A reference library for Canadian invertebrates with 1.5 million barcodes, voucher specimens, and DNA samples

Low-cost, high-volume imaging for entomological digitization

Large-scale digitization of natural history collections requires automation of image acquisition and processing. Reflecting this fact, various approaches, some highly sophisticated, have been developed to support imaging of museum specimens. However, most of these systems are complex and expensive, restricting their deployment. Here we describe a simple, inexpensive technique for imaging arthropods larger than 5 mm. By mounting a digital SLR camera on a CNC (computer numerical control) motor-drive rig, we created a system that captures high-resolution z-axis stacked images (6960 × 4640 pixels) of 95 specimens in 30 minutes. This system can be assembled inexpensively ($1000 USD without a camera) and it is easy to set-up and maintain. By coupling low cost with high production capacity, it represents a solution for digitizing any natural history collection.

Assessing arthropod biodiversity with DNA barcoding in Jinnah Garden, Lahore, Pakistan

Previous difficulties in arthropod taxonomy (such as limitations in conventional morphological approaches, the possibility of cryptic species and a shortage of knowledgeable taxonomists) has been overcome by the powerful tool of DNA barcoding. This study presents a thorough analysis of DNA barcoding in regards to Pakistani arthropods, which were collected from Lahore's Jinnah Garden. The 88 % (9,451) of the 10,792 specimens that were examined were able to generate DNA barcodes and 83% (8,974) of specimens were assigned 1,361 barcode index numbers (BINs). However, the success rate differed significantly between the orders of arthropods, from 77% for Thysanoptera to an astounding 93% for Diptera. Through morphological exams, DNA barcoding, and cross-referencing with the Barcode of Life Data system (BOLD), the Barcode Index Numbers (BINs) were assigned with a high degree of accuracy, both at the order (100%) and family (98%) levels. Though, identifications at the genus (37%) and species (15%) levels showed room for improvement. This underscores the ongoing need for enhancing and expanding the DNA barcode reference library. This study identified 324 genera and 191 species, underscoring the advantages of DNA barcoding over traditional morphological identification methods. Among the 17 arthropod orders identified, Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera from the class Insecta dominated, collectively constituting 94% of BINs. Expected malaise trap Arthropod fauna in Jinnah Garden could contain approximately 2,785 BINs according to Preston log-normal species distribution, yet the Chao-1 Index predicts 2,389.74 BINs. The Simpson Index of Diversity (1-D) is 0.989, signaling high species diversity, while the Shannon Index is 5.77, indicating significant species richness and evenness. These results demonstrated that in Pakistani arthropods, DNA barcoding and BOLD are an invaluable tool for improving taxonomic understanding and biodiversity assessment, opening the door for further eDNA and metabarcoding research.

Testing plastomes and nuclear ribosomal DNA sequences as the next-generation DNA barcodes for species identification and phylogenetic analysis in Acer

BACKGROUND

Acer is a taxonomically intractable and speciose genus that contains over 150 species. It is challenging to distinguish Acer species only by morphological method due to their abundant variations. Plastome and nuclear ribosomal DNA (nrDNA) sequences are recommended as powerful next-generation DNA barcodes for species discrimination. However, their efficacies were still poorly studied. The current study will evaluate the application of plastome and nrDNA in species identification and perform phylogenetic analyses for Acer.

RESULT

Based on a collection of 83 individuals representing 55 species (c. 55% of Chinese species) from 13 sections, our barcoding analyses demonstrated that plastomes exhibited the highest (90.47%) species discriminatory power among all plastid DNA markers, such as the standard plastid barcodes matK + rbcL + trnH-psbA (61.90%) and ycf1 (76.19%). And the nrDNA (80.95%) revealed higher species resolution than ITS (71.43%). Acer plastomes show abundant interspecific variations, however, species identification failure may be due to the incomplete lineage sorting (ILS) and chloroplast capture resulting from hybridization. We found that the usage of nrDNA contributed to identifying those species that were unidentified by plastomes, implying its capability to some extent to mitigate the impact of hybridization and ILS on species discrimination. However, combining plastome and nrDNA is not recommended given the cytonuclear conflict caused by potential hybridization. Our phylogenetic analysis covering 19 sections (95% sections of Acer) and 128 species (over 80% species of this genus) revealed pervasive inter- and intra-section cytonuclear discordances, hinting that hybridization has played an important role in the evolution of Acer.

CONCLUSION

Plastomes and nrDNA can significantly improve the species resolution in Acer. Our phylogenetic analysis uncovered the scope and depth of cytonuclear conflict in Acer, providing important insights into its evolution.

The InBIO Barcoding Initiative Database: DNA barcodes of Orthoptera from Portugal

Background

The InBIO Barcoding Initiative (IBI) Orthoptera dataset contains records of 420 specimens covering all the eleven Orthoptera families occurring in Portugal. Specimens were collected in continental Portugal from 2005 to 2021 and were morphologically identified to species level by taxonomists. A total of 119 species were identified corresponding to about 77% of all the orthopteran species known from continental Portugal.

New information

DNA barcodes of 54 taxa were made public for the first time at the Barcode of Life Data System (BOLD). Furthermore, the submitted sequences were found to cluster in 129 BINs (Barcode Index Numbers), 35 of which were new additions to the Barcode of Life Data System (BOLD). All specimens have their DNA barcodes publicly accessible through BOLD online database. Stenobothruslineatus is recorded for the first time for continental Portugal. This dataset greatly increases the knowledge on the DNA barcodes and distribution of Orthoptera from Portugal. All DNA extractions and most specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources.

Global arthropod beta-diversity is spatially and temporally structured by latitude

Global biodiversity gradients are generally expected to reflect greater species replacement closer to the equator. However, empirical validation of global biodiversity gradients largely relies on vertebrates, plants, and other less diverse taxa. Here we assess the temporal and spatial dynamics of global arthropod biodiversity dynamics using a beta-diversity framework. Sampling includes 129 sampling sites whereby malaise traps are deployed to monitor temporal changes in arthropod communities. Overall, we encountered more than 150,000 unique barcode index numbers (BINs) (i.e. species proxies). We assess between site differences in community diversity using beta-diversity and the partitioned components of species replacement and richness difference. Global total beta-diversity (dissimilarity) increases with decreasing latitude, greater spatial distance and greater temporal distance. Species replacement and richness difference patterns vary across biogeographic regions. Our findings support long-standing, general expectations of global biodiversity patterns. However, we also show that the underlying processes driving patterns may be regionally linked.

