Search

Megachile is one of the largest bee genera, including nearly 1,500 species, but very few chromosome-level assemblies exist for this group or the family Megachilidae. Here, we report the chromosome-level genome assembly of Megachile lagopoda collected from Xizang, China. Using PacBio CLR long reads and Hi-C data, we assembled a genome of 256.83 Mb with 96.08% of the assembly located on 16 chromosomes. Our assembly contains 266 scaffolds, with a scaffold N50 length of 15.6 Mb, and BUSCO completeness of 99.20%. We masked 27.10% (69.61 Mb) of the assembly as repetitive elements, identified 459 non-coding RNAs, and predicted 11,157 protein-coding genes. This high-quality genome of M. lagopoda represents an important step forward for our knowledge of megachilid genomics and bee evolution overall., (© 2024. The Author(s).)

Foraging behavior frequently plays a major role in driving the geographic distribution of animals. Buzzing to extract protein-rich pollen from flowers is a key foraging behavior used by bee species across at least 83 genera (these genera comprise ∼58% of all bee species). Although buzzing is widely recognized to affect the ecology and evolution of bees and flowering plants (e.g., buzz-pollinated flowers), global patterns and drivers of buzzing bee biogeography remain unexplored. Here, we investigate the global species distribution patterns within each bee family and how patterns and drivers differ with respect to buzzing bee species. We found that both distributional patterns and drivers of richness typically differed for buzzing species compared with hotspots for all bee species and when grouped by family. A major predictor of the distribution, but not species richness overall for buzzing members of four of the five major bee families included in analyses (Andrenidae, Halictidae, Colletidae, and to a lesser extent, Apidae), was the richness of poricidal flowering plant species, which depend on buzzing bees for pollination. Because poricidal plant richness was highest in areas with low wind and high aridity, we discuss how global hotspots of buzzing bee biodiversity are likely influenced by both biogeographic factors and plant host availability. Although we explored global patterns with state-level data, higher-resolution work is needed to explore local-level drivers of patterns. From a global perspective, buzz-pollinated plants clearly play a greater role in the ecology and evolution of buzzing bees than previously predicted., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Resource partitioning is considered a key factor in alleviating competitive interactions, enabling coexistence among consumer species. However, most studies have focused on resource partitioning between species, ignoring the potentially critical role of intraspecific variation in resource use. We investigated floral resource partitioning across species, colonies, and individuals in a species-rich bumblebee community in the diversification center of bumblebees. We used a total of 10,598 bumblebees belonging to 13 species across 5 years in the Hengduan Mountains of southwest China. First, we evaluated the influence of a comprehensive set of floral traits, including both those related to attractiveness (flower color and shape) and rewards (pollen, sugar ratio, nectar volume, sugar concentration, and amino acid content) on resource partitioning at the species level in bumblebee-plant networks. Then, we explored intraspecific resource partitioning on the colony and individual levels. Our results suggest that bumblebee species differ substantially in their use of the available floral resources, and that this mainly depends on flower attractiveness (floral color and shape). Interestingly, we also detected floral resource partitioning at the colony level within all commonest bumblebee species evaluated. In general, floral resource partitioning between bumblebee individuals decreased with species- and individual-level variation in body size (intertegular span). These results suggest that bumblebee species may coexist via the flexibility in their preferences for specific floral traits, which filters up to support the co-occurrence of high numbers of species and individuals in this global hotspot of species richness., (© 2024 The Ecological Society of America.)

Sequence data assembly is a foundational step in high-throughput sequencing, with untold consequences for downstream analyses. Despite this, few studies have interrogated the many methods for assembling phylogenomic UCE data for their comparative efficacy, or for how outputs may be impacted. We study this by comparing the most commonly used assembly methods for UCEs in the under-studied bee lineage Nomiinae and a representative sampling of relatives. Data for 63 UCE-only and 75 mixed taxa were assembled with five methods, including ABySS, HybPiper, SPAdes, Trinity and Velvet, and then benchmarked for their relative performance in terms of locus capture parameters and phylogenetic reconstruction. Unexpectedly, Trinity and Velvet trailed the other methods in terms of locus capture and DNA matrix density, whereas SPAdes performed favourably in most assessed metrics. In comparison with SPAdes, the guided-assembly approach HybPiper generally recovered the highest quality loci but in lower numbers. Based on our results, we formally move Clavinomia to Dieunomiini and render Epinomia once more a subgenus of Dieunomia. We strongly advise that future studies more closely examine the influence of assembly approach on their results, or, minimally, use better-performing assembly methods such as SPAdes or HybPiper. In this way, we can move forward with phylogenomic studies in a more standardized, comparable manner., (© 2024 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.)

