The Expanding Role of DNA Barcodes: Indispensable Tools for Ecology, Evolution, and Conservation

Diversity, Journal Year: 2022, Volume and Issue: 14(3), P. 213 - 213

Published: March 13, 2022

DNA barcoding has transformed the fields of ecology, evolution, and conservation by providing a rapid effective tool for species identification. The growth barcodes as resource biologists followed advances in computational sequencing technology that have enabled high-throughput applications. global barcode database is expanding to represent diversity on Earth thanks efforts international consortia biological collections. Today, instrumental advancing our understanding how evolve, they interact, we can slow down their extirpation extinction. This review focuses current applications sequences address fundamental lines research, well new which will play central role.

Language: Английский

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BOLD and GenBank revisited – Do identification errors arise in the lab or in the sequence libraries?

PLoS ONE, Journal Year: 2020, Volume and Issue: 15(4), P. e0231814 - e0231814

Published: April 16, 2020

Applications of biological knowledge, such as forensics, often require the determination materials to a species level. As such, DNA-based approaches identification, particularly DNA barcoding, are attracting increased interest. The capacity barcodes assign newly encountered specimens relies upon access informatics platforms, BOLD and GenBank, which host libraries reference sequences support comparison new them. parameterization these expands, barcoding has potential make valuable contributions in diverse applied contexts. However, recent publication called for caution after finding that both platforms performed poorly identifying 17 common insect species. This study follows up on this concern by asking if misidentifications reflected problems or query used test Because reanalysis revealed missteps acquiring analyzing were responsible most misidentifications, workflow is described minimize errors future investigations. present also limitations imposed lack polished species-level taxonomy many groups. In cases, applications can be strengthened mapping geographic distributions sequence-based proxies rather than waiting maturation formal taxonomic systems based morphology.

Language: Английский

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Forest Insect Biosecurity: Processes, Patterns, Predictions, Pitfalls

Annual Review of Entomology, Journal Year: 2022, Volume and Issue: 68(1), P. 211 - 229

Published: Oct. 6, 2022

The economic and environmental threats posed by non-native forest insects are ever increasing with the continuing globalization of trade travel; thus, need for mitigation through effective biosecurity is greater than ever. However, despite decades research implementation preborder, border, postborder preventative measures, insect invasions continue to occur, no evidence saturation, even predicted accelerate. In this article, we review measures used mitigate arrival, establishment, spread, impacts possible impediments successful these measures. Biosecurity successes likely under-recognized because they difficult detect quantify, whereas failures more evident in continued establishment additional species. There limitations existing systems at global country scales (for example, inspecting all imports impossible, phytosanitary perfect, knownunknowns cannot be regulated against, noncompliance an ongoing problem). should a shared responsibility across countries, governments, stakeholders, individuals.

Language: Английский

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The global spread and invasion capacities of alien ants

