The radiation of Hymenoptera illuminated by Bayesian inferences from the fossil record

Determining when lineages originated provides fundamental insights into the timing and pace of their diversification, improving our understanding of transformative paleoevents such as the Angiosperm Terrestrial Revolution (ATR)1 and Mid-Mesozoic Parasitoid Revolution (MMPR).2 As the MMPR overlaps with the ATR, improved age estimates help to disentangle the dynamics and temporal succession of these events that shaped modern ecosystems. Hymenoptera (ants, bees, and wasps) played an important role in the MMPR and ATR through their parasitoid and pollinating lineages. Parasitoids impact trophic networks, whereas pollinators interact with flowering plants.3,4 However, our understanding of Hymenoptera diversification remains limited by a lack of fossil-based studies and uncertainties in phylogenetic reconstructions. Combining fossil occurrences and macroevolutionary models, we estimated the origin and diversification of Hymenoptera lineages, considering changes in preservation over time and across taxa.5,6,7 Our results indicate that Hymenoptera diversification is multifaceted and lineage-specific. Sawflies diversified during the Paleozoic and Mesozoic in four episodes (middle Permian, Late Triassic to Middle Jurassic, Early Cretaceous, and the beginning of the Cenozoic) and experienced three extinction episodes (Middle Triassic, Late Jurassic, and mid-Cretaceous). The superfamily Xyeloidea originated during the middle Permian. Apocrita and parasitoid superfamilies emerged during the Early to Middle Triassic, diversified during the Late Jurassic and Early Cretaceous, and declined during the Late Cretaceous. We demonstrate that Hymenoptera experienced successive replacements during the MMPR-likely beginning in the Triassic-and synchronously with changes in floral assemblages of the ATR. We conclude with future directions to refine dating estimates from the fossil record.

What is Fragilaria koensabbei and does it matter what it is called? (Meta)barcoding and the science of taxonomy

Commentary is provided on the use of barcoding and metabarcoding in diatom studies and its broader relevance to the principles of taxonomy. The claims that taxonomy, however it is performed, is time-consuming and that it requires extensive expertise, due to a constantly evolving taxonomy, are questioned as good, even useful, criteria by which to judge a science.

MANGF: a reference library of DNA barcodes for Mantodea from French Guiana (Insecta, Dictyoptera)

Background

Mantodea plays a special role in the food chain as a group charismatic generalist predators. They regulate invertebrate populations while themselves being prey for many larger animals such as reptiles and birds. The present study focuses on Fench Guiana where about 78 species are known within eight families. This diversity represents a challenge for specimen identification.

New information

The MANGF project aims at developing a DNA metabarcoding approach to facilitate and enhance the monitoring of mantises as indicators in ecological studies. As a first step towards that goal, we assembled a library of DNA barcodes using the standard genetic marker for animals, i.e. a portion of the COI mitochondrial gene. In the present contribution, we release a library including 425 records representing 68 species in eight different families. Species were identified by expert taxonomists and each record is linked to a voucher specimen to enable future morphological examination. We also highlight and briefly discuss cases of low interspecific divergences, as well as cases of high intraspecific divergences that might represent cases of overlooked or cryptic diversity.

New frontiers in dinosaur exploration

Two hundred years after the naming of the first dinosaur, taxonomic studies remain an important component of dinosaur research. Around 50 new dinosaurs are named each year and are discovered from across the globe. The rate of new dinosaur discovery shows no signs of slowing, but not all geographical areas and temporal windows have been equally investigated. The potential for new dinosaur discoveries in India and Africa seems particularly high, while the Carnian, when dinosaurs probably originated, and the Middle Jurassic, when the major clades diversified, offer the best opportunities to make discoveries that will fundamentally change our understanding of dinosaur evolution. A major challenge to the discovery of new dinosaurs is funding. Frontier fieldwork is sometimes viewed as too risky to fund, while basic taxonomic work is considered to lack impact. As a consequence, we risk an 'extinction of experience', where researchers have limited training in the basic field- and specimen-based research that underpins our discipline. Going forward, new remote sensing techniques may help to find prospective areas, while three-dimensional scanning apps on smartphones will allow us to quickly record field data. Artificial intelligence is likely to be used increasingly for computed tomography segmentation and identification of problematic fossils.

Extracting specimen label data rapidly with a smartphone-a great help for simple digitization in taxonomy and collection management

We provide short tutorials in how to read out specimen label data from type- as well as handwritten labels in a rapid and easy way with a mobile phone. We apply them in general, but test them in particular for insect specimen labels, which are generally quite small. We provide alterative procedure instructions for Android and Apple based environments, as well as protocols for single and bulk scans. We expect that this way of data capture will be of great help for a simple digitization in taxonomy and collection management, independent from large industrial digitization pipelines. By omitting the step of taking/maintaining images of the labels, this approach is more rapid, cheaper, and environmentally more sustainable because no storage with carbon footprint is required for label images. We see the biggest advantage of this protocol in the use of readily available commercial devices, which are easy to handle, as they are used on a daily basis and can be replaced at relatively low cost when they come into (informatic) age, which is also a matter of cyber security.

Integrative taxonomy in helminth analysis: protocols and limitations in the twenty-first century

The term integrative taxonomy was coined in 2005 for the identification of microorganisms using morphological, molecular, pathological and ecological components. Since then, more than 200 scientific articles have been published using this term in the helminthology field in different geographical regions of the world, leading to accurate identifications of specimens and expanding the known biodiversity by describing novel species. Importantly, the responsible use of this approach has led to balanced results in which molecular data do not overshadow morphological, pathological or ecological information. By having different perspectives, new taxonomic situations have arrived including the definition of cryptic diversity, species complex and genotypes. In the present work, we present the main procedures and principles for conducting an integrative taxonomy study of parasitic helminth including collection and preservation of specimens, fixation and staining of worms for light microscopy and scanning electron microscopy, and histopathological, ecological and DNA analysis. This guide is aimed at researchers in their endeavor to analyze helminth parasites collected from wild or domestic animals with examples provided, but the protocols presented herein may be extrapolated for the analysis of helminths collected from other hosts (e.g. human or fish). One important aspect is that the recommendations presented herein derive from the authors' experiences, which will hopefully be of use to the reader.

Delimiting Species-Prospects and Challenges for DNA Barcoding

Discovering, describing and cataloguing global species diversity remains a fundamental challenge both for biodiversity research and for the management and conservation of biodiversity. Among animals, the challenge is particularly acute within the arthropods, which comprise approximately 85% of all described animals, with approximately 1 million described species. The true number of arthropod species is estimated to be in excess of 10 million species. This estimate is likely to be revised upward in the light of global DNA barcode sequencing initiatives that are cataloguing unprecedented levels of cryptic or overlooked diversity. The scale of diversity that is being recovered with barcode sequencing places further strain on a taxonomic system confronted by ever-limited global taxonomic capacity to verify and describe new species. It is predicted that the number of novel operational taxonomic units delimited by barcode sequencing is likely to eclipse the number of species described by Linnean taxonomy by as early as 2029. Unless addressed, this may see an increasing proportion of arthropod species falling outside of protective legislative frameworks as a consequence of their lack of formal description. Confronted with this challenge, there is increasing, but controversial, acceptance of species delimitation and species description based on barcode sequence clustering thresholds. In response to the evolving controversy surrounding this issue, it is both timely and important to identify and clarify prospects and challenges for DNA barcoding, with a specific focus on species delimitation to address important shortfalls and impediments in biodiversity research.

