines. Our results suggest an impact of subtle differences in biological characteristics on biogeographic history of individual lineages, when mostly lowland and flower-visiting lineages were able to disperse across sea channels.

The mitochondrial genome of Elodia flavipalpis Aldrich (Diptera: Tachinidae) and the evolutionary timescale of Tachinid flies

Tachinid flies are natural enemies of many lepidopteran and coleopteran pests of forests, crops, and fruit trees. In order to address the lack of genetic data in this economically important group, we sequenced the complete mitochondrial genome of the Palaearctic tachinid fly Elodia flavipalpis Aldrich, 1933. Usually found in Northern China and Japan, this species is one of the primary natural enemies of the leaf-roller moths (Tortricidae), which are major pests of various fruit trees. The 14,932-bp mitochondrial genome was typical of Diptera, with 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. However, its control region is only 105 bp in length, which is the shortest found so far in flies. In order to estimate dipteran evolutionary relationships, we conducted a phylogenetic analysis of 58 mitochondrial genomes from 23 families. Maximum-likelihood and Bayesian methods supported the monophyly of both Tachinidae and superfamily Oestroidea. Within the subsection Calyptratae, Muscidae was inferred as the sister group to Oestroidea. Within Oestroidea, Calliphoridae and Sarcophagidae formed a sister clade to Oestridae and Tachinidae. Using a Bayesian relaxed clock calibrated with fossil data, we estimated that Tachinidae originated in the middle Eocene.

MrBayes tgMC³: a tight GPU implementation of MrBayes

MrBayes is model-based phylogenetic inference tool using Bayesian statistics. However, model-based assessment of phylogenetic trees adds to the computational burden of tree-searching, and so poses significant computational challenges. Graphics Processing Units (GPUs) have been proposed as high performance, low cost acceleration platforms and several parallelized versions of the Metropolis Coupled Markov Chain Mote Carlo (MC³) algorithm in MrBayes have been presented that can run on GPUs. However, some bottlenecks decrease the efficiency of these implementations. To address these bottlenecks, we propose a tight GPU MC³ (tgMC³) algorithm. tgMC³ implements a different architecture from the one-to-one acceleration architecture employed in previously proposed methods. It merges multiply discrete GPU kernels according to the data dependency and hence decreases the number of kernels launched and the complexity of data transfer. We implemented tgMC³ and made performance comparisons with an earlier proposed algorithm, nMC³, and also with MrBayes MC³ under serial and multiply concurrent CPU processes. All of the methods were benchmarked on the same computing node from DEGIMA. Experiments indicate that the tgMC³ method outstrips nMC³ (v1.0) with speedup factors from 2.1 to 2.7×. In addition, tgMC³ outperforms the serial MrBayes MC³ by a factor of 6 to 30× when using a single GTX480 card, whereas a speedup factor of around 51× can be achieved by using two GTX 480 cards on relatively long sequences. Moreover, tgMC³ was compared with MrBayes accelerated by BEAGLE, and achieved speedup factors from 3.7 to 5.7×. The reported performance improvement of tgMC³ is significant and appears to scale well with increasing dataset sizes. In addition, the strategy proposed in tgMC³ could benefit the acceleration of other Bayesian-based phylogenetic analysis methods using GPUs.

Small mammal investigation in spotted fever focus with DNA-barcoding and taxonomic implications on rodents species from Hainan of China

Although mammals are a well-studied group of animals, making accurate field identification of small mammals is still complex because of morphological variation across developmental stages, color variation of pelages, and often damaged osteological and dental characteristics. In 2008, small mammals were collected for an epidemiological study of a spotted fever outbreak in Hainan, China. Ten species of small mammals were identified by morphological characters in the field, most using pelage color characters only. The study is extended here, in order to assess whether DNA barcoding would be suitable as an identification tool in these small mammals. Barcode clusters showed some incongruence with morphospecies, especially for some species of Rattus and Niviventer, so molecular delineation was carried out with an expanded dataset of combined cytochrome b (Cyt-b) and cytochrome c oxidase subunit I (COI) sequences. COI sequences were successfully amplified from 83% of collected mammals, but failed in all specimens of Suncus murinus, which were thus excluded in DNA barcoding analysis. Of note, ten molecular taxonomic units were found from samples of nine morphologically identified species. Accordingly, 11 species of small mammals were present in the investigated areas, including four Rattus species, three Niviventer species, Callosciurus erythraeus, Neohylomys hainanensis, Tupaia belangeri, and Suncus murinus. Based on the results of the phylogenetic and molecular delineation analyses, the systematic status of some rodent species should be redefined. R. rattus hainanicus and R. rattus sladeni are synonyms of R. andamanensis. R. losea from China and Southeast Asia comprises two independent species: R. losea and R. sakeratensis. Finally, the taxonomic status of three putative species of Niviventer should be further confirmed according to morphological, molecular and ecological characters.

