Systematic Entomology

Planthoppers (Hemiptera: Fulgoromorpha) are a species-rich and globally distributed insect clade with high economic, ecological, and evolutionary importance. However, the relationships among planthopper lineages and families remain unclear. Previous efforts based on inconsistent morphological traits, a few genes, or limited sampling often resulted in conflicting tree topologies. Here, we used genome-level data to assemble 1164 nuclear single-copy genes and 13 mitochondrial protein-coding genes for 149 planthopper species representing 19 out of 21 extant families. Additional markers were added from published mitogenomes, expanding our sampling to 285 species. These markers were used for Maximum Likelihood-based tree inference and dating analyses. The newly inferred phylogenies validated well-accepted relationships and recovered novel placements. Taxonomic conclusions include the establishment of a new family Borysthenidae stat. rev. within Delphacoidea and a new superfamily Meenoploidea superfam. nov. including redefined Kinnaridae stat. rev. and Meenoplidae stat. rev., the confirmation of the monophyletic family Achilixiidae outside the Achilidae-Derbidae clade, and the transfer of tribes Lyncidini and Amyclini to Dictyopharidae and the genus Madagascaritia to Fulgoridae. The time analyses based on 57 nuclear markers and 30 fossils dated the origin of crown Fulgoromorpha back to Guadalupian, Permian ([~]263 Ma), close to the maximum constraint at 267.3 Ma, while applying an older root constraint resulted in an origin in Mississippian, Carboniferous ([~]332 Ma). While future sampling of unstudied fauna in unexplored regions or habitats may change the topology, the current phylogenomic analysis will serve as a solid foundation for research into planthopper ecology, evolution, and significance.

1. Diptera represent a diverse insect order, including vectors of human and animal pathogens. Their accurate species identification remains a major bottleneck in ecological and epidemiological studies. Morphological identification requires taxonomic expertise, while molecular methods are costly and not universally reliable. Wing geometric morphometrics offers an alternative, but manual landmark annotation is time-consuming and introduces observer bias. 2. We developed ITHILDIN, an automated pipeline for landmark and semilandmark annotation of Diptera wings, combining UNet++ segmentation and an Hourglass landmark prediction model. Using mosquitoes as the primary model system, we extended an existing repository with 5,793 additional images. Models were trained on 5991 annotations of landmarks and segmentations and then evaluated on 12,522 images across 34 taxa. We assessed landmark prediction accuracy against human observers and ML-morph, evaluated species identification using Linear Discriminant Analysis on 17 homologous landmarks and 52 semilandmarks, and tested out-of-distribution generalisation by reproducing an independent study. Transferability was demonstrated by adapting the pipeline to the Dipteran families Drosophilidae and Glossinidae. 3. The Hourglass model achieved a mean landmark error of 4.5 pixels (95% CI: 4.3-4.6), within human observer variability (4.7 pixels, 95% CI: 4.4-5.0) and substantially outperforming ML-Morph (12.7 pixels, 95% CI: 11.1-14.2). The semilandmark-based approach for species identification achieved 91% balanced accuracy across 34 taxa, comparable to CNN performance (94%). On out-of-distribution data, the landmark pipeline generalised substantially better than the CNN and a soft-voting ensemble of the landmark and CNN classifiers achieved 88% balanced accuracy on a replicated study. 4. Combining geometric morphometrics with deep learning provides a reproducible, interpretable, and generalisable alternative to black-box CNN classifiers for Diptera wing analysis. By acting as a consistent single observer comparable to human annotation, the system eliminates inter-observer bias, enabling large-scale and cross-study morphometric analyses of Dipteran wings. The system is publicly available at www.ithildin.bnitm.de and transferable to other Diptera families with moderate retraining effort. Data availabilityImages used in this study are accessible under CC BY 4.0 license at https://doi.org/10.6019/S-BIAD1478. Downloadable and installable docker application can be accessed on the applications git page: https://anonymous.4open.science/r/ITHILDIN-4313/