Unveiling high solifuge diversity: Review of the genus Pseudocleobis Pocock, 1900 (Ammotrechidae) in Chile with the description of nine new species

The Pseudocleobis from Chile are revised. Pseudocleobis morsicans (Gervais, 1849) and P. chilensis Roewer, 1934 are considered species inquerenda. Pseudocleobis andinus (Pocock, 1899) is removed from the Chilean fauna, and its previous records are considered misidentifications. Pseudocleobis alticola Pocock, 1900 is recorded from Chile for the first time. Nine new species are described, Pseudocleobis elongatus n. sp., P. atacamensis n. sp., P. puna n. sp., P. krausi n. sp., P. choros n. sp., P. lalackama n. sp., P. mumai n. sp., P. cekalovici n. sp. and P. escuadra n. sp. The species can be distinguished by the male chelicera morphology. We discuss the relationship of Chilean Pseudocleobis with other species of the genus, based on morphology. This work increases the number of known Chilean solifuge species by almost 70%, revealing the high degree of diversification of this group in Chile.

Identifying the Knowledge and Capacity Gaps in Southeast Asian Insect Conservation

Insects represent most of terrestrial animal biodiversity, and multiple reports suggest that their populations are declining globally due to anthropogenic impacts. Yet, a high proportion of insect species remain undescribed and limited data on their population dynamics hamper insect conservation efforts. This is particularly critical in tropical biodiversity hotspots such as Southeast Asia. To identify knowledge and capacity gaps in Southeast Asian insect conservation, we performed a quantitative review of insect occurrence records, studies for the region and global '#conservation' posts from Twitter. We found that occurrence records increased over time, and were dominated by butterflies. Overall, studies were largely focused on pest and vector groups, and insect conservation and ecology studies were lacking in many countries. Despite an increase in local authorships and funding sources over time, the majority of these were still located outside of Southeast Asia. In '#conservation' posts, insects were highly under-represented and insect-related content was biased towards popular groups such as bees and butterflies. We suggest potential solutions to address these gaps, such as integrative taxonomic approaches, and increasing regional collaborations and public engagements. Crucially, we stress the need for political will and funding to overcome the impediments towards insect conservation efforts in Southeast Asia.

LIFEPLAN: A worldwide biodiversity sampling design

As the technology for mass identification of species is advancing rapidly, we developed a field sampling method that takes advantage of the emerging possibilities of combining sensor-based data with automated high-throughput data processing. This article describes the five field sampling methods used by the LIFEPLAN project to collect biodiversity data in a systematic manner, all over the world. These methods are designed for use by anyone with basic biology or ecology knowledge from the higher education or university level. We present the selection and characteristics of international sampling locations for urban and natural sites, as well as the nested scale design in the Nordic countries and Madagascar. We describe the steps to collect sequences of animal images (.jpg) from infrared triggered camera traps, audio data (.WAV) of environment sounds from audio recorders, invertebrate samples in ethanol from Malaise traps for DNA metabarcoding, as well as both soil samples and 24-hour air samples obtained from cyclone samplers for fungal DNA metabarcoding. To ensure the usability and consistency of the data for future use, we pay particular attention to the metadata collected. In specifying the current sampling protocols, we note that technology will continue to improve and evolve. Hardware will also change within a short time period, with the advantage of improving the equipment used for collecting samples. Thus, we present examples of the samples collected by each current sampling method, to be used as a baseline or in comparison with different equipment models.

Mosquito species identification accuracy of early deployed algorithms in IDX, A vector identification tool

Mosquito-borne diseases continue to pose a great threat to global public health systems due to increased insecticide resistance and climate change. Accurate vector identification is crucial for effective control, yet it presents significant challenges. IDX - an automated computer vision-based device capable of capturing mosquito images and outputting mosquito species ID has been deployed globally resulting in algorithms currently capable of identifying 53 mosquito species. In this study, we evaluate deployed performance of the IDX mosquito species identification algorithms using data from partners in the Southeastern United States (SE US) and Papua New Guinea (PNG) in 2023 and 2024. This preliminary assessment indicates continued improvement of the IDX mosquito species identification algorithms over the study period for individual species as well as average regional accuracy with macro average recall improving from 55.3 % [Confidence Interval (CI) 48.9, 61.7] to 80.2 % [CI 77.3, 84.9] for SE US, and 84.1 % [CI 75.1, 93.1] to 93.6 % [CI 91.6, 95.6] for PNG using a CI of 90 %. This study underscores the importance of algorithm refinement and dataset expansion covering more species and regions to enhance identification systems thereby reducing the workload for human experts, addressing taxonomic expertise gaps, and improving vector control efforts.

Genus Bithynia: morphological classification to molecular identification

Snails of the genus Bithynia, whose primary habitat is slow-flowing ponds and ditches, serve as the first intermediate hosts of liver fluke. Currently, approximately 200 million individuals worldwide are at risk of liver fluke infection, yet questions still persist regarding the taxonomic identification of Bithynia genus, a crucial player in the transmission of this disease. Accurate taxonomic classification of the Bithynia genus could significantly enhance current understanding of the disease's transmission mechanisms. In this article we comprehensively review the extensive research conducted on Bithynia genus, spanning past inquiries up to the latest findings. The primary emphasis is placed on exploring the taxonomic identification of this genus within various technological settings. We then present a consolidated analysis of the morphological taxonomic identification methods, highlighting their strengths and limitations. We also introduce a novel perspective on the future direction of identification and classification efforts for the members of this genus, emphasizing the crucial role Bithynia plays in the epidemiological cycle of liver fluke transmission. We conclude by urging researchers to prioritize the significance of the members of this genus in the epidemiological cycle of liver fluke transmission and in control measures for disease dissemination, within the context of the vector organisms.

The diversity of ignorance and the ignorance of diversity: origins and implications of "shadow diversity" for conservation biology and extinction

Biodiversity shortfalls and taxonomic bias can lead to inaccurate assessment of conservation priorities. Previous literature has begun to explore practical reasons why some species are discovered sooner or are better researched than others. However, the deeper socio-cultural causes for undiscovered and neglected biodiversity, and the value of collectively analysing species at risk of unrecorded, or "dark", extinction, are yet to be fully examined. Here, we argue that a new label (we propose "shadow diversity") is needed to shift our perspective from biodiversity shortfalls to living, albeit unknown, species. We suggest this linguistic shift imparts intrinsic value to these species, beyond scientific gaze and cultural systems. We review research on undiscovered, undetected and hidden biodiversity in the fields of conservation biology, macroecology and genetics. Drawing on philosophy, geography, history and sociology, we demonstrate that a range of socio-cultural factors (funding, education and historical bias) combine with traditional, practical impediments to limit species discovery and detection. We propose using a spectrum of shadow diversity which enables a complex, non-binary and comprehensive approach to biodiversity unknowns. Shadow diversity holds exciting potential as a tool to increase awareness, appreciation and support for the conservation of traditionally less studied wildlife species and sites, from soil microbes to less charismatic habitat fragments. We advocate for a shift in how the conservation community and wider public see biodiversity and an increase in popular support for conserving a wider range of life forms. Most importantly, shadow diversity provides appropriate language and conceptual frameworks to discuss species absent from conservation assessment and at potential risk of dark extinction.

Performance of DNA metabarcoding, standard barcoding and morphological approaches in the identification of insect biodiversity

For two decades, DNA barcoding and, more recently, DNA metabarcoding have been used for molecular species identification and estimating biodiversity. Despite their growing use, few studies have systematically evaluated these methods. This study aims to evaluate the efficacy of barcoding methods in identifying species and estimating biodiversity, by assessing their consistency with traditional morphological identification and evaluating how assignment consistency is influenced by taxonomic group, sequence similarity thresholds and geographic distance. We first analysed 951 insect specimens across three taxonomic groups: butterflies, bumblebees and parasitic wasps, using both morphological taxonomy and single-specimen COI DNA barcoding. An additional 25,047 butterfly specimens were identified by COI DNA metabarcoding. Finally, we performed a systematic review of 99 studies to assess average consistency between insect species identity assigned via morphology and COI barcoding and to examine the distribution of research effort. Species assignment consistency was influenced by taxonomic group, sequence similarity thresholds and geographic distance. An average assignment consistency of 49% was found across taxonomic groups, with parasitic wasps displaying lower consistency due to taxonomic impediment. The number of missing matches doubled with a 100% sequence similarity threshold and COI intraspecific variation increased with geographic distance. Metabarcoding results aligned well with morphological biodiversity estimates and a strong positive correlation between sequence reads and species abundance was found. The systematic review revealed an 89% average consistency and also indicated taxonomic and geographic biases in research effort. Together, our findings demonstrate that while problems persist, barcoding approaches offer robust alternatives to traditional taxonomy for biodiversity assessment.