The complete mitochondrial genome of Leucoptera malifoliella Costa (Lepidoptera: Lyonetiidae)

The mitochondrial genome (mitogenome) of Leucoptera malifoliella (=L. scitella) (Lepidoptera: Lyonetiidae) was sequenced. The size was 15,646 bp with gene content and order the same as those of other lepidopterans. The nucleotide composition of L. malifoliella mitogenome is highly A+T biased (82.57%), ranked just below Coreana raphaelis (82.66%) (Lepidoptera: Lycaenidae). All protein-coding genes (PCGs) start with the typical ATN codon except for the cox1 gene, which uses CGA as the initiation codon. Nine PCGs have the common stop codon TAA, four PCGs have the common stop codon T as incomplete stop codons, and nad4l and nad6 have TAG as the stop codon. Cloverleaf secondary structures were inferred for 22 tRNA genes, but trnS1(AGN) was found to lack the DHU stem. The secondary structure of rrnL and rrnS is generally similar to other lepidopterans but with some minor differences. The A+T-rich region includes the motif ATAGA, but the poly (T) stretch is replaced by a stem-loop structure, which may have a similar function to the poly (T) stretch. Finally, there are three long repeat (154 bp) sequences followed by one short repeat (56 bp) with four (TA)(n) intervals, and a 10-bp poly-A is present upstream of trnM. Phylogenetic analysis shows that the position of Yponomeutoidea, as represented by L. malifoliella, is the same as traditional classifications. Yponomeutoidea is the sister to the other lepidopteran superfamilies covered in the present study.

The integrative taxonomic approach reveals host specific species in an encyrtid parasitoid species complex

Integrated taxonomy uses evidence from a number of different character types to delimit species and other natural groupings. While this approach has been advocated recently, and should be of particular utility in the case of diminutive insect parasitoids, there are relatively few examples of its application in these taxa. Here, we use an integrated framework to delimit independent lineages in Encyrtus sasakii (Hymenoptera: Chalcidoidea: Encyrtidae), a parasitoid morphospecies previously considered a host generalist. Sequence variation at the DNA barcode (cytochrome c oxidase I, COI) and nuclear 28S rDNA loci were compared to morphometric recordings and mating compatibility tests, among samples of this species complex collected from its four scale insect hosts, covering a broad geographic range of northern and central China. Our results reveal that Encyrtus sasakii comprises three lineages that, while sharing a similar morphology, are highly divergent at the molecular level. At the barcode locus, the median K2P molecular distance between individuals from three primary populations was found to be 11.3%, well outside the divergence usually observed between Chalcidoidea conspecifics (0.5%). Corroborative evidence that the genetic lineages represent independent species was found from mating tests, where compatibility was observed only within populations, and morphometric analysis, which found that despite apparent morphological homogeneity, populations clustered according to forewing shape. The independent lineages defined by the integrated analysis correspond to the three scale insect hosts, suggesting the presence of host specific cryptic species. The finding of hidden host specificity in this species complex demonstrates the critical role that DNA barcoding will increasingly play in revealing hidden biodiversity in taxa that present difficulties for traditional taxonomic approaches.