A novel design of a portable funnel light trap (PFLT) was presented for collecting insects in ecological studies. The trap consists of a compact plastic box equipped with a light source and power source, along with two plastic polypropylene interception vanes. The PFLT costs 18.3 USD per unit and weighs approximately 300 g. A maximum of six PFLT units can be packed in one medium-sized backpack (32 cm × 45 cm × 15 cm, 20 L), making it easier to set up multiple units in remote areas wherein biodiversity research is needed. The low cost and weight of the trap also allows for large-scale deployment. The design is customizable and can be easily manufactured to fit various research needs. To validate the PFLT's efficacy in collecting insects across different habitat types, a series of field experiments were conducted in South Korea and Laos, where 37 trials were carried out. The PFLT successfully collected 7497 insects without experiencing battery issues or damage by rain or wind. Insect compositions and abundances differed across the three sampled habitat types: forests, grasslands, and watersides. This new FLT trap is an important tool for studying and protecting insect biodiversity, particularly in areas wherein conventional light traps cannot be deployed.

Species occurrence data are foundational for research, conservation, and science communication, but the limited availability and accessibility of reliable data represents a major obstacle, particularly for insects, which face mounting pressures. We present BeeBDC, a new R package, and a global bee occurrence dataset to address this issue. We combined >18.3 million bee occurrence records from multiple public repositories (GBIF, SCAN, iDigBio, USGS, ALA) and smaller datasets, then standardised, flagged, deduplicated, and cleaned the data using the reproducible BeeBDC R-workflow. Specifically, we harmonised species names (following established global taxonomy), country names, and collection dates and, we added record-level flags for a series of potential quality issues. These data are provided in two formats, "cleaned" and "flagged-but-uncleaned". The BeeBDC package with online documentation provides end users the ability to modify filtering parameters to address their research questions. By publishing reproducible R workflows and globally cleaned datasets, we can increase the accessibility and reliability of downstream analyses. This workflow can be implemented for other taxa to support research and conservation., (© 2023. The Author(s).)

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., (© 2023 John Wiley & Sons Ltd.)

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., (© 2023 John Wiley & Sons Ltd.)

Wild bees provide important pollination services, but they face numerous stressors that threaten them and their ecosystem services. Wild bees can be exposed to heavy metal pollution through the consumption of nectar, pollen, and water, which might cause bee decline. While some studies have measured heavy metal concentrations in honeybees, few studies have monitored heavy metal concentrations in wild bees or explored their potential effects on wild bee communities. To investigate the impact of heavy metal pollution on wild bee communities, heavy metal concentrations, including vanadium (V), chromium (Cr), nickel (Ni), cadmium (Cd), Zinc (Zn) and lead (Pb) in multiple wild bee species were measured. Multiple wild bee species, including: Xylocopa tranquabaroroum, Eucera floralia, Apis cerana, and small bee mixtures (representing multiple small wild bee species) were sampled from 18 sites in Quzhou, Zhejiang Province, China. The findings demonstrated that there were significant differences in heavy metal concentrations among different bee species. The concentrations of V, Zn, Cd, and Pb in X. tranquabaroroum, the largest bee species in this study, were lower than that in the other three sample groups. Furthermore, there were significant negative correlations between heavy metal pollution and wild bee diversity and species richness, but not with abundance. Particularly, there was no significant relationship between heavy metal pollution and the abundance of small bees. Given these worrying findings, monitoring multiple heavy metals in wild bees should be conducted for protecting wild bee diversity and securing their pollination services., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Inc. All rights reserved.)