Taxon sampling is a central aspect of phylogenetic study design, but it has received limited attention in the context of molecular dating and especially in the framework of total-evidence dating, a widely used dating approach that directly integrates molecular and morphological information from extant and fossil taxa. We here assess the impact of different outgroup sampling schemes on age estimates in a total-evidence dating analysis under the uniform tree prior. Our study group are Pimpliformes, a highly diverse, rapidly radiating group of parasitoid wasps of the family Ichneumonidae. We cover 201 extant and 79 fossil taxa, including the oldest fossils of the family from the Early Cretaceous and the first unequivocal representatives of extant subfamilies from the mid Paleogene. Based on newly compiled molecular data from ten nuclear genes and a morphological matrix that includes 222 characters, we show that age estimates become both older and less precise with the inclusion of more distant and more poorly sampled outgroups. In addition, we discover an artefact that might be detrimental for total-evidence dating: "bare-branch attraction", namely high attachment probabilities of, especially, older fossils to terminal branches for which morphological data are missing. After restricting outgroup sampling and adding morphological data for the previously attracting, bare branches, we recover a Middle and Early Jurassic origin for Pimpliformes and Ichneumonidae, respectively. This first age estimate for the group not only suggests an older origin than previously thought, but also that diversification of the crown group happened before the Cretaceous-Paleogene boundary. Our case study demonstrates that in order to obtain robust age estimates, total-evidence dating studies need to be based on a thorough and balanced sampling of both extant and fossil taxa, with the aim of minimizing evolutionary rate heterogeneity and missing morphological information.

Chloropidae, commonly known as grass flies, is a hyperdiverse family of true flies thriving in terrestrial ecosystems around the world with importance to conservation and economy. However, true grass fly diversity and evolutionary affinities are still largely unknown leading to an obscure classification at varied taxonomic levels. The massive lack of data on grass fly evolution hampers studies ranging from species discovery to diversification and provision of ecological services. To overcome this issue, we provide the first comprehensive phylogeny of worldwide Chloropidae using whole-genome shotgun sequencing to retrieve mitochondrial genes, ultraconserved elements and single-copy orthologs. With this, we generated genomic resources from all subfamilies, 95% of the tribes and 48% of the chloropid genera from all biogeographic regions which provides an invaluable resource for biodiversity studies worldwide. Overall, our results provide novel genomic data of over 100 fly species. We implemented dramatic changes in grass fly classification system that redefine one subfamily, propose three new tribes, reassign the tribal position of 59 genera, and synonymize four suprageneric taxa. In addition, we reveal a novel synapomorphy for the family, elucidate grass fly sister-group, and assess the utility of the mitochondrial genome alone to recover evolutionary relationships of a recent lineages of flies. This study is fundamental to mitigate the neglect associated with grass flies through an unprecedented source of genomic data, ultimately providing a novel framework for understanding the rapid evolution of the last and most species-rich radiation of flies.

Fossils provide unique opportunity to understand the tempo and mode of evolution and are essential for modeling the history of lineage diversification. Here, we interrogate the Mesozoic fossil record of the Aculeata, with emphasis on the ants (Formicidae), and conduct an extended series of ancestral state estimation exercises on distributions of tip-dated combined-evidence phylogenies. We developed and illustrated from ground-up a series of 576 morphological characters which we scored for 144 extant and 431 fossil taxa, including all families of Aculeata, Trigonaloidea, Evanioidea, and {dagger}Ephialtitoidea. We used average posterior probability support to guide composition of a target matrix of 303 taxa, for which we integrated strongly filtered ultraconserved element (UCE) data for 115 living species. We also implemented reversible jump MCMC (rjMCMC) and hidden state methods to model complex behavioral characters to test hypotheses about the pathway to obligate eusociality. In addition to revising the higher classification of all sampled groups to family or subfamily level using estimated character polarities to diagnose nodes across the phylogeny, we find that the mid-Cretaceous genera {dagger}Camelomecia and {dagger}Camelosphecia form a clade which is robustly supported as sister to all living and fossil Formicidae. For this reason, we name this extinct clade as {dagger}@@@idae fam. nov. and provide a definition for the expanded Formicoidea. Based on our results, we recognize three major phases in the early evolution of the ants: (1) origin of Formicoidea as ground-adapted huntresses during the Late Jurassic in the "stinging aggressor" guild (Aculeata) among various lineages of "sneaking parasitoids" (non-aculeate Vespina); (2) the first formicoid radiation during the Early Cretaceous, by the end of which all major extant linages originated; and (3) turnover of the Formicoidea at the end-Cretaceous leading to the second formicoid radiation. We conclude with a concentrated series of considerations for future directions of study with this dataset and beyond.