Checklists of extant harvestman (Arachnida: Opiliones) species for all the countries of the world

This study presents a comprehensive survey of the extant diversity of harvestmen (Arachnida: Opiliones), a pivotal taxon for biogeography and conservation studies, across Earth's geopolitical entities (here treated as "countries"). The rationale for recognizing more than 200 of these countries lato sensu worldwide is provided. The four most diverse of these countries are here further subdivided in states/provinces resulting in over 300 controlled vocabulary terms (geographic areas that contain harvestman records). These terms have been tagged to over 6900 species/subspecies of Opiliones, resulting in the generation of over 10,000 records. Checklists aiming for exhaustiveness are presented for valid extant Opiliones species/subspecies in each of these geographic areas, as documented in the World Catalogue of Opiliones (WCO) project, and geo maps are included to visually depict the distribution density of known species. Notably, this work marks the first-ever presentation of such checklists in the taxonomic literature for several countries, notably India, Indonesia, Papua New Guinea, and the Philippines. Brazil emerges as the most diverse country for harvestmen, with more than 1000 species, followed by Venezuela, Indonesia, and the United States, each hosting over 300 species. Checklists are individually provided for each state/province in these four countries. Elusive yet valid species are listed separately in their own section of nomina dubia, not entering the countries lists. Leiobunum rotundum argentatum Franganillo, 1926, is here elevated to Leiobunum argentatum Franganillo, 1926 new rank. Paropilio spinipes Roewer, 1956, is considered a junior subjective synonym of Opilio cirtanus C.L. Koch, 1839 syn. nov., Lacinius longisetus (Thorell, 1876) is considered a junior subjective synonym of Lacinius horridus (Panzer, 1794) syn. nov. The combination Rhopalocranaus hickmanni Caporiacco, 1951, is reinstated after this species appeared as Cranaus hickmanni in the literature. Some nomenclatural changes are established as a consequence of homonymy: (a) Paranemastoma graecum (Giltay, 1932) comb. nov. is the correct name for Nemastoma simplex Giltay, 1932 (currently combined as Paranemastoma simplex), a junior primary homonym of Nemastoma bacilliferum simplex Simon, 1913; (b) Belemulus annulatus remains permanently invalid as a junior secondary homonym replaced before 1961, so the replacement name to be used is Belemulus roeweri (Soares & Soares, 1948) comb. nov.; (c) Isaeus mexicanus Sørensen, 1932, must be reinstated as a species-group name rejected after 1960 due to secondary homonymy with Haehnelia mexicana Roewer, 1915; (d) Paranemastoma roeweri Staręga, 1978 is the correct name for Nemastoma redikorzevi Roewer, 1951, a junior primary homonym of Nemastoma redikorzevi Kharitonov, 1946; (e) the new name Neocynorta lanegra nom. nov. is proposed for Neocynorta lata (González-Sponga, 1992), originally Cynorta lata, which is a primary homonym of Cynorta lata Banks, 1909, currently in the genus Eucynortula; (f) the new name Neocynorta electrigena nom. nov. is proposed for Neocynorta punctata (González-Sponga, 2003), originally Paecilaema punctata, which is a primary homonym of Paecilaema punctata Sørensen, 1932, currently in the genus Anduzeia.

The voice of the little giants: Arcellinida testate amoebae in environmental DNA-based bioindication, from taxonomy free to haplotypic level

Bioindication, evaluating biological responses to environmental disturbances, is crucial for assessing the ecological status of an ecosystem. While historical bioindication relied on macroscopic organisms, the introduction of environmental DNA (eDNA) techniques allows the application of protists without the necessity of morphological identification. In this study, we propose a novel bioindication methodology utilizing Arcellinida, a group of top predators among protists, as bioindicators of freshwater ecosystems. For that purpose, we first characterized the Arcellinida diversity over 1 year at three different points of Lake Sanabria, an ancient glacier lake known to be subjected to anthropogenic disturbances. We compared this diversity with an undisturbed control site. Second, we characterized the Arcellinida diversity in other ecosystems to generate the ecological background to test the connectivity between them. Results indicate limited connectivity between the different ecosystems and an edge effect between terrestrial and aquatic ecosystems. Disturbed freshwater ecosystems exhibited reduced Arcellinida diversity at both specific and infraspecific levels, providing valuable insight into recent disturbances. Arcellinida-based bioindication provides a sensitive, accurate and easy-to-interpret protocol for monitoring disturbances in freshwater ecosystems. It represents a valuable tool for environmental assessments and conservation strategies.

Most soil and litter arthropods are unidentifiable based on current DNA barcode reference libraries

We are far from knowing all species living on the planet. Understanding biodiversity is demanding and requires time and expertise. Most groups are understudied given problems of identifying and delimiting species. DNA barcoding emerged to overcome some of the difficulties in identifying species. Its limitations derive from incomplete taxonomic knowledge and the lack of comprehensive DNA barcode libraries for so many taxonomic groups. Here, we evaluate how useful barcoding is for identifying arthropods from highly diverse leaf litter communities in the southern Appalachian Mountains (USA). We used 3 reference databases and several automated classification methods on a data set including several arthropod groups. Acari, Araneae, Collembola, Coleoptera, Diptera, and Hymenoptera were well represented, showing different performances across methods and databases. Spiders performed the best, with correct identification rates to species and genus levels of ~50% across databases. Springtails performed poorly, no barcodes were identified to species or genus. Other groups showed poor to mediocre performance, from around 3% (mites) to 20% (beetles) correctly identified barcodes to species, but also with some false identifications. In general, BOLD-based identification offered the best identification results but, in all cases except spiders, performance is poor, with less than a fifth of specimens correctly identified to genus or species. Our results indicate that the soil arthropod fauna is still insufficiently documented, with many species unrepresented in DNA barcode libraries. More effort toward integrative taxonomic characterization is needed to complete our reference libraries before we can rely on DNA barcoding as a universally applicable identification method.

Alike but genetically divergent: The resurrection of Urotrygon asterias (Jordan & Gilbert, 1883) from its closest relatives, the Munda and the Blotched stingray

The genus Urotrygon comprises small- to medium-sized endemic round rays on the American continent and has undergone several synonymization processes. Here, we used an integrative taxonomic approach, including meristic, morphometric, and mtDNA analyses, to resolve the particularly intricate relationship among Urotrygon munda Gill, 1863, Urotrygon chilensis (Günther, 1872), and Urotrygon asterias (Jordan & Gilbert, 1883). The latter species is currently a synonym of U. munda but is also considered the U. chilensis "northern morphotype." These taxonomic entities have historically been confounded, mainly due to their phenotypical resemblance along their geographic distribution in the eastern Pacific. We assessed 78 specimens (43 "northern" and 30 "southern morphotypes" of U. chilensis, as well as 5 U. munda) using 19 external variables for taxonomic and morphometric analysis. Distinct meristic patterns, including pectoral and pelvic ceratotrichia, vertebrae number, and thorn distribution along the dorsal midline, were observed in the series-type specimens of the three taxonomic entities. Our multivariate morphometric analyses consistently differentiated the three groups as distinct taxonomic entities, with an overall classification accuracy of 66.7%. The meristic results also provided reliable information distinguishing the three entities. Based on the nicotinamide adenine dinucleotide (NADH2) and cytochrome oxidase subunit I (COI) genes, our phylogenetic analysis were consistent with the morphometric and meristic data, supporting these three entities as distinct species having their own evolutionary lineages. Our comprehensive approach confidently demonstrated that the northern U. chilensis morphotype matched and corresponded to the description of the Starry round ray, U. asterias, confirming its taxonomic resurrection as a valid species distinct from U. chilensis and U. munda. The geographic distribution of U. asterias spans from the tropical west coast of Mexico (including the Gulf of California) to Costa Rica, revealing that microevolutionary processes have well-defined population clades within this range. Furthermore, U. chilensis is unequivocally established as the sole Urotrygon species occurring south of the Guayaquil marine ecoregion. In addition, the public COI and NADH2 sequences available for Urotrygon hosted in the ad hoc online databases were found to be misidentified, emphasizing the need for rigorous taxonomic scrutiny in this group. Finally, our research underscores the significance of an integrative approach that combines morphometric, meristic, and molecular techniques with historical data to disentangle the complexities of closely related taxa.