Bees are the most significant pollinators of flowering plants. This partnership began ca. 120 million years ago, but the uncertainty of how and when bees spread across the planet has greatly obscured investigations of this key mutualism. We present a novel analysis of bee biogeography using extensive new genomic and fossil data to demonstrate that bees originated in Western Gondwana (Africa and South America). Bees likely originated in the Early Cretaceous, shortly before the breakup of Western Gondwana, and the early evolution of any major bee lineage is associated with either the South American or African land masses. Subsequently, bees colonized northern continents via a complex history of vicariance and dispersal. The notable early absences from large landmasses, particularly in Australia and India, have important implications for understanding the assembly of local floras and diverse modes of pollination. How bees spread around the world from their hypothesized Southern Hemisphere origin parallels the histories of numerous flowering plant clades, providing an essential step to studying the evolution of angiosperm pollination syndromes in space and time., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 Elsevier Inc. All rights reserved.)

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., (© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

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., (© 2022 Institute of Zoology, Chinese Academy of Sciences.)

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., (© 2022 Institute of Zoology, Chinese Academy of Sciences.)

Wildlife trade is a major driver of biodiversity loss, yet whilst the impacts of trade in some species are relatively well-known, some taxa, such as many invertebrates are often overlooked. Here we explore global patterns of trade in the arachnids, and detected 1,264 species from 66 families and 371 genera in trade. Trade in these groups exceeds millions of individuals, with 67% coming directly from the wild, and up to 99% of individuals in some genera. For popular taxa, such as tarantulas up to 50% are in trade, including 25% of species described since 2000. CITES only covers 30 (2%) of the species potentially traded. We mapped the percentage and number of species native to each country in trade. To enable sustainable trade, better data on species distributions and better conservation status assessments are needed. The disparity between trade data sources highlights the need to expand monitoring if impacts on wild populations are to be accurately gauged and the impacts of trade minimised., (© 2022. The Author(s).)

Integrative taxonomy is central to modern taxonomy and systematic biology, including behavior, niche preference, distribution, morphological analysis, and DNA barcoding. However, decades of use demonstrate that these methods can face challenges when used in isolation, for instance, potential misidentifications due to phenotypic plasticity for morphological methods, and incorrect identifications because of introgression, incomplete lineage sorting, and horizontal gene transfer for DNA barcoding. Although researchers have advocated the use of integrative taxonomy, few detailed algorithms have been proposed. Here, we develop a convolutional neural network method (morphology-molecule network [MMNet]) that integrates morphological and molecular data for species identification. The newly proposed method (MMNet) worked better than four currently available alternative methods when tested with 10 independent data sets representing varying genetic diversity from different taxa. High accuracies were achieved for all groups, including beetles (98.1% of 123 species), butterflies (98.8% of 24 species), fishes (96.3% of 214 species), and moths (96.4% of 150 total species). Further, MMNet demonstrated a high degree of accuracy ($>$98%) in four data sets including closely related species from the same genus. The average accuracy of two modest subgenomic (single nucleotide polymorphism) data sets, comprising eight putative subspecies respectively, is 90%. Additional tests show that the success rate of species identification under this method most strongly depends on the amount of training data, and is robust to sequence length and image size. Analyses on the contribution of different data types (image vs. gene) indicate that both morphological and genetic data are important to the model, and that genetic data contribute slightly more. The approaches developed here serve as a foundation for the future integration of multimodal information for integrative taxonomy, such as image, audio, video, 3D scanning, and biosensor data, to characterize organisms more comprehensively as a basis for improved investigation, monitoring, and conservation of biodiversity. [Convolutional neural network; deep learning; integrative taxonomy; single nucleotide polymorphism; species identification.]., (© The Author(s) 2021. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Anthidiini, a large bee tribe characterized by light-colored maculations, represents nearly 1,000 pollinator species, but no genomes are yet available for this tribe. Here, we report a chromosome-level genome assembly of Anthidium xuezhongi collected from the Tibetan Plateau. Using PacBio long reads and Hi-C data, we assembled a genome of 189.14 Mb with 99.94% of the assembly located in 16 chromosomes. Our assembly contains 23 scaffolds, with the scaffold N50 length of 12.53 Mb, and BUSCO completeness of 98.70% (n = 1,367). We masked 25.98 Mb (13.74%) of the assembly as repetitive elements, identified 385 noncoding RNAs, and predicted 10,820 protein-coding genes (99.20% BUSCO completeness). Gene family evolution analyses identified 9,251 gene families, of which 31 gene families experienced rapid evolution. Interspecific chromosomal variation among A. xuezhongi, Bombus terrestris, and Apis mellifera showed strong chromosomal syntenic relationships. This high-quality genome assembly is a valuable resource for evolutionary and comparative genomic analyses of bees., (© The Author(s) 2022. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Andrena camellia Wu is one of the primary pollinators of Camellia oleifera A. in China. In this paper, the essential number of individuals for efficient pollination by this species was calculated via two criteria, based on various indicators including counts of pollen grains in provisions, from single visits, and from single foraging trips overall; single flower visit duration; single flight period duration; number of eggs laid by a single female over their lifetime; and the average number of flowers per plant. Based on the number of pollen grains collected per flower visit, the essential number of females necessary is 2107 in a 1-ha Camellia oleifera garden with 1800 plants, while only 1998 female individuals are essentially needed when estimated based on the mean number of pollen grains collected in a single flight period. We argue that the essential number estimated by the former method is more reasonable and accurate for practical applications.

