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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.

We report one year (2013-2014) of biomonitoring an insect community in a tropical old-growth rain forest, during construction of an industrial-level geothermal electricity project. This is the first-year reaction by the species-rich insect biodiversity; six subsequent years are being analyzed now. The site is on the margin of a UNESCO Natural World Heritage Site, Área de Conservación Guanacaste (ACG), in northwestern Costa Rica. This biomonitoring is part of Costa Rica's ongoing efforts to sustainably retain its wild biodiversity through biodevelopmental integration with its societies. Essential tools are geothermal engineering needs, entomological knowledge, insect species-rich forest, government-NGO integration, common sense, DNA barcoding for species-level identification, and Malaise traps. This research is tailored for integration with its society at the product level. We combine an academic view with on-site engineering decisions. This biomonitoring requires alpha-level DNA barcoding combined with centuries of morphology-based entomological taxonomy and ecology. Not all desired insect community analyses are performed; they are for data from subsequent years combined with this year. We provide enough analysis to be used by both guilds now. This biomonitoring has shown, for the first year, that the geothermal project impacts only the biodiversity within a zone less than 50 m from the project margin. Key words: DNA barcode, geothermal project, Costa Rica, biomonitoring with insects, ICE/ACG/SINAC/MINAE/GDFCF. Les auteurs rapportent les résultats d'une première année (2013-2014) de biosurveillance d'une communauté d'insectes dans une forêt tropicale ancienne, au cours de la construction d'un complexe industriel de génération d'électricité géothermique. Il s'agit de la première année de réaction de cette communauté d'insectes riche en espèces; six années subséquentes sont en cours d'analyse. Le site est situé à la marge d'un site du Patrimoine mondial de l'UNESCO, l'Área de Conservación Guanacaste (ACG), dans le nord-ouest du Costa Rica. Ce travail de biosurveillance s'inscrit dans les efforts en cours au Costa Rica pour maintenir de manière durable sa biodiversité sauvage via une intégration bio-développementale avec ses sociétés. Les outils essentiels en sont les besoins en génie géothermique, les connaissances en entomologie, une forêt riche en espèces, une intégration gouvernement-ONG, le sens commun, le codage à barres de l'ADN pour l'identification au niveau de l'espèce et les pièges Malaise. Cette recherche est faite sur mesure pour favoriser l'intégration avec la société au niveau du produit. Les auteurs combinent une vision académique avec la prise de décisions d'ingénierie sur le site. La biosurveillance nécessite un codage à barres de niveau alpha combiné avec une taxonomie et une écologie séculaires fondées sur la morphologie. Ce ne sont pas toutes les analyses de communautés d'insectes qui sont réalisées; elles le seront pour les données des années subséquentes lorsque celles-ci auront été combinées aux données de cette année. Les auteurs réalisent suffisamment d'analyses pour être utiles aux deux guildes pour l'instant. Cette biosurveillance a montré, pour la première année, que le projet de géothermie touche uniquement la biodiversité située dans une zone à moins de 50 m de la marge du projet. [Traduit par la Rédaction] Mots-clés: codes-barres à l'ADN, projet de géothermie, Costa Rica, biosurveillance d'insectes, ICE/ACG/SINAC/MINAE/GDFCF., Introduction Philosophical The detailed reactions of the biodiversity of whole terrestrial communities of tropical wild eukaryotic biodiversity, to industrial-scale perturbations, have not yet become a major topic of research interest [...]