Robotic specimen processing is transforming biodiversity discovery by replacing labor-intensive handling with scalable systems that can simultaneously generate high-quality specimen images. We demonstrate that these images can be leveraged by deep learning to efficiently extract key biological information and guide targeted specimen processing. Using a model dark taxon, the Phoridae (Diptera), the workflow performs three core tasks: sex identification, specimen orientation classification, and anatomical segmentation. Sex identification allows selective retention of diagnostically informative specimens, avoiding wasted effort on non-diagnostic individuals. Orientation classification enables specimens in the desired orientation to proceed immediately, while suboptimally oriented specimens can be repositioned for informative processing. Anatomical segmentation allows targeted processing of specimens displaying diagnostic characters or targeted analysis of specific anatomical regions in subsequent workflow steps. Comparative analysis of model architectures shows task-specific selection is crucial: a Convolutional Neural Network achieved an accuracy of 0.94 for orientation, a Vision Transformer achieved 0.88 for sex, and a U-Net precisely segmented nine anatomical regions with a mean IoU of 0.78. These results demonstrate that robotic imaging combined with deep learning provides a validated foundation for high-throughput, targeted specimen processing, maximising efficiency and utility for taxonomic and trait-based analyses, and supporting scalable, sustainable biodiversity workflows.

Despite tropical psocids comprise ~60% of species diversity within the Psocidae (Insecta, Psocodea), previous studies on the Psocidae phylogeny have poorly sampled tropical species (<40% species in trees). Here we discuss the evolution and systematics of the Psocidae based on the most comprehensive species-level sampling of the Psocidae. We sequenced and inferred the phylogenetic position of 43 previously unsampled Neotropical species from COI, H3, WNT, 18S, 16S, and 12S. Based on our phylogenies we found that Neotropical psocids are generally not closely related to morphologically similar taxa in the Holarctic region. Consequently, the monophyletic status for the major groups within Psocidae (subfamilies and tribes) is recovered only when Holarctic groups are sampled (7-10 of 11 higher-level groups are monophyletic) but violated when Neotropical species are included in the dataset (1 of 11 higher-level groups are monophyletic). Leveraging the largest phylogeny of the Psocidae, our study pinpoints the downfalls of simply extending taxonomic knowledge from lineages of a certain area to inform diversity and evolution of lineages in other regions. HighlightsO_LITropical psocids comprise >60% of the extant family richness C_LIO_LIPrevious phylogenies have undersampled Tropical psocids C_LIO_LIHolarctic and Neotropical species are classified under the same morphological groups C_LIO_LIHolarctic and Neotropical generally correspond to evolutionarily distinct lineages C_LIO_LIPhylogenies based on Holarctic psocids poorly inform evolution in the Neotropics C_LI

The microcaddisfly family Hydroptilidae is the most species-rich within the insect order Trichoptera and has a global distribution. The taxonomy and systematics of this group remains understudied in proportion to its diversity. Here, we present a phylogenetic assessment of subfamily relationships that includes five of the six Hydroptilidae subfamilies (Hydroptilinae, Leucotrichiinae, Ochrotrichiinae, Orthotrichiinae, and Stactobiinae) using publicly available molecular data. Our analyses recovered Leucotrichiinae, Ochrotrichiinae, and Stactobiinae as monophyletic and Hydroptilinae as paraphyletic. Based on the diversity and distribution of taxa, much more representation of species is needed to fully understand the relationships of subfamilies; however, our results suggest a need to revisit the placement of Ithytrichia, which concurs with other recent molecular work on Hydroptilidae. Further clarity into the relationships of Hydroptilidae will be important for understanding the variability and phylogenetic signal of ecological traits.

