Towards holistic insect monitoring: species discovery, description, identification and traits for all insects

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2024, Volume and Issue: 379(1904)

Published: May 5, 2024

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 operational units subsequently tested/validated as a second source (e.g. morphology). New described using barcodes, images short diagnoses, abundance collected both new specimen discovery become raw material training artificial intelligence identification algorithms collecting trait such body size, feeding modes. Additional can vouchers by genomic tools developed ecologists. Applying this pipeline few per site will lead greatly improved regardless whether composition sample is determined images, metabarcoding or megabarcoding. article part theme issue 'Towards toolkit global biodiversity monitoring'.

Language: Английский

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Molecular Delimitation of Evolutionary Significant Units Reveals Hidden Geographic Drivers of Extinction Risk Within Island Arthropods

Diversity and Distributions, Journal Year: 2025, Volume and Issue: 31(1)

Published: Jan. 1, 2025

ABSTRACT Aim Globally, arthropod biodiversity is under threat, with increased risk of species‐level extinctions, and this threat particularly acute on oceanic islands. A fundamental first step towards understanding extinction to understand genetic connectivity among the constituent populations a species. Our aim develop implement protocol characterise island within species reveal otherwise hidden range size drivers extinction. Location Canary Islands, Spain. Methods We based mtDNA sequence data for delimitation evolutionary significant units (ESUs) evaluate beetle spider distributed across multiple Results results that more than half analysed are comprised two or ESUs. also find low dispersal ability was predictor ESUs Coleoptera, but no difference Araneae. Main Conclusions Most consistent early stage differentiation incipient speciation, some exceeding conservative interspecific threshold, thus indicative cryptic suggest extending our approach integration other traits may provide refined predictive framework risks

Language: Английский

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Hotspot of Exotic Benthic Marine Invertebrates Discovered in the Tropical East Atlantic: DNA Barcoding Insights From the Bijagós Archipelago, Guinea‐Bissau

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(3)

Published: March 1, 2025

This study aimed to explore and document putative exotic marine benthic invertebrate species in the Bijagós Archipelago, Guinea-Bissau, enhance understanding of biodiversity address extent introductions. The research was conducted a UNESCO Biosphere Reserve located Guinea-Bissau. involved region's first scuba-diving survey biodiversity. DNA barcoding employed assist identification species. Molecular phylogenetic analyses were with available barcodes ensure accurate taxonomic assignments, detect cryptic species, investigate phylogeography taxa. resulted discovery 28 new records for including octocorals, scleractinians, hydroids, bryozoans, barnacles, ascidians. Among these, six documented time East Atlantic: Stragulum bicolor, Nemalecium lighti, Diphasia sp., Amathia alternata, A. distans, Symplegma rubra. revealed pervasive diversity within previously listed as exotic, suggesting that some, such hydroids Plumularia setacea, Obelia geniculata, Dynamena disticha, are not due their restricted biogeographic distributions. Many other reported introduced present only few genetic lineages capable long-distance dispersal human activities. highlights considerable gaps knowledge West African suggests substantial underestimation anthropogenic trade between Tropical Atlantic Americas, Indo-Pacific, Mediterranean, Africa. Detailed genomic necessary species' biogeography adaptive traits. Our findings challenge current classifications underscore need improved monitoring management prevent spread non-native

Language: Английский

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Barcode 100K Specimens: In a Single Nanopore Run

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 10, 2024

It is a global priority to better manage the biosphere, but action must be informed by comprehensive data on abundance and distribution of species. The acquisition such information currently constrained high costs. DNA barcoding can speed registration unknown animal species, most diverse kingdom eukaryotes, as BIN system automates their recognition. However, inexpensive sequencing protocols are critical census all species likely require analysis billion or more specimens. Barcoding involves extraction followed PCR with last step dominating costs until 2017. By enabling highly multiplexed samples, Sequel platforms from Pacific BioSciences slashed 90%, these instruments only deployed in core facilities because expense. Sequencers Oxford Nanopore Technologies provide an escape capital service costs, low sequence fidelity has, recently, adoption. improved performance its latest flow cells (R10.4.1) erases this barrier. This study demonstrates that MinION cell characterise amplicon pool derived 100,000 specimens while Flongle process one several thousand. At $0.01 per specimen, now least expensive barcode workflow.

