Emerging technologies revolutionise insect ecology and monitoring

Trends in Ecology & Evolution, Journal Year: 2022, Volume and Issue: 37(10), P. 872 - 885

Published: July 8, 2022

Insects are the most diverse group of animals on Earth, but their small size and high diversity have always made them challenging to study. Recent technological advances potential revolutionise insect ecology monitoring. We describe state art four technologies (computer vision, acoustic monitoring, radar, molecular methods), assess advantages, current limitations, future potential. discuss how these can adhere modern standards data curation transparency, implications for citizen science, integration among different monitoring programmes technologies. argue that they provide unprecedented possibilities it will be important foster international via collaboration.

Language: Английский

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When details matter: Integrative revision of Holarctic Coelophthinia Edwards (Diptera, Mycetophilidae), including mapping of its mitogenome, leads to the description of four new pseudocryptic species

Biodiversity Data Journal, Journal Year: 2023, Volume and Issue: 11

Published: Feb. 14, 2023

The small genus Coelophthinia Edwards, 1941 of the subfamily Gnoristinae (Diptera, Mycetophilidae) is so far known to harbour four species from Palaearctic, Nearctic and Neotropical Regions. Extensive DNA barcoding fungus gnats family Mycetophilidae through International Barcode Life project (iBOL) have initiated integrative studies resulting in taxonomic upgrades a better understanding many their delimitation. opportunity was also taken describe mitogenome member for first time. give evidence splitting European C. thoracica into three different species. Four new are described USA, Japan Nordic Region Europe, cirra Kerr sp. n. , itoae Kurina lata Kjaerandsen loraasi raising number Holarctic two six. analysed.

Language: Английский

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The InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of cuckoo wasps, with the description of new species from the Iberian Peninsula (Hymenoptera, Chrysididae)

Biodiversity Data Journal, Journal Year: 2023, Volume and Issue: 11

Published: March 1, 2023

DNA barcoding technologies have provided a powerful tool for the fields of ecology and systematics. Here, we present part InBIO Barcoding Initiative Database: contribution to knowledge on barcodes cuckoo wasps (Hymenoptera, Chrysididae) dataset representing 144 specimens 103 species, covering approximately 44% Iberian 21% European fauna. The (IBI – Portuguese terrestrial invertebrate biodiversity) aims fill gap taxa. All extractions are deposited in IBI collection at CIBIO, Research Center Biodiversity Genetic Resources University Mons (Belgium) Natur-Museum Lucerne (Switzerland). This increases distribution 102 species wasps. A total 52 from 11 different genera, were new additions Barcode Life Data System (BOLD), with another 44 added under-represented taxa BOLD. their publicly accessible through BOLD online database. Nine wasp newly recorded Portugal. Additionally, two science described: Chrysis crossi Rosa, sp. nov. southern Portugal Hedychridium calcarium eastern Spain. Several taxonomic changes proposed Hedychrum rutilans Dahlbom, 1845 is found consist that can be sympatry, s. str. viridaureum Tournier, 1877 stat. Stilbum westermanni confirmed as distinct calens (Fabricius, 1781), latter not Iberia; barcoded material Australia represents amethystium 1775) resurr.; identified chloropygum Buysson, 1888 actually belongs caputaureum Trautmann & Trautmann, 1919, first record this Iberia. Philoctetes parvulus (Dahlbom, 1845) synonym punctulatus 1845). lusitanica Bischoff, 1910 valid species. hebraeica Linsenmaier, 1959 raised status.