Insect orders have been defined and stable for decades, with few notable exceptions (e.g., Blattodea and Psocoptera). One of the few remaining questions of order-level monophyly is that of Mecoptera in respect to the phylogenetic placement of Siphonaptera (fleas). We used a large set of transcriptomic nucleotide sequence data representing 56 species and more than 3,000 single-copy genes to resolve the evolutionary history of Antliophora, including fleas (Siphonaptera), scorpionflies and relatives (Mecoptera), and true flies (Diptera). We find that fleas and mecopterans together are the sister group of flies. However, our data and/or analyses are unable to distinguish whether fleas are sister to a monophyletic Mecoptera, or whether they arose from within extant mecopteran families, rendering Mecoptera paraphyletic. We did not detect parameter bias in our dataset after applying a broad range of detection methods. Counter to a previous hypothesis that placed fleas within Mecoptera as the sister group to wingless boreids (snow fleas), we found a potential sister group relationship between fleas and the enigmatic family Nannochoristidae. Although we lack conclusive evidence, it seems possible that fleas represent the most-species rich group of modern mecopterans and that their parasitic lifestyle and morphological adaptations have simply made them unrecognizable in respect to their order-level classification.

Phylogenetic analyses using morphological data currently require hand-crafted character matrices, limiting the number of taxa that can be included. Here I explore how Deep Learning and Computer Vision approaches typically applied to image classification tasks, may be used to infer phylogenetic relationships among bivalves. A convolutional neural network (CNN) was trained on thousands of images showing species of 75 bivalve families. The predictions of the CNN on a large number of bivalve images are then interpreted as an indication of how similar these bivalves are to each other, are averaged by the families to which the species belonged, and visualized in a cluster diagram. In this cluster diagram, significantly more families clustered with members of their subclasses than expected by chance, confirming the feasibility of the approach. To address the issue of convergent evolution, two further CNNs were trained, on the same images but grouped by the orders and subclasses to which the species belonged. Combining predictions for the same images but on different taxonomic levels improved the inferred phylogenetic relationships also of families that the CNNs had not been trained on. Finally, this combined tree is merged with five published phylogenetic trees into a supertree, representing the largest single phylogeny of the Bivalvia to date, encompassing 128 families, including six exclusively fossil families and nine extant families for which presently no molecular data are available. Issues inherent to the approach and suggestions for future directions are discussed.

Bees are presumed to have arisen in the early to mid-Cretaceous coincident with the fragmentation of the southern continents and concurrently with the early diversification of the flowering plants. Among the main groups of bees, Andreninae sensu lato comprise about 3000 species widely distributed with greatest and disjunct diversity in arid areas of North America, South America, and the Palearctic region. Here, we present the first comprehensive dated phylogeny and historical biogeographic analysis for andrenine bees, including representatives of all currently recognized tribes. Our analyses rely on a dataset of 106 taxa and 7952 aligned nucleotide positions from one mitochondrial and six nuclear loci. Andreninae is strongly supported as a monophyletic group and the recovered phylogeny corroborates the commonly recognized clades for the group. Thus, we propose a revised tribal classification that is congruent with our phylogenetic results. The time-calibrated phylogeny and ancestral range reconstructions of Andreninae reveal a fascinating evolutionary history with Gondwana patterns that are unlike those observed in other subfamilies of bees. Andreninae arose in South America during the Late Cretaceous around 90 Million years ago (Ma) and the origin of tribes occurred through a relatively long time-window from this age to the Miocene. The early evolution of the main lineages took place in South America until the beginning of Paleocene with North American fauna origin from it and Palearctic from North America as results of multiple lineage interchanges between these areas by long-distance dispersal or hopping through landmass chains. Overall, our analyses provide strong evidence of amphitropical distributional pattern currently observed in Andreninae in the American continent as result at least three periods of possible land connections between the two American landmasses, much prior to the Panama Isthmus closure. The andrenine lineages reached the Palearctic region through four dispersal events from North America during the Eocene, late Oligocene and early Miocene, most probably via the Thulean Bridge. The few lineages with Afrotropical distribution likely originated from a Palearctic ancestral in the Miocene around 10 Ma when these regions were contiguous, and the Sahara Desert was mostly vegetated making feasible the passage by several organisms. Incursions of andrenine bees to North America and then onto the Old World are chronological congruent with distinct periods when open-vegetation habitats were available for trans-continental dispersal and at the times when aridification and temperature decline offered favorable circumstances for bee diversification.

