Published: Jan. 1, 2024
Language: Английский
Molecular Ecology Resources, Journal Year: 2022, Volume and Issue: 23(4), P. 742 - 755
Published: Dec. 8, 2022
Assessment of biodiversity using metabarcoding data, such as from bulk or environmental DNA sampling, is becoming increasingly relevant in ecology, sciences and monitoring. Thereby, the taxonomic identification species their sequences relies strongly on reference databases that link genetic to names. These vary completeness availability, depending group studied region targeted. The incompleteness an important argument explain nondetection by supposedly present. However, there exist further generally overlooked problems with can lead false inaccurate inferences assignment. Here, we synthesize all possible inherent databases. In particular, identify a complete, mutually nonexclusive list seven classes challenges when it comes selecting, developing database for are: (i) mislabelling, (ii) sequencing errors, (iii) sequence conflict, (iv) (v) low resolution, (vi) missing taxa (vii) intraspecific variants. For each problem identified, provide description consequences assignment process. We illustrate respective examples taken literature obtained quantitative analyses public databases, GenBank BOLD. Finally, discuss solutions identified how navigate them. Only raising users' awareness limitations data will adequate interpretations these be achieved.
Language: Английский
Citations
77
Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: unknown
Published: Oct. 4, 2024
Abstract Mitigating ongoing losses of insects and their key functions (e.g. pollination) requires tracking large‐scale long‐term community changes. However, doing so has been hindered by the high diversity insect species that prohibitively investments time, funding taxonomic expertise when addressed with conventional tools. Here, we show these concerns can be through a comprehensive, scalable cost‐efficient DNA metabarcoding workflow. We use 1815 samples from 75 Malaise traps across Germany 2019 2020 to demonstrate how incorporated into monitoring networks for less than 50 € per sample, including supplies, labour maintenance. validated detected using two publicly available databases (GBOL GBIF) judgement experts. With an average 1.4 M sequence reads sample uncovered 10,803 species, which 83.9% were represented single Operational Taxonomic Unit (OTU). estimated another 21,043 plausible argue either lack reference barcode or are undescribed. The total 31,846 is similar number known (~35,500). Because capture only subset insects, our approach identified many likely unknown new science. Our reproducible workflow (~80% OTU‐similarity among years) provides blueprint biodiversity other components in near real time.
Language: Английский
Citations
11
Environmental DNA, Journal Year: 2022, Volume and Issue: 5(2), P. 326 - 342
Published: Dec. 18, 2022
Abstract Metabarcoding of environmental DNA (eDNA) is a powerful tool for describing biodiversity, such as finding keystone species or detecting invasive in samples. Continuous improvements the method and advances sequencing platforms over last decade have meant this approach now widely used biodiversity sciences biomonitoring. For its general use, hinges on correct identification taxa. However, past studies shown how crucially depends important decisions during sampling, sample processing, subsequent handling data. With no clear consensus to best practice, particularly latter has led varied bioinformatic approaches recommendations data preparation taxonomic identification. In study, using large freshwater fish eDNA sequence dataset, we compared frequently zero‐radius Operational Taxonomic Unit (zOTU) our raw reads assigned it taxonomically (i) combination with publicly available reference sequences (open databases) (ii) an OSU (Operational Sequence Units) database approach, curated generated from specimen barcoding (closed database). We show both gave comparable results common species. commonalities between decreased read abundance were thus less reliable not rare The success zOTU depended suitability, rather than size, database. Contrastingly, often enabled species‐level identifications, yet resolution recent phylogenetic age need include target group coverage, outgroups full annotation databases avoid misleading annotations that can occur when short amplicon sizes commonly metabarcoding studies. Finally, make suggestions improve construction use future.
Language: Английский
Citations
20
European Journal of Phycology, Journal Year: 2023, Volume and Issue: 59(2), P. 127 - 156
Published: Nov. 28, 2023
Effective monitoring of non-indigenous seaweeds and combatting their effects relies on a solid confirmation the status respective species. We critically analysed presumed seaweed species reported from Mediterranean Sea, Northeast Atlantic Ocean Macaronesia, resulting in list 140 whose nature is undisputed. For an additional 87 it unclear if they are native or (cryptogenic species) identity requires (data deficient species). discuss factors underlying both taxonomic biogeographic uncertainties outline recommendations to reduce uncertainty about seaweeds. Our dataset consisted over 19,000 distribution records, half which can be attributed only five (Sargassum muticum, Bonnemaisonia hamifera, Asparagopsis armata, Caulerpa cylindracea Colpomenia peregrina), while 56 (40%) recorded no more than once twice. In addition, our analyses revealed considerable variation diversity between geographic regions. The Eastern Sea home largest fraction species, majority have Red Indo-Pacific origin entered mostly via Suez Canal. Non-indigenous with ranges situated Northwest Pacific make up large total Western Lusitania Northern Europe, followed by Australasian origin. Uncertainty remains, however, regarding range substantial study area. so far as first detections serve proxy for introduction rate seaweeds, these do not reveal decrease rate, indicating that current measures policies insufficient battle spread
Language: Английский
Citations
12
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown
Published: May 7, 2023
Abstract Mitigating ongoing losses of insects and their key functions (e.g., pollination) requires accurately tracking large-scale long-term community changes. However, doing so has been notoriously hindered by uniquely high insect species diversity that prohibitively investments time, funding, taxonomic expertise. Here, we show these concerns can be addressed through a comprehensive, scalable cost-efficient DNA metabarcoding workflow. We use 1,815 samples from 75 Malaise traps across Germany 2019 2020 to demonstrate how incorporated into monitoring networks for less than 50 € per sample, including supplies, labor maintenance. With on average 1.4M sequence reads sample uncovered 10,803 validated species, which 83.9% were represented single OTU. estimated another 21,403 plausible likely either lack reference barcode or are undescribed. The total 31,846 is similar the number known (∼35,500). Because capture only subset insects, our approach identified many unknown new science. Our reproducible workflow (∼80% OTU-similarity among years) provides blueprint biodiversity other components in near real time.
