Systematic Entomology最新文献

As larger amounts of DNA sequence data become available, so does the need for heuristic metrics summarizing the quality of such datasets. This creates two seemingly conflicting outcomes for the phylogenomics community: so called ‘point-and-click’ algorithms make analysis of genomic data easier, but automation may perpetuate biases caused by uncritical reliance on algorithms. Here, based on nine ultraconserved element (UCE) datasets from arthropods, we demonstrate that relying solely on the Completeness metric—a common tool to report amounts of missing data (MD) and inform choices about filtering loci—underestimates the actual amount of non-randomly distributed MD and fails to prevent possible biases introduced by it. By only counting terminals sampled for each locus, Completeness overlooks the amount of MD in loci containing sequences that are truncated or gappy. Thus, datasets assessed for data quality only by this metric, and reported to be ‘complete’, can retain substantial MD concentrated in some terminals with extreme amounts of it, which may affect estimation of parameters often interpreted as biologically meaningful measures by phylogenetic algorithms (e.g., branch lengths). We demonstrate this by showing that MD could drive the generation of long branches and affect the support values of nodes containing taxa with high amounts of MD. Finally, we offer six recommendations authors can employ alongside or alternatively to Completeness, to keep the community standards of data quality strong.

Typhlocybinae is one of the most diverse groups of leafhoppers, constituting an important component of phytophagous insect diversity. The traditional tribal-level phylogenetic relationships within this subfamily remain contentious, with differing hypotheses implying distinct evolutionary histories. This study contributes to resolving these controversies using phylogenomics. We newly sequenced low-coverage whole genomes for 54 species spanning the six classic tribes of Typhlocybinae. From these data, we extracted thousands of universal single-copy orthologs (USCOs) and ultraconserved elements (UCEs). Robust tribal-level phylogenies were reconstructed using multiple dataset matrices (USCO50, USCO70, USCO90, USCO_fna, ClipKIT_USCO70, UCE_fna) and tree-building strategies, including partitioned maximum likelihood with homogeneous models, unpartitioned heterogeneous mixture models and the multi-species coalescent (MSC) model. A particular focus was placed on elucidating the complex taxonomic status between Zyginellini and Typhlocybini, integrating molecular results with morphological evidence. Our findings indicate that the choice of molecular marker type and modelling methods can influence the inferred tribal-level relationships. Data filtering improves tribal-level support. The final analyses reveal that Zyginellini is not monophyletic but is intermixed with Typhlocybini, although some Zyginellini lineages appear to have originated earlier than the Old World Typhlocybini. The other four tribes of Typhlocybinae are all monophyletic. The tribal-level phylogenetic relationship is: ((Zyginellini_Typhlocybini) + (Dikraneurini + Erythroneurini)) + (Alebrini + Empoascini). Furthermore, integrating wing venation morphology with previous molecular evidence, we propose the Eualebrina subtribe nov. of Typhlocybini (sensu lato). This study provides unprecedented genomic-scale data for Typhlocybinae and offers a framework to address similar phylogenetic challenges in other organisms.

DNA barcoding, the use of a standard DNA fragment for species identification, has emerged as a major field of biodiversity research. The effectiveness of this approach rests on the premise that much less variation exists within species than between them. While exceptions occur, this has been demonstrated in many animal taxa where the COI gene is effective in species discrimination. Sawflies are an exception to this pattern because DNA barcodes often fail to distinguish congeneric species. Using high-throughput single-molecule DNA sequencing to recover COI sequences from thousands of sawflies, we found that single individuals often possess multiple, seemingly functional, full-length DNA barcodes (i.e., unrecognizable as nuclear pseudogenes)—a phenomenon not documented at similar prevalence in any animal taxon. While the evolutionary causes of multiple variants require further investigation, our observation is remarkable as it violates the one-barcode-one-specimen assumption. The presence of multiple variants of barcodes within individuals does not jeopardize the concept, but it introduces a complexity for species inventories based on metabarcoding. They will overestimate the species count when barcode-based operational species units are used as species proxies. Similarly, DNA barcode reference libraries must consider how best to deal with the high frequency of multiple intra-individual variants.