AO_SCPLOWBSTRACTC_SCPLOWThis study reconstructs the phylogeny of an expansive set of Neotropical leaf beetles in the subfamily Chrysomelinae. From 33 species in the genus Platyphora Gistel, and an additional 37 species representing 16 beetle genera, five genes, three nuclear, and two mitochondrial, were sequenced and used to obtain a well-supported molecular phylogeny using both Bayesian and Maximum Likelihood. The subtribes Chrysomelina and Doryphorina (sensu Daccordi 1982) were monophyletic, while the genus Platyphora was polyphyletic. The genus Leptinotarsa Chevrolat is confirmed to be distinct from Stilodes Chevrolat. Host plant family was recorded for both adults and larvae using direct observations where possible. Ancestral host plant use was reconstructed using Bayesian trait analyses. A complicated history of host plant switches among a restricted set of plant families is revealed: In the paraphyletic Platyphora, one clade that includes Proseicela and Leptinotarsa had two switches from Asclepiadiodeae to Solanaceae, one switch to Moraceae, and one switch to Malpighiaceae, another Platyphora clade had switches between Asteraceae and Rauvolfioideae, and from Rauvolfioideae to Asclepiadiodeae, with other members of the same clade feeding on Boraginaceae and Convolvulaceae. All species included in the clade containing Tritaenia and Stilodes fed on Malpighiaceae, and all species included in the Cosmogramma and Calligrapha clade fed on Malvaceae.

Based on a previously published but realigned matrix for Santalales, we find many relationships that were weakly or unsupported in previous studies are here much better supported, providing a more robust foundation upon which to discuss Santalales classification. In the maximum likelihood analysis, we recovered the same basic relationships as in the previous studies, but with two major differences: i) Balanophoraceae in the broad sense are monophyletic and well supported as embedded in Santalaceae (rather than biphyletic and outside Santalaceae) and ii) most of the former Olacaceae form a moderately supported clade (rather than a weakly supported grade). In the parsimony analysis, the position of Balanophoraceae s.l. is not well supported (although their broader circumscription is). We outline three possible options for a classification of the order and propose a new familial and subfamilial classification for Santalales. This hopefully provides a stable, user- friendly taxonomic framework that is phylogenetically well supported and more consistent with historical usage than some recently proposed systems, and provides taxa that can be more readily diagnosed morphologically. We recommend recognition of nine families (in phylogenetic sequence): Strombosiaceae, Erythropalaceae, Olacaceae, Opiliaceae, Santalaceae, Misodendraceae, Schoepfiaceae and Loranthaceae, plus an unresolved position for Balanophoraceae (including Mystropetalaceae), which we propose to exclude from Santalaceae until more evidence of their relationships to that family is available from nuclear genes. Four new subfamilies, Gaiadendroideae, Comandroideae, Nanodeoideae and Thesioideae, are proposed, and a new combination, Loranthus obtusifolius, is made.