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., Competing Interests: Declaration of Interests The authors declare no competing interests., (Copyright © 2020 The Author(s). Published by Elsevier Inc. All rights reserved.)

Background: Invasive species are increasingly driving biodiversity decline, and knowledge of colonization dynamics, including both drivers and dispersal modes, are important to prevent future invasions. The bee species Megachile sculpturalis (Hymenoptera: Megachilidae), native to East-Asia, was first recognized in Southeast-France in 2008, and has since spread throughout much of Europe. The spread is very fast, and colonization may result from multiple fronts., Result: To track the history of this invasion, codominant markers were genotyped using Illumina sequencing and the invasion history and degree of connectivity between populations across the European invasion axis were investigated. Distinctive genetic clusters were detected with east-west differentiations in Middle-Europe., Conclusion: We hypothesize that the observed cluster formation resulted from multiple, independent introductions of the species to the European continent. This study draws a first picture of an early invasion stage of this wild bee and forms a foundation for further investigations, including studies of the species in their native Asian range and in the invaded range in North America.

The Chinese bees of the genus Anthidium Fabricius, 1804, are reviewed. Twenty-one species are confirmed to occur in China, five of which are described and illustrated as new Chinese endemics: Anthidium (Anthidium) pseudomontanum Niu Zhu, sp. nov., A. (A.) pseudophilorum Niu Zhu, sp. nov., A. (A.) tasitiense Niu Zhu, sp. nov., A. (A.) xuezhongi Niu Zhu, sp. nov., and A. (Proanthidium) qingtaoi Niu Zhu, sp. nov.. The previously unknown female of A. (A.) kashmirense Mavromoustakis, 1937 and male of A. (P.) kashgarense (Cockerell, 1911) are described for the first time. Anthidium (A.) furcatum Wu, 2004 (junior primary homonym, nec Anthidium furcatum Ducke, 1908) is replaced with its valid and available synonym A. (A.) striatum Wu, 2004. New synonymies are also established for A. (A.) kashmirense Mavromoustakis, 1937 = A. (A.) nigroventrale Wu, 1982, syn. nov., and A. (A.) florentinum (Fabricius, 1775) = A. (A.) helianthinum Wu, 2004, syn. nov. The non-Chinese Anthidium amabile Alfken, 1933 (junior primary homonym, nec Anthidium porterae var. amabile Cockerell, 1904) is unavailable and the available name Anthidium (Proanthidium) minimum Pasteels, 1969, is valid for this species. Updated synonymies and distributional data are provided for some widespread Palaearctic species including two now adventive in the New World. For Chinese species, the distribution and floral associations of each are provided along with illustrations and a key to the known species.

The Belt and Road Initiative (BRI) represents the largest infrastructure and development project in human history, and presents risks and opportunities for ecosystems, economies, and communities. Some risks (habitat fragmentation, roadkill) are obvious, however, many of the BRI's largest challenges for development and conservation are not obvious and require extensive consideration to identify. In this first BRI Horizon Scan, we identify 11 frontier issues that may have large environmental and social impacts but are not yet recognised. More generally, the BRI will increase China's participation in international environmental governance. Thus, new cooperative modes of governance are needed to balance geopolitical, societal, and environmental interests. Upgrading and standardising global environmental standards is essential to safeguard ecological systems and human societies., (Published by Elsevier Ltd.)