The cicada tribe Platypleurini, characterized by a remarkably flattened body, is distributed mainly in the Afrotropical and Oriental regions with a few species also occurring in the eastern Palearctic Region. Prior phylogenetic analyses revealed polyphyly among Oriental genera, and phylogeny and phylogeographical patterns of related ‘sibling’ species remain unclear. Here we investigated the phylogenetic relationships of representative platypleurines and population differentiation of two Oriental species using molecular data combined with genomic data of their obligate endosymbionts Karelsulcia and Hodgkinia. We revealed that platypleurines and Karelsulcia exhibit congruent phylogenies at both the species and population levels, and that Karelsulcia has undergone continuous genomic erosion, manifested as varying degrees of pseudogenization. The phylogeny of Hodgkinia also reflects that of platypleurines, and its genomes underwent further splitting and expansion concomitant with the diversification of host cicadas. The initial divergence of Platypleurini and that of the major Afrotropical and Asian lineages were ca. 44.58 Ma and ca. 37.27 Ma, respectively, corresponding to the initial collision between the Arabian Plate and the Eurasian Plate during the Late Eocene and Early Oligocene. We established Asianopleura gen. nov., reassigned Eopycna coelestia to Neoplatypleura and described E. autumnalis sp. nov. Both E. repanda and N. coelestia comb. nov. diverged into distinct phylogroups during the Late Miocene and Early Pliocene, indicating that contemporaneous geological activities and climatic oscillations acted as pivotal drivers in the diversification of these mountain specialists. This study yields novel insights into ecological diversification of Platypleurini and co-evolutionary dynamics between cicadas and associated endosymbionts.

The historical classification of dung beetles (subfamily Scarabaeinae) based on classical morphology has been repeatedly shown to be artificial due to widespread homoplasy. Previous attempts to revise, redefine and stabilize the classification within a molecular phylogenetic framework resulted in 101 genera treated as incertae sedis. Among these unplaced taxa are all genera endemic to Australia, New Guinea, New Caledonia and New Zealand. Here we examine tribal classifications among the subfamily Scarabaeinae based on ultraconserved elements (UCEs), with a targeted sampling aimed at examining systematic relationships of the Australasian endemic genera that, until now, have remained poorly supported. On the basis of these results, we reinstate a tribal name previously synonymous with Deltochilini. Mentophilini Lacordaire stat. rest. and sensu n. includes 31 genera endemic to Australasia. Additionally, a new tribe is proposed for a distinct lineage that is supported by both morphology and phylogeny. Boletoscapterini trib. n. consists of a single Australian genus, Boletoscapter Matthews. We discuss the validity of the tribe Epilissini and recommend not recognizing the tribe until future revisionary work redefines the distinct clades. Following these taxonomic changes, 23 tribes within Scarabaeinae are recognized as valid and 47 scarabaeine genera remain unplaced.

The majority of moths are terrestrial throughout their life cycle. An exception is the subfamily Acentropinae (Lepidoptera: Crambidae), a diverse group of aquatic moths comprising nearly 700 species. Acentropinae represent the largest lineage of moths with at least one life stage adapted to an aquatic environment. Despite their unique biology, their evolutionary relationships remain poorly understood. The most comprehensive study on acentropine phylogeny is over 70 years old and predates the use of modern analytical methods. Few studies since then have attempted to reconstruct the phylogeny of Acentropinae, and those that did are limited in taxon and character/gene sampling. We tested hypotheses of acentropine relationships by reconstructing a genus-level phylogeny based on 360 loci and 22 genera of Acentropinae. Our phylogeny provides strong support for the monophyly of Acentropinae, a basal division between two tribes, Argyractini Lange and Acentropini Stephens. The tribe Nymphulini Duponchel syn. nov. is found to be a junior synonym of Acentropini. Within this tribe, we find support for some previously defined family-group clades (the ‘terrestrial’ clade, the ‘flowing water’ clade, and the Aulacodes clade), and we discuss novel morphological features that are potential synapomorphies of these clades. Our study provides a foundation for future research on the ecology and evolution of aquatic Lepidoptera.