DNA barcoding, phylogeography and evolutionary dynamics of Chrysichthys auratus

This study embarked on an exploration into the genetic structure and evolutionary history of the Chrysichthys auratus species, leveraging PCR amplification, phylogenetic trees, and haplotype networks. Specific DNA segments were successfully amplified and visualized through electrophoresis. Newly obtained sequences were Bank into GenBank and given accession numbers (OR730807-OR730808-OR730809). The Neighbor-Joining method provided insights into the evolutionary relationships among taxa, further augmented by bootstrap values and the Tamura 3-parameter method. A comprehensive geographical haplotype network showcased pronounced genetic differentiation, especially between remote populations. Nonetheless, shared haplotypes between proximate regions indicated either ancestral genetic connections or ongoing gene flow. Employing the COI-DNA barcodes, an in-depth understanding of intra- and inter-populational genetic diversity was achieved. The study's findings unravel the intricate genetic landscape and evolutionary dynamics of C. auratus, offering novel perspectives into its demographic history across its vast native habitat.

New faunistic data on Diptera (Hexapoda, Insecta) from the Ziarat Juniperus forest ecosystem (Pakistan)

Background

This study presents the first faunistic record and DNA barcoding for some Diptera species recorded from the Juniperus forest ecosystem of Balochistan, Pakistan. DNA barcoding was used to explore species diversity of Dipterans and collections carried out using a Malaise trap between December 2018 to December 2019. This process involved sequencing the 658 bp Cytochrome Oxidase I (COI) gene.

New information

Amongst the collected Diptera specimens, nine families were identified, representing 13 genera. These species include Atherigonasoccata (Rondani, 1871), Atherigonavaria (Schiner, 1868), Chironomusdorsalis (Meigen, 1818), Eupeodescorollae (Linnaeus, 1758), Eristalistenax (Linnaeus,1758), Goniaornata (Meigen, 1826), Luciliasericata (Meigen, 1826), Paragusquadrifasciatus (Linnaeus, 1758), Polleniarudis (Fabricius, 1794), Raviniapernix (Thompson, 1869), Sarcophagadux (Thompson, 1869), Trupaneaamoena (Schiner, 1868) and Wohlfahrtiabella (Linnaeus, 1758). The families Syrphidae and Sarcophagidae exhibited the highest representation, each comprising three genera and three species. They were followed by the family Muscidae, which had a single genus and two species. Anthomyiidae, Chironomidae, Calliphoridae, Polleniidae, Tachinidae and Tephritidae were represented by only one genus and one species. A nique Barcode Index Number (BIN) was allotted to Tachinidae (specie i.e Goniaornata). The results indicated that barcoding through cytochrome oxidase I is an effective approach for the accurate identification and genetic studies of Diptera species. This discovery highlights the significant diversity of this insect order in study region. Furthermore, a comprehensive list of other Diptera species remains elusive because of difficulties in distinguishing them, based on morphology and a lack of professional entomological knowledge.

Towards a Canary Islands barcode database for soil biodiversity: revealing cryptic and unrecorded mite species diversity within insular soils

Soil arthropod diversity contributes to a high proportion of the total biodiversity on Earth. However, most soil arthropods are still undescribed, hindering our understanding of soil functioning and global biodiversity estimations. Inventorying soil arthropods using conventional taxonomical approaches is particularly difficult and costly due to the great species richness, abundance and local-scale heterogeneity of mesofauna communities and the poor taxonomic background knowledge of most lineages. To alleviate this situation, we have designed and implemented a molecular barcoding framework adapted to soil fauna. This pipeline includes different steps, starting with a morphology-based selection of specimens which are imaged. Then, DNA is extracted non-destructively. Both images and voucher specimens are used to assign a taxonomic identification, based on morphology that is further checked for consistency with molecular information. Using this procedure, we studied 239 specimens of mites from the Canary Islands including representatives of Mesostigmata, Sarcoptiformes and Trombidiformes, of which we recovered barcode sequences for 168 specimens that were morphologically identified to 49 species, with nine specimens that could only be identified at the genus or family levels. Multiple species delimitation analyses were run to compare molecular delimitations with morphological identifications, including ASAP, mlPTP, BINs and 3% and 8% genetic distance thresholds. Additionally, a species-level search was carried out at the Biodiversity Databank of the Canary Islands (BIOTA) to evaluate the number of species in our dataset that were not previously recorded in the archipelago. In parallel, a sequence-level search of our sequences was performed against BOLD Systems. Our results reveal that multiple morphologically identified species correspond to different molecular lineages, which points to significant levels of unknown cryptic diversity within the archipelago. In addition, we evidenced that multiple species in our dataset constituted new records for the Canary Islands fauna and that the information for these lineages within online genetic repositories is very incomplete. Our study represents the first systematic effort to catalogue the soil arthropod mesofauna of the Canary Islands and establishes the basis for the Canary Islands Soil Biodiversity barcode database. This resource will constitute a step forward in the knowledge of these arthropods in a region of special interest.

Creating Virtuous Cycles for DNA Barcoding: A Case Study in Science Innovation, Entrepreneurship, and Diplomacy

This chapter on the history of the DNA barcoding enterprise attempts to set the stage for the more scholarly contributions in this volume by addressing the following questions. How did the DNA barcoding enterprise begin? What were its goals, how did it develop, and to what degree are its goals being realized? We have taken a keen interest in the barcoding movement and its relationship to taxonomy, collections, and biodiversity informatics more broadly considered. This chapter integrates our two different perspectives on barcoding. DES was the Executive Secretary of the Consortium for the Barcode of Life from 2004 to 2017, with the mission to support the success of DNA barcoding without being directly involved in generating barcode data. RDMP viewed barcoding as an important entry into the landscape of biodiversity data, with many potential linkages to other components of that landscape. We also saw it as a critical step toward the era of international genomic research that was sure to follow. Like the Mercury Program that paved the way for lunar landings by the Apollo Program, we saw DNA barcoding as the proving grounds for the interdisciplinary and international cooperation that would be needed for success of whole-genome research.