Current Biology, Journal Year: 2023, Volume and Issue: 33(3), P. 566 - 571.e3

Published: Jan. 6, 2023

Many alien species are neither cultivated nor traded but spread unintentionally, and their global movements, capacities to invade ecosystems, susceptibility detection by biosecurity measures poorly known.1Elton C.S. The Ecology of Invasions Plants Animals. Methuen, 1958Crossref Google Scholar,2Pyšek P. Richardson D.M. Pergl J. Jarošík V. Sixtová Z. Weber E. Geographical taxonomic biases in invasion ecology.Trends Ecol. Evol. 2008; 23: 237-244https://doi.org/10.1016/j.tree.2008.02.002Abstract Full Text PDF PubMed Scopus (573) Scholar,3Diagne C. Leroy B. Vaissière A.C. Gozlan R.E. Roiz D. Jarić I. Salles J.M. Bradshaw C.J.A. Courchamp F. High rising economic costs biological invasions worldwide.Nature. 2021; 592: 571-576https://doi.org/10.1038/s41586-021-03405-6Crossref (419) Scholar,4Hulme P.E. Trade, transport trouble: managing invasive pathways an era globalization.J. Appl. 2009; 46: 10-18https://doi.org/10.1111/j.1365-2664.2008.01600.xCrossref (1729) Scholar We addressed these key knowledge gaps for ants, a ubiquitous group stowaway contaminant organisms that include some the world's most damaging species.5Angulo Hoffmann B.D. Ballesteros-Mejia L. Taheri A. Balzani Bang Renault Cordonnier M. Bellard Diagne et al.Economic ants worldwide.Biol. Invas. 2022; 24: 2041-2060https://doi.org/10.1007/s10530-022-02791-wCrossref (24) Scholar,6Weber N.A. Tourist ants.Ecology. 1939; 20: 442-446https://doi.org/10.2307/1930408Crossref Scholar,7McGlynn T.P. worldwide transfer ants: geographical distribution ecological invasions.J. Biogeogr. 1999; 26: 535-548https://doi.org/10.1046/j.1365-2699.1999.00310.xCrossref (330) Scholar,8Suarez A.V. Holway D.A. Ward P.S. role opportunity unintentional introduction nonnative ants.Proc. Natl. Acad. Sci. USA. 2005; 102: 17032-17035https://doi.org/10.1073/pnas.0506119102Crossref (127) Scholar,9Suarez McGlynn Tsutsui N.D. Biogeographic patterns introduced ants.in: Lach Parr Abott K. Ant. Ecology. Oxford University Press, 2010: 233-244Google Scholar,10Bertelsmeier Globalization anthropogenic social insects.Curr. Opin. Insect 16-23https://doi.org/10.1016/j.cois.2021.01.006Crossref (36) assembled dataset over 146,000 occurrence records comprehensively map human-mediated 520 ant across 525 regions globally. From descriptions environments which were collected within individual regions—such as imported cargoes, buildings, outdoor settings—we determined whether different barriers had been overcome11Blackburn T.M. Pyšek Bacher S. Carlton J.T. Duncan R.P. Wilson J.R.U. A proposed unified framework invasions.Trends 2011; 333-339https://doi.org/10.1016/j.tree.2011.03.023Abstract (1578) classified under three levels capacity corresponding increasing threat. found sources sinks For instance, although diversity indoor-confined peaked Palearctic realm, able establish outdoors Nearctic Oceanian realms, mainly originated from Neotropical Oriental realms. also border interceptions missed two-thirds with naturalization capacity, many associated litter soil. Our study documents vast globally while highlighting avenues more targeted responses, such prioritizing screening imports hotspots high improving cryptic invertebrates dwelling substrates.

Language: Английский

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The Future of DNA Barcoding: Reflections from Early Career Researchers

Diversity, Journal Year: 2021, Volume and Issue: 13(7), P. 313 - 313

Published: July 9, 2021

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

Language: Английский

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Lack of Statistical Rigor in DNA Barcoding Likely Invalidates the Presence of a True Species' Barcode Gap

Frontiers in Ecology and Evolution, Journal Year: 2022, Volume and Issue: 10

Published: April 14, 2022

DNA barcoding has been largely successful in satisfactorily exposing levels of standing genetic diversity for a wide range taxonomic groups through the employment only one or few universal gene markers. However, sufficient coverage geographically-broad intra-specific haplotype variation within genomic databases like Barcode Life Data Systems (BOLD) and GenBank remains relatively sparse. As reference sequence libraries continue to grow exponentially size, there is now need identify novel ways meaningfully analyzing vast amounts available barcode data. This an important issue address promptly routine tasks specimen identification species discovery, which have seen broad adoption areas as diverse regulatory forensics resource conservation. Here, it demonstrated that interpretation data lacking statistical rigor. To highlight this, focus set specifically on key concept become household name field: gap. Arguments outlined herein center animal taxa stem from three angles: (1) improper allocation sampling effort necessary capture adequate within-species variation, (2) failing properly visualize interspecific distances, (3) inconsistent, inappropriate use, absence inferential procedures gap analyses. Furthermore, simple solutions are can greatly propel use tool irrefutably match unknowns knowns basis with high degree confidence. Proposed methods examined illustrated application Canadian Pacific fish case study.

Language: Английский

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Technological innovations enhance invasive species management in the anthropocene

BioScience, Journal Year: 2023, Volume and Issue: 73(4), P. 261 - 279

Published: April 1, 2023

Abstract Curbing the introduction, spread, and impact of invasive species remains a longstanding management policy prerogative. In recent decades, globalization environmental change have further complicated efforts to execute science-based actions that address these challenges. New technologies offer exciting opportunities advance invasion science knowledge, enhance actions, guide strategies but are increasingly complex inaccessible most practitioners. present article, we synthetic perspective innovative with applications for related pathway intervention, spread prevention, mitigation, public engagement. We also describe tools augment big data processing required by some methods (e.g., remote sensing, mobile application data), such as automated image text recognition built on machine learning. Finally, explore challenges successful integration emerging into management, focusing pipelines enable practitioners integrate practice while recognizing logistic financial constraints.