Despite intense interest in bees, no genomes are available for the bee family Colletidae. Colletes gigas, one of the largest species of the genus Colletes in the world, is an ideal candidate to fill this gap. Endemic to China, C. gigas has been the focus of studies on its nesting biology and pollination of the economically important oil tree Camellia oleifera, which is chemically defended. To enable deeper study of its biology, we sequenced the whole genome of C. gigas using single-molecule real-time sequencing on the Pacific Bioscience Sequel platform. In total, 40.58 G (150×) of long reads were generated and the final assembly of 326 scaffolds was 273.06 Mb with a N50 length of 8.11 Mb, which captured 94.4% complete Benchmarking Universal Single-Copy Orthologs. We predicted 11,016 protein-coding genes, of which 98.50% and 84.75% were supported by protein- and transcriptome-based evidence, respectively. In addition, we identified 26.27% of repeats and 870 noncoding RNAs. The bee phylogeny with this newly sequenced colletid genome is consistent with available results, supporting Colletidae as sister to Halictidae when Stenotritidae is not included. Gene family evolution analyses identified 9,069 gene families, of which 70 experienced significant expansions (33 families) or contractions (37 families), and it appears that olfactory receptors and carboxylesterase may be involved in specializing on and detoxifying Ca. oleifera pollen. Our high-quality draft genome for C. gigas lays the foundation for insights on the biology and behavior of this species, including its evolutionary history, nesting biology, and interactions with the plant Ca. oleifera., (© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Genomic data sets are increasingly central to ecological and evolutionary biology, but far fewer resources are available for invertebrates. Powerful new computational tools and the rapidly decreasing cost of Illumina sequencing are beginning to change this, enabling rapid genome assembly and reference marker extraction. We have developed and tested a practical workflow for developing genomic resources in nonmodel groups with real-world data on Collembola (springtails), one of the most dominant soil animals on Earth. We designed universal molecular marker sets, single-copy orthologues (BUSCOs) and ultraconserved elements (UCEs), using three existing and 11 newly generated genomes. Both marker types were tested in silico via marker capture success and phylogenetic performance. The new genomes were assembled with Illumina short reads and 9,585-14,743 protein-coding genes were predicted with ab initio and protein homology evidence. We identified 1,997 benchmarking universal single-copy orthologues (BUSCOs) across 14 genomes and created and assessed a custom BUSCO data set for extracting single-copy genes. We also developed a new UCE probe set containing 46,087 baits targeting 1,885 loci. We successfully captured 1,437-1,865 BUSCOs and 975-1,186 UCEs across 14 genomes. Phylogenomic reconstructions using these markers proved robust, giving new insight on deep-time collembolan relationships. Our study demonstrates the feasibility of generating thousands of universal markers from highly efficient whole-genome sequencing, providing a valuable resource for genome-scale investigations in evolutionary biology and ecology., (© 2020 John Wiley & Sons Ltd.)

Five Chinese species of Nomia (Gnathonomia) Pauly, 2005 are treated in this paper: Nomia fusciventris Zhang Niu, sp. nov. from Fujian Province is described as a new species; N. aurata Bingham, 1897 and N. wahisi Pauly, 2009 are recorded from China for the first time, and the male of N. pieli Cockerell, 1931 is newly reported. An updated diagnosis is provided for the subgenus Nomia (Gnathonomia) to accommodate Chinese endemic species which lack the white integumental bands found in most previously described forms. A key to the known Chinese species is provided.

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., Competing Interests: None declared., (© 2019 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

The Chinese bees of the genus Trachusa Panzer, 1804 are reviewed. Nine species are confirmed to occur in China. Three new species are described and illustrated: Trachusa (Paraanthidium) pingdaensis Niu, sp. nov., T. (P.) staabi Niu, sp. nov. and T. (P.) wuae Niu, sp. nov. The distribution of each species is given. An illustrated key to the Chinese species is provided.

