The School Malaise Trap Program: Coupling educational outreach with scientific discovery

Taxonomic identification accuracy from BOLD and GenBank databases using over a thousand insect DNA barcodes from Colombia

Recent declines of insect populations at high rates have resulted in the need to develop a quick method to determine their diversity and to process massive data for the identification of species of highly diverse groups. A short sequence of DNA from COI is widely used for insect identification by comparing it against sequences of known species. Repositories of sequences are available online with tools that facilitate matching of the sequences of interest to a known individual. However, the performance of these tools can differ. Here we aim to assess the accuracy in identification of insect taxonomic categories from two repositories, BOLD Systems and GenBank. This was done by comparing the sequence matches between the taxonomist identification and the suggested identification from the platforms. We used 1,160 COI sequences representing eight orders of insects from Colombia. After the comparison, we reanalyzed the results from a representative subset of the data from the subfamily Scarabaeinae (Coleoptera). Overall, BOLD systems outperformed GenBank, and the performance of both engines differed by orders and other taxonomic categories (species, genus and family). Higher rates of accurate identification were obtained at family and genus levels. The accuracy was higher in BOLD for the order Coleoptera at family level, for Coleoptera and Lepidoptera at genus and species level. Other orders performed similarly in both repositories. Moreover, the Scarabaeinae subset showed that species were correctly identified only when BOLD match percentage was above 93.4% and a total of 85% of the samples were correctly assigned to a taxonomic category. These results accentuate the great potential of the identification engines to place insects accurately into their respective taxonomic categories based on DNA barcodes and highlight the reliability of BOLD Systems for insect identification in the absence of a large reference database for a highly diverse country.

Excluding spatial sampling bias does not eliminate oversplitting in DNA-based species delimitation analyses

DNA barcoding and DNA-based species delimitation are major tools in DNA taxonomy. Sampling has been a central debate in this context, because the geographical composition of samples affects the accuracy and performance of DNA barcoding. Performance of complex DNA-based species delimitation is to be tested under simpler conditions in absence of geographic sampling bias. Here, we present an empirical dataset sampled from a single locality in a Southeast-Asian biodiversity hotspot (Laos: Phou Pan mountain). We investigate the performance of various species delimitation approaches on a megadiverse assemblage of herbivorous chafer beetles (Coleoptera: Scarabaeidae) to infer whether species delimitation suffers in the same way from exaggerate infraspecific variation despite the lack of geographic genetic variation that led to inconsistencies between entities from DNA-based and morphology-based species inference in previous studies. For this purpose, a 658 bp fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) was analyzed for a total of 186 individuals of 56 morphospecies. Tree-based and distance-based species delimitation methods were used. All approaches showed a rather limited match ratio (max. 77%) with morphospecies. Poisson tree process (PTP) and statistical parsimony network analysis (TCS) prevailingly over-splitted morphospecies, while 3% clustering and Automatic Barcode Gap Discovery (ABGD) also lumped several species into one entity. ABGD revealed the highest congruence between molecular operational taxonomic units (MOTUs) and morphospecies. Disagreements between morphospecies and MOTUs have to be explained by historically acquired geographic genetic differentiation, incomplete lineage sorting, and hybridization. The study once again highlights how important morphology still is in order to correctly interpret the results of molecular species delimitation.

The Future of DNA Barcoding: Reflections from Early Career Researchers

Over the last two decades, the use of DNA barcodes has transformed our ability to identify and assess life on our planet. Both strengths and weaknesses of the method have been exemplified through thousands of peer-reviewed scientific articles. Given the novel sequencing approaches, currently capable of generating millions of reads at low cost, we reflect on the questions: What will the future bring for DNA barcoding? Will identification of species using short, standardized fragments of DNA stand the test of time? We present reflected opinions of early career biodiversity researchers in the form of a SWOT analysis and discuss answers to these questions.

