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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., (© 2021 John Wiley & Sons Ltd.)

The School Malaise Trap Program (SMTP) provides a technologically sophisticated and scientifically relevant educational experience that exposes students to the diversity of life, enhancing their understanding of biodiversity while promoting environmental stewardship. Since 2013, the SMTP has allowed 15,000 students at 350 primary and secondary schools to explore insect diversity in Canadian schoolyards. Students at each school collected hundreds of insects for an analysis of DNA sequence variation that enabled their rapid identification to a species. Through this hands-on approach, they participated in a learning exercise that conveys a real sense of scientific discovery. As well, the students contributed valuable data to the largest biodiversity genomics initiative ever undertaken: the International Barcode of Life project. To date, the SMTP has sequenced over 80,000 insect specimens, which includes representatives of 7,990 different species, nearly a tenth of the Canadian fauna. Both surprisingly and importantly, the collections generated the first DNA barcode records for 1,288 Canadian species.

Despite 250 years of modern taxonomy, there remains a large biodiversity knowledge gap. Most species remain unknown to science. DNA barcoding can help address this gap and has been used in a variety of educational contexts to incorporate original research into school curricula and informal education programmes. A growing body of evidence suggests that actively conducting research increases student engagement and retention in science. We describe case studies in five different educational settings in Canada and the USA: a programme for primary and secondary school students (ages 5-18), a year-long professional development programme for secondary school teachers, projects embedding this research into courses in a post-secondary 2-year institution and a degree-granting university, and a citizen science project. We argue that these projects are successful because the scientific content is authentic and compelling, DNA barcoding is conceptually and technically straightforward, the workflow is adaptable to a variety of situations, and online tools exist that allow participants to contribute high-quality data to the international research effort. Evidence of success includes the broad adoption of these programmes and assessment results demonstrating that participants are gaining both knowledge and confidence. There are exciting opportunities for coordination among educational projects in the future.This article is part of the themed issue 'From DNA barcodes to biomes'., (© 2016 The Authors.)

Background: Coleoptera is the most diverse order of insects (>300,000 described species), but its richness diminishes at increasing latitudes (e.g., ca. 7400 species recorded in Canada), particularly of phytophagous and detritivorous species. However, incomplete sampling of northern habitats and a lack of taxonomic study of some families limits our understanding of biodiversity patterns in the Coleoptera. We conducted an intensive biodiversity survey from 2006-2010 at Churchill, Manitoba, Canada in order to quantify beetle species diversity in this model region, and to prepare a barcode library of beetles for sub-arctic biodiversity and ecological research. We employed DNA barcoding to provide estimates of provisional species diversity, including for families currently lacking taxonomic expertise, and to examine the guild structure, habitat distribution, and biogeography of beetles in the Churchill region., Results: We obtained DNA barcodes from 3203 specimens representing 302 species or provisional species (the latter quantitatively defined on the basis of Molecular Operational Taxonomic Units, MOTUs) in 31 families of Coleoptera. Of the 184 taxa identified to the level of a Linnaean species name, 170 (92.4%) corresponded to a single MOTU, four (2.2%) represented closely related sibling species pairs within a single MOTU, and ten (5.4%) were divided into two or more MOTUs suggestive of cryptic species. The most diverse families were the Dytiscidae (63 spp.), Staphylinidae (54 spp.), and Carabidae (52 spp.), although the accumulation curve for Staphylinidae suggests that considerable additional diversity remains to be sampled in this family. Most of the species present are predatory, with phytophagous, mycophagous, and saprophagous guilds being represented by fewer species. Most named species of Carabidae and Dytiscidae showed a significant bias toward open habitats (wet or dry). Forest habitats, particularly dry boreal forest, although limited in extent in the region, were undersampled., Conclusions: We present an updated species list for this region as well as a species-level DNA barcode reference library. This resource will facilitate future work, such as biomonitoring and the study of the ecology and distribution of larvae.