Large-scale observational data from citizen science efforts are becoming increasingly common in ecology, and researchers often choose between these and data from intensive local-scale studies for their analyses. This choice has potential trade-offs related to spatial scale, observer variance, and interannual variability. Here we explored this issue with phenology by comparing models built using data from the large-scale, citizen science USA National Phenology Network (USA-NPN) effort with models built using data from more intensive studies at Long Term Ecological Research (LTER) sites. We built statistical and process based phenology models for species common to each data set. From these models, we compared parameter estimates, estimates of phenological events, and out-of-sample errors between models derived from both USA-NPN and LTER data. We found that model parameter estimates for the same species were most similar between the two data sets when using simple models, but parameter estimates varied widely as model complexity increased. Despite this, estimates for the date of phenological events and out-of-sample errors were similar, regardless of the model chosen. Predictions for USA-NPN data had the lowest error when using models built from the USA-NPN data, while LTER predictions were best made using LTER-derived models, confirming that models perform best when applied at the same scale they were built. This difference in the cross-scale model comparison is likely due to variation in phenological requirements within species. Models using the USA-NPN data set can integrate parameters over a large spatial scale while those using an LTER data set can only estimate parameters for a single location. Accordingly, the choice of data set depends on the research question. Inferences about species-specific phenological requirements are best made with LTER data, and if USA-NPN or similar data are all that is available, then analyses should be limited to simple models. Large-scale predictive modeling is best done with the larger-scale USA-NPN data, which has high spatial representation and a large regional species pool. LTER data sets, on the other hand, have high site fidelity and thus characterize inter-annual variability extremely well. Future research aimed at forecasting phenology events for particular species over larger scales should develop models that integrate the strengths of both data sets., (© 2018 The Authors. Ecology published by Wiley Periodicals, Inc. on behalf of Ecological Society of America.)

Anthophora (Micranthophora) comprises the largest subgenus of Anthophora in the Western Hemisphere, with 26 species. Though previously synonymized with the Anthophora (Heliophila), A. (Micranthophora) is here confirmed as a subgenus, morphological and multi-gene molecular phylogenetic evidence refute this and the synonymy of A. (Micranthophora) to A. (Heliophila) is formally rejected. Characters for (Micranthophora) are given and a key to species is provided. Seven new species are described: Anthophora (Micranthophora) caudata Orr, sp. nov.; Anthophora (Micranthophora) chihuahua Orr, sp. nov.; Anthophora (Micranthophora) escalante Orr, sp. nov.; Anthophora (Micranthophora) parkeri Orr, sp. nov.; Anthophora (Micranthophora) rara Orr, sp. nov.; Anthophora (Micranthophora) striata Orr, sp. nov.; and Anthophora (Micranthophora) timberlakei Orr, sp. nov. Further, four new synonyms are enacted: A. arthuri and A. flexipes to A. albata, A. nigritula to A. exigua, and A. xanthochlora to A. pachyodonta. Distributional and phenological data, as well as known details of nesting biology and floral specialization, are provided. Future research directions and species of potential conservation interest are also discussed.

Background: The native bee fauna of Mississippi, USA has been historically poorly sampled, but is of particular relevance to determine range limits for species that occur in the southern United States. Currently published literature includes 184 species of bees that occur within the state of Mississippi. Additions to the list of native bees known for Mississippi are reported with notes on range, ecology and resources for identification., New Information: The geographic ranges of seven additional species are extended into the state of Mississippi: Andrena (Melandrena) obscuripennis Smith, 1853, Anthemurgus passiflorae Robertson, 1902, Dieunomia bolliana (Cockerell 1910), Diadasia (Diadasia) enavata (Cresson 1872), Peponapis crassidentata (Cockerell 1949), Triepeolus subnitens Cockerell and Timberlake, 1929 and Brachynomada nimia (Snelling and Rozen 1987). These records raise the total number of published species known from the state to 191. Anthemurgus and Brachynomada are also genera new to Mississippi.

The cleptoparasitic bee genus Townsendiella Crawford (Nomadinae, Townsendiellini) is a rare group restricted to the southwestern United States and adjacent Mexico, whose taxonomy and biology remain poorly known. This paper describes Townsendiella ensifera sp. n., the first known record of this genus from Pinnacles National Park. A key to the species of the genus is provided. Several potential areas of future research are also discussed.

