Systematic Entomology

Arcellidae is a family of testate amoebae within Arcellinida (Amoebozoa), comprising three recognized genera: Arcella, Galeripora, and Antarcella. Although species in the family have been studied for nearly two centuries, many historically described taxa and major morphological groups remain unsampled at the molecular level. Here, we provide a comprehensive review of Arcellidae and generate new cytochrome c oxidase subunit I (COI) sequences for arcellid species from Canadian peatlands, focusing on tall-shelled Arcella historically classified in section Altae sensu Deflandre. COI phylogenetic analyses recover a strongly supported monophyletic clade corresponding to North American representatives of Altae, providing the first molecular corroboration of this morphologically defined group. Within this clade, we redescribe Arcella leidyana based on modern material from Eeyou Istchee (Quebec). We further describe Galeripora purdoni sp. nov. from a calcareous fen in eastern Ontario, representing a novel terrestrial lineage within the genus, and redescribe Galeripora artocrea, which we transfer to Arcella based on congruent molecular and morphological evidence. Phylogenomic analyses of Arcellidae isolates from the Protist 10,000 Genomes Project reveal an additional deep lineage basal to Arcella and Galeripora. Together, these results highlight hidden diversity and demonstrate the importance of integrative approaches for resolving arcellid systematics and refining its classification.

Webspinners (Insecta: Embioptera) are an unusual insect order that are known for their subsocial behavior and prolific silk-production. Due to their unique foreleg silk glands, and spider-like ability to produce silk throughout their entire life cycle, webspinners are hypothesized to have evolved silk independently from other arthropod lineages. To date, there are no reference-quality genomes available for the order, preventing the study of their silk gene origination and diversification. Here, we assembled PacBio HiFi reference genomes and characterized the silk genes present in two webspinner species, Aposthonia ceylonica and Oligotoma nigra. The genomes reveal multiple full-length copies of the primary Embioptera silk gene, e-fibroin, that have undergone both ancestral and recent gene duplications within the group. For both species, all e-fibroin paralogs show the presence of complex repeat units consisting of multiple exons and introns that are remarkably homogenized across each gene. We also used CT-scanning of the internal silk glands to provide details concerning the localization of silk production in foreleg tarsi, and interspecific morphology. Article summaryThis study introduces the first high-quality genomes for webspinners, enabling new research on silk for evolutionary biologists and materials scientists alike. The authors sequenced two embiopteran species, Aposthonia ceylonica and Oligotoma nigra, to compare silk genes and gland structure using micro-computed tomography, an imaging method that shows internal anatomy in detail. They found multiple copies of the primary silk gene in both species that likely arose from multiple duplication events at different evolutionary times. These silk genes exhibit unusual gene structure with hierarchically organized repeat units that are highly homogenized within a gene. The findings show that silk genes have a complex evolutionary history in webspinners and provide a foundation for studying silk diversity within the order, and in the broader context of insect silk.

Catenulids are free-living flatworms, common in eutrophic freshwaters such as ponds, ditches, or peatbogs, with most of the diversity described from tropical regions to date. Although the majority of the species have been described from warmer climates, most molecular studies have been done on specimens from temperate zones in Europe. We addressed this gap by sampling for exotic species in localities available in a temperate climate. In this study, we investigated catenulid diversity in the greenhouses at the University of Warsaw Botanic Garden and recorded two species known only from tropical areas (Stenostomum paraguayense and Suomina evelinae) and one exotic species recorded previously from a greenhouse in Poland (Stenostomum corderoi). Additionally, in the latter species, we provide evidence for environmentally induced coloration of sensory pits, which has not been reported thus far. We placed the collected species on a phylogeny using barcoding of 18S, 28S, and COI genes and retrieved paraphyly of the family Catenulidae, with S. evelinae forming a sister group to the genus Paracatenula, and hence we propose a revision of its systematic position. In total, we recorded six species, including three with a wide cosmopolitan distribution (C. turgida, S. grande and S. tuberculosum), and provided sequences for five of them, three of which had no previous molecular records (S. paraguayense, S. evelinae and S. corderoi). Thus, we confirm that greenhouses represent an important source of exotic species for taxonomic work on microscopic invertebrates.