Principles for Constructing DNA Barcode Reference Libraries

All DNA barcode methods rely on reference sequences linked to well-curated voucher specimens. Definitions for and locations of DNA barcode reference libraries are not standardized, and vary throughout the literature. Standardizing, and centralizing reference specimens would provide an unambiguous source, analogous to reference genomes, to reproduce identifications and improve a library. This chapter proposes a working definition of a DNA barcode reference library, consistent with DNA barcode data standards, along with principles and methods to consider when producing or using such a library. These methods allow explicit traceback to sequence-sources which elevate the value of voucher specimens, and create a potential for community curation.

Assessment of the DNA barcode libraries for the study of the poorly-known rove beetle (Staphylinidae) fauna of West Siberia

Staphylinidae, or rove beetles, are one of the mega-diverse and abundant families of the ground-living terrestrial arthropods that is taxonomically poorly known even in the regions adjacent to Europe where the fauna has been investigated for the longest time. Since DNA barcoding is a tool to accelerate biodiversity research, here we explored if the currently-available COI barcode libraries are representative enough for the study of rove beetles of West Siberia. This is a vast region adjacent to Europe with poorly-known fauna of rove beetles and from where not a single DNA barcode has hitherto been produced for Staphylinidae. First, we investigated the faunal similarity between the rove beetle faunas of the climatically compatible West Siberia in Asia, Fennoscandia in Europe and Canada and Alaska in North America. Second, we investigated barcodes available for Staphylinidae from the latter two regions in BOLD and GenBank, the world's largest DNA barcode libraries. We conclude that the rather different rove beetle faunas of Fennoscandia, on the one hand and Canada and Alaska on the other hand, are well covered in both barcode libraries that complement each other. We also find that even without any barcodes originating from specimens collected in West Siberia, this coverage is helpful for the study of rove beetles there due to the significant number of widespread species shared between West Siberia and Fennoscandia and due to the even larger number of shared genera amongst all three investigated regions. For the first time, we compiled a literature-based checklist for 726 species of the West Siberian Staphylinidae supplemented by their occurrence dataset submitted to GBIF. Our script written for mining unique (i.e. not redundant) barcodes for a given geographic area across global libraries is made available here and can be adopted for any other regions.

Diversity and Distribution of Mites (ACARI) Revealed by Contamination Survey in Public Genomic Databases

Acari (mites and ticks) are a biodiverse group of microarthropods within the Arachnida. Because of their diminutive size, mites are often overlooked. We hypothesized that mites, like other closely related microorganisms, could also contaminate public genomic database. Here, using a strategy based on DNA barcodes previously reported, we scanned contaminations related to mites (Acari, exclusive of Ixodida) in Genbank WGS/TSA database. In 22,114 assemblies (17,845 animal and 4269 plant projects), 1717 contigs in 681 assemblies (3.1%) were detected as mite contaminations. Additional taxonomic analysis showed the following: (1) most of the contaminants (1445/1717) were from the specimens of Magnoliopsida, Insecta and Pinopsida; (2) the contamination rates were higher in plant or TSA projects; (3) mite distribution among different classes of hosts varied considerably. Additional phylogenetic analysis of these contaminated contigs further revealed complicated mite-host associations. Overall, we conducted a first systemic survey and analysis of mite contaminations in public genomic database, and these DNA barcode related mite contigs will provide a valuable resource of information for understanding the diversity and phylogeny of mites.

A workflow for expanding DNA barcode reference libraries through 'museum harvesting' of natural history collections

Natural history collections are the physical repositories of our knowledge on species, the entities of biodiversity. Making this knowledge accessible to society - through, for example, digitisation or the construction of a validated, global DNA barcode library - is of crucial importance. To this end, we developed and streamlined a workflow for 'museum harvesting' of authoritatively identified Diptera specimens from the Smithsonian Institution's National Museum of Natural History. Our detailed workflow includes both on-site and off-site processing through specimen selection, labelling, imaging, tissue sampling, databasing and DNA barcoding. This approach was tested by harvesting and DNA barcoding 941 voucher specimens, representing 32 families, 819 genera and 695 identified species collected from 100 countries. We recovered 867 sequences (> 0 base pairs) with a sequencing success of 88.8% (727 of 819 sequenced genera gained a barcode > 300 base pairs). While Sanger-based methods were more effective for recently-collected specimens, the methods employing next-generation sequencing recovered barcodes for specimens over a century old. The utility of the newly-generated reference barcodes is demonstrated by the subsequent taxonomic assignment of nearly 5000 specimen records in the Barcode of Life Data Systems.

Enhancing DNA barcode reference libraries by harvesting terrestrial arthropods at the Smithsonian's National Museum of Natural History

The use of DNA barcoding has revolutionised biodiversity science, but its application depends on the existence of comprehensive and reliable reference libraries. For many poorly known taxa, such reference sequences are missing even at higher-level taxonomic scales. We harvested the collections of the Smithsonian's National Museum of Natural History (USNM) to generate DNA barcoding sequences for genera of terrestrial arthropods previously not recorded in one or more major public sequence databases. Our workflow used a mix of Sanger and Next-Generation Sequencing (NGS) approaches to maximise sequence recovery while ensuring affordable cost. In total, COI sequences were obtained for 5,686 specimens belonging to 3,737 determined species in 3,886 genera and 205 families distributed in 137 countries. Success rates varied widely according to collection data and focal taxon. NGS helped recover sequences of specimens that failed a previous run of Sanger sequencing. Success rates and the optimal balance between Sanger and NGS are the most important drivers to maximise output and minimise cost in future projects. The corresponding sequence and taxonomic data can be accessed through the Barcode of Life Data System, GenBank, the Global Biodiversity Information Facility, the Global Genome Biodiversity Network Data Portal and the NMNH data portal.