The zoobank LSID for this publication is: urn:lsid:zoobank.org:pub:B95DE9C4-E516-4D20-978F-A1B3C4C45BA0.

Omethidae are a small family of soft-bodied beetles, which are classified in the superfamily Elateroidea. The family is composed of 13 extant and one fossil genera and 69 species described from the Americas and East Asia. Members of Omethidae have a particularly heterogeneous morphology, with current members originally described in Cantharidae, Drilidae, Lampyridae, Telegeusidae and Phengodidae. Morphological and molecular-based phylogenetic hypotheses are still highly divergent, with morphology-based phylogenies recovering Telegeusinae related to Phengodidae, and multigene phylogenies recovering Telegeusinae as closely related to Omethidae. We implemented a genome skimming sequencing approach to produce genomic data for representatives of all Omethidae subfamilies. The resulting dataset is the first phylogenomic study produced for the family. Our results corroborated previous multigene phylogenies, and recovered Omethidae sister to Artematopodidae, and Telegeusinae as a subfamily of Omethidae, and also rejected the relationships of Telegeusinae with Phengodidae. In contrast to previous molecular-based hypotheses, Driloniinae were recovered as a sister group to the remaining Omethidae, rendering the following topology: (Artematopodidae + (Driloniinae + (Telegeusinae + (Omethinae + Matheteinae)))). We reviewed the family and presented an updated diagnosis for Omethidae and its subfamilies, as well as identification keys for the subfamilies and genera, and a checklist for all described extant and extinct species.

Aotearoa New Zealand is home to a remarkable number of endemic taxa, some of which have existed on the archipelago since before the breakup of Gondwana. The mite harvesters (suborder Cyphophthalmi), tiny non-spider arachnids that dwell in forest leaf litter and caves, are one such group. The mite harvester family Pettalidae Shear exhibits a classic Gondwanan distribution with notable diversity in Aotearoa, which is home to three pettalid genera. Our research focuses on the evolution of the most widespread and speciose Aotearoa pettalid genus, Rakaia Hirst, 1926. Through phylogenetic analysis, we provide a window into patterns of ancient diversification and infer historical biogeographic trends. We generated subgenomic data through target enrichment of ultraconserved elements (UCEs) using an Arachnida-specific probe set; the 50% and 75% taxon-occupancy matrix retrieved 848 and 585 loci, respectively. In addition to generating the first fully resolved phylogeny of Rakaia, we performed a molecular clock analysis and tested for shifts in diversification rates in order to explore the effect of geological events such as the Oligocene Drowning, the uplift of Kā Tiritiri o te Moana, and forest habitat contraction and fragmentation during the Last Glacial Maximum.

The family Gerridae, commonly known as water striders, are true bugs (Hemiptera, Heteroptera) that skate on the surface of waterbodies ranging from small streams to large rivers, ponds, lakes and even the open ocean. Eight extant subfamilies and eight tribes are traditionally recognized in this family. Furthermore, Microveliinae and Haloveliinae (traditionally in Veliidae) have also been classified as Gerridae by some authors lately. Here, we used a low-coverage shotgun sequencing to infer the phylogenetic relationships of Gerridae, showing new insights into the evolutionary history and taxonomic status of this taxon. Our study represents the first molecular analysis that includes representatives of all subfamilies and tribes. Nineteen specimens analysed were from museum collections and over 25 years old. Maximum-likelihood and Bayesian inference analyses support the monophyly of all subfamilies except Gerrinae, which is paraphyletic. Our analyses further revealed the non-monophyly of Gerrini, Metrobatini and Trepobatini, as well as for the genera Aquarius Schellenberg and Tenagogonus Stål (both Gerrinae). A molecular clock analysis showed that Gerridae originated during the mid-Cretaceous, with most subfamilies diversifying during the Late Cretaceous or early Paleogene. The results highlight issues with the current classification of Gerridae and the need for a careful taxonomic review of some taxa of this family.