The Mammal Diversity Database (MDD) is an open-access resource providing up-to-date taxonomic, nomenclatural, and geographic data for global mammal species. Since its launch in 2018, the MDD has transformed the traditionally static process of updating mammalian taxonomy into regular online releases reflecting the latest published research. To build on this foundation, we here present version 2.0 of the MDD (MDD2), which catalogues 6,759 living and recently extinct mammal species, representing net increases of 4.1% and 24.8% over MDD version 1.0 and Mammal Species of the World, 3rd edition (MSW3), respectively. Additionally, we identify a net increase of 68.8% (+2,754; 3,149 splits + de novo, 395 lumps) species since 1980 at a rate of [~]65 species/year based on past totals from 14 mammalian compendia, leading to projections of [~]7,084 species by 2030 and [~]8,382 by 2050 if these trends continue. Key updates in MDD2 include: (i) codings of US state, country, continent, and biogeographic realm geographic categories for each species; (ii) a comprehensive nomenclatural dataset for 50,230 valid and synonymous species-rank names, curated with type locality and specimen information for the first time; and (iii) integration between the MDD and the databases Hesperomys and Batnames for greater data accuracy and completeness. These updates bridge critical gaps in the taxonomic and nomenclatural information needed for ongoing revisions and assessments of mammalian species diversity. Using these data, we evaluate temporal and geographic trends over the past 267 years, identifying four major time periods of change in mammalian taxonomy and nomenclature: (i) the initial monographic description of traditionally charismatic species (1758-1880); (ii) the peak of descriptive taxonomy, describing subspecies, and publishing in journals (1881-1939); (iii) the shift toward revisionary taxonomy and polytypic species (1940- 1999); and (iv) the current technology-driven period of integrative revisionary taxonomy (2000- present). Geographically, new species recognition since MSW3 has been concentrated in equatorial, mountainous, and island regions, highlighting areas of high mammal endemism (e.g., Madagascar, Philippines, Andes, East Africa, Himalayas, Atlantic Forests). However, gaps in 21st century taxonomic activity are identified in West and Central Africa, India, and some parts of Indonesia. Currently lagging conservation assessments are alarming, with 25% of the MDD2-recognized mammal species allocated to the understudied conservation threat categories of Data Deficient (11%) or Not Evaluated (14%), underscoring the need for greater taxonomic integration with conservation organizations. Governance advancements in MDD2 include the establishment of external taxonomic subcommittees to guide data collection and curation, a rewritten website that improves access and scalability, a cross-platform application that provides offline access, and new partnerships to continue linking MDD data to global biodiversity infrastructure. By providing up-to-date mammalian taxonomic and nomenclatural data--including links to the text of original name descriptions, type localities, and type specimen collections--the MDD provides an integrative resource for mammalogists and conservationists to more easily track the status of their study organisms. Teaser Text: The Mammal Diversity Database 2.0, listing 6,759 mammal species and 50,230 species-level synonyms, unifies 267 years of taxonomic, nomenclatural, and geographic data to track global mammal biodiversity and provide a continually updated resource for the mammalogical community. Teaser Image: Figure 3. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/640393v1_fig3.gif" ALT="Figure 3"> View larger version (34K): org.highwire.dtl.DTLVardef@1012e67org.highwire.dtl.DTLVardef@8d99d7org.highwire.dtl.DTLVardef@6f21b9org.highwire.dtl.DTLVardef@f23fd_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 3.C_FLOATNO Type locality locations for species-rank mammal taxa described from 1 January 2000 to 15 August 2024. Map gray-scale country coloration represents the total number of currently valid species type localities found per country described within this period. Colored dots represent the exact georeferenced type locality of all currently valid species (red circles) and names currently considered synonyms and subspecies (blue diamonds) in MDD2. Most coordinates were generated from the original description of each name when included directly in publication, while others were georeferenced using GeoLocate or WikiMedia GeoHack place coordinates when not included in the original description publication. The georeferenced localities were mapped and both programmatically and visually vetted for accuracy. Latitude and longitude in decimal degrees is included for each of the names mapped here in the MDD2 synonym list, Supplementary Data SD2. C_FIG

Although several methods exist for extracting and sequencing historical DNA originating from drypreserved insect specimens deposited in natural history museums, no consensus exists as to what is the optimal approach. We demonstrate that a customized, low-cost archival DNA extraction protocol ([~] {euro}10 per sample), in combination with Ultraconserved Elements (UCEs), is an effective tool for insect phylogenomic studies. We successfully tested our approach by sequencing DNA from scarab dung beetles preserved in both wet and dry collections, including unique primary type and rare historical specimens from internationally important natural history museums in London, Paris and Helsinki. The focal specimens comprise enigmatic dung beetle genera (Nesosisyphus, Onychotechus and Helictopleurus) that varied in age and preservation. The oldest specimen, the holotype of the now possibly extinct Mauritian endemic Nesosisyphus rotundatus, was collected in 1944. We obtained high-quality DNA from all studied specimens to enable the generation of a UCE-based dataset that revealed an insightful and well-supported phylogenetic tree of dung beetles. The resulting phylogeny suggested the reclassification of Onychotechus (previously incertae sedis) within the tribe Coprini. Our approach demonstrates the feasibility and effectiveness of combining DNA data from historic and recent museum specimens to provide novel insights. The proposed archival DNA protocol is available at DOI 10.17504/protocols.io.81wgbybqyvpk/v1 HighlightsO_LIWe combined custom low-cost archival DNA extractions and Ultraconserved Element phylogenomics C_LIO_LIDNA from rare museum specimens of enigmatic dung beetles revealed their phylogenetic connections C_LIO_LIGenomic data was obtained from the holotype of a potentially extinct monoinsular endemic species C_LIO_LIGenomic data allowed a rare and enigmatic species of previously unknown affinity to be classified C_LIO_LIThe morphology of museum specimens remained intact following non-destructive DNA extraction C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/564347v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@34aad0org.highwire.dtl.DTLVardef@1ba597dorg.highwire.dtl.DTLVardef@1493c2dorg.highwire.dtl.DTLVardef@10dd2eb_HPS_FORMAT_FIGEXP M_FIG C_FIG

