Environmental DNA最新文献

{"title":"Challenges in Detecting Ecological Interactions Using Sedimentary Ancient DNA Data","authors":"Fiona Margaret Callahan,&nbsp;Jacky Kaiyuan Li,&nbsp;Rasmus Nielsen","doi":"10.1002/edn3.70067","DOIUrl":"https://doi.org/10.1002/edn3.70067","url":null,"abstract":"<p>With increasing availability of ancient and modern environmental DNA technology, whole-community species occurrence and abundance data over time and space is becoming more available. Sedimentary ancient DNA data can be used to infer associations between species, which can generate hypotheses about biotic interactions, a key part of ecosystem function and biodiversity science. Here, we have developed a realistic simulation to evaluate five common methods from different fields for this type of inference. We find that across all methods tested, false discovery rates of interspecies associations are high under simulation conditions where the assumptions of the methods are violated in a variety of ecologically realistic ways. Additionally, we find that for more realistic simulation scenarios, with sample sizes that are currently realistic for this type of data, models are typically unable to detect interactions better than random assignment of associations. Different methods perform differentially well depending on the number of taxa in the dataset. Some methods (SPIEC-EASI, SparCC) assume that there are large numbers of taxa in the dataset, and we find that SPIEC-EASI is highly sensitive to this assumption while SparCC is not. Additionally, we find that for many methods, default calibration can result in high false discovery rates. We find that for small numbers of species, no method consistently outperforms logistic and linear regression, indicating a need for further testing and methods development.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70067","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143749813","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reconstruction of Marimo Population Dynamics Over 200 Years Using Molecular Markers and Fossil Plankton Remains","authors":"Jotaro Urabe,&nbsp;Isamu Wakana,&nbsp;Hajime Ohtsuki,&nbsp;Masayuki K. Sakata,&nbsp;Yurie Otake,&nbsp;Ryotaro Ichige,&nbsp;Michinobu Kuwae,&nbsp;Toshifumi Minamoto","doi":"10.1002/edn3.70085","DOIUrl":"https://doi.org/10.1002/edn3.70085","url":null,"abstract":"<p>Recent efforts have focused on reconstructing the historical abundance of unfossilized organisms using environmental DNA preserved in sediments (sedDNA). This information is crucial for understanding long-term changes in ecosystems. However, because sedDNA is prone to degradation, its quantification may not always provide accurate estimates of past abundances. To address this issue, we developed a novel method to correct for sedDNA degradation by incorporating plankton remains and applied it to estimate the historical abundance of marimo—large spherical colonies of the green alga <i>Aegagropila brownii</i> (formerly <i>A. linnaei</i>)—in Lake Akan, Japan, which is the only known habitat for large marimo. We first quantified marimo sedDNA in lake sediments dating back over 200 years. We then used our new method to estimate historical changes in their abundance from sedDNA. Analyses revealed that marimo were historically 10–100 times more abundant than they are today, but that their abundance declined in the early 20th century when influxes of muddy water and water level fluctuations occurred due to deforestation and the operation of a hydroelectric power plant. These findings align with historical eyewitness accounts, indicating that, when corrected for degradation using fossilized remains, sedDNA can be a powerful tool for reconstructing the past abundance of unfossilized organisms.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70085","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143741526","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Breaking the Standard: Can Oxford Nanopore Technologies Sequencing Compete With Illumina in Protistan Amplicon Studies?","authors":"Dana Bludau,&nbsp;Guido Sieber,&nbsp;Manan Shah,&nbsp;Aman Deep,&nbsp;Jens Boenigk,&nbsp;Daniela Beisser","doi":"10.1002/edn3.70084","DOIUrl":"https://doi.org/10.1002/edn3.70084","url":null,"abstract":"<p>Advancements in sequencing technologies have revolutionized environmental research, leading to a superior understanding of ecosystem functions. In recent years, high-throughput sequencing techniques evolved from short-read Illumina sequencing to long-read Oxford Nanopore Technologies (ONT) sequencing. While Illumina still