Fisheries and aquatic sciences, Journal Year: 2025, Volume and Issue: 28(3), P. 152 - 162
Published: March 1, 2025
Language: Английский
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
Citations
30
International Journal of Biological Macromolecules, Journal Year: 2023, Volume and Issue: 233, P. 123549 - 123549
Published: Feb. 4, 2023
Language: Английский
Citations
20
Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)
Published: March 15, 2024
Abstract DNA barcoding is an essential tool in modern biodiversity sciences. Despite considerable work to barcode the tree of life, many groups, including insects, remain partially or totally unreferenced, preventing from reaching its full potential. Aquatic especially three orders Ephemeroptera, Plecoptera, and Trichoptera (EPT), are key freshwater quality indicators worldwide. Among them, Plecoptera (stoneflies), which among most sensitive aquatic insects habitat modification, play a central role river monitoring surveys. Here, we present update reference database for (meta)barcoding Switzerland, now covering all 118 species known this country. Fresh specimens, mostly rare localized species, were collected, 151 new CO1 barcodes generated. These merged with 422 previously published sequences, resulting dataset 573 barcoded specimens. Our was delimited 115 clusters based on priori morphological identifications, 17% newly reported 4% globally. clusters, 85% showed complete congruence morphology. Distance-based analysis indicated local gaps 97% clusters. This study significantly improves Swiss stoneflies, enhancing future identification accuracy monitoring. Additionally, reveals cryptic diversity incongruence between morphology barcodes, both presenting valuable opportunities integrative taxonomic studies. Voucher extractions available developments, metabarcoding environmental
Language: Английский
Citations
7
Scientific Reports, Journal Year: 2021, Volume and Issue: 11(1)
Published: Feb. 26, 2021
Abstract The current decline of wild bees puts important ecosystem services such as pollination at risk. Both inventory and monitoring programs are needed to understand the causes bee decline. Effective insect relies on both mass-trapping methods coupled with rapid accurate identifications. Identifying using only morphology can be challenging, in particular, specimens from mass-trapped samples which often poor condition. We generated DNA barcodes for 2931 representing 157 species (156 named one unnamed species) 28 genera. Automated cluster delineation reveals 172 BINs (Barcodes Index Numbers). A total 36 (22.93%) were found highly urbanized areas. majority specimens, 96.17% barcoded form reciprocally exclusive groups, allowing their unambiguous identification. This includes several closely related notoriously difficult identify. 137 (87.26%) show a “one-to-one” match between BIN assignment. Fourteen (8.92%) deep conspecific lineages no apparent morphological differentiation. Only two pairs shared same making identification alone uncertain. Therefore, our barcoding reference library allows reliable by non-experts vast Loire Valley.
Language: Английский
Citations
40
Molecular Ecology Resources, Journal Year: 2022, Volume and Issue: 22(8), P. 3161 - 3175
Published: July 5, 2022
Plastid genome and nuclear ribosomal DNA (nrDNA) arrays, proposed recently as "super-barcodes," might provide additional discriminatory power overcome the limitations of traditional barcoding loci, yet super-barcodes need to be tested for their effectiveness in more plant groups. Morphological homoplasy among Schima species makes genus a model testing efficacy super-barcodes. In this study, we generated multiple data sets comprising standard barcodes (matK, rbcL, trnH-psbA, nrITS) (plastid genome, nrDNA arrays) across 58 individuals from 12 out 13 China. No samples were correctly assigned using while only 27.27% with accessions distinguished plastid its partitioned sets-the lowest estimated rate super-barcode success literature so far. For other taxa similarly divergence low levels genetic variation, incomplete lineage sorting, hybridization or taxonomic oversplitting are all possible causes failure. Taken together, our study suggests that by no means immune challenges imposed evolutionary complexity. We therefore call developing multilocus markers discrimination
Language: Английский
Citations
24
Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)
Published: July 28, 2023
Abstract The alarming rate of climate change demands new management strategies to protect coral reefs. Environments such as mangrove lagoons, characterized by extreme variations in multiple abiotic factors, are viewed potential sources stress-tolerant corals for assisted evolution and propagation. However, biological trade-offs adaptation extremes poorly known. Here, we investigate the reef-building Porites lutea thriving both reef sites show that stress-tolerance comes with compromises genetic energetic mechanisms skeletal characteristics. We observe reduced diversity gene expression variability corals, a disadvantage under future harsher selective pressure. find density, thickness higher porosity skeletons from mangroves, symptoms metabolic energy redirection stress response functions. These findings demonstrate need caution when utilizing human interventions, current survival may compromise competitive fitness.