DNA Barcode Library of Megadiverse Lepidoptera in an Alpine Nature Park (Italy) Reveals Unexpected Species Diversity

Species inventories are a prerequisite for biodiversity monitoring and conservation, particularly in protected areas. However, the possibilities of a standardized survey of species diversity using DNA barcoding have so far hardly been implemented, especially in species-rich groups. A first-time molecular-based and nearly complete inventory of the megadiverse insect order Lepidoptera in a protected area in the Alps (Cottian Alps, Italy) was intended to test the possibilities and reliability of DNA-based identifications. From voucher material collected between 2019 and 2022, we successfully sequenced 1213 morphospecies that grouped into 1204 BINs (barcode index numbers), whereas DNA barcoding failed for another 18 species. A total of 35 species shared a BIN with one or more taxa, but a majority of 19 species could still be discriminated by divergent sequences. A total of 12 morphospecies split into two BINs. These species and a further 22 taxa with unique BINs and barcode divergences >2% to the nearest neighbor require taxonomic re-assessment. Two additional cryptic species from the study area were described recently. Finally, 16 species are newly recorded for Italy. Our study, therefore, demonstrates the importance of DNA barcoding for both faunistics and the discovery of cryptic diversity, even in apparently well-studied protected areas.

The first DNA barcode library of Chironomidae from the Tibetan Plateau with an evaluation of the status of the public databases

The main aim of this study was to curate a COI barcode library of Chironomidae from the Tibetan Plateau (TP) as an essential supplement to the public database. Another aim is to evaluate the current status of the public database of Chironomidae in aspects of taxonomic coverage, geographic representation, barcode quality, and efficiency for molecular identification, the Tibetan Plateau, China. In this study, 512 individuals of Chironomidae from the TP were identified based on morphological taxonomy and barcode analysis. The metadata of public records of Chironomidae were downloaded from the BOLD, and the quality of the public barcodes was ranked using the BAGS program. The reliability of the public library for molecular identification was evaluated with the newly curated library using the BLAST method. The newly curated library comprised 159 barcode species of 54 genera, of which 58.4% of species were likely new to science. There were great gaps in the taxonomic coverage and geographic representation in the public database, and only 29.18% of barcodes were identified at the species level. The quality of the public database was of concern, with only 20% of species being determined as concordant between BINs and morphological species. The accuracy of molecular identification using the public database was poor, and about 50% of matched barcodes could be correctly identified at the species level at the identity threshold of 97%. Based on these data, some recommendations are included here for improving barcoding studies on Chironomidae. The species richness of Chironomidae from the TP is much higher than ever recorded. Barcodes from more taxonomic groups and geographic regions are urgently needed to fill the great gap in the current public database of Chironomidae. Users should take caution when public databases are adopted as reference libraries for the taxonomic assignment.

A manager's guide to using eDNA metabarcoding in marine ecosystems

Environmental DNA (eDNA) metabarcoding is a powerful tool that can enhance marine ecosystem/biodiversity monitoring programs. Here we outline five important steps managers and researchers should consider when developing eDNA monitoring program: (1) select genes and primers to target taxa; (2) assemble or develop comprehensive barcode reference databases; (3) apply rigorous site occupancy based decontamination pipelines; (4) conduct pilot studies to define spatial and temporal variance of eDNA; and (5) archive samples, extracts, and raw sequence data. We demonstrate the importance of each of these considerations using a case study of eDNA metabarcoding in the Ports of Los Angeles and Long Beach. eDNA metabarcoding approaches detected 94.1% (16/17) of species observed in paired trawl surveys while identifying an additional 55 native fishes, providing more comprehensive biodiversity inventories. Rigorous benchmarking of eDNA metabarcoding results improved ecological interpretation and confidence in species detections while providing archived genetic resources for future analyses. Well designed and validated eDNA metabarcoding approaches are ideally suited for biomonitoring applications that rely on the detection of species, including mapping invasive species fronts and endangered species habitats as well as tracking range shifts in response to climate change. Incorporating these considerations will enhance the utility and efficacy of eDNA metabarcoding for routine biomonitoring applications.

Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods

Metazoan metabarcoding is emerging as an essential strategy for inventorying biodiversity, with diverse projects currently generating massive quantities of community-level data. The potential for integrating across such data sets offers new opportunities to better understand biodiversity and how it might respond to global change. However, large-scale syntheses may be compromised if metabarcoding workflows differ from each other. There are ongoing efforts to improve standardization for the reporting of inventory data. However, harmonization at the stage of generating metabarcode data has yet to be addressed. A modular framework for harmonized data generation offers a pathway to navigate the complex structure of terrestrial metazoan biodiversity. Here, through our collective expertise as practitioners, method developers, and researchers leading metabarcoding initiatives to inventory terrestrial biodiversity, we seek to initiate a harmonized framework for metabarcode data generation, with a terrestrial arthropod module. We develop an initial set of submodules covering the 5 main steps of metabarcode data generation: (i) sample acquisition; (ii) sample processing; (iii) DNA extraction; (iv) polymerase chain reaction amplification, library preparation, and sequencing; and (v) DNA sequence and metadata deposition, providing a backbone for a terrestrial arthropod module. To achieve this, we (i) identified key points for harmonization, (ii) reviewed the current state of the art, and (iii) distilled existing knowledge within submodules, thus promoting best practice by providing guidelines and recommendations to reduce the universe of methodological options. We advocate the adoption and further development of the terrestrial arthropod module. We further encourage the development of modules for other biodiversity fractions as an essential step toward large-scale biodiversity synthesis through harmonization.

DNA barcodes reveal striking arthropod diversity and unveil seasonal patterns of variation in the southern Atlantic Forest

The Atlantic Forest harbors 7% of global biodiversity and possesses high levels of endemism, but many of its component taxa remain unstudied. Due to the importance of tropical forests and the urgency to protect them, there is a compelling need to address this knowledge gap. To provide more information on its arthropod fauna, a Malaise trap was deployed for 12 months in a semi-degraded area of the southern Upper Paraná ecoregion of the Atlantic Forest. All specimens were DNA barcoded and the Barcode Index Number (BIN) system was employed to assign each specimen to a species proxy. DNA barcodes were obtained from 75,500 arthropods that included representatives of 8,651 BINs. Nearly 81% of these BINs were first records, highlighting the high rates of endemism and lack of study of arthropods from the Atlantic Forest. Diptera was the most abundant order, followed by Hemiptera, Lepidoptera and Hymenoptera. Diptera was also the most species-rich order, followed by Hymenoptera, Lepidoptera, and Coleoptera, a result consistent with studies in other biogeographic regions. Insects were most abundant in winter and most diverse in autumn and winter. This pattern, however, was caused mainly by the dynamics of dipteran diversity as other orders differed in their seasonal variation. The BIN composition of the insect community varied sharply through the year and also differed between the two consecutive summers included in the sampling period. The study of the 38 commonest BINs showed that seasonal patterns of abundance were not order-specific. Temperature had the strongest impact on seasonal abundance variation. Our results highlight the striking and understudied arthropod diversity of the highly fragmented Atlantic Forest, the predominance of dipterans, and the fact that abundance and richness in this insect community peak in the coolest months. Standardized studies like this generate fast and reliable biodiversity inventories and unveil ecological patterns, thus providing valuable information for conservation programs.