Contextualising samples: supporting reference genomes of European biodiversity through sample and associated metadata collection

The European Reference Genome Atlas (ERGA) consortium aims to generate a reference genome catalogue for all of Europe's eukaryotic biodiversity. The biological material underlying this mission, the specimens and their derived samples, are provided through ERGA's pan-European network. To demonstrate the community's capability and capacity to realise ERGA's ambitious mission, the ERGA Pilot project was initiated. In support of the ERGA Pilot effort to generate reference genomes for European biodiversity, the ERGA Sampling and Sample Processing committee (SSP) was formed by volunteer experts from ERGA's member base. SSP aims to aid participating researchers through (i) establishing standards for and collecting of sample/specimen metadata; (ii) prioritisation of species for genome sequencing; and (iii) development of taxon-specific collection guidelines including logistics support. SSP serves as the entry point for sample providers to the ERGA genomic resource production infrastructure and guarantees that ERGA's high-quality standards are upheld throughout sample collection and processing. With the volume of researchers, projects, consortia, and organisations with interests in genomics resources expanding, this manuscript shares important experiences and lessons learned during the development of standardised operational procedures and sample provider support. The manuscript details our experiences in incorporating the FAIR and CARE principles, species prioritisation, and workflow development, which could be useful to individuals as well as other initiatives.

A protocol to evaluate the taxonomic health of Neotropical species of Nasutitermes (Termitidae, Nasutitermitinae)

Herein a protocol is proposed to summarize the taxonomic situation for species, using the Neotropical Nasutitermes Dudley (Nasutitermitinae) as a test. The objective of this protocol is to allow comparisons between the available taxonomic information for species, and to provide objective criteria for assessing the information gaps for each taxon in order to prioritize topics for future investigation. Key aspects of taxonomic practice (condition of type specimens, helpfulness of descriptions and figures, compilation of distribution data, molecular data) were noted, the data were tabulated, and the taxa ranked. In addition, specific notes for each species have been included that may help to improve the solutions to the problems raised here.

Using DNA barcoding to identify high-priority taxa (Hymenoptera: Ichneumonidae) from Great Smoky Mountains National Park

The All Taxa Biodiversity Inventory (ATBI) in Great Smoky Mountains National Park (GSMNP) seeks to document every species of living thing in the park. The ATBI is decades in progress, yet some taxa remain virtually untouched by taxonomists. Such "high priority" taxa include the hyper-diverse parasitoid wasp family Ichneumonidae. Despite the positive and multifaceted effects ichneumonids have on their environment, only a small percentage of those collected in the park have been identified as species, mostly to their complex morphology and overwhelming diversity. Recently, DNA barcoding has transformed biodiversity inventories, streamlining the process to be more rapid and efficient. To test the effectiveness of barcoding 20 + year-old specimens of Ichneumonidae and catalog new records for GSMNP, COI was amplified from 95 ichneumonid morphospecies collected from Andrew's Bald, NC. Species identifications were confirmed morphologically. Eighty-one ichneumonids generated sequence data, representing 16 subfamilies and 44 genera. The subfamily Oxytorinae is newly recorded from GSMNP, along with 10 newly recorded genera and 23 newly recorded species across Ichneumonidae. These results contribute significantly to the ATBI by adding new park records for a high-priority taxon and demonstrate the effectiveness of applying DNA barcoding to samples in long-term storage or those lacking immediate taxonomic expertise.

Synchronised monitoring of plant and insect diversity: a case study using automated Malaise traps and DNA-based methods

The occurrence and distribution of insects and their possible associations with plant species are largely unknown in Germany and baseline data to monitor future trends are urgently needed. Using newly-designed automated Malaise trap multi-samplers, the occurrence of insect species and their potential associations with plants was monitored synchronously at two contrasting field sites in Germany: an urban botanical garden and a forest research station. Taxa were identified by metabarcoding of the insects and the plant traces present in the preservative ethanol of the Malaise trap samples. For comparison, a botanical survey was conducted in the vicinity of the traps. Across both sites, we identified a total of 1290 exact sequence variants (ESVs) assigned to Insecta, of which 205 are known to be pollinators. In the botanical garden, we detected the occurrence of 128 plant taxa, of which 41 also had one of their known insect pollinator species detected. Insect species richness was highest in May, mainly attributed to an increase in Diptera. These results present a case study of the applicability of automated sampling and DNA-based methods to monitor the timings of flowering and corresponding activity of plant-visiting insects.

Taxonomic Impediment for Conservation: The Case of Bees in an Undersampled Tropical Mid-Elevation Site, San Martín, Peru

In this first field survey of an entire bee fauna for any part of Peru, we report a total of 1796 bees belonging to 181 species or morphospecies in four families. The taxonomic impediment was pronounced with only 80 species of 181 that could be named. With such a high proportion of undetermined species, it is not possible to adequately compare pollinator communities across different studies, assess historical changes or analyze endemism patterns to document ecology, behavior and evolution of the species and genera. This information is required to provide a sound basis for policymakers to protect habitats for the conservation of native pollinators.

Spotting mistakes: Reappraisal of Spotted Drum Stellifer punctatissimus (Meek & Hildebrand, 1925) (Teleostei: Sciaenidae) reveals species misidentification trends and suggests latitudinal sexual dimorphism

A major part of the described species is understudied, falling into the Linnean shortfall. This is a major concern for cryptic species, which require integrative approaches to better evaluate their diversity. We conducted morphological analyses using specimens of Stellifer punctatissimus, S. gomezi, and S. menezesi to reassess their taxonomical identity. We evaluated the allometric and sexual components of the morphology of the Stellifer punctatissimus species complex, and tested and discussed species hypotheses. The combined evidence of our work and previous studies agrees with the current morphological hypothesis of three species, as opposed to the two-lineage molecular hypothesis. However, as cryptic species, they overlap in most their traits, especially females and juveniles. Previously unaccounted variation of allometric and sexually dimorphic characters in this species complex revealed a confounding effect that might explain past and current taxonomic errors. Taxonomical practice of using body depth as a diagnostic character had led to juveniles and females being, respectively, described as a different species or wrongfully identified. Hence, taxonomical studies demand better assessment of allometric and sexual dimorphism components. Herein, we present new characters in a key to the Atlantic species of Stellifer, which disclose size and sexual variation unnoticed in previous studies. The contrasting growth patterns among these species could imply distinct habitat use. As a result, it could be suggested that such species are under different threats, which highlights the need of differential management and conservation strategies.