Language: Английский
Citations
16
Ecology and Evolution, Journal Year: 2023, Volume and Issue: 13(9)
Published: Sept. 1, 2023
Methodological and biological considerations are intertwined when studying cryptic species. A potentially large component of modern biodiversity, the frequency species among taxonomic groups is not well documented. The term "cryptic species" imprecisely used in scientific literature, causing ambiguity interpreting their evolutionary ecological significance. This study reviews how have been defined, discussing implications for taxonomy biology, explores these with a case based on recently published literature extant shelled marine gastropods. Reviewed gastropods were recorded by Records presented authors variable levels confidence but difficult to disentangle from inherent biases effort. These complexities notwithstanding, most gastropod discussed
Language: Английский
Citations
13
Biological Conservation, Journal Year: 2023, Volume and Issue: 280, P. 109963 - 109963
Published: Feb. 22, 2023
Biodiversity loss has accelerated over the past century and freshwater species overall are among those experiencing greatest declines. Genetic resources have potential to help evaluate full magnitude of this represent a key tool effectively allocate conservation monitor success restoration efforts. The power genetic will be realized when daunting task referencing all DNA sequences organisms is complete. Here, we quantified availability distribution barcode genome data for macroscopic in Canada, country rich inland water thus particularly vulnerable aquatic losses. Impressively, most (86 %) were represented by barcodes recorded BOLD Systems database, while very few had genomes available (<4 NCBI database. We identified deficiencies northern regions taxa assessed as at risk or without sufficient information status classification. As expected, speciose insect group lower-than-average number records per high proportion deficient adequate coverage. This study highlights where future sequencing should prioritized within initiatives such Canada BioGenome Project BIOSCAN provides workflow that could applied internationally inform management plans mitigate biodiversity loss.
Language: Английский
Citations
11
Apidologie, Journal Year: 2024, Volume and Issue: 55(1)
Published: Jan. 17, 2024
Abstract Honey bees ( Apis spp.) are important pollinators in many natural and agro-ecosystems across the world. Effective means of surveying wild populations therefore key to their conservation management. One available survey method infers honey bee colony density from genotype drones (males) sampled sites known as Drone Congregation Areas (DCAs). While this approach has been commonly used for Western A. mellifera ), its feasibility other species is unknown. Here, we investigate drone congregation behaviour Asian cerana north-east Australia suitability inferring density. As population invasive, surveys case can aid monitoring population’s growth spread. Over 5 years, identified 30 DCAs, which were stable time. DCAs sheltered areas beside tree-lines or openings forest canopy. joined during 1–2-h afternoon intervals could be at heights 2–24 m via adhesive lines attached helium balloons carrying lures coated queen pheromone. Drones more likely present a DCA temperature increased, though abiotic factors did not predict overall abundance. low numbers even where was extremely low. Based on genotyping inferred sibship between 2016 2021, estimate Australia’s range 1.1–8.1 colonies/km 2 . This extrapolates total size 11,000–83,000 colonies, with refined estimates requiring better knowledge flight distance effect habitat We conclude that based possible propose part toolkit methods monitor both native invasive ranges.
Language: Английский
Citations
4
Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 24(5)
Published: March 25, 2024
Abstract Recent declines in insect abundances, especially populations of wild pollinators, pose a threat to many natural and agricultural ecosystems. Traditional species monitoring relies on morphological character identification is inadequate for efficient standardized surveys. DNA barcoding has become standard approach molecular organisms, aiming overcome the shortcomings traditional biodiversity monitoring. However, its efficacy depends completeness reference databases. Large efforts are (almost entirely) lacking European countries such patchy data limit Europe‐wide analyses precisely how apply bee identification. Here, we advance towards an effective bees. We conducted high‐effort survey bees at junction central southern Europe barcoded all collected morphospecies. For global analyses, complemented our barcode dataset with relevant delimitation, general genus‐specific gaps examined error rate repositories. found that (i) sixth specimens from Slovenia could not be reliably identified, (ii) delimitation methods show numerous systematic discrepancies, (iii) there no gap across (iv) genus specific, but only after curating errors Intense sampling underrepresented regions strict curation repositories needed enhance use
Language: Английский
Citations
4