More than 80% of all animal species remain unknown to science. Most these live in the tropics and belong taxa that combine small body size with high specimen abundance large richness. For such clades, using morphology for discovery is slow because numbers specimens must be sorted based on detailed microscopic investigations. Fortunately, could greatly accelerated if DNA sequences used sorting species. Morphological verification "molecular operational taxonomic units" (mOTUs) then dissection...

DNA barcodes are a useful tool for discovering, understanding, and monitoring biodiversity which critical tasks at time of rapid loss. However, widespread adoption requires cost-effective simple barcoding methods. We here present workflow that satisfies these conditions. It was developed via "innovation through subtraction" thus minimal lab equipment, can be learned within days, reduces the barcode sequencing cost to < 10 cents, allows fast turnaround from specimen sequence by using portable...

Abstract New, rapid, accurate, scalable, and cost-effective species discovery delimitation methods are needed for tackling “dark taxa,” here defined as groups which $&amp;lt;$10$\%$ of all described the estimated diversity exceeds 1,000 species. Species these taxa should be based on multiple data sources (“integrative taxonomy”) but collecting types risks impeding a process that is already too slow. We develop large-scale integrative taxonomy (LIT), an explicit method where preliminary...

Most of arthropod biodiversity is unknown to science. Consequently, it has been unclear whether insect communities around the world are dominated by same or different taxa. This question can be answered through standardized sampling followed estimation species diversity and community composition with DNA barcodes. Here this approach applied flying insects sampled 39 Malaise traps placed in five biogeographic regions, eight countries numerous habitats (>225,000 specimens belonging >25,000 458...

Rapid habitat loss and degradation are responsible for population decline in a growing number of species. Understanding the natural history these species is important designing conservation strategies, such as enhancements or ex-situ conservation. The acquisition observational data may be difficult rare declining species, but metagenomics metabarcoding can provide novel kinds information. Here we use methods analysing fecal samples from an endangered colobine primate, banded leaf monkey...

Abstract Faecal samples are of great value as a non‐invasive means to gather information on the genetics, distribution, demography, diet and parasite infestation endangered species. Direct shotgun sequencing faecal DNA could give these simultaneously, but this approach is largely untested. Here, we used two characterize red‐shanked doucs langurs ( P ygathrix nemaeus ) that were fed known foliage, fruits, vegetables cereals. Illumina HiSeq produced ~74 67 million paired reads for samples,...

Freshwater habitats are of high conservation value and provide a wide range ecosystem services. Effective management requires regular monitoring. However, conventional methods based on direct observation or specimen collection so invasive, expensive labour-intensive that frequent monitoring is uncommon. Here, we test whether the evaluation environmental DNA (eDNA) from water simple protocol can be used for assessing biodiversity. We use universal metazoan primers characterizing eDNA across...

Abstract DNA barcodes are useful for species discovery and identification, but obtaining currently requires a well‐equipped molecular laboratory is time‐consuming, and/or expensive. We here address these issues by developing barcoding pipeline Oxford Nanopore Min ION ™ demonstrating that one flow cell can generate ~500 specimens despite the high basecall error rates of reads. The overcomes errors first summarizing all reads same tagged amplicon as consensus barcode. Consensus overall...

Abstract Biologists frequently sort specimen‐rich samples to species. This process is daunting when based on morphology, and disadvantageous if performed using molecular methods that destroy vouchers (e.g., metabarcoding). An alternative barcoding every specimen in a bulk sample then presorting the specimens DNA barcodes, thus mitigating downstream morphological work presorted units. Such “reverse workflow” too expensive Sanger sequencing, but we here demonstrate feasible with an...

Abstract Most arthropod species are undescribed and hidden in specimen‐rich samples that difficult to sort using morphological characters. For such samples, sorting putative with DNA barcodes is an attractive alternative, but needs cost‐effective techniques suitable for use many laboratories around the world. Barcoding portable inexpensive MinION sequencer produced by Oxford Nanopore Technologies (ONT) could be useful presorting because it requires little space inexpensive. However,...

Holistic insect monitoring needs scalable techniques to overcome taxon biases, determine species abundances, and gather functional traits for all species. This requires that we address taxonomic impediments the paucity of data on abundance, biomass traits. We here outline how these deficiencies could be addressed at scale. The workflow starts with large-scale barcoding (megabarcoding) specimens from mass samples obtained biomonitoring sites. barcodes are then used group into molecular...