A DNA barcode survey of insect biodiversity in Pakistan

Although Pakistan has rich biodiversity, many groups are poorly known, particularly insects. To address this gap, we employed DNA barcoding to survey its insect diversity. Specimens obtained through diverse collecting methods at 1,858 sites across Pakistan from 2010-2019 were examined for sequence variation in the 658 bp barcode region of the cytochrome c oxidase 1 (COI) gene. Sequences from nearly 49,000 specimens were assigned to 6,590 Barcode Index Numbers (BINs), a proxy for species, and most (88%) also possessed a representative image on the Barcode of Life Data System (BOLD). By coupling morphological inspections with barcode matches on BOLD, every BIN was assigned to an order (19) and most (99.8%) were placed to a family (362). However, just 40% of the BINs were assigned to a genus (1,375) and 21% to a species (1,364). Five orders (Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera) accounted for 92% of the specimens and BINs. More than half of the BINs (59%) are so far only known from Pakistan, but others have also been reported from Bangladesh (13%), India (12%), and China (8%). Representing the first DNA barcode survey of the insect fauna in any South Asian country, this study provides the foundation for a complete inventory of the insect fauna in Pakistan while also contributing to the global DNA barcode reference library.

Unearthing soil arthropod diversity through DNA metabarcoding

DNA metabarcoding has the potential to greatly advance understanding of soil biodiversity, but this approach has seen limited application for the most abundant and species-rich group of soil fauna-the arthropods. This study begins to address this gap by comparing information on species composition recovered from metabarcoding two types of bulk samples (specimens, soil) from a temperate zone site and from bulk soil samples collected at eight sites in the Arctic. Analysis of 22 samples (3 specimen, 19 soil) revealed 410 arthropod OTUs belonging to 112 families, 25 orders, and nine classes. Studies at the temperate zone site revealed little overlap in species composition between soil and specimen samples, but more overlap at higher taxonomic levels (families, orders) and congruent patterns of α- and β-diversity. Expansion of soil analyses to the Arctic revealed locally rich, highly dissimilar, and spatially structured assemblages compatible with dispersal limited and environmentally driven assembly. The current study demonstrates that DNA metabarcoding of bulk soil enables rapid, large-scale assessments of soil arthropod diversity. However, deep sequence coverage is required to adequately capture the species present in these samples, and expansion of the DNA barcode reference library is necessary to improve taxonomic resolution of the sequences recovered through this approach.

Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR

Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means to catalogue, explore, and monitor the richness and biogeography of life on Earth. However, exploiting their full potential requires tools that connect biodiversity infrastructures and resources. As a research infrastructure developing services and technical solutions that help integrate and coordinate life science resources across Europe, ELIXIR is a key player. To identify opportunities, highlight priorities, and aid strategic thinking, here we survey approaches by which molecular technologies help inform understanding of biodiversity. We detail example use cases to highlight how DNA sequencing is: resolving taxonomic issues; Increasing knowledge of marine biodiversity; helping understand how agriculture and biodiversity are critically linked; and playing an essential role in ecological studies. Together with examples of national biodiversity programmes, the use cases show where progress is being made but also highlight common challenges and opportunities for future enhancement of underlying technologies and services that connect molecular and wider biodiversity domains. Based on emerging themes, we propose key recommendations to guide future funding for biodiversity research: biodiversity and bioinformatic infrastructures need to collaborate closely and strategically; taxonomic efforts need to be aligned and harmonised across domains; metadata needs to be standardised and common data management approaches widely adopted; current approaches need to be scaled up dramatically to address the anticipated explosion of molecular data; bioinformatics support for biodiversity research needs to be enabled and sustained; training for end users of biodiversity research infrastructures needs to be prioritised; and community initiatives need to be proactive and focused on enabling solutions. For sequencing data to deliver their full potential they must be connected to knowledge: together, molecular sequence data collection initiatives and biodiversity research infrastructures can advance global efforts to prevent further decline of Earth's biodiversity.

Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR

Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means to catalogue, explore, and monitor the richness and biogeography of life on Earth. However, exploiting their full potential requires tools that connect biodiversity infrastructures and resources. As a research infrastructure developing services and technical solutions that help integrate and coordinate life science resources across Europe, ELIXIR is a key player. To identify opportunities, highlight priorities, and aid strategic thinking, here we survey approaches by which molecular technologies help inform understanding of biodiversity. We detail example use cases to highlight how DNA sequencing is: resolving taxonomic issues; Increasing knowledge of marine biodiversity; helping understand how agriculture and biodiversity are critically linked; and playing an essential role in ecological studies. Together with examples of national biodiversity programmes, the use cases show where progress is being made but also highlight common challenges and opportunities for future enhancement of underlying technologies and services that connect molecular and wider biodiversity domains. Based on emerging themes, we propose key recommendations to guide future funding for biodiversity research: biodiversity and bioinformatic infrastructures need to collaborate closely and strategically; taxonomic efforts need to be aligned and harmonised across domains; metadata needs to be standardised and common data management approaches widely adopted; current approaches need to be scaled up dramatically to address the anticipated explosion of molecular data; bioinformatics support for biodiversity research needs to be enabled and sustained; training for end users of biodiversity research infrastructures needs to be prioritised; and community initiatives need to be proactive and focused on enabling solutions. For sequencing data to deliver their full potential they must be connected to knowledge: together, molecular sequence data collection initiatives and biodiversity research infrastructures can advance global efforts to prevent further decline of Earth's biodiversity.

Do the evolutionary interactions between moths and bats promote niche partitioning between bats and birds?