Language: Английский

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PROTAX-GPU: a scalable probabilistic taxonomic classification system for DNA barcodes

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

Published: May 5, 2024

DNA-based identification is vital for classifying biological specimens, yet methods to quantify the uncertainty of sequence-based taxonomic assignments are scarce. Challenges arise from noisy reference databases, including mislabelled entries and missing taxa. PROTAX addresses these issues with a probabilistic approach classification, advancing on that rely solely sequence similarity. It provides calibrated partially populated hierarchy, accounting taxa lack references incorrect annotation. While effective smaller scales, global application necessitates substantially larger libraries, goal previously hindered by computational barriers. We introduce PROTAX-GPU, scalable algorithm capable leveraging Barcode Life Data System (>14 million specimens) as database. Using graphics processing units (GPU) accelerate similarity nearest-neighbour operations JAX library Python integration, we achieve over 1000 × speedup compared central unit (CPU)-based implementation without compromising PROTAX's key benefits. PROTAX-GPU marks significant stride towards real-time DNA barcoding, enabling quicker more efficient species in environmental assessments. This capability opens up new avenues monitoring analysis biodiversity, our ability understand respond ecological dynamics. article part theme issue 'Towards toolkit insect biodiversity monitoring'.

Language: Английский

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DNA Barcoding of German Cuckoo Wasps (Hymenoptera: Chrysididae) Suggests Cryptic Species in Several Widely Distributed Species

Insects, Journal Year: 2024, Volume and Issue: 15(11), P. 850 - 850

Published: Oct. 30, 2024

Germany is home to a rich cuckoo wasp fauna (Hymenoptera: Chrysididae) with about 108 species. However, several nomenclatural changes, the lack of identification keys, and discovery cryptic species difficult identify based on external morphology have made challenge. COI barcoding has been instrumental in some could help alleviate above problems, but reliable large reference database containing barcodes lacking. We present more than 800 specimens 101 native lay foundation for barcode-based German An analysis barcode sequences suggested groups that are largely consistent current taxonomy group. found few cases over- or undersplitting taxa. In common species, high degree divergence suggests presence need be further assessed by integrative approaches. Our library will enhance researchers' ability reliably within this fascinating group insects, particular identifying life stages offer no morphological features species-level identification.

Language: Английский

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Current State of DNA Barcoding of Sciaroidea (Diptera)—Highlighting the Need to Build the Reference Library

Insects, Journal Year: 2022, Volume and Issue: 13(2), P. 147 - 147

Published: Jan. 29, 2022

DNA barcoding has tremendous potential for advancing species knowledge many diverse groups of insects, potentially paving way machine identification and semi-automated monitoring whole insect faunas. Here, I review the current state superfamily Sciaroidea (Diptera), a group consisting eight understudied fly families where described in world makes up some 10% (≈16,000 species) all Diptera. World data were extracted from Barcode Life online database BoldSystems (BOLD) contrasted with results experiences Nordic project to build reference library. Well over 1.2 million (1,224,877) specimens have been submitted barcoding, giving barcode-compliant sequences resulting 56,648 so-called barcode index numbers (BINs, machine-generated proxies species). Although BINs on BOLD already represent 3.5 times number species, merely 2850 named (described or interim names, 5% BINs) currently assigned BIN. The other 95% remain as dark taxa figuring frontier publications statistics representing diversity within family. In region, however, substantial progress made towards building complete library, making 55% BOLD. Another major source (31%) comes COI mined GenBank, generated through phylogenetic integrative studies outside Building quality library insects such requires heavy investment, both pre sequence post sequence, by trained taxonomists curate voucher collections, continually improve describe new species. Only when are properly calibrated rigorously quality-checked can great classical taxonomic metabarcoding, eDNA ecology be realized.

Language: Английский

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Plant DNA barcode library for native flowering plants in the arid region of northwestern China

Molecular Ecology Resources, Journal Year: 2023, Volume and Issue: 23(6), P. 1389 - 1402

Published: April 6, 2023

DNA barcoding is a well-established tool for rapid species identification and biodiversity monitoring. A reliable traceable barcode reference library with extensive coverage necessary but unavailable many geographical regions. The arid region in northwestern China, vast area of about 2.5 million km2 , ecologically fragile often overlooked studies. In particular, data from the China are lacking. We develop evaluate efficacy an native flowering plants China. Plant specimens were collected, identified vouchered this purpose. database utilized four markers, namely rbcL, matK, ITS ITS2, 1816 accessions (representing 890 385 genera 72 families), consisted 5196 sequences. Individual barcodes varied resolution rates: species- genus-level rates ITS2 79.9%-51.1%/76.1%, 79.9%-67.2%/88.9%, 85.0%-72.0%/88.2% 81.0%-67.4%/84.9%, respectively. three-barcode combination rbcL + matK (RMI) revealed higher (75.5%/92.1%, respectively). total 110 plastomes newly generated as super-barcodes to increase seven species-rich genera, Astragalus, Caragana, Lactuca, Lappula, Lepidium, Silene Zygophyllum. Plastomes compared standard their combination. suggest future databases include super-barcodes, especially complex genera. plant current study provides valuable resource biological investigations regions