Polytypic species with large ranges may harbor unrecognized diversity because taxonomy ranks populations differing subtly in plumage as subspecies. The Ruddy Foliage-gleaner (Clibanornis rubiginosus) exemplifies this problem. It ranges from Mexico to Brazil, with 15 subspecies, and forms a non-monophyletic complex with two congeners, yet its songs had not been compared. We measured ten spectral and temporal variables on 104 recordings covering 14 of 15 subspecies. Bayesian linear mixed models showed three song groups: eight subspecies west of the Andes share a single-note song, whereas Amazonian and Guianan populations add a short introductory note and sing longer, lower-pitched songs. Within this group, watkinsorum sings the lowest-pitched and longest song and is phylogenetically closer to C. cinnamomeigula than to its Amazonian neighbors. The third group is C. cinnamomeigula alone, a white-eyed taxon in an otherwise dark-eyed group. Its high-pitched, vibrato song resembles none other in the genus. One-note and two-note songs differ in kind without intermediates, and every two-note taxon sequenced to date falls in one clade, so C. rubiginosus is paraphyletic. We recognize four species, C. rubiginosus sensu stricto, C. cinnamomeigula, C. watkinsorum, and C. obscurus. This raises Clibanornis from five species to eight and divides its only polytypic species.

Among Madagascar primates, the sportive lemurs (family Lepilemuridae) have seen their species diversity increase from eight in 2005 to 26 in 2009 mostly by applying the phylogenetic species concept to DNA barcode data. Despite the genus being speciose, only one case of sympatry is known from northern Madagascar, where two sportive lemur species described based on low mtDNA divergence, Lepilemur ankaranensis and Lepilemur milanoii, were found to co-occur at the center of their joint distribution range. Here, to clarify the taxonomy of these two species and examine their sympatry, we apply an integrative taxonomic framework to genomic and morphological data from 84 individuals of L. ankaranensis and L. milanoii, encompassing their entire distribution range and the forest of Analafiana, beyond their southernmost limit. Using clustering, multivariate, and isolation by distance analyses, we find no evidence of a sympatric zone and show that despite clear genetic differentiation between regions, the genomic and morphological diversity of the L. ankaranensis, L. milanoii-Analafiana group is clinal and explained by geographic distance. These results clarify that L. milanoii is a junior synonym of L. ankaranensis and that the Analafiana forest population belongs to L. ankaranensis, extending its distribution. It further implies that the 'sympatric' zone, the Andrafiamena forest, hosts conspecific individuals with slightly differentiated mtDNA backgrounds, rather than slightly differentiated sympatric species. Lastly, we re-evaluate the IUCN conservation metrics of L. ankaranensis, which continue to qualify as Endangered (EN) under the B1ab(i-v) criteria.

Motivation: The Interactive Tree of Life (iTOL) is widely used to display and annotate phylogenetic trees, but managing its format-sensitive annotation files impede reproducible high-throughput analyses. Among the maintained Python packages and versions evaluated, none combined template generation, taxonomic monophyly assessment and iTOL batch operations. Results: PyiTOL validates inputs, generates 31 iTOL template schemas (22 accepted by the live batch uploader), performs LCA-based monophyly classification with nested-monophyly detection, sampling-completeness states and polyphyletic subgroup decomposition, plus API upload and session replay. On a topology-constructed benchmark, all calls matched prespecified labels for 4,389 groups; on a 700-genome tree, binary mono/non-mono calls agreed with ETE4 for 409 genera; 17,294 GTDB R232 genera were processed in about 17 s. Availability and Implementation: PyiTOL 1.0.3 (Python [≥]3.10; Linux, macOS and Windows) is MIT-licensed at https://github.com/ZengZichao/PyiTOL and archived with test data at Zenodo (https://doi.org/10.5281/zenodo.22106806).

Biodiversity aggregators such as GBIF provide unprecedented access to global biodiversity data, yet their representativeness remains uneven across space and taxa. This study examined the spatial and taxonomic structure of global vascular plant data available on GBIF. Six filters were applied to the GBIF vascular plant dataset, resulting in the removal of 54% of all records. Together, the filters explained more than 90% of the identified spatial issues, with duplicate and missing coordinates accounting for most of the variation. A higher number of occurrence records was associated with a greater number of spatial issues. Record distributions became progressively more even at finer taxonomic levels, from orders to species. The time series of occurrences for species, genera, and families increased sharply after 1800 and continued to rise, with no apparent stabilisation. Of the 824 ecoregions covered, 73 accounted for 72% of all occurrence records. These ecoregions spanned all continents but were strongly concentrated in Europe, followed by North America and Oceania. The analyses reveal four key patterns: (1) data volume is positively associated with spatial issues; (2) a small number of taxa account for a large proportion of records, whereas many are represented by relatively few; (3) occurrence data aggregated by GBIF have increased continuously since 1800; and (4) record coverage remains highly uneven across the world's ecoregions. These results highlight the substantial contribution of biodiversity data aggregators to expanding access to biological information while demonstrating the persistent spatial and taxonomic biases that shape their contents. Such biases should be explicitly considered when assessing data completeness and quality and when using aggregated occurrence records to infer global biodiversity patterns.