Standards and Best Practices for Monitoring and Benchmarking Insects

Benchmark studies of insect populations are increasingly relevant and needed amid accelerating concern about insect trends in the Anthropocene. The growing recognition that insect populations may be in decline has given rise to a renewed call for insect population monitoring by scientists, and a desire from the broader public to participate in insect surveys. However, due to the immense diversity of insects and a vast assortment of data collection methods, there is a general lack of standardization in insect monitoring methods, such that a sudden and unplanned expansion of data collection may fail to meet its ecological potential or conservation needs without a coordinated focus on standards and best practices. To begin to address this problem, we provide simple guidelines for maximizing return on proven inventory methods that will provide insect benchmarking data suitable for a variety of ecological responses, including occurrence and distribution, phenology, abundance and biomass, and diversity and species composition. To track these responses, we present seven primary insect sampling methods—malaise trapping, light trapping, pan trapping, pitfall trappings, beating sheets, acoustic monitoring, and active visual surveys—and recommend standards while highlighting examples of model programs. For each method, we discuss key topics such as recommended spatial and temporal scales of sampling, important metadata to track, and degree of replication needed to produce rigorous estimates of ecological responses. We additionally suggest protocols for scalable insect monitoring, from backyards to national parks. Overall, we aim to compile a resource that can be used by diverse individuals and organizations seeking to initiate or improve insect monitoring programs in this era of rapid change.

The genus Vipio Latreille (Hymenoptera, Braconidae) in the Neotropical Region

The genus Vipio Latreille is revised for the Neotropical region (south of Nicaragua). All species are fully illustrated. Thirteen species are recognised of which five (V.boliviensis, V.carinatus, V.godoyi, V.hansoni, and V.lavignei) are described as new, all with descriptions attributable to Inayatullah, Shaw & Quicke. All previously described Neotropical species are redescribed. A key is included for the identification of the Vipio species known from the Americas south of Nicaragua, and all species are illustrated.

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

The reliable taxonomic identification of organisms through DNA sequence data requires a well parameterized library of curated reference sequences. However, it is estimated that just 15% of described animal species are represented in public sequence repositories. To begin to address this deficiency, we provide DNA barcodes for 1,500,003 animal specimens collected from 23 terrestrial and aquatic ecozones at sites across Canada, a nation that comprises 7% of the planet's land surface. In total, 14 phyla, 43 classes, 163 orders, 1123 families, 6186 genera, and 64,264 Barcode Index Numbers (BINs; a proxy for species) are represented. Species-level taxonomy was available for 38% of the specimens, but higher proportions were assigned to a genus (69.5%) and a family (99.9%). Voucher specimens and DNA extracts are archived at the Centre for Biodiversity Genomics where they are available for further research. The corresponding sequence and taxonomic data can be accessed through the Barcode of Life Data System, GenBank, the Global Biodiversity Information Facility, and the Global Genome Biodiversity Network Data Portal.

DNA barcodes reveal 63 overlooked species of Canadian beetles (Insecta, Coleoptera)

This study demonstrates the power of DNA barcoding to detect overlooked and newly arrived taxa. Sixty-three species of Coleoptera representing 25 families are studied based on DNA barcode data and morphological analysis of the barcoded specimens. Three of the species involve synonymies or previous taxonomic confusion in North America, while the first Canadian records are published for 60 species. Forty-two species are adventive in North America, and 40 of these adventive species originate from the Palaearctic region. Three genera are recorded from the Nearctic region for the first time: Coelostoma Brullé, 1835 (Hydrophilidae), Scydmoraphes Reitter, 1891 (Staphylinidae), and Lythraria Bedel, 1897 (Chrysomelidae). Two new synonymies are established: Mycetoporus triangulatus Campbell, 1991 (Staphylinidae) is a junior synonym of Mycetoporus reichei Pandellé, 1869, syn. nov. while Bledius philadelphicus Fall, 1919 (Staphylinidae) is a junior synonym of Bledius gallicus (Gravenhorst, 1806), syn. nov. The previously suggested move of Ctenicera tigrina (Fall, 1901) to the genus Pseudanostirus Dolin, 1964 (Elateridae) is formalized, resulting in Pseudanostirus tigrinus (Fall, 1901), comb. nov.