The relationship between species diversity and environmental parameters is poorly understood for the mobile macrofauna of deep-sea habitats due to under-sampling and subsequent lack of accurate taxonomic information. To redress this, cytochrome oxidase c subunit I (COI) DNA sequences were used to estimate species diversity and to compare phoxocephalid amphipod assemblages among 20 stations encompassing a range of environmental conditions. Two regions, east (Chatham Rise) and west (Challenger Plateau) of New Zealand were sampled to depths of 200-1200 m with an epibenthic sled. Using a comparison among identified morphospecies, we found a clear gap in sequence divergences between 6% and 13% and used a 6% threshold to designate molecular operational taxonomic units (MOTUs), as a surrogate to putative species. DNA sequences (n = 297) revealed high total diversity (n = 49 MOTUs), as well as high beta diversity (28 MOTUs found at single location only). Novel phoxocephalid MOTUs were found at most stations, especially on Challenger Plateau and the flanks of Chatham Rise. Analyses of interstation assemblages revealed a major split between regions, indicating minimal overlap in taxon distributions. A cluster of highly similar stations was identified, broadly distributed over the crest of Chatham Rise, in association with elevated food availability, probably resulting from higher surface productivity and relatively shallow depth. Accordingly, multivariate analysis revealed a strong correlation between phoxocephalid assemblages and food supply. This study highlights the value of molecular approaches, in particular COI sequences, for quantifying and comparing diversity in under-sampled and/or under-studied taxa., (© 2012 Blackwell Publishing Ltd.)

DNA barcoding is a promising approach to the diagnosis of biological diversity in which DNA sequences serve as the primary key for information retrieval. Most existing software for evolutionary analysis of DNA sequences was designed for phylogenetic analyses and, hence, those algorithms do not offer appropriate solutions for the rapid, but precise analyses needed for DNA barcoding, and are also unable to process the often large comparative datasets. We developed a flexible software tool for DNA taxonomy, named TaxI. This program calculates sequence divergences between a query sequence (taxon to be barcoded) and each sequence of a dataset of reference sequences defined by the user. Because the analysis is based on separate pairwise alignments this software is also able to work with sequences characterized by multiple insertions and deletions that are difficult to align in large sequence sets (i.e. thousands of sequences) by multiple alignment algorithms because of computational restrictions. Here, we demonstrate the utility of this approach with two datasets of fish larvae and juveniles from Lake Constance and juvenile land snails under different models of sequence evolution. Sets of ribosomal 16S rRNA sequences, characterized by multiple indels, performed as good as or better than cox1 sequence sets in assigning sequences to species, demonstrating the suitability of rRNA genes for DNA barcoding.

Background Traditional biomonitoring approaches have delivered a basic understanding of biodiversity, but they cannot support the large-scale assessments required to manage and protect entire ecosystems. This study used DNA metabarcoding to assess spatial and temporal variation in species richness and diversity in arthropod communities from 52 protected areas spanning 3 Canadian ecoregions. Results This study revealed the presence of 26,263 arthropod species in the 3 ecoregions and indicated that at least another 3,000–5,000 await detection. Results further demonstrate that communities are more similar within than between ecoregions, even after controlling for geographical distance. Overall α-diversity declined from east to west, reflecting a gradient in habitat disturbance. Shifts in species composition were high at every site, with turnover greater than nestedness, suggesting the presence of many transient species. Conclusions Differences in species composition among their arthropod communities confirm that ecoregions are a useful synoptic for biogeographic patterns and for structuring conservation efforts. The present results also demonstrate that metabarcoding enables large-scale monitoring of shifts in species composition, making it possible to move beyond the biomass measurements that have been the key metric used in prior efforts to track change in arthropod communities. [ABSTRACT FROM AUTHOR]

Two regions of mitochondrial (mt) DNA, cytochrome c oxidase subunit 1 (COI) and 16S rRNA, were sequenced in nine species of Betta from Thailand and Indonesia. Most species showed little intraspecific COI variation (adjusted mean = 0·48%) including the putative species Betta sp. Mahachai, but one species ( Betta smaragdina) included three lineages showing much greater divergence (7·03-13·48%) that probably represent overlooked species. These findings were confirmed by maximum likelihood analysis and Bayesian inference, which revealed well-supported corresponding monophyletic clades. Based on these results and morphological differences, the putative species Betta sp. Mahachai from central Thailand is a species distinct from other members of the B. splendens group and represents a new and hitherto undescribed species. Furthermore, this study also demonstrated the probable existence of two overlooked Betta species found in the Khorat plateau basin, illustrating the utility of mitochondrial genetic markers in the revelation of overlooked diversity. [ABSTRACT FROM AUTHOR]