Background: Selumetinib (AZD6244, ARRY-142886)+docetaxel increases median overall survival (OS) and significantly improves progression-free survival (PFS) and objective response rate (ORR) compared with docetaxel alone in patients with KRAS mutant, stage IIIB/IV non-small-cell lung cancer (NSCLC; NCT00890825)., Methods: Retrospective analysis of OS, PFS, ORR and change in tumour size at week 6 for different sub-populations of KRAS codon mutations., Results: In patients receiving selumetinib+docetaxel and harbouring KRAS G12C or G12V mutations there were trends towards greater improvement in OS, PFS and ORR compared with other KRAS mutations., Conclusion: Different KRAS mutations in NSCLC may influence selumetinib/docetaxel sensitivity.

Taxonomy has far-reaching effects throughout biology, and incorrect taxonomy can be detrimental in many ways. Polymorphic species complexes, many of which exist in the bee genus Anthophora Latreille, lend themselves to such difficulties. This study employs environmental niche mapping (ENM) and traditional morphological analyses to investigate the validity of the subjective synonymy of Anthophora (Heliophila) curta Provancher with the senior synonym A. squammulosa Dours. Eleven of fifty morphological characters consistently differentiate the two putative species, with an additional five characters sometimes separating them. Additionally, based on over 1000 georeferenced museum specimens, the geographic ranges of the two taxa do not overlap. The two entities also react differently to the bioclimatic variables based on correlation analysis. We further tested the two-species hypothesis by constructing ENMs with informative bioclimatic variables associated with locality records. Their modelled distributions overlapped less than 1%, suggesting discrete environmental boundaries. The variables which contributed most to each species' model also differed. These differences are explored in relation to their habitats. The combined morphological and biogeographic analysis indicates that A. curta and A. squammulosa are distinct species. Based on the accumulated evidence the synonymy is formally rejected and A. curta is recognized as a valid species. Five additional taxa (A. bispinosa Cockerell, A. franciscana Cockerell, A. usticauda Cockerell, A. u. cinerior Cockerell, A. zamoranella Cockerell) are newly synonymized with A. squammulosa and Anthophora curta var. melanops Cockerell is newly synonymized with A. curta. Implications outside of taxonomy are discussed.

Background: Analysis of tumour samples for mutations is becoming increasingly important in driving personalised therapy in cancer. As more targeted therapies are developed, options to survey mutations in multiple genes in a single tumour sample will become ever more attractive and are expected to become the mainstay of molecular diagnosis in non-small cell lung cancer (NSCLC) in the future., Materials and Methods: 238 non-small cell lung cancer (NSCLC) tumour samples were analysed using a custom panel of 82 mutation assays across 14 oncogenes including KRAS and EGFR using Sequenom iPlex Matrix Assisted Laser Desorption/Ionisation Time of Flight Mass Spectrometry (MALDI-TOF). We compared the data generated for KRAS mutations to those detected by Amplification Refractory Mutation System (ARMS) based DxS TheraScreen K-RAS Mutation Kit., Results: The ARMS detected mutations in 46/238 tumour samples. For samples with mutations detected by both approaches, 99.1% overall agreement was observed. The MALDI-TOF method detected an additional 6 samples as KRAS mutation positive and also provided data on concomitant mutations including PIK3CA and TP53., Conclusions: The Sequenom MALDI-TOF method provides a sensitive panel-based approach which makes efficient use of patient diagnostic samples. This technology could provide an opportunity to deliver comprehensive screening of relevant biomarkers to the clinic earlier in disease management, without the need for repeat biopsy and allow for additional downstream analysis in NSCLC where available tissue may have been exhausted.