Systematic challenges and opportunities in insect monitoring: a Global South perspective

Insect monitoring is pivotal for assessing biodiversity and informing conservation strategies. This study delves into the complex realm of insect monitoring in the Global South-world developing and least-developed countries as identified by the United Nations Conference on Trade and Development-highlighting challenges and proposing strategic solutions. An analysis of publications from 1990 to 2024 reveals an imbalance in research contributions between the Global North and South, highlighting disparities in entomological research and the scarcity of taxonomic expertise in the Global South. We discuss the socio-economic factors that exacerbate the issues, including funding disparities, challenges in collaboration, infrastructure deficits, information technology obstacles and the impact of local currency devaluation. In addition, we emphasize the crucial role of environmental factors in shaping insect diversity, particularly in tropical regions facing multiple challenges including climate change, urbanization, pollution and various anthropogenic activities. We also stress the need for entomologists to advocate for ecosystem services provided by insects in addressing environmental issues. To enhance monitoring capacity, we propose strategies such as community engagement, outreach programmes and cultural activities to instill biodiversity appreciation. Further, language inclusivity and social media use are emphasized for effective communication. More collaborations with Global North counterparts, particularly in areas of molecular biology and remote sensing, are suggested for technological advancements. In conclusion, advocating for these strategies-global collaborations, a diverse entomological community and the integration of transverse disciplines-aims to address challenges and foster inclusive, sustainable insect monitoring in the Global South, contributing significantly to biodiversity conservation and overall ecosystem health. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.

Sharing insect data through GBIF: novel monitoring methods, opportunities and standards

Technological advancements in biological monitoring have facilitated the study of insect communities at unprecedented spatial scales. The progress allows more comprehensive coverage of the diversity within a given area while minimizing disturbance and reducing the need for extensive human labour. Compared with traditional methods, these novel technologies offer the opportunity to examine biological patterns that were previously beyond our reach. However, to address the pressing scientific inquiries of the future, data must be easily accessible, interoperable and reusable for the global research community. Biodiversity information standards and platforms provide the necessary infrastructure to standardize and share biodiversity data. This paper explores the possibilities and prerequisites of publishing insect data obtained through novel monitoring methods through GBIF, the most comprehensive global biodiversity data infrastructure. We describe the essential components of metadata standards and existing data standards for occurrence data on insects, including data extensions. By addressing the current opportunities, limitations, and future development of GBIF's publishing framework, we hope to encourage researchers to both share data and contribute to the further development of biodiversity data standards and publishing models. Wider commitments to open data initiatives will promote data interoperability and support cross-disciplinary scientific research and key policy indicators. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.

Tree of life metabarcoding can serve as a biotic benchmark for shifting baselines in urbanized estuaries

Urbanization of estuaries drastically changed existing shorelines and bathymetric contours, in turn modifying habitat for marine foundational species that host critical biodiversity. And yet we lack approaches to characterize a significant fraction of the biota that inhabit these ecosystems on time scales that align with rates of urbanization. Environmental DNA (or eDNA) metabarcoding that combines multiple assays targeting a broad range of taxonomic groups can provide a solution, but we need to determine whether the biological communities it detects ally with different habitats in these changing aquatic environments. In this study, we tested whether tree of life metabarcoding (ToL-metabarcoding) data extracted from filtered seawater samples correlated with four known geomorphic habitat zones across a heavily urbanized estuary (Sydney Harbour, Australia). Using this method, we substantially expanded our knowledge on the composition and spatial distribution of marine biodiversity across the tree of life in Sydney Harbour, particularly for organisms where existing records are sparse. Excluding terrestrial DNA inputs, we identified significant effects of both distance from the mouth of Sydney Harbour and geomorphic zone on biological community structure in the ToL-metabarcoding dataset (entire community), as well as in each of the taxonomic subgroups that we considered (fish, macroinvertebrates, algae and aquatic plants, bacteria). This effect appeared to be driven by taxa as a collective versus a few individual taxa, with each taxon explaining no more than 0.62% of the variation between geomorphic zones. Similarly, taxonomic richness was significantly higher within geomorphic zones with large sample sizes, but also decreased by 1% with each additional kilometer from the estuary mouth, a result consistent with a reduction in tidal inputs and available habitat in upper catchments. Based on these results, we suggest that ToL-metabarcoding can be used to benchmark biological monitoring in other urbanized estuaries globally, and in Sydney Harbour at future time points based on detection of bioindicators across the tree of life. We also suggest that robust biotic snapshots can be archived following extensive curation of taxonomic assignments that incorporates ecological affinities, supported by records from relevant and regional biodiversity repositories.

Identification of fish specimens of the Tocantins River, Brazil, using DNA barcoding

The fish fauna of the Tocantins River possesses many endemic species; however, it is little studied in molecular terms and is quite threatened by the construction of several hydroelectric dams. Therefore, the objective of this study was to identify the ichthyofauna of the Tocantins River using DNA barcoding. For this, collections were carried out in five points of this river, which resulted in the capture of 725 individuals from which partial sequences of the cytochrome oxidase subunit I (COI) gene were obtained for genetic analysis. A total of 443 haplotypes were recovered with the mean intraspecific K2P genetic distance of 1.82%. Altogether, 138 species were identified based on morphological criteria, which was a quantity that was much lower than that indicated by the four molecular methods (assemble species by automatic partitioning [ASAP], barcode index number [BIN], generalized mixed Yule coalescent (GMYC), and Bayesian Poisson tree processes [bPTP]) through which 152-157 molecular entities were identified. In all, 41 unique BINs were obtained based on the data generated in the BOLDSystems platform. According to the result indicated by ASAP (species delimitation approach considered the most appropriate in the present study), there was an increase of 17 molecular entities (12.32%), when compared to the number of species identified through their morphological criteria, as it can show cryptic diversity, candidates for new species, and misidentifications. There were 21 incongruities indicated between the different identification approaches for species. Therefore, it is suggested that these taxonomic problems be cautiously evaluated by experts to solve such taxonomic issues.

Heteroptera research in Latin America and the Caribbean (Insecta, Hemiptera): status and perspectives in the 21st century

Latin American and the Caribbean regions (LAC) harbor one of the most biodiverse areas of the world, the Neotropics. True bugs (Hemiptera: Heteroptera) are a diverse lineage of insects, with more than 45,000 species, particularly speciose in the Neotropical region. True bugs are fundamental in the dynamics of natural and modified ecosystems, with several species critical to agriculture and public health. We compiled Heteroptera research in LAC from 1998-2022 using bibliographic databases. Productivity, collaborative networks, and the main topics studied were analyzed. A total of 1,651 Heteroptera studies from LAC were found, with continuous growth being 2021 the most prolific. Four categories (Taxonomy of extant species, Faunistic inventories and new records, Pest species biology, and Community ecology) represent most of the published research. About 60 percent of the records evaluated correspond to five families (Pentatomidae, Reduviidae, Coreidae, Miridae, and Rhyparochromidae). We emphasize the need to keep working on Heteroptera taxonomy because it will allow further advances in other areas such as phylogenetic analyses, biogeography, ecology, and natural history, among others. The results of our analyses characterize the current state of heteropterology in the region, establishing a baseline for future studies and efforts to broaden the knowledge of the group.

Microplastics as an emerging threat to amphibians: Current status and future perspectives

Given their pervasiveness in the environment, particularly in aquatic ecosystems, plastics are posing a growing concern worldwide. Many vertebrates and invertebrates in marine, freshwater, and terrestrial ecosystems exhibit microplastic (MP) uptake and accumulation. Some studies have indicated the fatal impacts of MPs on animals and their possible transfer through food chains. Thus, it is crucial to study MP pollution and its impacts on environment-sensitive and globally threatened animal groups, such as amphibians, which also play an important role in the energy transfer between ecosystems. Unfortunately, research in this field is lacking and sources of organized information are also scarce. Hence, we systematically reviewed published literature on MPs in amphibians to fill the existing knowledge gap. Our review revealed that most of the previous studies have focused on MP bioaccumulation in amphibians, whereas, only a few research highlighted its impacts. We found that more than 80% of the studied species exhibited MP accumulation. MPs were reported to persist in different organs for a long time and get transferred to other trophic levels. They can also exhibit cytotoxic and mutagenic effects and may have fatal impacts. Moreover, they can increase the disease susceptibility of amphibians. Our study concludes the MPs as a potential threat to amphibians and urges increasing the scope and frequency of research on MP pollution and its impacts on this vulnerable animal group. We also provide a generalized method for studying MPs in amphibians with future perspectives and research directions. Our study is significant for extending the knowledge of MPs and their impacts on amphibians and guiding prospective research.