Reconstructing ancestral morphologies on a phylogenetic tree is a central task in evolutionary morphometrics. Established reconstruction methods, including multivariate Brownian-motion approaches, rely on linear assumptions and do not directly model the correlations between landmarks within a shape, which can oversimplify the reconstructed morphology. The DICAROS method (Diffeomorphic Independent Contrasts for Ancestral Reconstruction of Shapes; Severinsen et al., 2026) instead fuses sibling shapes along branches with large-deformation diffeomorphic (LDDMM) landmark dynamics that model these correlations, so that ancestors remain on the shape manifold. DICAROS was shown to outperform ordinary least-squares, Brownian-motion, and penalized-likelihood reconstruction, particularly on non-symmetric trees. The dicaros package repackages that pipeline as a documented, pip-installable tool that runs on arbitrary landmark datasets from a single command. It handles 2D and 3D landmarks, Newick and NEXUS trees, a choice of Euclidean or Frechet species means, optional anchor-based alignment, and tips backed by a single specimen, and it returns the reconstructed shapes for all nodes together with the tree relabelled at its internal nodes. We demonstrate dicaros on two new datasets: a 2D leaf dataset (217 species) and a 3D guenon skull dataset (22 species).

Complex biomechanical innovations are often treated as discrete evolutionary breakthroughs, yet their diversification within large radiations remains poorly understood. Beetle leg joints provide a striking example: some weevils possess screw-like coxa-trochanteral articulations in which rotation and axial displacement are mechanically coupled, resembling engineered screw-and-nut mechanisms. Whether these joints represent isolated mechanical extremes, discrete adaptive types or part of a broader continuum of phenotypic variation has remained unknown. Here we combine synchrotron X-ray microtomography, landmark-free atlas-based morphometrics, quantitative functional morphology and phylogenetic comparative analyses to examine the mesocoxa-trochanteral joint in 68 specimens representing seven sampled family-level groups across early-diverging and derived weevil lineages. We show that screw joint evolution combines continuous variation in trochanteral shape with a restricted set of mechanically plausible joint-character combinations, rather than forming sharply separated morphological classes. True screw-and-nut joints are not confined to a distinct region of morphospace, indicating that overall form and mechanical configuration are not necessarily coupled. The occurrence of this configuration in the early diverging Caridae shows that it is not restricted to more derived families. Three-dimensional helix fitting revealed a mosaic geometry, with winding angle showing the clearest relationship with overall shape and joint architecture, whereas axial pitch varied largely independently of shape, size and lineage. Together, these patterns show that screw joint components diversified with different degrees of evolutionary integration. These results recast the weevil screw joint from a singular biomechanical curiosity into a diversified evolutionary system. They suggest that complex functional structures can evolve through the gradual recombination and differential persistence of structurally constrained and evolutionary flexible components, rather than through a single shift from simple to fully specialized designs.

Background: Reproducible taxonomic collapsing and geological-timescale annotation of time-calibrated phylogenetic trees in R often require coordination among several packages and repeated code for label parsing, clade validation, plotting, and export. Workflow-managed analyses additionally benefit from non-interactive configuration, predictable diagnostics, and machine-readable exit status. Results: We present Rclade, an R package that consolidates the multi-package coordination required for taxonomic collapsing into a streamlined, single-function interface. Rclade provides (1) custom ggproto objects (GeomPolygonStraight/GeomSegmentStraight) that bypass coord_munch() interpolation to achieve straight-edge rendering of collapsed triangles in circular layouts; (2) automatic detection and parsing of four taxonomic-label formats (GTDB, Silva, NCBI, embedded) plus user-supplied custom regex, with explicit input-validation contracts and parsing-accuracy evaluation on real and derived test sets; and (3) workflow embeddability through YAML configuration, library-mode APIs, and standard Unix exit codes. Benchmarks on synthetic and real datasets (200-10,000 synthetic tips and real reference trees up to 10,122 tips; 5 replicates at every scale under a unified fully rendered measurement protocol) show that the full-pipeline overhead is modest for interactive use (median {approx}0.87 s in-session rendering and {approx}8.4 s process-level wall-clock at 10,000 tips). Conclusions: Rclade is a convenience layer over the ggtree/deeptime ecosystem that reduces boilerplate while adding targeted technical improvements for circular-layout rendering and format heterogeneity management.