Molecular evolution of cytochrome C oxidase-I protein of insects living in Saudi Arabia

The study underpins barcode characterization of insect species collected from Saudi Arabia and explored functional constraints during evolution at the DNA and protein levels to expect the possible mechanisms of protein evolution in insects. Codon structure designated AT-biased insect barcode of the cytochrome C oxidase I (COI). In addition, the predicted 3D structure of COI protein indicated tyrosine in close proximity with the heme ligand, depicted substitution to phenylalanine in two Hymenopteran species. This change resulted in the loss of chemical bonding with the heme ligand. The estimated nucleotide substitution matrices in insect COI barcode generally showed a higher probability of transversion compared with the transition. Computations of codon-by-codon nonsynonymous substitutions in Hymenopteran and Hemipteran species indicated that almost half of the codons are under positive evolution. Nevertheless, codons of COI barcode of Coleoptera, Lepidoptera and Diptera are mostly under purifying selection. The results reinforce that codons in helices 2, 5 and 6 and those in loops 2–3 and 5–6 are mostly conserved and approach strong purifying selection. The overall results argue the possible evolutionary position of Hymenopteran species among those of other insects.

Expedited assessment of terrestrial arthropod diversity by coupling Malaise traps with DNA barcoding 1

Monitoring changes in terrestrial arthropod communities over space and time requires a dramatic increase in the speed and accuracy of processing samples that cannot be achieved with morphological approaches. The combination of DNA barcoding and Malaise traps allows expedited, comprehensive inventories of species abundance whose cost will rapidly decline as high-throughput sequencing technologies advance. Aside from detailing protocols from specimen sorting to data release, this paper describes their use in a survey of arthropod diversity in a national park that examined 21 194 specimens representing 2255 species. These protocols can support arthropod monitoring programs at regional, national, and continental scales.

Stigmella multispicata Rociene. & Stonis, an Asian leafminer on Siberian elm, now widespread in eastern North America (Lepidoptera, Nepticulidae)

Stigmellamultispicata Rocienė & Stonis, 2014, previously known from the single male holotype from Primorye, Russia, is reported as a new invasive species mining leaves of Siberian elm, Ulmuspumila L., in eastern North America. Both adults and leafmines have been reported from many sites as unidentified Nepticulidae since 2010. Crucial for the identification was a match of the DNA barcode of a single larva collected on Ulmuspumila in Beijing with adults from North America. The single larva constitutes a new record for China. Stigmellamultispicata is closely related to the European S.ulmivora (Fologne, 1860), feeding likewise on Ulmus, but differs in details of external morphology and genitalia, particularly in the female, where S.multispicata has a remarkable elongated narrow ovipositor, suitable for oviposition in underside hairy leaf vein axils, where all mines start. In North America S.multispicata is the only Ulmus-feeding nepticulid with green larvae. Currently the species is known from USA: Illinois, Indiana, Iowa, Maryland, Massachusetts, Minnesota, New York, Ohio, Tennessee, Wisconsin, and Canada: Ontario and Québec. In Sagaponack, on Long Island, New York, larvae have been reported to occur en masse on Siberian elms from at least two sites. The current distribution could be reconstructed thanks also to many online photographs from observation websites. The species is redescribed, with the first descriptions of female, larva, and leafmine, and compared with S.ulmivora, which is fully redescribed. The two native North American nepticulid Ulmus leafminers, S.apicialbella (Chambers, 1873) and Ectoedemiaulmella (Braun, 1912), are diagnosed and new provincial and state records are provided. A key to linear mines on Ulmus in North America is provided. We suspect that trade of live plants through nurseries played a role in the sudden spread of this invasive species.