Geochemical, mineralogical records, and statistical approaches in establishing sedimentary in the environment of a Mediterranean coastal system: case of Sebkha El-Guettiate (southeastern Tunisia)

The current study was conducted within the context of the Holocene era in Sebkha El-Guettiate, located in southeastern Tunisia. The aim was to determine the factors influencing the geochemical and mineralogical composition of sediments and to elucidate the sedimentary characteristics of the Holocene within the Sebkha core. We examined a sediment core extending 100 cm from this Sebkha, subjecting it to comprehensive analysis to uncover its sedimentological, mineralogical, and geochemical properties. Several techniques were employed to strengthen and validate the connections between geochemical and mineralogical analyses, including X-ray diffraction (XRD), X-ray fluorescence (XRF), scanning electron microscopy (SEM), and infrared (IR) spectroscopy, among others. Furthermore, statistical analyses utilizing principal component analysis (PCA) were applied to the results of the geochemical and mineralogical studies, aiding in the identification of patterns and relationships. A comprehensive mineralogical assessment of the core's sediments revealed the presence and interpretation of carbonate minerals, evaporite minerals, and detrital minerals. Through the application of infrared (IR) spectrometer techniques to all sediment samples, we gained insight into the mineralogical components and the distribution of key elements such as quartz, kaolinite, calcite, feldspar, and organic carbon. The geochemical composition demonstrated a clear dominance of silica (SiO2), accompanied by fluctuations in carbonate percentages (CaCO3). The prominent major elements, primarily magnesium (Mg) and calcium (Ca) originating from dolomitization, sodium (Na) and chlorine (Cl) from halite, and calcium (Ca) from gypsum, exhibited varying levels. Results from Rock-Eval 6 pyrolysis indicated that the organic matter within the sediments is generally a mixture of terrestrial and aquatic origins. This study provides practical information that underscores the diverse origins contributing to Sebkha sediment formation, often influenced by saline systems.

Diversity of true bugs (Insecta: Hemiptera: Heteroptera) from the El Impenetrable National Park, Argentina

The study of the Heteroptera (Hemiptera) fauna of the El Impenetrable National Park, resulted in an inventory composed of: Alydidae (2 spp.), Aradidae (1 sp.), Belostomatidae (5 spp.), Berytidae (1 sp.), Blissidae (1 sp.), Coreidae (11 spp.), Corixidae (2 spp.), Geocoridae (1 sp.), Gerridae (1 sp.), Hebridae (1 sp.), Largidae (4 spp.), Lygaeidae (5 spp.), Miridae (17 spp.), Nabidae (1 sp.), Notonectidae (1 sp.), Oxycarenidae (1 sp.), Pachygronthidae (1 sp.), Pachynomidae (2 spp.), Pentatomidae (16 spp.), Pleidae (1 sp.), Pyrrhocoridae (1 sp.), Reduviidae (30 spp.), Rhopalidae (5 spp.), Rhyparochromidae (12 spp.), Saldidae (1 sp.), Scutelleridae (2 spp.), Tingidae (1 sp.), and Veliidae (1 sp.). These findings include six new records for the Argentinean fauna: Prytanes foedus (Stl), Saldula pallipes (Fabricius), Camirus brevilinea (Walker), Atopozelus opsimus Elkins, Doldina bicarinata Stl, Rocconota sextuberculata St and 39 new records for Chaco Province.

Species delimitation of tea plants (Camellia sect. Thea) based on super-barcodes

BACKGROUND

The era of high throughput sequencing offers new paths to identifying species boundaries that are complementary to traditional morphology-based delimitations. De novo species delimitation using traditional or DNA super-barcodes serve as efficient approaches to recognizing putative species (molecular operational taxonomic units, MOTUs). Tea plants (Camellia sect. Thea) form a group of morphologically similar species with significant economic value, providing the raw material for tea, which is the most popular nonalcoholic caffeine-containing beverage in the world. Taxonomic challenges have arisen from vague species boundaries in this group.

RESULTS

Based on the most comprehensive sampling of C. sect. Thea by far (165 individuals of 39 morphospecies), we applied three de novo species delimitation methods (ASAP, PTP, and mPTP) using plastome data to provide an independent evaluation of morphology-based species boundaries in tea plants. Comparing MOTU partitions with morphospecies, we particularly tested the congruence of MOTUs resulting from different methods. We recognized 28 consensus MOTUs within C. sect. Thea, while tentatively suggesting that 11 morphospecies be discarded. Ten of the 28 consensus MOTUs were uncovered as morphospecies complexes in need of further study integrating other evidence. Our results also showed a strong imbalance among the analyzed MOTUs in terms of the number of molecular diagnostic characters.

CONCLUSION

This study serves as a solid step forward for recognizing the underlying species boundaries of tea plants, providing a needed evidence-based framework for the utilization and conservation of this economically important plant group.

Facilitating taxonomy and phylogenetics: An informative and cost-effective protocol integrating long amplicon PCRs and third-generation sequencing

Phylogenetic inference has become a standard technique in integrative taxonomy and systematics, as well as in biogeography and ecology. DNA barcodes are often used for phylogenetic inference, despite being strongly limited due to their low number of informative sites. Also, because current DNA barcodes are based on a fraction of a single, fast-evolving gene, they are highly unsuitable for resolving deeper phylogenetic relationships due to saturation. In recent years, methods that analyse hundreds and thousands of loci at once have improved the resolution of the Tree of Life, but these methods require resources, experience and molecular laboratories that most taxonomists do not have. This paper introduces a PCR-based protocol that produces long amplicons of both slow- and fast-evolving unlinked mitochondrial and nuclear gene regions, which can be sequenced by the affordable and portable ONT MinION platform with low infrastructure or funding requirements. As a proof of concept, we inferred a phylogeny of a sample of 63 spider species from 20 families using our proposed protocol. The results were overall consistent with the results from approaches based on hundreds and thousands of loci, while requiring just a fraction of the cost and labour of such approaches, making our protocol accessible to taxonomists worldwide.

New records of Provanna (Gastropoda, Provannidae) from the Costa Rica Margin and an identification key for the genus

Consistent species identification is foundational to biological research and requires coordination among a diversity of researchers and institutions. However, such consistency may be hindered for rare organisms where specimens, identification resources, and taxonomic experts are few. This is often the case for deep-sea taxonomic groups. For example, the deep-sea gastropod genus Provanna Dall, 1918 is common at chemosynthetic sites throughout the world's oceans, yet no formal guide to these species has yet been produced. Recent exploration has recovered new specimens of Provanna from hydrocarbon seeps off the Pacific Costa Rica Margin. The current work assesses the species identity of these specimens using shell morphology, radular morphology, and genetic barcoding (mitochondrial CO1 and nuclear H3). Records of occurrence for P.laevis Warén & Ponder, 1991, P.ios Warén & Bouchet, 1986, and P.pacifica Warén & Bouchet, 1986 are herein presented from the Costa Rica Margin. A critical taxonomic review of the 29 extant species within this genus was conducted and their genetic, morphological, and biogeographical distinction assessed. In this review, genetic and morphological support was found for nearly all current species delineations except for P.glabraOkutani et al., 1992, syn. nov. and P.laevis, syn. nov., which are herein synonymized to P.laevis, and for P.ios, syn. nov. and P.goniata Warén & Bouchet, 1986, syn. nov., which are synonymized to P.ios. Finally, the first species identification key for the extant species in this genus is presented. This work clarifies the taxonomy and systematics of this deep-sea gastropod genus and contributes a novel polytomous key for use in future research.