Sinia rhodoleuca, the sole species of the monotypic genus Sinia (Ochnaceae), was previously transferred to Sauvagesia based mainly on morphological similarities. However, its phylogenetic position has remained unresolved because molecular data for the species were unavailable. Here, we generated genomic data for Sinia rhodoleuca and reconstructed its phylogenetic position within Sauvagesieae. Our phylogenomic analyses consistently recovered Sinia rhodoleuca as sister to Indosinia, whereas the Neotropical Sauvagesia formed a distantly related lineage, rendering Sauvagesia broadly circumscribed non-monophyletic. Comparative morphological evidence further supports the close relationship between Sinia and Indosinia, particularly in their closely parallel secondary veins, lacerate stipules, and prominent petaloid staminodes, while differences in floral characters support their recognition as distinct genera. We therefore reinstate Sinia as a distinct genus and provide a revised taxonomic treatment of Sinia rhodoleuca. Our study demonstrates how phylogenomic evidence can resolve long-standing taxonomic uncertainties and reveal evolutionary relationships obscured by morphological similarity.

Deep learning tools are increasingly used today, particularly in medical segmentation. A gap nonetheless remains in automating segmentation for insects. This work addresses the following question: can a generalist segmentation model, trained on several phylogenetically related orthopteran species, reliably automate head tissue segmentation from micro-CT images? To answer this, we used nnU-Net, a self-configuring 3D deep learning segmentation framework originally developed for medical imaging, whose core function, learning to recognize tissues of interest, applies directly to this context. Six anatomical classes were automated, comparing two training strategies: sequential fine-tuning, which adds species one at a time under the assumption that progressive learning would strengthen predictive power, and from-scratch training, in which the model learns the entire dataset simultaneously. The fine-tuning model (ModelB) reached a Dice coefficient (a measure of overlap between automated segmentation and manual ground truth, ranging from 0 to 1) of 0.7715, compared to 0.7664 for the from-scratch model (ModelC). Although both models produced accurate automated segmentations, no significant difference was found between the two training strategies (paired Wilcoxon test, n = 24, p = 0.243). Despite a dataset limited to 20 individuals and the absence of one method clearly outperforming the other, the models remain usable across the three species studied (Gryllus bimaculatus, Loxoblemmus equestris, L. doenitzi), including in the presence of pronounced sexual dimorphism. It reduces a 20 hour segmentation task to under a minute.

Forecasting species population dynamics is a central challenge in computational ecology, yet existing approaches rarely combine flexible nonlinear modelling, support for count-based ecological data, and systematic uncertainty quantification within a single, scalable framework. Here we introduce reserBUGS, an open-source Python framework for ecological forecasting based on reservoir computing, a recurrent neural network architecture in which only a simple readout layer is trained while a fixed high-dimensional dynamical system encodes temporal memory and nonlinear dependencies. reserBUGS integrates species abundance time series with environmental covariates retrieved automatically from global climate products, generates probabilistic ensemble forecasts, and provides tools for forecast evaluation and reliability assessment. We evaluated reserBUGS using insect abundance time series from available biodiversity monitoring datasets, comparing its performance against seven statistical and machine-learning baselines over one- to five-year forecast horizons. Reservoir-based models consistently outperformed alternatives in both predicting future abundance and capturing forecast uncertainty, with environmental predictors increasing the proportion of stable forecasts and contributing additional predictive value beyond historical abundance dynamics alone, particularly at 3-4-year forecast horizons. Probabilistic forecasts further enabled the identification of conditions associated with reduced predictive skill, providing a practical basis for communicating forecast confidence to end users. While default configurations already achieved competitive performance across a taxonomically and geographically diverse set of time series, hyperparameter optimisation revealed substantial room for performance gains through series-specific tuning. reserBUGS offers a computationally efficient and extensible framework for ecological forecasting that is well suited to the short, heterogeneous time series typical of biodiversity monitoring programmes. Its combination of flexible nonlinear modelling, probabilistic uncertainty quantification, and automated environmental data integration addresses key practical barriers to the adoption of modern forecasting methods in conservation and ecological research.