Utility of the DNA barcoding gene fragment for parasitic wasp phylogeny (Hymenoptera: Ichneumonoidea): data release and new measure of taxonomic congruence

The enormous cytochrome oxidase subunit I (COI) sequence database being assembled from the various DNA barcoding projects as well as from independent phylogenetic studies constitutes an almost unprecedented amount of data for molecular systematics, in addition to its role in species identification and discovery. As part of a study of the potential of this gene fragment to improve the accuracy of phylogenetic reconstructions, and in particular, exploring the effects of dense taxon sampling, we have assembled a data set for the hyperdiverse, cosmopolitan parasitic wasp superfamily Ichneumonoidea, including the release of 1793 unpublished sequences. Of approximately 84 currently recognized Ichneumonoidea subfamilies, 2500 genera and 41,000 described species, barcoding 5'-COI data were assembled for 4168 putative species-level terminals (many undescribed), representing 671 genera and all but ten of the currently recognized subfamilies. After the removal of identical and near-identical sequences, the 4174 initial sequences were reduced to 3278. We show that when subjected to phylogenetic analysis using both maximum likelihood and parsimony, there is a broad correlation between taxonomic congruence and number of included sequences. We additionally present a new measure of taxonomic congruence based upon the Simpson diversity index, the Simpson dominance index, which gives greater weight to morphologically recognized taxonomic groups (subfamilies) recovered with most representatives in one or a few contiguous groups or subclusters.

Phylogenetic reconstruction and DNA barcoding for closely related pine moth species (Dendrolimus) in China with multiple gene markers

Unlike distinct species, closely related species offer a great challenge for phylogeny reconstruction and species identification with DNA barcoding due to their often overlapping genetic variation. We tested a sibling species group of pine moth pests in China with a standard cytochrome c oxidase subunit I (COI) gene and two alternative internal transcribed spacer (ITS) genes (ITS1 and ITS2). Five different phylogenetic/DNA barcoding analysis methods (Maximum likelihood (ML)/Neighbor-joining (NJ), "best close match" (BCM), Minimum distance (MD), and BP-based method (BP)), representing commonly used methodology (tree-based and non-tree based) in the field, were applied to both single-gene and multiple-gene analyses. Our results demonstrated clear reciprocal species monophyly for three relatively distant related species, Dendrolimus superans, D. houi, D. kikuchii, as recovered by both single and multiple genes while the phylogenetic relationship of three closely related species, D. punctatus, D. tabulaeformis, D. spectabilis, could not be resolved with the traditional tree-building methods. Additionally, we find the standard COI barcode outperforms two nuclear ITS genes, whatever the methods used. On average, the COI barcode achieved a success rate of 94.10-97.40%, while ITS1 and ITS2 obtained a success rate of 64.70-81.60%, indicating ITS genes are less suitable for species identification in this case. We propose the use of an overall success rate of species identification that takes both sequencing success and assignation success into account, since species identification success rates with multiple-gene barcoding system were generally overestimated, especially by tree-based methods, where only successfully sequenced DNA sequences were used to construct a phylogenetic tree. Non-tree based methods, such as MD, BCM, and BP approaches, presented advantages over tree-based methods by reporting the overall success rates with statistical significance. In addition, our results indicate that the most closely related species D. punctatus, D. tabulaeformis, and D. spectabilis, may be still in the process of incomplete lineage sorting, with occasional hybridizations occurring among them.

Anti-predator defence drives parallel morphological evolution in flea beetles

Complex morphological or functional traits are frequently considered evolutionarily unique and hence useful for taxonomic classification. Flea beetles (Alticinae) are characterized by an extraordinary jumping apparatus in the usually greatly expanded femur of their hind legs that separates them from the related Galerucinae. Here, we examine the evolution of this trait using phylogenetic analysis and a time-calibrated tree from mitochondrial (rrnL and cox1) and nuclear (small subunits and large subunits) genes, as well as morphometrics of femora using elliptic Fourier analysis. The phylogeny strongly supports multiple independent origins of the metafemoral spring and therefore rejects the monophyly of Alticinae, as defined by this trait. Geometric outline analysis of femora shows the great plasticity of this structure and its correlation with the type and diversity of the metafemoral springs. The recognition of convergence in jumping apparatus now resolves the long-standing difficulties of Galerucinae-Alticinae classification, and cautions against the value of trait complexity as a measure of taxonomic significance. The lineage also shows accelerated species diversification rates relative to other leaf beetles, which may be promoted by the same ecological factors that also favour the repeated evolution of jumping as an anti-predation mechanism.