Two new species of Glaphyropyga Schiner (Diptera: Asilidae: Asilinae) from Peru

Two new species in the strictly Neotropical genus Glaphyropyga Schiner, 1866 are described from Peru; Glaphyropyga andina sp. nov. and Glaphyropyga monticola sp. nov., both from Cuzco, elevating to 14 the number of known species in this genus. A distribution map for the Peruvian species is given and a key to the known species is proposed.

Species Diagnosis and DNA Taxonomy

The use of DNA has helped to improve and speed up species identification and delimitation. However, it also provides new challenges to taxonomists. Incongruence of outcome from various markers and delimitation methods, bias from sampling and skewed species distribution, implemented models, and the choice of methods/priors may mislead results and also may, in conclusion, increase elements of subjectivity in species taxonomy. The lack of direct diagnostic outcome from most contemporary molecular delimitation approaches and the need for a reference to existing and best sampled trait reference systems reveal the need for refining the criteria of species diagnosis and diagnosability in the current framework of nomenclature codes and good practices to avoid nomenclatorial instability, parallel taxonomies, and consequently more and new taxonomic impediment.

A review of the genus Muusoctopus (Cephalopoda: Octopoda) from Arctic waters

We report two Arctic species of incirrate octopods new to science. One is formally described here as Muusoctopus aegir Golikov, Gudmundsson & Sabirov sp. nov. while the other, Muusoctopus sp. 1, is not formally described due to a limited number of samples (all are immature individuals). These two species differ from each other, and from other Muusoctopus, especially in: 1) absence of stylets (in M. aegir sp. nov.); 2) proportions of mantle and head; 3) funnel organ morphology (W-shaped with medial and marginal limbs of equal length in M. aegir sp. nov., or medial are slightly longer; V V-shaped with medial limbs slightly longer and broader than marginal in Muusoctopus sp. 1); 4) sucker and gill lamellae counts; 5) relative arm length and sucker diameter; and 6) male reproductive system relative size and morphology. Species of Muusoctopus now comprise four of 12 known Arctic cephalopods. Additionally, this study provides: a) new data on the morphology and reproductive biology of M. johnsonianus and M. sibiricus, and a diagnosis of M. sibiricus; b) the equations to estimate mantle length and body mass from beak measurements of M. aegir sp. nov. and M. johnsonianus; c) a cytochrome c oxidase subunit I gene barcode for M. sibiricus; d) new data on the ecology and distribution of all studied species; and e) a data table for the identification of northern North Atlantic and Arctic species of Muusoctopus.

Black gold rush - Evaluating the efficiency of the Fractionator in separating Hymenoptera families in a meadow ecosystem over a two week period

In the face of insect decline, monitoring projects are launched widely to assess trends of insect populations. Collecting over long time periods results in large numbers of samples with thousands of individuals that are often just stored in freezers waiting to be further processed. As the time-consuming process of sorting and identifying specimens prevents taxonomists from working on mass samples, important information on species composition remains unknown and taxonomically neglected species remain undiagnosed. Size fractioning of bulk samples can improve sample handling and, thus, can help to overcome the taxonomic impediment. In this paper, we evaluate the efficiency of the fractionator in separating Hymenoptera families from a Malaise trap sample of a meadow ecosystem over a two week interval to make them available for further morphological identification. The fractionator system by Buffington and Gates (2008) was used to separate the sample in two size classes - a large (macro) and a small (micro) fraction - and Hymenoptera specimens were then counted and identified on family level. In total, 2,449 Hymenoptera specimens were found in the macro fraction and 3,016 in the micro fraction (5,465 specimens in total). For 24 out of 34 Hymenoptera families (71%), separation was significant. This study illustrates the efficiency of the fractionator and its potential to improve workflows dealing with specimen-rich Malaise trap samples.

Darwin's feathers: Eco-evolutionary biology, predictions and policy

The scientific community is often asked to predict the future state of the environment and, to do so, the structure (biodiversity) and the functions (ecosystem functioning) of the investigated systems must be described and understood. In his "handful of feathers" metaphor, Charles Darwin explained the difference between simple and predictable systems, obeying definite laws, and complex (and unpredictable) systems, featured by innumerable components and interactions among them. In order not to waste efforts in impossible enterprises, it is crucial to ascertain if accurate predictions are possible in a given domain, and to what extent they might be reliable. Since ecology and evolution (together forming "natural history") deal with complex historical systems that are extremely sensitive to initial conditions and to contingencies or 'black swans', it is inherently impossible to accurately predict their future states. Notwithstanding this impossibility, policy makers are asking the community of ecological and evolutionary biologists to predict the future. The struggle for funding induces many supposed naturalists to do so, also because other types of scientists (from engineers to modellers) are keen to sell predictions (usually in form of solutions) to policy makers that are willing to pay for them. This paper is a plea for bio-ecological realism. The "mission" of ecologists and evolutionary biologists (natural historians) is not to predict the future state of inherently unpredictable systems, but to convince policy makers that we must live with uncertainties. Natural history, however, can provide knowledge-based wisdom to face the uncertainties about the future. Natural historians produce scenarios that are of great help in figuring out how to manage our relationship with the rest of nature.

Population Genomics of Pooled Samples: Unveiling Symbiont Infrapopulation Diversity and Host-Symbiont Coevolution

Microscopic symbionts represent crucial links in biological communities. However, they present technical challenges in high-throughput sequencing (HTS) studies due to their small size and minimal high-quality DNA yields, hindering our understanding of host-symbiont coevolution at microevolutionary and macroevolutionary scales. One approach to overcome those barriers is to pool multiple individuals from the same infrapopulation (i.e., individual host) and sequence them together (Pool-Seq), but individual-level information is then compromised. To simultaneously address both issues (i.e., minimal DNA yields and loss of individual-level information), we implemented a strategic Pool-Seq approach to assess variation in sequencing performance and categorize genetic diversity (single nucleotide polymorphisms (SNPs)) at both the individual-level and infrapopulation-level for microscopic feather mites. To do so, we collected feathers harboring mites (Proctophyllodidae: Amerodectes protonotaria) from four individual Prothonotary Warblers (Parulidae: Protonotaria citrea). From each of the four hosts (i.e., four mite infrapopulations), we conducted whole-genome sequencing on three extraction pools consisting of different numbers of mites (1 mite, 5 mites, and 20 mites). We found that samples containing pools of multiple mites had more sequencing reads map to the feather mite reference genome than did the samples containing only a single mite. Mite infrapopulations were primarily genetically structured by their associated individual hosts (not pool size) and the majority of SNPs were shared by all pools within an infrapopulation. Together, these results suggest that the patterns observed are driven by evolutionary processes occurring at the infrapopulation level and are not technical signals due to pool size. In total, despite the challenges presented by microscopic symbionts in HTS studies, this work highlights the value of both individual-level and infrapopulation-level sequencing toward our understanding of host-symbiont coevolution at multiple evolutionary scales.