Three new species of sun orchid (Thelymitra) endemic to Aotearoa New Zealand are here described. These are T. palustris, T. scabrifolia and T. semaphora. The morphological distinctiveness of these three species has been acknowledged for decades; however, their taxonomic status has remained unresolved. Evidence from existing karyological data, recently generated DNA sequence data (LFY and ycf1) and morphological studies from historical and fresh collections are used here to support their formal description. Both, T. palustris and T. semaphora are restricted to wet habitats north of Auckland (North Island). Thelymitra scabrifolia inhabits mostly scrub, and it has a similar northern North Island distribution, but is has been found also in Manawat[a]whi / Three Kings Islands and historically in Otago (South Island). All three species are polyploids and are of conservation concern.

Orchid bees (Euglossini, Apidae) are Neotropical insects whose species-level identification can depend on minute morphological characters, some difficult to see or analyze. In such cases, DNA barcoding may facilitate identification by comparing standardized DNA sequences with reference libraries. The mitochondrial cytochrome c oxidase I (COI) marker widely used in animals does not, however, provide uniform species-level resolution across bee lineages. We developed an adaptive-length nuclear ribosomal DNA (nrDNA) barcoding framework based on overlapping Nanopore-sequenced markers spanning approximately 500 to 5500 bp for 114 Euglossini species. By matching barcode length to specimen quality, material with varied preservation histories was processed within a single analysis. Leave-k-out validation with IDTAXA achieved more than 96% identification success for two longer barcodes, while performance was lower for the shortest. Combining barcode lengths within one reference library maintained high identification success, and confidence filtering reduced overclassification when species were absent from the reference library. For orchid bees, this framework permits affordable high-throughput identification and supports targeted taxonomic verification and revision. Combining adaptive barcode lengths in one analytical framework offers a general design principle for long-read reference-library construction. Its performance must now be tested in other groups.

Dense semilandmarks describe 3D surfaces with hundreds to thousands of points, and sliding them by bending energy or Procrustes distance is a near-universal default. Three questions remain open: does dense sampling add shape beyond fixed landmarks, how many points are needed, and does sliding help or harm? Real specimens cannot answer them: the true correspondence is unknown. We tested two workflows, ALPACA (single-template registration) and DeCAL (landmark-anchored correspondence), on 496 mouse skulls at 250-1,000 points, with and without sliding, scored by surface reconstruction. We repeated it on 500 synthetic skulls with exact correspondence, measuring each point's distance to its true homologue. Dense semilandmarks lowered error for almost every specimen; the fixed landmarks added little but supplied anchoring the semilandmarks could not, and the anchored method was more accurate. The benefit saturated near 250 points for ALPACA but kept improving to 1,000 for DeCAL. Procrustes-distance sliding harmed every configuration; bending-energy sliding helped only a poor, landmark-free correspondence, vanishing once anatomical anchors spanned the form. Match the sliding decision to the correspondence in hand: relax a poor one, leave a good one alone, never slide toward the mean. Known-correspondence specimens offer a general test of landmarking and sliding against ground truth.

FigTree is a long-standing phylogenetic tree viewer, but its GUI-centered workflow does not itself provide a versioned, batch-replayable record of styling operations. We present FigTreeKit, a Python package that serializes a supported subset of FigTree 1.4.4 annotations (!hilight, !color, and !font), audits taxonomy mappings before topology-gated clade collapse, retains selected BEAST-style metadata in the tested fixtures, and invokes a patched FigTree renderer for headless PNG, PDF, and SVG output. Across 60 independently generated balanced trees with 50-10,000 taxa (10 trees per size, each timed 10 times as technical replicates), the tree-level log-log slope of export time was 0.96 (95% confidence interval [CI], 0.91-1.01), which is compatible with approximately linear scaling over the tested range but does not prove it. The 189,801-taxon GTDB R232 bacterial reference tree was parsed and exported as a large-data scalability demonstration. On the 10,122-taxon GTDB R232 archaeal reference tree, the scripted workflow assessed 179 order-level groups; 142 multi-tip groups produced non-trivial collapses, whereas 37 singleton groups did not alter the display. The software is accompanied by 796 passing tests, a golden conformance corpus that includes acceptance tests against the bundled FigTree JAR, deterministic scenario-based topology checks, and an overall statement coverage of 81%, reported as a descriptive engineering metric. FigTreeKit is released under the GPL-2.0-or-later license as the figtreekit package on PyPI, with source code, documentation, and benchmark data archived on Zenodo.