Robber flies or assassin flies (Diptera: Asilidae) are a diverse family of venomous predators. The most recent classification organizes Asilidae into 14 subfamilies based on a comprehensive morphological phylogeny, but many of these have not been supported in a subsequent molecular study using traditional molecular markers. To address questions of monophyly in Asilidae, we leveraged the recently developed Diptera-wide UCE baitset to compile seven datasets comprising 151 robber flies and 146 - 2,508 loci, varying in the extent of missing data. We also studied the behavior of different nodal support metrics, as the non-parametric bootstrap is known to perform poorly with large genomic datasets. Our ML phylogeny was fully resolved and well-supported, but partially incongruent with the coalescent phylogeny. Further examination of the datasets suggested the possibility that GC bias had influenced gene tree inference and subsequent species tree analysis. The subfamilies Brachyrhopalinae, Dasypogoninae, Dioctriinae, Stenopogoninae, Tillobromatinae, Trigonomiminae, and Willistonininae were not recovered as monophyletic in either analysis, consistent with a previous molecular study. The inter-subfamily relationships are summarized as follows: Laphriinae and Dioctriinae (in part) are successively sister to the remaining subfamilies, which form two clades; the first consists of a grade of Stenopogoninae (in part), Willistonininae (in part), Bathypogoninae+Phellinae, Stichopogoninae, Leptogastrinae, Ommatiinae, and Asilinae; the second clade consists of a thoroughly paraphyletic assemblage of genera from Dioctriinae (in part), Trigonomiminae, Stenopogoninae (in part), Tillobromatinae, Brachyrhopalinae, and Dasypogoninae. We find that nodal support does not significantly vary with missing data. Furthermore, the bootstrap appears to overestimate nodal support, as has been reported from many recent studies. Gene concordance and site concordance factors seem to perform better, but may actually underestimate support. We instead recommend quartet concordance as a more appropriate estimator of nodal support. Our comprehensive phylogeny demonstrates that the higher classification of Asilidae is far from settled, and it will provide a much-needed foundation for a thorough revision of the subfamily classification.

AO_SCPLOWBSTRACTC_SCPLOWWhile DNA characters are increasingly used for phylogenetic inference, taxa delimitation and identification, their use for formal description of taxa (i.e. providing either a formal description or a diagnosis) remains scarce and inconsistent. The impediments are neither nomenclatural, nor conceptual, but rather methodological issues: lack of agreement of what DNA character should be provided, and lack of a suitable operational algorithm to identify such characters. Furthermore, the reluctance of using DNA data in taxonomy may also be due to the concerns of insufficient reliability of DNA characters as robustness of the DNA based diagnoses has never been thoroughly assessed. Removing these impediments will enhance integrity of systematics, and will enable efficient treatment of traditionally problematic cases, such as for example, cryptic species. We have developed a novel versatile and scalable algorithm MolD to recover diagnostic combinations of nucleotides (DNCs) for pre-defined groups of DNA sequences, corresponding to taxa. We applied MolD to four published monolocus datasets to examine 1) which type of DNA characters compilation allows for more robust diagnosis, and 2) how the robustness of DNA based diagnosis changes depending on the sampled fraction of taxons diversity. We demonstrate that the redundant DNCs, termed herein sDNCs, allow for higher robustness. Furthermore, we show that a reliable DNA-based diagnosis may be obtained when a rather small fraction of the entire data set is available. Based on our results we propose improvements to the existing practices of handling DNA data in taxonomic descriptions, and discuss a workflow of contemporary systematic study, where the integrative taxonomy part precedes the proposition of a DNA based diagnosis and the diagnosis itself can be efficiently used as a DNA barcode. Our analysis fills existing methodological gaps, thus setting stage for a wider use of the DNA data in taxa description.