Ecological theory suggests that the coexistence of species is promoted by the partitioning of available resources, as in dietary niche partitioning where predators partition prey. Yet, the mechanisms underlying dietary niche partitioning are not always clear. We used fecal DNA metabarcoding to investigate the diets of seven nocturnal insectivorous bird and bat species. Low diet overlap (2%-22%) supported resource partitioning among all species. Differences in diet corresponded with species identity, prey detection method, and foraging behavior of predators. Insects with ultrasonic hearing capabilities were consumed significantly more often by birds than bats, consistent with an evolved avoidance of echolocating strategies. In turn, bats consumed a greater proportion of noneared insects such as spruce budworms. Overall, our results suggest that evolutionary interactions among bats and moths translate to dietary niche partitioning and coexistence among bats and nocturnal birds.

Revealing morphological characteristics of Goniodorididae genera (Mollusca: Nudibranchia)

Detailed knowledge of the anatomy of the species is an essential element in taxonomic studies, since it allows the comparison and differentiation of separate groups of taxa. It becomes especially important when considering type species, as the subsequent identification of the species that compose the taxa is based on its characteristics, considered common in the group. However, despite its relevance, there are still numerous species without detailed descriptions, being especially significant among invertebrates. The family Goniodorididae is a little-known group of nudibranchs that includes eight recognized genera: Okenia, Goniodoris, Ancula, Lophodoris, Spahria, Trapania, Goniodoridella and Murphydoris. Several of their species are not completely described, including type species, and the systematics of the family is still unclear. Here we study in detail the external morphology and internal anatomy of the type species of five of the eight Goniodorididae genera using microcomputed tomography and scanning electron microscopy. We include the species Okenia elegans, Goniodoris nodosa, Ancula gibbosa, Goniodoridella savignyi and Murphydoris singaporensis as well as one species of Trapania, T. graeffei. We describe for the first time the detailed internal anatomy of the type species Goniodoridella savignyi. The diagnostic features of each genus are compared, and a preliminary framework is shown to clarify their systematics and identifications.

A DNA barcode reference library of Portuguese mosquitoes

Mosquitoes are important biological vectors of pathogens and species identification in all life stages is the first step for effective monitoring and control of mosquito-borne diseases. Molecular methods for species identification have been developed over the last years to overcome the limitations of the taxonomic identification based on morphology. DNA barcoding, using a fragment of the mitochondrial cytochrome oxidase I (COI) gene, can be used for species identification but a reliable and comprehensive reference database of verified sequences is required. In this study, we aimed to generate a DNA barcode reference library for the identification of mosquito species from Portuguese mosquito fauna, including most relevant vector species. Mosquitoes captured under the National Vector Surveillance Program (REVIVE) were processed for DNA extraction, COI gene fragment amplification and sequencing. Nighty-eight barcode sequences were obtained, representing 26 species and 6 genera. Sequences were submitted to GenBank and BOLD and were used for validation of phenetic classification. Barcode Index Number (BIN) assignment and Automatic Barcode Gap Discovery (ABGD) were used and clustered COI sequences into twenty-five molecular operational taxonomic units (MOTUs). This is the first comprehensive study that combines morphological and molecular identification of most mosquito species present in Portugal aiming to offer a reliable framework for mosquito species identification.

Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron

Standard plant DNA barcodes based on 2-3 plastid regions, and nrDNA ITS show variable levels of resolution, and fail to discriminate among species in many plant groups. Genome skimming to recover complete plastid genome sequences and nrDNA arrays has been proposed as a solution to address these resolution limitations. However, few studies have empirically tested what gains are achieved in practice. Of particular interest is whether adding substantially more plastid and nrDNA characters will lead to an increase in discriminatory power, or whether the resolution limitations of standard plant barcodes are fundamentally due to plastid genomes and nrDNA not tracking species boundaries. To address this, we used genome skimming to recover near-complete plastid genomes and nuclear ribosomal DNA from Rhododendron species and compared discrimination success with standard plant barcodes. We sampled 218 individuals representing 145 species of this species-rich and taxonomically difficult genus, focusing on the global biodiversity hotspots of the Himalaya-Hengduan Mountains. Only 33% of species were distinguished using ITS+matK+rbcL+trnH-psbA. In contrast, 55% of species were distinguished using plastid genome and nrDNA sequences. The vast majority of this increase is due to the additional plastid characters. Thus, despite previous studies showing an asymptote in discrimination success beyond 3-4 plastid regions, these results show that a demonstrable increase in discriminatory power is possible with extensive plastid genome data. However, despite these gains, many species remain unresolved, and these results also reinforce the need to access multiple unlinked nuclear loci to obtain transformative gains in species discrimination in plants.

Integrative taxonomy of Nearctic and Palaearctic Aleocharinae: new species, synonymies, and records (Coleoptera, Staphylinidae)