Recent technological advances allow for the large-scale acquisition of genetic and morphological data: high-throughput sequencing has transformed the field of genomics while synchrotron X-ray microtomography enables rapid, noninvasive 3D imaging. However, integrating these approaches for the same specimens is challenging because X-rays can fragment DNA, and DNA extraction damages internal morphology, particularly relevant for small bodied organisms, such as insects. We systematically tested multiple extraction protocols and irradiation conditions across three model insect species. We irradiated more than 1,000 specimens under varying conditions and tested DNA quality through DNA barcoding and UCE sequencing. Our results demonstrate that high-quality DNA and high-resolution tomograms can be obtained from the same individuals, provided that the parameters are carefully optimized and rapid SR-CT scanning precedes DNA extraction. In this respect, our findings establish practical guidelines for combining genomics and phenomics, paving the way for comprehensive integrative digitization of biodiversity.

Citizen science observations are abundant, but conservation requires turning uneven records into reliable predictions and directing new surveys to where information is missing. We developed a biodiversity platform for Japan that is updated monthly and integrates 2.32 million records to predict 8,297 species across seven taxonomic groups. Shared representation models outperformed species-specific models in four groups and extended predictions to species with few records. Five independent datasets, including structured monitoring, environmental DNA and complete forest inventories, confirmed that the models ranked observed species and occupied sites above alternatives, with median AUCs of 0.724 to 0.894 across sites and 0.650 to 0.841 across species. For any user-selected area, the platform returns candidate species, distribution predictions, a biodiversity map corrected for uneven observation effort, a conservation priority map for native species and a map recommending where to survey next. This map highlights places where species with few records are predicted to occur despite limited sampling. Independent observations showed that areas ranked highly by this predicted potential contained many such species, indicating that model predictions can help direct surveys toward knowledge gaps. New observations are incorporated into monthly updates, creating a national feedback system connecting citizen science, local conservation decisions and future surveys.

Resolving deep phylogenetic relationships requires integrating multiple lines of evidence, as distinct evolutionary forces shape signals from different genomic markers. Here, we investigate the systematics of the controversial APPD lineage (Anomiidae, Placunidae, Plicatulidae, and, by inference, Dimyidae) within Pectinida sensu lato using phylogenomic, comparative genomic, transcriptomic, proteomic, and morphological approaches. Our analyses consistently recover APPD as a monophyletic lineage sister to Limida and Pectinoidea, divergent at [~]428 Mya. With three novel high-quality genomes, extensive progressive chromosomal fusions demonstrate a reduction in chromosome number of the APPD lineage (6-13), compared with an ancestral 20 molluscan linkage groups (MLGs). Accompanied by extensive intrachromosomal gene-order scrambling, we identify one functional centromere in Placuna vitream flanked by two vestigial centromeric remnants on a single chromosome, providing a potential resource for investigating centromere inactivation and neocentromere formation. Mitochondrial genomes of APPD lineage exhibit unprecedented plasticity in translational decoding: Pododesmus employs the invertebrate mitochondrial code; Heteranomia employs +1 translational frameshifting to bypass in-frame TAG codons, whereas in Anomia, Enigmonia, Placuna, and Plicatulidae, TAA is reassigned to tyrosine and confirmed by proteomic evidence, which supports mitochondrial frameshifting in APPD lineage and defines a novel translation table for bivalves. Integrating phylogenetic distinctiveness, deep divergence, extreme karyotypic restructuring, unique mitochondrial features, and morphological diagnosability, we elevate the APPD lineage into Anomiida ord. nov. This revision resolves long-standing uncertainties for Pectinida sensu stricto and Limida, and establishes the APPD lineage as a valuable system for investigating chromosome fusion, centromere evolution, codon reassignment, and translational recoding. ClassificationBiological Sciences; Evolution SIGNIFICANCE STATEMENTWe have re-examined a controversial group of marine bivalves (Anomiidae, Placunidae, Plicatulidae, and Dimyidae). Our integrative approach shows that these animals split from scallops and their relatives more than 428 million years ago and have undergone drastic chromosomal fusions that reduced their chromosome number from 20 to as few as 6. Additionally, some species evolved unusual ways of reading their mitochondrial genetic code, either reassigning the stop codon to tyrosine or using +1 translational frameshifting to skip stop signals. The combination of deep evolutionary time and genomic divergence warrants recognizing them as a new order, Anomiida ord. nov. This work, as a case study, demonstrates how chromosome fusion and genetic code variation contribute to invertebrate diversity.