Language: Английский

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Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: A case study on beach meiofauna

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 24(7)

Published: July 31, 2024

Abstract Molecular techniques like metabarcoding, while promising for exploring diversity of communities, are often impeded by the lack reference DNA sequences available taxonomic annotation. Our study explores benefits combining targeted barcoding and morphological taxonomy to improve metabarcoding efficiency, using beach meiofauna as a case study. Beaches globally important ecosystems inhabited meiofauna, microscopic animals living in interstitial space between sand grains, which play key role coastal biodiversity ecosystem dynamics. However, research on faces challenges due limited expertise sparse sampling. We generated 775 new cytochrome c oxidase I barcodes from specimens collected along Netherlands' west coast combined them with NCBI GenBank database. analysed alpha beta 561 samples 24 North Sea beaches, region extensively studied both enriched database without additional barcodes. results show 2.5‐fold increase sequence annotation doubling species‐level Operational Taxonomic Units (OTUs) identification when annotating data enhanced Additionally, our analyses revealed bell‐shaped curve OTU richness across intertidal zone, aligning more closely analysis patterns, defined community dissimilarity patterns supralittoral sites. highlights importance expanding molecular databases assessments, ultimately improving understanding ecosystems.

Language: Английский

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The first report from Poland and larvae description of Eukiefferiella dittmari Lehmann, 1972 (Diptera: Chironomidae) based on morphological and molecular characteristics

Zootaxa, Journal Year: 2025, Volume and Issue: 5570(1), P. 169 - 178

Published: Jan. 15, 2025

Eukiefferiella is a large genus in the family Chironomidae with over 50 species worldwide. Their immature stages have so far been described many western Palearctic. Nevertheless, some are still known only from adult males. Presented below description of dittmari Lehmann, 1972 larvae first recorded Poland pristine river Rawka. The were collected water moss and identified to level using DNA barcode BOLD database. E. belong ilkleyensis group having bifid SIII seta, mentum wide central tooth four pairs lateral teeth. At genetic morphological level, sister Nearctic endobryonia, also an aquatic dweller. phylogenetic relation these two should be further investigated.

Language: Английский

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Delimiting Species—Prospects and Challenges for DNA Barcoding

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 6, 2025

ABSTRACT Discovering, describing and cataloguing global species diversity remains a fundamental challenge both for biodiversity research the management conservation of biodiversity. Among animals, is particularly acute within arthropods, which comprise approximately 85% all described with 1 million species. The true number arthropod estimated to be in excess 10 This estimate likely revised upward light DNA barcode sequencing initiatives that are unprecedented levels cryptic or overlooked diversity. scale being recovered places further strain on taxonomic system confronted by ever‐limited capacity verify describe new It predicted novel operational units delimited eclipse Linnean taxonomy as early 2029. Unless addressed, this may see an increasing proportion falling outside protective legislative frameworks consequence their lack formal description. Confronted challenge, there increasing, but controversial, acceptance delimitation description based sequence clustering thresholds. In response evolving controversy surrounding issue, it timely important identify clarify prospects challenges barcoding, specific focus address shortfalls impediments research.