The nature of science: The fundamental role of natural history in ecology, evolution, conservation, and education

There is a contemporary trend in many major research institutions to de-emphasize the importance of natural history education in favor of theoretical, laboratory, or simulation-based research programs. This may take the form of removing biodiversity and field courses from the curriculum and the sometimes subtle maligning of natural history research as a "lesser" branch of science. Additional threats include massive funding cuts to natural history museums and the maintenance of their collections, the extirpation of taxonomists across disciplines, and a critical under-appreciation of the role that natural history data (and other forms of observational data, including Indigenous knowledge) play in the scientific process. In this paper, we demonstrate that natural history knowledge is integral to any competitive science program through a comprehensive review of the ways in which they continue to shape modern theory and the public perception of science. We do so by reviewing how natural history research has guided the disciplines of ecology, evolution, and conservation and how natural history data are crucial for effective education programs and public policy. We underscore these insights with contemporary case studies, including: how understanding the dynamics of evolutionary radiation relies on natural history data; methods for extracting novel data from museum specimens; insights provided by multi-decade natural history programs; and how natural history is the most logical venue for creating an informed and scientifically literate society. We conclude with recommendations aimed at students, university faculty, and administrators for integrating and supporting natural history in their mandates. Fundamentally, we are all interested in understanding the natural world, but we can often fall into the habit of abstracting our research away from its natural contexts and complexities. Doing so risks losing sight of entire vistas of new questions and insights in favor of an over-emphasis on simulated or overly controlled studies.

How we study cryptic species and their biological implications: A case study from marine shelled gastropods

Methodological and biological considerations are intertwined when studying cryptic species. A potentially large component of modern biodiversity, the frequency of cryptic species among taxonomic groups is not well documented. The term "cryptic species" is imprecisely used in scientific literature, causing ambiguity when interpreting their evolutionary and ecological significance. This study reviews how cryptic species have been defined, discussing implications for taxonomy and biology, and explores these implications with a case study based on recently published literature on extant shelled marine gastropods. Reviewed gastropods were recorded by species. Records of cryptic gastropods were presented by authors with variable levels of confidence but were difficult to disentangle from inherent biases in the study effort. These complexities notwithstanding, most gastropod species discussed were not cryptic. To the degree that this review's sample represents extinct taxa, the results suggest that a high proportion of shelled marine gastropod species are identifiable for study in the fossil record. Much additional work is needed to provide a more adequate understanding of the relative frequency of cryptic species in shelled marine gastropods, which should start with more explicit definitions and targeted case studies.

Marine Flora of French Polynesia: An Updated List Using DNA Barcoding and Traditional Approaches

Located in the heart of the South Pacific Ocean, the French Polynesian islands represent a remarkable setting for biological colonization and diversification, because of their isolation. Our knowledge of this region's biodiversity is nevertheless still incomplete for many groups of organisms. In the late 1990s and 2000s, a series of publications provided the first checklists of French Polynesian marine algae, including the Chlorophyta, Rhodophyta, Ochrophyta, and Cyanobacteria, established mostly on traditional morphology-based taxonomy. We initiated a project to systematically DNA barcode the marine flora of French Polynesia. Based on a large collection of ~2452 specimens, made between 2014 and 2023, across the five French Polynesian archipelagos, we re-assessed the marine floral species diversity (Alismatales, Cyanobacteria, Rhodophyta, Ochrophyta, Chlorophyta) using DNA barcoding in concert with morphology-based classification. We provide here a major revision of French Polynesian marine flora, with an updated listing of 702 species including 119 Chlorophyta, 169 Cyanobacteria, 92 Ochrophyta, 320 Rhodophyta, and 2 seagrass species-nearly a two-fold increase from previous estimates. This study significantly improves our knowledge of French Polynesian marine diversity and provides a valuable DNA barcode reference library for identification purposes and future taxonomic and conservation studies. A significant part of the diversity uncovered from French Polynesia corresponds to unidentified lineages, which will require careful future taxonomic investigation.

The future of tropical insect diversity: strategies to fill data and knowledge gaps

The decline of insect diversity is a much-discussed, yet understudied phenomenon, particularly in the tropics, where the majority of insect abundance, diversity and biomass is found. Integrated approaches involving traditional taxonomic methods, new molecular approaches, and novel monitoring and identification tools and applications are needed to address related and challenging questions regarding how many species of tropical insects exist, their distributions and natural history, the relative impacts of global change drivers on insect diversity across complex tropical landscapes, and the effects of insect declines on ecosystem functions and services. The main barriers to addressing these challenges are a lack of capacity and funding for research on insects in tropical countries and a lack of recognition of their importance for ecosystem functioning and human wellbeing. Insects must be brought into policy agendas, local capacity and funding through cross-boundary collaborations and equitable scientific practices increased, and their importance emphasized.

Tightening the requirements for species diagnoses would help integrate DNA-based descriptions in taxonomic practice

Modern advances in DNA sequencing hold the promise of facilitating descriptions of new organisms at ever finer precision but have come with challenges as the major Codes of bionomenclature contain poorly defined requirements for species and subspecies diagnoses (henceforth, species diagnoses), which is particularly problematic for DNA-based taxonomy. We, the commissioners of the International Commission on Zoological Nomenclature, advocate a tightening of the definition of "species diagnosis" in future editions of Codes of bionomenclature, for example, through the introduction of requirements for specific information on the character states of differentiating traits in comparison with similar species. Such new provisions would enhance taxonomic standards and ensure that all diagnoses, including DNA-based ones, contain adequate taxonomic context. Our recommendations are intended to spur discussion among biologists, as broad community consensus is critical ahead of the implementation of new editions of the International Code of Zoological Nomenclature and other Codes of bionomenclature.

From identification to forecasting: the potential of image recognition and artificial intelligence for aphid pest monitoring

Insect monitoring has gained global public attention in recent years in the context of insect decline and biodiversity loss. Monitoring methods that can collect samples over a long period of time and independently of human influences are of particular importance. While these passive collection methods, e.g. suction traps, provide standardized and comparable data sets, the time required to analyze the large number of samples and trapped specimens is high. Another challenge is the necessary high level of taxonomic expertise required for accurate specimen processing. These factors create a bottleneck in specimen processing. In this context, machine learning, image recognition and artificial intelligence have emerged as promising tools to address the shortcomings of manual identification and quantification in the analysis of such trap catches. Aphids are important agricultural pests that pose a significant risk to several important crops and cause high economic losses through feeding damage and transmission of plant viruses. It has been shown that long-term monitoring of migrating aphids using suction traps can be used to make, adjust and improve predictions of their abundance so that the risk of plant viruses spreading through aphids can be more accurately predicted. With the increasing demand for alternatives to conventional pesticide use in crop protection, the need for predictive models is growing, e.g. as a basis for resistance development and as a measure for resistance management. In this context, advancing climate change has a strong influence on the total abundance of migrating aphids as well as on the peak occurrences of aphids within a year. Using aphids as a model organism, we demonstrate the possibilities of systematic monitoring of insect pests and the potential of future technical developments in the subsequent automated identification of individuals through to the use of case data for intelligent forecasting models. Using aphids as an example, we show the potential for systematic monitoring of insect pests through technical developments in the automated identification of individuals from static images (i.e. advances in image recognition software). We discuss the potential applications with regard to the automatic processing of insect case data and the development of intelligent prediction models.

Illustrated keys and a DNA barcode reference library of the amphibians and terrestrial reptiles (Amphibia, Reptilia) of São Tomé and Príncipe (Gulf of Guinea, West Africa)

The herpetofauna of São Tomé and Príncipe consists of nine species of amphibians, all endemic, and 21 species of terrestrial reptiles, of which 17 are endemic. Our current knowledge regarding its natural history, ecology, and distribution is limited. Here two important tools are provided to support researchers, conservationists, and local authorities in the identification of the country's herpetofauna: an illustrated key to the herpetofauna of the two islands and surroundings islets and a DNA barcode reference library. The keys allow a rapid and unambiguous morphological identification of all occurring species. The DNA barcodes for the entire herpetofauna of the country were produced from 79 specimens, all of which are deposited in museum collections. The barcodes generated are available in online repositories and can be used to provide unambiguous molecular identification of most of the species. Future applications and use of these tools are briefly discussed.