The use of DNA barcoding is well established for specimen identification and large-scale biodiversity discovery, but remains underutilized time-sensitive applications such as rapid species discovery in field stations, identifying pests, citizen science projects, authenticating food. main reason that existing express workflows are either too expensive or can only be used very well-equipped laboratories by highly-trained staff. We here show an alternative workflow combining extraction with...

DNA barcoding was proposed in 2003, the Consortium for Barcode of Life established 2004, and movement has since attracted more than $80 million funding. Here we investigate how many species multicellular animals have been barcoded. We compare numbers a public database (GenBank as January 2012) with those Database (BOLD) find that GenBank contains COI (cytochrome c oxidase subunit 1) sequences ca. 60 000 while BOLD reports barcodes 150 species. The discrepancy is likely due to large amount...

New techniques for the species-level sorting of millions specimens are needed in order to accelerate species discovery, determine how many live on earth, and develop efficient biomonitoring techniques. These methods should be reliable, scalable, cost-effective, as well being largely insensitive low-quality genomic DNA, given that this is usually all can obtained from museum specimens. Mini-barcodes seem satisfy these criteria, but it unclear they perform when compared with full-length...

Characterizing trophic networks is fundamental to many questions in ecology, but this typically requires painstaking efforts, especially identify the diet of small generalist predators. Several attempts have been devoted develop suitable molecular tools determine predatory interactions through gut content analysis, and challenge has achieve simultaneously high taxonomic breadth resolution. General practical methods are still needed, preferably independent PCR amplification barcodes, recover...

Abstract Background The world’s fast disappearing mangrove forests have low plant diversity and are often assumed to also a species-poor insect fauna. We here compare the tropical arthropod fauna across freshwater swamp six different forest types (rain-, swamp, dry-coastal, urban, mangroves) based on 140,000 barcoded specimens belonging ca. 8500 species. Results find that globally imperiled habitat “mangroves” is an overlooked hotspot for diversity. Our study reveals species-rich (&gt;3000...

Abstract We are entering the sixth mass extinction with little data for “dark taxa”, although they comprise most species. Much of neglect is due to fact that conventional taxonomic methods struggle handling thousands specimens belonging hundreds thus here propose a new strategy we call taxonomy”. It addresses (i) impediments, (ii) lack biodiversity baselines and (iii) low impact revisionary research. Taxonomic impediments reduced by carrying out revisions at small geographic scales keep...

Millions of species remain undescribed, requiring molecular and morphological diagnoses. However, no efficient software reliably derives tests -state-specific contrastive- UITOTO addresses this gap by identifying, testing, visualizing Diagnostic Molecular Combinations (DMCs). The uses a weighted random sampling algorithm based on the Jaccard Index for building candidate DMCs. It then selects DMCs with highest specificity stability, meeting user-defined thresholds exclusive character states....

Abstract New, rapid, accurate, scalable, and cost-effective species discovery delimitation methods are needed for tackling “dark taxa”, that we here define as clades which &lt;10% of all described the estimated diversity exceeds 1000 species. Species these taxa should be based on multiple data sources (“integrative taxonomy”) but collecting types risks impeding a process is already too slow. We develop explicit to avoid this by applying Large-scale Integrative Taxonomy (LIT). Preliminary...

Abstract Halting biodiversity decline is one of the most critical challenges for humanity, but monitoring hampered by taxonomic impediments. One impediment large number undescribed species (here called “dark taxon impediment”) while another caused superficial descriptions which can only be resolved consulting type specimens (“superficial description impediment”). Recently, Sharkey et al. (2021) proposed to address dark Costa Rican braconid wasps describing 403 based on barcode clusters...

DNA obtained from invertebrates (iDNA) can be metabarcoded in order to survey vertebrate communities. However, little attention has been paid the interaction between invertebrate and species. Here, we tested for specialization by sampling dung carrion fly community of a swamp forest remnant along disturbance gradient (10 sites: 80-310 m road). Approximately, 60% baited 407 flies yielded 294 identifications based on two COI fragments 16S. A bipartite network analysis found no statistically...