A chromosome-level genome assembly of the forestry pest Coronaproctus castanopsis.

As an important forestry pest, Coronaproctus castanopsis (Monophlebidae) has caused serious damage to the globally valuable Gutianshan ecosystem, China. In this study, we assembled the first chromosome-level genome of the female specimen of C. castanopsis by merging BGI reads, HiFi long reads and Hi-C data. The assembled genome size is 700.81 Mb, with a scaffold N50 size of 273.84 Mb and a contig N50 size of 12.37 Mb. Hi-C scaffolding assigned 98.32% (689.03 Mb) of C. Castanopsis genome to three chromosomes. The BUSCO analysis (n = 1,367) showed a completeness of 91.2%, comprising 89.2% of single-copy BUSCOs and 2.0% of multicopy BUSCOs. The mapping ratio of BGI, second-generation RNA, third-generation RNA and HiFi reads are 97.84%, 96.15%, 97.96%, and 99.33%, respectively. We also identified 64.97% (455.3 Mb) repetitive elements, 1,373 non-coding RNAs and 10,542 protein-coding genes. This study assembled a high-quality genome of C. castanopsis, which accumulated valuable molecular data for scale insects.

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.

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.

The Whole Genome of Colletes collaris (Hymenoptera: Colletidae): An Important Step in Comparative Genomics of Cellophane Bees.

Gaining knowledge on bees is of the utmost importance due to the paramount role that they play in angiosperm pollination. Herein, we provide the first genome assembly of Colletes collaris, a pan-Eurasian cellophane bee. We sequenced 50.53 Gbp of long-read data plus 57.36 Gbp of short-read data in Oxford Nanopore Technologies and Illumina platforms, respectively. The genome assembly consisted of 374.75 Mbp distributed across 374 contigs, with L50 and N50 of 9 and 8.96 Mbp, respectively. We predicted the genome to comprise 20,399 protein-coding genes, 467,947 repeats, and 4,315 non-coding RNA genes. The transcriptome and mitochondrial genome of the species were also assembled. Gene family analysis with 15 insect species identified 14,417 families, 9,517 of them found in C. collaris. A dated phylogenomic analysis revealed high numbers of orthogroups experiencing rapid evolution within Colletes.

Evolutionary timescale of chalcidoid wasps inferred from over one hundred mitochondrial genomes.

Chalcidoidea is one of the most biologically diverse groups among Hymenoptera. Members are characterized by extraordinary parasitic lifestyles and extensive host ranges, among which several species attack plants or serve as pollinators. However, higher-level chalcidoid relationships remain controversial. Here, we performed mitochondrial phylogenomic analyses for major clades (18 out of 25 families) of Chalcidoidea based on 139 mitochondrial genomes. The compositional heterogeneity and conflicting backbone relationships in Chalcidoidea were assessed using various datasets and tree inferences. Our phylogenetic results supported the monophyly of 16 families and polyphyly of Aphelinidae and Pteromalidae. Our preferred topology recovered the relationship (Mymaridae+(Signiphoridae+Leucospidae)+(Chalcididae+((Perilampidae+Eucharitidae)+ remaining Chalcidoidea)))). The monophyly of Agaonidae and Sycophaginae was rejected, while the gall-associated ((Megastigmidae+Ormyridae)+(Ormocerinae+Eurytomidae)) relationship was supported in most results. A six-gene inversion may be a synapomorphy for most families, whereas other derived gene orders may introduce confusion in phylogenetic signals at deeper nodes. Dating estimates suggested that Chalcidoidea arose near the Jurassic/Cretaceous boundary and that two dynamic shifts in diversification occurred during the evolution of Chalcidoidea. We hypothesized that the potential codiversification between chalcidoids and their hosts may be crucial for accelerating the diversification of Chalcidoidea. Ancestral state reconstruction analyses supported the hypothesis that gall-inducers were mainly derived from parasitoids of gall-inducers, while other gall-inducers were derived from phytophagous groups. Taken together, these findings advance our understanding of mitochondrial genome evolution in the major interfamilial phylogeny of Chalcidoidea.

Impacts of Taxon-Sampling Schemes on Bayesian Tip Dating Under the Fossilized Birth-Death Process.

Evolutionary timescales can be inferred by molecular-clock analyses of genetic data and fossil evidence. Bayesian phylogenetic methods such as tip dating provide a powerful framework for inferring evolutionary timescales, but the most widely used priors for tree topologies and node times often assume that present-day taxa have been sampled randomly or exhaustively. In practice, taxon sampling is often carried out so as to include representatives of major lineages, such as orders or families. We examined the impacts of different densities of diversified sampling on Bayesian tip dating on unresolved fossilized birth-death (FBD) trees, in which fossil taxa are topologically constrained but their exact placements are averaged out. We used synthetic data generated by simulations of nucleotide sequence evolution, fossil occurrences, and diversified taxon sampling. Our analyses under the diversified-sampling FBD process show that increasing taxon-sampling density does not necessarily improve divergence-time estimates. However, when informative priors were specified for the root age or when tree topologies were fixed to those used for simulation, the performance of tip dating on unresolved FBD trees maintains its accuracy and precision or improves with taxon-sampling density. By exploring three situations in which models are mismatched, we find that including all relevant fossils, without pruning off those that are incompatible with the diversified-sampling FBD process, can lead to underestimation of divergence times. Our reanalysis of a eutherian mammal data set confirms some of the findings from our simulation study, and reveals the complexity of diversified taxon sampling in phylogenomic data sets. In highlighting the interplay of taxon-sampling density and other factors, the results of our study have practical implications for using Bayesian tip dating to infer evolutionary timescales across the Tree of Life. [Bayesian tip dating; eutherian mammals; fossilized birth-death process; phylogenomics; taxon sampling.].