Biodiversity research in tropical ecosystems--popularized as the most biodiverse habitats on Earth--often neglects invertebrates, yet invertebrates represent the bulk of local species richness. Insect communities in particular remain strongly impeded by both Linnaean and Wallacean shortfalls, and identifying species often remains a formidable challenge inhibiting the use of these organisms as indicators for ecological and conservation studies. Here we use DNA barcoding as an alternative to the traditional taxonomic approach for characterizing and comparing the diversity of moth communities in two different ecosystems in Gabon. Though sampling remains very incomplete, as evidenced by the high proportion (59%) of species represented by singletons, our results reveal an outstanding diversity. With about 3500 specimens sequenced and representing 1385 BINs (Barcode Index Numbers, used as a proxy to species) in 23 families, the diversity of moths in the two sites sampled is higher than the current number of species listed for the entire country, highlighting the huge gap in biodiversity knowledge for this country. Both seasonal and spatial turnovers are strikingly high (18.3% of BINs shared between seasons, and 13.3% between sites) and draw attention to the need to account for these when running regional surveys. Our results also highlight the richness and singularity of savannah environments and emphasize the status of Central African ecosystems as hotspots of biodiversity. Key words: community ecology, DNA barcodes, Lepidoptera, taxonomic deficit, tropical Africa. La recherche sur la biodiversite dans les ecosystemes tropicaux--presentes comme les habitats les plus riches en biodiversite sur la Terre--neglige souvent les invertebres qui constituent pourtant la part la plus importante de cette richesse en especes. Les communautes d'insectes en particulier sont particulierement affectees par les lacunes de connaissances, tant d'un point de vue taxonomique (le deficit Linneen) que du point de vue de notre comprehension de la distribution des especes (le deficit Wallaceen), de telle maniere que l'identification des especes demeure un defi considerable, limitant l'utilisation de ces de ces organismes comme indicateurs dans le cadre d'etudes d'ecologie et de conservation. Dans ce travail, les auteurs utilisent les codes-barres ADN comme alternative a l'approche taxonomique conventionnelle pour caracteriser et comparer la diversite des communautes de papillons de nuit au sein de deux ecosystemes contrastes au Gabon. Bien que l'echantillonnage demeure tres incomplet, comme en temoigne la grande proportion (59 %) d'especes presentes sous forme de singleton, les resultats revelent une diversite extraordinaire. Avec ses 3500 specimens sequences, lesquels englobent 1385 BIN (<< Barcode Index Number >>, assimiles a des especes) au sein de 23 familles, la diversite des papillons de nuit au sein des deux sites echantillonnes est plus elevee que le nombre total d'especes jusqu'alors repertoriees pour le pays entier. Ceci souligne les lacunes enormes en matiere de connaissance de la biodiversite de ce pays. Le taux de remplacement des especes, tant saisonnier que spatial, est etonnamment eleve (18,3 % des BIN partages entre saisons, 13,3 % entre les deux sites), ce qui indique la necessite d'en tenir compte lors de la realisation d'inventaires regionaux. Ces resultats soulignent egalement la richesse et la singularite des savanes et font ressortir le fait que les ecosystemes de l'Afrique Centrale constituent des zones extremement riches en biodiversite. Mots-cles : ecologie des communautes, codes-barres ADN, lepidopteres, deficit taxonomique, Afrique tropicale., Introduction Tropical ecosystems host unrivalled species richness (Kier et al. 2005; Myers 1984; Myerset al. 2000),a fact that has long captivated public attention and raised concerns about the way to [...]

Madagascar is a prime evolutionary hotspot globally, but its unique biodiversity is under threat, essentially from anthropogenic disturbance. There is a race against time to describe and protect the Madagascan endangered biota. Here we present a first molecular characterization of the micromoth fauna of Madagascar. We collected 1572 micromoths mainly using light traps in both natural and anthropogenically disturbed habitats in 24 localities across eastern and northwest Madagascar. We also collected 1384 specimens using a Malaise trap in a primary rain forest at Andasibe, eastern Madagascar. In total, we DNA barcoded 2956 specimens belonging to 1537 Barcode Index Numbers (BINs), 88.4% of which are new to BOLD. Only 1.7% of new BINs were assigned to species. Of 47 different families found, Dryadaulidae, Bucculatricidae, Bedelliidae, Batrachedridae, and Blastobasidae are newly reported for Madagascar and the recently recognized Tonzidae is confirmed. For test faunas of Canada and Australia, 98.9%-99.4% of Macroheterocera BINs exhibited the molecular synapomorphy of a phenylalanine in the 177th complete DNA barcode codon. Non-macroheteroceran BINs could thus be sifted out efficiently in the Malaise sample. The Madagascar micromoth fauna shows highest affinity with the Afrotropics (146 BINs also occur in the African continent). We found 22 recognised pests or invasive species, mostly occurring in disturbed habitats. Malaise trap samples show high temporal turnover and alpha diversity with as many as 507 BINs collected; of these, astonishingly, 499 (98.4%) were novel to BOLD and 292 (57.6%) were singletons. Our results provide a baseline for future surveys across the island. Key words: Africa, invasive alien species, Lepidoptera, Malaise trap, plant pests. Madagascar est un haut lieu de l'evolution au niveau mondial, mais sa biodiversite unique est menacee, essentiellement en raison de perturbations anthropogeniques. Une course contre la montre est engagee pour decrire et proteger le biote malgache menace. Dans ce travail, les auteurs presentent une premiere caracterisation moleculaire des << microlepidopteres >> de Madagascar. Les auteurs ont recolte 1572 specimens en utilisant principalement des pieges lumineux (dans des milieux tantot naturels, tantot perturbes par l'Homme) au sein de 24 localites dispersees a travers l'est et le nord-ouest de Madagascar. Ils ont aussi collecte 1384 specimens a l'aide d'un piege Malaise dans une foret primaire humide a Andasibe. Au total, les codes-barres ADN ont ete sequences pour 2956 specimens correspondant a 1537 BIN, dont 88,4 % sont inedits dans BOLD. Seuls 1,7 % des nouveaux BIN ont ete assignes a une espece connue. Parmi les 47 familles trouvees, les Dryadaulidae, Bucculatricidae, Bedelliidae, Batrachedridae et Blastobasidae sont signales pour la premiere fois de Madagascar. La faune etudiee presente la plus grande affinite avec l'ecozone afrotropicale (dans laquelle se retrouvent 146 BIN). Les auteurs ont trouve 22 ravageurs connus ou especes envahissantes, principalement dans les habitats perturbes. Les specimens provenant des pieges Malaise different au fil du temps et presentent une grande diversite alpha, leur total pouvant atteindre 507 BIN. Parmi ceux-ci, etonnamment, 499 (98,4 %) sont inedits dans BOLD et 292 (57,6 %) ont ete vus une seule fois. Ces resultats fournissent un referentiel pour de futures etudes dans d'autres regions de l'ile. Mots-cles : Afrique, especes envahissantes, Lepidoptera, piege Malaise, ravageurs de plantes., Introduction Madagascar is one of the top priority global hotspots for biodiversity conservation with high endemicity and under large anthropogenic pressure (Vences et al. 2009). There is an urgent need [...]