Language: Английский

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Webs of intrigue: museum genomics elucidate relationships of the marronoid spider clade (Araneae)

Insect Systematics and Diversity, Journal Year: 2023, Volume and Issue: 7(5)

Published: Sept. 1, 2023

Abstract Relationships among spider families that lack support through other lines of evidence (e.g., morphology) have recently been uncovered molecular phylogenetics. One such group is the “marronoid” clade, which contains about 3,400 described species in 9 families. Marronoids run gamut life history strategies, with social species, producing a variety silk types, and occurring range extreme environments. Despite recognition ecological variability group, there remains uncertainty family- level relationships, leaving diverse ecologies without an evolutionary context. The phylogenies produced to date relatively low nodal support, are few defined morphological synapomorphies, internal relationships many remain unclear. We use 93 exemplars from all marronoid ultraconserved element loci captured silico combination 48 novel low-coverage whole genomes genomic data Sequence Read Archive (SRA) produce 50% occupancy matrix 1,277 set probes. These were used infer phylogeny clade evaluate familial within combined single-locus (Sanger) legacy further increase taxonomic sampling. Our results indicate clearly well-supported provide for both monophyly paraphyly currently clade. propose changes accordance resulting phylogenetic hypothesis, including elevating Cicurinidae (restored status) Macrobunidae (new rank).

Language: Английский

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High-throughput biodiversity surveying sheds new light on the brightest of insect taxa

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2025, Volume and Issue: 292(2046)

Published: May 1, 2025

DNA metabarcoding of species-rich taxa is becoming a popular high-throughput method for biodiversity inventories. Unfortunately, its accuracy and efficiency remain unclear, as results mostly pertain to poorly known in underexplored regions. This study evaluates what an extensive sampling effort combined with can tell us about the lepidopteran fauna Sweden—one best-understood insect one most-surveyed countries world. We deployed 197 Malaise traps across Sweden year, generating 4749 bulk samples metabarcoding, compared existing data sources. detected more than half (1535) 2990 Swedish species 323 not reported during period by other providers. Full-length barcoding confirmed three new country, substantial range extensions two eight genetically distinct barcode variants potentially representing species, which has since been described. Most records represented small, inconspicuous from surveyed regions, highlighting components overlooked traditional surveying. These findings demonstrate that highly efficient accurate method, capable yielding significant discoveries even most well faunas.

Language: Английский

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DNA Barcode Library of Megadiverse Lepidoptera in an Alpine Nature Park (Italy) Reveals Unexpected Species Diversity

Diversity, Journal Year: 2023, Volume and Issue: 15(2), P. 214 - 214

Published: Feb. 2, 2023

Species inventories are a prerequisite for biodiversity monitoring and conservation, particularly in protected areas. However, the possibilities of standardized survey species diversity using DNA barcoding have so far hardly been implemented, especially species-rich groups. A first-time molecular-based nearly complete inventory megadiverse insect order Lepidoptera area Alps (Cottian Alps, Italy) was intended to test reliability DNA-based identifications. From voucher material collected between 2019 2022, we successfully sequenced 1213 morphospecies that grouped into 1204 BINs (barcode index numbers), whereas failed another 18 species. total 35 shared BIN with one or more taxa, but majority 19 could still be discriminated by divergent sequences. 12 split two BINs. These further 22 taxa unique barcode divergences >2% nearest neighbor require taxonomic re-assessment. Two additional cryptic from study were described recently. Finally, 16 newly recorded Italy. Our study, therefore, demonstrates importance both faunistics discovery diversity, even apparently well-studied

Language: Английский

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