Language: Английский

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“Dark taxonomy”: A new protocol for overcoming the taxonomic impediments for dark taxa and broadening the taxon base for biodiversity assessment

Cladistics, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 16, 2025

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 number low. The risk error delimiting species based on two types data. furthermore show dark taxonomy can yield important baseline using samples obtained biomonitoring traps. Lastly, argue research be improved publishing papers addressing different readerships. principles illustrated our treatment Singapore's fungus gnats (Mycetophilidae) only Malaise trap samples. first batch ( N = 1454) contains 120 species, which 115 science, reducing increasing described Oriental 25%. Species delimitation started DNA barcodes estimate Molecular Operational Units (MOTUs) before “LIT” (Large‐scale Integrative Taxonomy) was used obtain boundaries integrating morphological molecular To test completeness revision, next analysed second 1493 found >97% belonged delimited batch. Indeed, contained 18 rare MOTUs, i.e. study suggests single revision simultaneously names all relevant Overall, believe taxonomy” quickly ready large unknown taxon biomonitoring.

Language: Английский

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Exploring the water mite fauna (Acari, Hydrachnidia) of the Madeira archipelago: DNA Barcoding reveals a remarkable species endemicity

Zootaxa, Journal Year: 2025, Volume and Issue: 5621(5), P. 501 - 513

Published: April 21, 2025

Water mites represent the group with highest degree of endemism among all macroinvertebrates living in freshwater habitats Madeira. The water mite fauna this archipelago has been well known for a long time, but until now they have not molecularly investigated. So far, 25 species recorded, most them endemic to library presented here covers 584 COI DNA barcodes grouped into 23 Barcode Index Numbers (BINs), which genetic (more than 80% Madeira fauna). Our study shows that barcode clusters generated by Life Data Systems (BOLD) matches morphological identifications specimens, one exception family Lebertiidae. A large-scale comparison new sequences those available public databases such as BOLD confirmed uniqueness diversity inhabiting Neumania atlantida Lundblad, 1941, previously synonymized N. uncinata Walter, 1927, is resurrected valid species. Additionally, data revealed Sperchon brevirostris Koenike, 1895, common freshwaters Europe and Macaronesia, consists multiple lineages, restricted Finally, our research three Madeira, i.e., Hydrachna skorikowi Piersig, 1900, Arrenurus bicuspidator Berlese, 1885 Lebertia algeriensis 1942. latter species, found be running waters island, may first documented potentially, if invasive, then non-indigenous ecosystems

Language: Английский

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Fast, Flexible, Feasible: A Transparent Framework for Evaluating eDNA Workflow Trade-offs in Resource-Limited Settings

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 18, 2025

Abstract Environmental DNA (eDNA) analysis enables biodiversity monitoring by detecting organisms from trace genetic material, but high reagent costs, cold-chain logistics, and computational demands limit its broader use, particularly in resource-limited settings. To address these challenges improve accessibility, we systematically evaluated multiple workflow components, including four extraction methods, two primer sets, three Nanopore basecalling models, demultiplexing pipelines. Across 144 combinations tested an aquarium with 15 fish species, mapped trade-offs between cost, sensitivity, processing speed using a hierarchical Bayesian model, to assess where time resource savings are possible without compromising detection. Workflows the Qiagen Blood Tissue (BT) kit provided highest recovering all species of sampled community within 3–5 hours Oxford sequencing when paired MiFish-U set high-accuracy (HAC) basecalling. Chelex, alternative lower-cost method, required extended (>24 hours) reach comparable species-detection rates. DirectPCR QuickExtract offered field-friendly alternatives that achieved recovery ∼10–12 hours, though their cost-effectiveness varied. While MarVer1 was designed broaden vertebrate detection, it recovered same as MiFish-U, fewer total reads. Real-time trials (0–61 revealed high-efficiency workflows (BT + HAC) reached detection plateaus rapidly, indicating can be reduced sacrificing accuracy. The OBITools4 bioinformatics pipeline enabled automated discarded more reads than alternative, ONTbarcoder2.3, which retained low-abundance taxa at cost manual curation. Rather identifying single “best” workflow, this study provides transparent decision framework for prioritizing speed, sensitivity eDNA applications, supporting scalable, cost-effective monitoring,

Language: Английский

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