A long tradition of separate Nearctic and Palaearctic taxonomic studies of the diverse aleocharine rove beetles (Coleoptera: Staphylinidae) has obscured the recognition of Holarctic species and detection of adventive species in both regions. Recently, integrated study of the two regions through detailed morphological comparisons and development of an authoritatively identified DNA barcode reference library has revealed the degree to which these two aleocharine faunas are interconnected, both naturally and through human activity. Here this approach is adopted to recognize new species, reveal Holarctic species, and recognize adventive species in both North America and Europe. The following new species are described: Isoglossatriangularis Klimaszewski, Brunke & Pentinsaari, sp. nov. from British Columbia; Gnypetaimpressicollis Klimaszewski, Brunke & Pentinsaari, sp. nov., from Ontario, Maryland and North Carolina; Aloconotapseudogregaria Klimaszewski, Brunke & Pentinsaari, sp. nov., from Ontario and Virginia; and Philhygrapseudolaevicollis Klimaszewski, Brunke & Pentinsaari, sp. nov. from eastern Canada. Dasygnypetavelata and Philhygraangusticauda are revealed to be Holarctic species, resulting in the following synonymies: Dasygnypetavelata (Erichson, 1839) = Gnypetaminuta Klimaszewski & Webster, 2008, syn. nov. and Philhygraangusticauda (Bernhauer, 1909) = Atheta (Philhygra) pinegensis Muona, 1983, syn. nov. The Nearctic species Hylotaochracea (and genus Hylota), Thecturotatenuissima, and Trichiusarobustula are newly reported from the Palaearctic region as adventive, resulting in the following synonymies: Hylotaochracea Casey, 1906 = Stichoglossa (Dexiogyia) forticornis Strand, 1939, syn. nov.; Thecturotatenuissima Casey, 1893 = Athetamarchii Dodero, 1922, syn. nov.; and Trichiusarobustula Casey, 1893 = T.immigrata Lohse, 1984, syn. nov. The Palaearctic species Amarocharaforticornis, Anomognathuscuspidatus, Oligotapumilio, and Parocyusarubicunda are newly confirmed from the Nearctic region as adventive, resulting in the following synonymies: Parocyusarubicunda (Erichson, 1837) = Chiloporaamericana Casey, 1906, syn. nov. and Anomognathuscuspidatus (Erichson, 1839) = Thecturaamericana Casey, 1893, syn. nov. The genus Dasygnypeta, sensu nov. is newly reported from North America, Paradilacra is newly reported from eastern North America, and Haploglossa is newly reported from Canada, resulting in the following synonymy: Paradilacradensissima (Bernhauer, 1909) = Gnypetasaccharina Klimaszewski & Webster, 2008, syn. nov. Native Cypheawallisi is newly reported from across Canada and C.curtula is removed from the Nearctic fauna. The status of both Gyrophaenaaffinis and Homalotaplana is uncertain but these species are no longer considered to be adventive in North America. Three new combinations are proposed: Dasygnypetabaranowskii (Klimaszewski, 2020) and D.nigrella (LeConte, 1863) (both from Gnypeta) and Mocytascopula (Casey, 1893) (from Acrotona). Dolosota Casey, 1910, syn. nov. (type species Eurypronotascopula Casey), currently a subgenus of Acrotona, is therefore synonymized with Mocyta Mulsant & Rey, 1874. Additionally, four new Canadian records and 18 new provincial and state records are reported.

Exploring the vertebrate fauna of the Bird's Head Peninsula (Indonesia, West Papua) through DNA barcodes

Biodiversity knowledge is widely heterogeneous across the Earth's biomes. Some areas, due to their remoteness and difficult access, present large taxonomic knowledge gaps. Mostly located in the tropics, these areas have frequently experienced a fast development of anthropogenic activities during the last decades and are therefore of high conservation concerns. The biodiversity hotspots of Southeast Asia exemplify the stakes faced by tropical countries. While the hotspots of Sundaland (Java, Sumatra, Borneo) and Wallacea (Sulawesi, Moluccas) have long attracted the attention of biologists and conservationists alike, extensive parts of the Sahul area, in particular the island of New Guinea, have been much less explored biologically. Here, we describe the results of a DNA-based inventory of aquatic and terrestrial vertebrate communities, which was the objective of a multidisciplinary expedition to the Bird's Head Peninsula (West Papua, Indonesia) conducted between 17 October and 20 November 2014. This expedition resulted in the assembly of 1005 vertebrate DNA barcodes. Based on the use of multiple species-delimitation methods (GMYC, PTP, RESL, ABGD), 264 molecular operational taxonomic units (MOTUs) were delineated, among which 75 were unidentified and an additional 48 were considered cryptic. This study suggests that the diversity of vertebrates of the Bird's Head is severely underestimated and considerations on the evolutionary origin and taxonomic knowledge of these biotas are discussed.

First description of a widespread Mytilus trossulus-derived bivalve transmissible cancer lineage in M. trossulus itself

Two lineages of bivalve transmissible neoplasia (BTN), BTN1 and BTN2, are known in blue mussels Mytilus. Both lineages derive from the Pacific mussel M. trossulus and are identified primarily by their unique genotypes of the nuclear gene EF1α. BTN1 is found in populations of M. trossulus from the Northeast Pacific, while BTN2 has been detected in populations of other Mytilus species worldwide but not in M. trossulus itself. Here we examined M. trossulus from the Sea of Japan (Northwest Pacific) for the presence of BTN. Using hemocytology and flow cytometry of the hemolymph, we confirmed the presence of disseminated neoplasia in our specimens. Cancerous mussels possessed the BTN2 EF1α genotype and two mitochondrial haplotypes with different recombinant control regions, similar to that of common BTN2 lineages. This is the first report of BTN2 in its original host species M. trossulus. A comparison of all available BTN and M. trossulus COI sequences suggests a common and recent origin of BTN2 diversity in populations of M. trossulus outside the Northeast Pacific, possibly in the Northwest Pacific.

A DNA barcode-based survey of wild urban bees in the Loire Valley, France

The current decline of wild bees puts important ecosystem services such as pollination at risk. Both inventory and monitoring programs are needed to understand the causes of wild bee decline. Effective insect monitoring relies on both mass-trapping methods coupled with rapid and accurate identifications. Identifying wild bees using only morphology can be challenging, in particular, specimens from mass-trapped samples which are often in poor condition. We generated DNA barcodes for 2931 specimens representing 157 species (156 named and one unnamed species) and 28 genera. Automated cluster delineation reveals 172 BINs (Barcodes Index Numbers). A total of 36 species (22.93%) were found in highly urbanized areas. The majority of specimens, representing 96.17% of the species barcoded form reciprocally exclusive groups, allowing their unambiguous identification. This includes several closely related species notoriously difficult to identify. A total of 137 species (87.26%) show a "one-to-one" match between a named species and the BIN assignment. Fourteen species (8.92%) show deep conspecific lineages with no apparent morphological differentiation. Only two species pairs shared the same BIN making their identification with DNA barcodes alone uncertain. Therefore, our DNA barcoding reference library allows reliable identification by non-experts for the vast majority of wild bee species in the Loire Valley.