Language: Английский
Citations
10
Journal of Animal Ecology, Journal Year: 2023, Volume and Issue: 92(8), P. 1575 - 1588
Published: June 1, 2023
Abstract Research in freshwater ecosystems has always had a strong focus on ecological interactions. The vast majority of studies, however, have investigated trophic interactions and food webs, overlooking wider suite non‐trophic (e.g. facilitation, competition, symbiosis parasitism) the networks they form. Without complete understanding all potential interactions, ranging from mutualistic through to antagonistic, we may be missing important processes with consequences for ecosystem assembly, structure function. Ecological can constructed at different scales, genes ecosystems, but also local global, as such there is significant opportunity put them work research. To expand beyond need leverage technological methodological advances look recent research marine terrestrial systems—which are far more advanced terms detecting, measuring contextualising Future studies should emerging technologies aid merging wide range into advance our ultimately increase efficacy conservation, management, restoration other applications.
Language: Английский
Citations
10
Neotropical Ichthyology, Journal Year: 2025, Volume and Issue: 23(1)
Published: Jan. 1, 2025
Abstract Genetic information is crucial for species identification, population genetics structure, evolutionary relationships, and biodiversity monitoring. It helps address gaps related to Linnean (taxonomic uncertainty) Darwinian (phylogenetic knowledge) shortfalls. Understanding these can guide data collection reduce This study focuses on compiling genetic 748 fish in the Tocantins-Araguaia basin, examining number of unique genomic regions individual sampled per species. We also investigated factors that determine availability by linking it with macroecological predictors. Our findings reveal fewer than one-third endemic have resources available. The shortfall - lack phylogenetic knowledge a key factor limiting data, experiencing more this having less information. underscores need increased sampling better assess biological like structure.
Language: Английский
Citations
0
Ecology and Evolution, Journal Year: 2024, Volume and Issue: 14(2)
Published: Feb. 1, 2024
Abstract The Guizhou golden monkey ( Rhinopithecus brelichi ) is a critically endangered wildlife species, and understanding its diet composition may be useful for assessing feeding strategies. DNA metabarcoding was used to determine the dietary diversity of R. . extracted from 31 faecal samples amplified chloroplast rbcL mitochondrial COI sequenced using Illumina NovaSeq platform. A comparative analysis sequences revealed that five most abundant plant genera were Magnolia , Morinda Viburnum Tetradium Eurya In winter, mostly consumed shrubs, herbs shrubs/trees according habit with higher abundances comparatively. families in animal Psychodidae, Trichinellidae, Staphylinidae, Scarabaeidae Trichoceridae. This study first show winter diets based on metabarcoding. These results provide an important basis wild which inhabits only Fanjingshan National Nature Reserve, China.
Language: Английский
Citations
3
Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 24(4)
Published: March 1, 2024
Abstract Biomonitoring of marine life has been enhanced in recent years by the integration innovative DNA‐based approaches, which offer advantages over more laborious techniques (e.g. microscopy). However, trade‐offs between throughput, sensitivity and quantitative measurements must be made when choosing prevailing molecular methodologies (i.e. metabarcoding or qPCR/dPCR). Thus, aim present study was to demonstrate utility a microfluidic‐enabled high‐throughput PCR platform (HTqPCR) for rapid cost‐effective development validation multi‐species biomonitoring toolkit, using larvae 23 commercially targeted bivalve crustacean species as case study. The workflow divided into three main phases: definition (off‐) target taxa establishment reference databases (PHASE 1); selection/development assessment assays 2); protocol optimization field 3). 42 were eventually chosen validated. Genetic signal not only showed good correlation with direct visual counts microscopy but also ability provide data at highest taxonomic resolution (species level) time‐ fashion. This developed demonstrating considerable this state‐of‐the‐art technology boosting developmental testing application panels monitoring management natural resources. Once developed, approach provides cost time‐effective alternative compared other approaches metabarcoding). In addition, it is transferable wide range will aid future programmes.
Language: Английский
Citations
2
Environmental DNA, Journal Year: 2023, Volume and Issue: unknown
Published: Nov. 29, 2023
The sequencing revolution requires accurate taxonomic classification of DNA sequences. Key to making assignments are curated, comprehensive reference barcode databases. However, the generation and curation such databases has remained challenging given large continuously growing volumes both sequence data novel targets. Monitoring research applications require a greater diversity specialized gene regions targeted taxa then currently curated by professional staff. Thus there is need for an easy implement computational tool that can generate metabarcoding libraries any bespoke locus. We address this reimagining CRUX from Anacapa Toolkit present rCRUX package in R which, like it's predecessor, relies on homology PCR primer compatibility instead keyword-searches avoid limitations user-defined metadata. typical workflow involves searching plausible seed amplicons (
Language: Английский
Citations
4