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.

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.

Key to Ooctonus Haliday (Hymenoptera: Mymaridae) in China, with one new species and three new country records.

A new species of Ooctonus Haliday (Hymenoptera: Mymaridae), O. innermongolicus Aishan Hu sp. nov., is described from Inner Mongolia and Tibet, China. Eight other species of the genus, including the three new records O. hemipterus Haliday, O. lokomotiv Triapitsyn and O. spartak Triapitsyn, are also reported and illustrated. A key to females is provided for the 18 species of Ooctonus known from China.

Notes on the Genus Aceratoneuromyia Girault (Hymenoptera: Eulophidae).

Fruit flies in the family Tephritidae are well known as economically important pests of edible fruits and can often cause serious damage and losses to both agriculture and the economy. One of the common parasitoids of fruit flies, Aceratoneuromyia indica (Silvestri), has been used in biological programs. However, the biocontrol utilities of parasitoids are impeded by the difficulties of proper identification. Species of the genus Aceratoneuromyia Girault (Hymenoptera: Eulophidae), usually developed as parasitoids of fruit flies, are studied here. Trjapitzinichus Kostjukov and Kosheleva is proposed as a new synonym under Aceratoneuromyia. Three new species of Aceratoneuromyia, A. bilinis Huangfu and Cao sp. nov., A. carinata Cao and Zhu sp. nov., and A. trilinus Cao and Zhu sp. nov., are described and illustrated from China. Aceratoneuromyia indica is also treated here with diagnosis and illustrations. DNA barcodes of A. bilinis and A. indica and a key to the world species of Aceratoneuromyia are provided. This study provided important identification information of parasitoids with morphology and molecular evidence, which is useful for imperative needs regarding the identity of parasitoids attacking fruit flies.

A new species and a newly recorded subgenus of Lipotriches Gerstaecker, 1858 (Hymenoptera, Apoidea, Halictidae, Nomiinae) from China.

Two Chinese species of the genus Lipotriches Gerstaecker, 1858 are treated in this paper. Lipotriches (Lipotriches) guihongi Zhang & Niu, sp. nov. is recognized as a new species and Lipotriches (Maynenomia) nanensis (Cockerell, 1929) is a new species and subgenus record for China. The number of Chinese species of the subfamily Nomiinae and genus Lipotriches are updated to 47 and 15, respectively.

Testing the systematic status of Homalictus and Rostrohalictus with weakened cross-vein groups within Halictini (Hymenoptera: Halictidae) using low-coverage whole-genome sequencing.

The halictid genus Lasioglossum, as one of the most species-rich bee groups with persistently contentious subgeneric boundaries, is one of the most challenging bee groups from a systematic standpoint. An enduring question is the relationship of Lasioglossum and Homalictus, whether all halictine bees with weakened distal wing venation comprise one or multiple genera. Here, we analyzed the phylogenetic relationships among the subgroups within Lasioglossum s.l. based on thousands of single-copy orthologs and ultraconserved elements, which were extracted from 23 newly sequenced low-coverage whole genomes alongside a published genome (22 ingroups plus 2 outgroups). Both marker sets provided consistent results across maximum likelihood and coalescent-based species tree approaches. The phylogenetic and topology test results show that the Lasioglossum and Hemihalictus series are reciprocally monophyletic and Homalictus and Rostrohalictus are valid subgenera of Lasioglossum. Consequently, we lower Homalictus to subgenus status within Lasioglossum again, and we also raise Rostrohalictus to subgenus status from its prior synonymy with subgenus Hemihalictus. Lasioglossum przewalskyi is also transferred to the subgenus Hemihalictus. Ultimately, we redefine Lasioglossum to include all halictine bees with weakened distal wing venation.

Chinese Species of the Genus Pseudanaphes Noyes & Valentine (Hymenoptera: Mymaridae) with Description of a New Species.

The fairyfly Mymaridae (Hymenoptera: Chalcidoidea) are widely distributed worldwide, but species of this family have rarely been collected and recorded from the Qinghai-Tibet Plateau. In this study, mymarids collected in Tibet, China, are identified based on morphology and molecular data. Two species of the genus Pseudanaphes Noyes & Valentine are treated and illustrated here, including a known species, P. zhaoi Lin, and a new species, P. yadongicus Aishan & Cao sp. nov. In addition, a key to the world species of Pseudanaphes (females) and DNA barcodes for P. yadongicus and P. zhaoi are provided.

Review of the genus Pleurotroppopsis Girault (Hymenoptera: Eulophidae) with interspecific phylogenetic relationships based on morphological characters.

This study is dedicated to the late Dr. John LaSalle, and reviews the world species of Pleurotroppopsis Girault (Hymenoptera: Eulophidae); fourteen species are treated, of which two are newly described: P. dactylispae Cao & Zhu sp. nov. from China and P. peukscutella Cao & Zhu sp. nov. from Malaysia. On the basis of morphological characters, tentative relationships among genera allied to Pleurotroppopsis are discussed. A revised definition of Pleurotroppopsis is presented based on study of type specimens of all species and a critical review of previous studies on the genus. In addition, parsimony analyses were conducted to infer a phylogeny of Pleurotroppopsis species based on a unique data matrix of morphological characters. Keys to genera allied to Pleurotroppopsis and to known species of Pleurotroppopsis are provided.