Insect diversity in the Saharo-Arabian region: Revealing a little-studied fauna by DNA barcoding

Although insects dominate the terrestrial fauna, sampling constraints and the poor taxonomic knowledge of many groups have limited assessments of their diversity. Passive sampling techniques and DNA-based species assignments now make it possible to overcome these barriers. For example, Malaise traps collect specimens with minimal intervention while the Barcode Index Number (BIN) system automates taxonomic assignments. The present study employs Malaise traps and DNA barcoding to extend understanding of insect diversity in one of the least known zoogeographic regions, the Saharo-Arabian. Insects were collected at four sites in three countries (Egypt, Pakistan, Saudi Arabia) by deploying Malaise traps. The collected specimens were analyzed by sequencing 658 bp of cytochrome oxidase I (DNA barcode) and assigning BINs on the Barcode of Life Data Systems. The year-long deployment of a Malaise trap in Pakistan and briefer placements at two Egyptian sites and at one in Saudi Arabia collected 53,092 specimens. They belonged to 17 insect orders with Diptera and Hymenoptera dominating the catch. Barcode sequences were recovered from 44,432 (84%) of the specimens, revealing the occurrence of 3,682 BINs belonging to 254 families. Many of these taxa were uncommon as 25% of the families and 50% of the BINs from Pakistan were only present in one sample. Family and BIN counts varied significantly through the year, but diversity indices did not. Although more than 10,000 specimens were analyzed from each nation, just 2% of BINs were shared by Pakistan and Saudi Arabia, 4% by Egypt and Pakistan, and 7% by Egypt and Saudi Arabia. The present study demonstrates how the BIN system can circumvent the barriers imposed by limited access to taxonomic specialists and by the fact that many insect species in the Saharo-Arabian region are undescribed.

Improved protocols to accelerate the assembly of DNA barcode reference libraries for freshwater zooplankton

Currently, freshwater zooplankton sampling and identification methodologies have remained virtually unchanged since they were first established in the beginning of the XX century. One major contributing factor to this slow progress is the limited success of modern genetic methodologies, such as DNA barcoding, in several of the main groups. This study demonstrates improved protocols which enable the rapid assessment of most animal taxa inhabiting any freshwater system by combining the use of light traps, careful fixation at low temperatures using ethanol, and zooplankton-specific primers. We DNA-barcoded 2,136 specimens from a diverse array of taxonomic assemblages (rotifers, mollusks, mites, crustaceans, insects, and fishes) from several Canadian and Mexican lakes with an average sequence success rate of 85.3%. In total, 325 Barcode Index Numbers (BINs) were detected with only three BINs (two cladocerans and one copepod) shared between Canada and Mexico, suggesting a much narrower distribution range of freshwater zooplankton than previously thought. This study is the first to broadly explore the metazoan biodiversity of freshwater systems with DNA barcodes to construct a reference library that represents the first step for future programs which aim to monitor ecosystem health, track invasive species, or improve knowledge of the ecology and distribution of freshwater zooplankton.

Diversity of parasitoid and parasitic wasps across a latitudinal gradient: Using public DNA records to work within a taxonomic impediment

The diversity of insect parasitoids (Hymenoptera) has long been thought to be anomalous because it doesn’t appear to increase rapidly with decreasing latitude. However, due to the presence of undiscovered cryptic species and the under-sampling of hyper-diverse tropical areas, such apparently anomalous gradients may, in fact, be artifacts of limited geographic and taxonomic sampling. We attempted to circumvent such taxonomic impediments by elucidating a diversity/latitude relationship for parasitoid wasps, using publicly available DNA sequences to quantify diversity (via a species proxy molecular operational taxonomic unit (the DNA Barcode Index Number) and phylogenetic diversity) across a latitudinal gradient of ∼5000 km. We compared these diversity values to the abiotic factors (temperature and precipitation) that may drive the diversity/latitude relationship. We found no significant relationship between either diversity measure with latitude or with the environmental variables. Although ours is the first work to enumerate different DNA-based measures of parasitoid diversity across this geographic scale in a standardized fashion using publicly available sequences, further standardized collections over long time periods and a rapid movement of sequences into the public arena are needed to facilitate the further testing of macroecological trends elucidated with public DNA sequence libraries.