In developed countries, colorectal cancer (CRC) is the third most common malignancy, but it is the second most frequent cause of cancer-related death. Clinicians are still faced with numerous challenges in the treatment of this disease, and future approaches which target the molecular features of the disorder will be critical for success in this disease setting. Genetic analyses of many solid tumours have shown that up to 100 protein-encoding genes are mutated. Within CRC, numerous genetic alterations have been identified in a number of pathways. Therefore, understanding the molecular pathology of CRC may present information on potential routes for treatment and may also provide valuable prognostic information. This will be particularly pertinent for molecularly targeted treatments, such as anti-vascular endothelial growth factor therapies and anti-epidermal growth factor receptor (EGFR) monoclonal antibody therapy. KRAS and BRAF mutations have been shown to predict response to anti-EGFR therapy. As EGFR can also signal via the phosphatidylinositol 3-kinase (PI3K) kinase pathway, there is considerable interest in the potential roles of members of this pathway (such as PI3K and PTEN) in predicting treatment response. Therefore, a combined approach of new techniques that allow identification of these biomarkers alongside interdisciplinary approaches to the treatment of advanced CRC will aid in the treatment decision-making process and may also serve to guide future therapeutic approaches.

Background: Large-scale gene expression studies have not yielded the expected insight into genetic networks that control complex processes. These anticipated discoveries have been limited not by technology, but by a lack of effective strategies to investigate the data in a manageable and meaningful way. Previous work suggests that using a pre-determined seed-network of gene relationships to query large-scale expression datasets is an effective way to generate candidate genes for further study and network expansion or enrichment. Based on the evolutionary conservation of gene relationships, we test the hypothesis that a seed network derived from studies of retinal cell determination in the fly, Drosophila melanogaster, will be an effective way to identify novel candidate genes for their role in mouse retinal development., Methodology/principal Findings: Our results demonstrate that a number of gene relationships regulating retinal cell differentiation in the fly are identifiable as pairwise correlations between genes from developing mouse retina. In addition, we demonstrate that our extracted seed-network of correlated mouse genes is an effective tool for querying datasets and provides a context to generate hypotheses. Our query identified 46 genes correlated with our extracted seed-network members. Approximately 54% of these candidates had been previously linked to the developing brain and 33% had been previously linked to the developing retina. Five of six candidate genes investigated further were validated by experiments examining spatial and temporal protein expression in the developing retina., Conclusions/significance: We present an effective strategy for pursuing a systems biology approach that utilizes an evolutionary comparative framework between two model organisms, fly and mouse. Future implementation of this strategy will be useful to determine the extent of network conservation, not just gene conservation, between species and will facilitate the use of prior biological knowledge to develop rational systems-based hypotheses.

Molecular characterization of tumour material will become increasingly important in selecting patients for clinical trials and offering appropriate treatment for patients in clinical practice. Recent advances in the field have indicated that the molecular characteristics of a tumour can be determined from circulating tumour cells and circulating tumour DNA; thus, a simple blood sample could provide these data in a simple, convenient and efficient manner. This article discusses progress towards guiding treatment decisions through measuring tumour-derived factors in the circulation., (Copyright (c) 2010 Elsevier Ltd. All rights reserved.)

Background: This study investigated the potential clinical utility of circulating free DNA (cfDNA) as a source of BRAF mutation detection in patients enrolled into a phase II study of AZD6244, a specific MEK1/2 inhibitor, in patients with advanced melanoma., Methods: BRAF mutations were detected using Amplification Refractory Mutation System allele-specific PCR. BRAF mutation status was assessed in serum-derived cfDNA from 126 patients enrolled into the study and from 94 matched tumour samples., Results: Of 94 tumour samples, 45 (47.9%) were found to be BRAF mutation positive (BRAF+). Serum-derived cfDNA was BRAF+ in 33 of 126 (26.2%) samples, including in five samples for which tumour data were unavailable. Of BRAF+ tumours, 25 of 45 (55.6%) were BRAF+ in cfDNA. In three cases in which the tumour was negative, cfDNA was BRAF+. Progression-free survival (PFS) of patients with BRAF+ tumour and cfDNA was not significantly different compared with tumour BRAF+ but cfDNA BRAF-negative patients, indicating that cfDNA BRAF detection is not associated with poorer prognosis on PFS in stage III/IV advanced melanoma., Conclusions: These data demonstrate the feasibility of BRAF mutation detection in cfDNA of patients with advanced melanoma. Future studies should aim to incorporate BRAF mutation testing in cfDNA to further validate this biomarker for patient selection.