Language: Английский

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eDNA metabarcoding of small plankton samples to detect fish larvae and their preys from Atlantic and Pacific waters

Scientific Reports, Journal Year: 2021, Volume and Issue: 11(1)

Published: March 31, 2021

Zooplankton community inventories are the basis of fisheries management for containing fish larvae and their preys; however, visual identification early-stage (the "missing biomass") is difficult laborious. Here, eDNA metabarcoding was employed to detect zooplankton species interest from open coastal waters. High-Throughput sequencing (HTS) environmental samples using small water volumes has been proposed whose DNA most abundant. We analyzed 6-L taken subtropical tropical waters Cytochrome oxidase I (COI) gene as metabarcode. In ocean, several commercial invertebrate important in diet were found metabarcodes confirmed individual barcoding. Comparing Atlantic, Mediterranean, Red Sea, Pacific we a lower taxonomic depth OTU assignments than those temperate ones, suggesting large gaps reference databases areas; thus higher effort barcoding oceans highly recommended. This similar simplified sampling protocols could be applied early detection fisheries.

Language: Английский

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Forest leaf litter beetles of Taiwan: first DNA barcodes and first insight into the fauna

Deutsche Entomologische Zeitschrift, Journal Year: 2024, Volume and Issue: 71(1), P. 17 - 47

Published: Jan. 8, 2024

We report the publication of 953 DNA barcodes forest leaf litter beetles from central Taiwan, in total representing 334 species 36 beetle families. This is first bulk data Taiwanese Leaf Litter project focused on uncovering under-explored diversity across Taiwan. Based these data, we provide records following taxa for Taiwan: family Sphindidae (genus Aspidiphorus Ziegler, 1821); tribes Trichonychini, Ctenistini, and Bythinoplectini (all Staphylinidae: Pselaphinae); genera Gyrelon Hinton, 1942, Thyroderus Sharp, 1885, Cautomus 1885 Cerylonidae), Dermatohomoeus Hlisnikovský, 1963 (Leiodidae), Paraploderus Herman, 1970 (Staphylinidae: Oxytelinae), Thinocharis Kraatz, 1859 Paederinae), Cephennodes Reitter, 1884, Napoconnus Franz, 1957 (both Scydmaeninae), Bicava Belon, 1884 (Latridiidae), Otibazo Morimoto, 1961, Seleuca Pascoe, 1871 Acallinus 1962 Curculionidae); Oodes (Lachnocrepis) japonicus (Bates, 1873) (Carabidae: Licininae), Drusilla obliqua (Bernhauer, 1916) Aleocharinae) Coccotrypes advena Blandford, 1894 (Curculionidae: Scolytinae). The Anapleus Horn, 1873 (Histeridae) Batraxis 1882 Pselaphinae) have been confirmed. male Sivacrypticus taiwanicus Kaszab, 1964 (Archeocrypticidae) described time. jenpani Hu, Fikáček & Matsumoto, sp. nov. (Cerylonidae) described, illustrated, compared with related species. associated larvae 42 adults, are concisely illustrating some these: , Perigona cf. nigriceps Dejean, 1831 Carabidae), Ptilodactyla (Ptilodactylidae), Maltypus ryukyuanus Wittmer, (Cantharidae), Myrmecocephalus brevisulcus (Pace, 2008), Diochus sp., Mimopinophilus Staphylinidae), Stelidota multiguttata 1877, Lasiodites inaequalis (Grouvelle, 1914) Nitidulidae), Lagria scutellaris Pic, 1910, Anaedus spinicornis 1973 Tenebrionidae). also cases Rickettsia infections Scydmaeninae Pselaphinae. All (sequences, metadata, voucher photos) made public BOLD database a Zenodo Archive.

Language: Английский

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Molecular characterization and demographic insights into soybean bud borer (Lepidoptera: Tortricidae) in Brazil

Journal of Insect Science, Journal Year: 2024, Volume and Issue: 24(2)

Published: Feb. 14, 2024

Abstract The soybean bud borer, a pest in Brazil, was initially identified as Crocidosema aporema (Walsingham 1914) (Lepidoptera: Tortricidae). Outbreaks of this species have recently increased, but identification remains uncertain, and the historical factors associated with its geographic distribution Brazil are little known. Here, we conducted characterization phylogeographic analysis based on molecular morphological evidence. Ninety individuals bud-borers Lepidoptera were collected different regions Brazil. We sequenced COI COII mitochondrial genes examined wing patterns male genital morphology. DNA barcoding approach revealed that 10 Argyrotaenia sphaleropa (Meyrick 1909) Tortricidae) 80 genus Zeller. morphology adult genitalia wings proved to be insufficient confirm Brazilian C. aporema, originally described from high-elevation site Costa Rica. Furthermore, genetic distance between putative specimens Rica (ranging 5.2% 6.4%) supports hypothesis not referable aporema. Our single strain (i.e., species) low diversity crops. found no indication structure related among populations or edaphoclimatic regions. population expansion borer coincides increase area production suggesting expanded farming has allowed significant effective size pest.

Language: Английский

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