Capturing phylogenetic signal from a massive radiation can be daunting. The superfamily Chalcidoidea is an excellent example of a hyperdiverse group that has remained recalcitrant to phylogenetic resolution. Chalcidoidea are mostly parasitoid wasps that until now included 27 families, 87 subfamilies and as many as 500,000 estimated species. We combined 1007 exons obtained with Anchored Hybrid Enrichment with 1048 Ultra-Conserved Elements (UCEs) for 433 taxa including all extant families, over 95% of all subfamilies and 356 genera chosen to represent the vast diversity of the superfamily. Going back and forth between molecular results and our collective morphological and biological knowledge, we detected insidious bias driven by the saturation of nucleotide data and highlighted morphological convergences. Our final results are based on a concatenated analysis of the least saturated exons and UCE data sets (2054 loci, 284,106 sites). Our analyses support a sister relationship with Mymarommatoidea. Seven of the previously recognized families were not monophyletic, so foundations for a new classification are discussed. Biology appears potentially more informative than morphology, as illustrated by the elucidation of a clade of plant gall associates and a clade of taxa with planidial first-instar larvae. The phylogeny suggests a shift from smaller soft-bodied wasps to larger and more heavily sclerotized wasps. Deep divergences in Chalcidoidea coincide with an increase in insect families in the fossil record, and an early shift to phytophagy corresponds with the beginning of the "Angiosperm Terrestrial Revolution". Our dating analyses suggest a Middle Jurassic origin of 174 Ma (167.3-180.5 Ma) and a crown age of 162.2 Ma (153.9-169.8 Ma) for Chalcidoidea. During the Cretaceous, Chalcidoidea underwent a rapid radiation in southern Gondwana with subsequent dispersals to the Northern Hemisphere. This scenario is discussed with regard to knowledge about host taxa of chalcid wasps, their fossil record, and Earths paleogeographic history.

1. Informative and consistent taxonomy above the species level is essential to communication about evolution, biodiversity, and conservation, and yet the practice of taxonomy is considered opaque and subjective by non-taxonomist scientists and the public alike. While various proposals have tried to make the basis for ranking and inclusiveness of taxa more transparent and objective, widespread adoption of these ideas has lagged. 2. Here, we present TaxonomR, an interactive online decision-support tool to evaluate alternative taxonomic classifications. This tool implements an approach that quantifies the criteria commonly used in taxonomic treatments and allows the user to interactively manipulate weightings for different criteria to compare scores for taxonomic groupings under those weights. 3. We use the butterfly taxon Argynnis to demonstrate how different weightings applied to common taxonomic criteria result in fundamentally different genus-level classifications that are predominantly used in different continents and geographic regions. These differences are objectively compared and quantified using TaxonomR to evaluate the kinds of criteria that have been emphasized in earlier classifications, and the nature of the support for current alternative taxonomic arrangements. 4. The main role of TaxonomR is to make taxonomic decisions transparent via an explicit prioritization scheme. TaxonomR is not a prescriptive application. Rather, it aims to be a tool for facilitating our understanding of alternative taxonomic classifications that can, in turn, potentially support global harmony in biodiversity assessments through evidence-based discussion and community-wide resolution of historically entrenched taxonomic tensions.

The ichneumonid subfamily Eucerotinae has been thought to be almost absent from the tropics, with the only known Afrotropical species found in Madagascar. We report the subfamily to be present in the mainland Afrotropics, and describe a new species, Euceros species 1 from Uganda and Cameroon (name not yet shown in preprint). The subfamily had likely not been observed in the mainland Afrotropics before due to low abundances and insufficient sampling. More Eucerotinae likely remain to be discovered in tropical Africa and Asia, although tropical America may genuinely have few eucerotine species. Much more extensive sampling will be needed before it is possible to make confident estimates of how eucerotine diversity is distributed globally.