Current understanding of ecological and evolutionary processes underlying island biodiversity is heavily shaped by empirical data from plants and birds, although arthropods comprise the overwhelming majority of known animal species, and as such can provide key insights into processes governing biodiversity. Novel high throughput sequencing (HTS) approaches are now emerging as powerful tools to overcome limitations in the availability of arthropod biodiversity data, and hence provide insights into these processes. Here, we explored how these tools might be most effectively exploited for comprehensive and comparable inventory and monitoring of insular arthropod biodiversity. We first reviewed the strengths, limitations and potential synergies among existing approaches of high throughput barcode sequencing. We considered how this could be complemented with deep learning approaches applied to image analysis to study arthropod biodiversity. We then explored how these approaches could be implemented within the framework of an island Genomic Observatories Network (iGON) for the advancement of fundamental and applied understanding of island biodiversity. To this end, we identified seven island biology themes at the interface of ecology, evolution and conservation biology, within which collective and harmonized efforts in HTS arthropod inventory could yield significant advances in island biodiversity research. [ABSTRACT FROM AUTHOR]

Abstract: It is essential that any DNA barcode reference library be based upon correctly identified specimens. The Barcode of Life Data Systems (BOLD) requires information such as images, geo-referencing, and [...]

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 offsite 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. [ABSTRACT FROM AUTHOR]

Abstract: The ability of a 650 base pair section of the mitochondrial cytochrome c oxidase I (COI) gene to provide species-level identifications has been demonstrated for large taxonomic assemblages of [...]

Arthropod abundance, biomass and taxonomic diversity are key metrics often used to assess the efficacy of restoration efforts. Gathering these metrics is a slow and laborious process, quantified by an expert manually sorting and weighing arthropod specimens. We present a tool to accelerate bulk arthropod classification and biomass estimates utilizing machine learning methods for computer vision.Our approach requires pre‐sorted arthropod samples to create a training dataset. We construct a dataset considering 18 terrestrial arthropod functional groups collected in southern Ontario, Canada. The dataset contains 517 high‐resolution images with approximately 20 individuals per image taken from either a petri dish or a bulk tray. Our tool uses the watershed algorithm to obtain precisely cropped individuals without any object annotations. After manually sorting cropped images of biological 'debris' and petri dish edges, three classifiers, DenseNet121, ResNet101 and MobileNetv2, each with trade‐offs of computational efficiency versus accuracy, are trained and compared to predict arthropod functional groups for each cropped individual. To calculate biomass, we compare seven linear and nonlinear models considering the arthropod pixel masks obtained using the watershed algorithm, in combination with images of a single function group with recorded weights, to calculate the per pixel density per functional group.From our experimentation, we recommend using DenseNet121 as it had the highest top‐1 functional group classification accuracy, likely a result of being the model with the largest number of parameters, with 86.14% considering the 20 labelled classes (18 arthropods plus debris and petri dish edge) in comparison to ResNet101 (85.10%) and MobileNetv2 (84.94%). For biomass estimation, we recommend using the average per pixel density which had the highest ranked performance considering both total error, 0.043 g (0.855% error), and cumulative class‐specific error, 1.62 g (40.67% average error across all classes), in comparison to the total ground truth biomass of 5.10 g. Our estimated Simpson's Index of Diversity was 0.9404 in comparison to the ground truth 0.9408.Our method simultaneously classifies >1,000 arthropods to functional groupings while estimating total and class specific biomass, without any computer vision bounding box or mask annotations, all from a single photo. We release our code and dataset to further research efforts in computer vision for arthropod classification. [ABSTRACT FROM AUTHOR]

Although the butterflies of North America have received considerable taxonomic attention, overlooked species and instances of hybridization continue to be revealed. The present study assembles a DNA barcode reference library for this fauna to identify groups whose patterns of sequence variation suggest the need for further taxonomic study. Based on 14,626 records from 814 species, DNA barcodes were obtained for 96% of the fauna. The maximum intraspecific distance averaged 1/4 the minimum distance to the nearest neighbor, producing a barcode gap in 76% of the species. Most species (80%) were monophyletic, the others were para- or polyphyletic. Although 15% of currently recognized species shared barcodes, the incidence of such taxa was far higher in regions exposed to Pleistocene glaciations than in those that were ice-free. Nearly 10% of species displayed high intraspecific variation (>2.5%), suggesting the need for further investigation to assess potential cryptic diversity. Aside from aiding the identification of all life stages of North American butterflies, the reference library has provided new perspectives on the incidence of both cryptic and potentially over-split species, setting the stage for future studies that can further explore the evolutionary dynamics of this group. [ABSTRACT FROM AUTHOR]