Methodological considerations for monitoring soil/litter arthropods in tropical rainforests using DNA metabarcoding, with a special emphasis on ants, springtails and termites

Robust data to refute or support claims of global insect decline are currently lacking, particularly for the soil fauna in the tropics. DNA metabarcoding represents a powerful approach for rigorous spatial and temporal monitoring of the taxonomically challenging soil fauna. Here, we provide a detailed field protocol, which was successfully applied in Barro Colorado Island (BCI) in Panama, to collect soil samples and arthropods in a tropical rainforest, to be later processed with metabarcoding. We also estimate the proportion of soil/litter ant, springtail and termite species from the local fauna that can be detected by metabarcoding samples obtained either from Berlese-Tullgren (soil samples), Malaise or light traps. Each collecting method detected a rather distinct fauna. Soil and Malaise trap samples detected 213 species (73%) of all target species. Malaise trap samples detected many ant species, whereas soil samples were more efficient at detecting springtail and termite species. With respect to long-term monitoring of soil-dwelling and common species (more amenable to statistical trends), the best combination of two methods were soil and light trap samples, detecting 94% of the total of common species. A protocol including 100 soil, 40 Malaise and 80 light trap samples annually processed by metabarcoding would allow the long-term monitoring of at least 11%, 18% and 16% of species of soil/litter ants, springtails and termites, respectively, present on BCI, and a high proportion of the total abundance (up to 80% of all individuals) represented by these taxa.

BAGS: An automated Barcode, Audit & Grade System for DNA barcode reference libraries

Biodiversity studies greatly benefit from molecular tools, such as DNA metabarcoding, which provides an effective identification tool in biomonitoring and conservation programmes. The accuracy of species-level assignment, and consequent taxonomic coverage, relies on comprehensive DNA barcode reference libraries. The role of these libraries is to support species identification, but accidental errors in the generation of the barcodes may compromise their accuracy. Here, we present an R-based application, Barcode, Audit & Grade System (BAGS) (https://github.com/tadeu95/BAGS), that performs automated auditing and annotation of cytochrome c oxidase subunit I (COI) sequences libraries, for a given taxonomic group of animals, available in the Barcode of Life Data System (BOLD). This is followed by implementing a qualitative ranking system that assigns one of five grades (A to E) to each species in the reference library, according to the attributes of the data and congruency of species names with sequences clustered in barcode index numbers (BINs). Our goal is to allow researchers to obtain the most useful and reliable data, highlighting and segregating records according to their congruency. Different tests were performed to perceive its usefulness and limitations. BAGS fulfils a significant gap in the current landscape of DNA barcoding research tools by quickly screening reference libraries to gauge the congruence status of data and facilitate the triage of ambiguous data for posterior review. Thereby, BAGS has the potential to become a valuable addition in forthcoming DNA metabarcoding studies, in the long term contributing to globally improve the quality and reliability of the public reference libraries.

Water Mite Diversity (Acariformes: Prostigmata: Parasitengonina: Hydrachnidiae) from Karst Ecosystems in Southern of Mexico: A Barcoding Approach

Water mites represent the most diverse and abundant group of Arachnida in freshwater ecosystems, with about 6000 species described; however, it is estimated that this number represents only 30% of the total expected species. Despite having strong biotic interactions with their community and having the potential to be exceptional bioindicators, they are frequently excluded from studies of water quality or ecology, due to actual and perceived difficulties of taxonomic identification in this group. The objective of this study is to use the variations in the sequences of the mitochondrial cytochrome oxidase subunit I (COI), also known as the DNA barcodes region, as a tool to assess the diversity of water mites at 24 sites in the Yucatan Peninsula of Mexico. We found 77 genetic groups or putative species corresponding to 18 genera: Arrenurus, Atractides, Centrolimnesia, Eylais, Geayia, Hydrodroma, Hydryphantes, Hygrobates, Koenikea, Krendowskia, Limnesia, Limnochares, Mamersellides, Mideopsis, Neumania, Piona, Torrenticola, and Unionicola. This was significant, since there are only 35 species described for this region. Furthermore, this molecular information has allowed us to infer that there are characteristic assemblies per site. These data will facilitate the incorporation of water mites in different studies while the curatorial work continues to assign a Linnaean name.

Trans-Atlantic Distribution and Introgression as Inferred from Single Nucleotide Polymorphism: Mussels Mytilus and Environmental Factors

Large-scale climate changes influence the geographic distribution of biodiversity. Many taxa have been reported to extend or reduce their geographic range, move poleward or displace other species. However, for closely related species that can hybridize in the natural environment, displacement is not the only effect of changes of environmental variables. Another option is subtler, hidden expansion, which can be found using genetic methods only. The marine blue mussels Mytilus are known to change their geographic distribution despite being sessile animals. In addition to natural dissemination at larval phase—enhanced by intentional or accidental introductions and rafting—they can spread through hybridization and introgression with local congeners, which can create mixed populations sustaining in environmental conditions that are marginal for pure taxa. The Mytilus species have a wide distribution in coastal regions of the Northern and Southern Hemisphere. In this study, we investigated the inter-regional genetic differentiation of the Mytilus species complex at 53 locations in the North Atlantic and adjacent Arctic waters and linked this genetic variability to key local environmental drivers. Of seventy-nine candidate single nucleotide polymorphisms (SNPs), all samples were successfully genotyped with a subset of 54 SNPs. There was a clear interregional separation of Mytilus species. However, all three Mytilus species hybridized in the contact area and created hybrid zones with mixed populations. Boosted regression trees (BRT) models showed that inter-regional variability was important in many allele models but did not prevail over variability in local environmental factors. Local environmental variables described over 40% of variability in about 30% of the allele frequencies of Mytilus spp. For the 30% of alleles, variability in their frequencies was only weakly coupled with local environmental conditions. For most studied alleles the linkages between environmental drivers and the genetic variability of Mytilus spp. were random in respect to “coding” and “non-coding” regions. An analysis of the subset of data involving functional genes only showed that two SNPs at Hsp70 and ATPase genes correlated with environmental variables. Total predictive ability of the highest performing models (r² between 0.550 and 0.801) were for alleles that discriminated most effectively M. trossulus from M. edulis and M. galloprovincialis, whereas the best performing allele model (BM101A) did the best at discriminating M. galloprovincialis from M. edulis and M. trossulus. Among the local environmental variables, salinity, water temperature, ice cover and chlorophyll a concentration were by far the greatest predictors, but their predictive performance varied among different allele models. In most cases changes in the allele frequencies along these environmental gradients were abrupt and occurred at a very narrow range of environmental variables. In general, regions of change in allele frequencies for M. trossulus occurred at 8–11 psu, 0–10 °C, 60%–70% of ice cover and 0–2 mg m⁻³ of chlorophyll a, M. edulis at 8–11 and 30–35 psu, 10–14 °C and 60%–70% of ice cover and for M. galloprovincialis at 30–35 psu, 14–20 °C.