dominates the sequencing market and offers high accuracy with low error rates, it is limited by shorter read lengths. ONT provides much longer reads, allowing for greater taxonomic resolution but at the cost of higher error rates. Since existing comparative amplicon analyses deal almost exclusively with prokaryotes, it is uncertain if ONT can serve as a reliable alternative to Illumina regarding protistic metabarcoding approaches. Therefore, this study focuses on comparing error rates, taxonomic classification accuracy, and the community composition of sequences obtained from Illumina and ONT sequencing of the 18S V9 rRNA gene region as well as the full-length 18S rRNA gene from sediment samples. In addition, the applicability of the recently updated Natrix2 amplicon processing pipeline for both sequencing approaches was evaluated. While higher error rates were observed for ONT reads, especially for short reads, the full-length ONT 18S sequences achieved greater taxonomic classification accuracy down to the species level. Illumina V9 sequencing, by contrast, provided reliable classification only down to the phylum level. An analysis of community compositions revealed significant taxonomic differences between the sequencing approaches, with ONT identifying more subtle responses of species to external influences. Nevertheless, the basic community patterns were detectable with all sequencing approaches. To conclude, this study showed for the first time that particularly full-length 18S ONT sequencing can serve as a reliable alternative to Illumina V9 sequencing for protist analysis and may even outperform Illumina depending on the specific research objectives.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70084","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143726916","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Water Volume, Biological and PCR Replicates Influence the Characterization of Deep-Sea Pelagic Fish Communities","authors":"Pedro A. Peres,&nbsp;Heather Bracken-Grissom","doi":"10.1002/edn3.70086","DOIUrl":"https://doi.org/10.1002/edn3.70086","url":null,"abstract":"<p>The pelagic deep sea is challenging to investigate due to logistical constraints regarding access and collection of samples; however, environmental DNA (eDNA) can potentially revolutionize our understanding of this ecosystem. Although recent advancements are being made regarding eDNA technology and autonomous underwater vehicles, no investigation has been performed to assess the impact of different experimental designs using gear found on many research vessels (i.e., CTD mounted with Niskin bottles). Here, we investigated the effects of sampled water volume, biological and PCR replicates in characterizing deep-sea pelagic biodiversity at the level of species and exact sequence variants (ESVs, representing intraspecific variation). Samples were collected at a nighttime depth of 450 m in the northern Gulf of Mexico using Niskin bottles, and we targeted the fish community using the MiFish primer (12S rRNA). Our results show that 1 L is insufficient to characterize deep-sea pelagic fish communities. The 5 L and 10 L treatments detected similar community structure (i.e., the combination of number of species and relative occurrence) and numbers of species per biological replicate; however, the 10 L treatment detected a higher total number of species, more ESVs, and a different community structure when considering ESVs. We found that five biological replicates can detect up to 80% of the number of species detected in each of the 5 L and 10 L treatments, near the saturation point. PCR replicates also had an important role in species and ESV detection, which implies increasing PCR replicates if water volume is limited. We suggest that future studies collect at least 5 L, 5 or more field replicates, and 5–10 PCR replicates to adequately investigate deep-sea pelagic biodiversity using eDNA, considering resource limitations. Our study provides guidance for future eDNA studies and a potential route to expand eDNA studies at a global scale.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70086","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143726917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The First eDNA-Based Assessment at the World's Most Remote Inhabited Islands: Investigating Marine Vertebrate Diversity at Tristan da Cunha","authors":"Megan M. A. Elsmore,&nbsp;Sarah Dalesman,&nbsp;James P. Glass,&nbsp;Jéssica Escobar-Porras,&nbsp;Charles R. Treleven,&nbsp;Sarah Helyar,&nbsp;Paul W. Shaw,&nbsp;Niall J. McKeown","doi":"10.1002/edn3.70081","DOIUrl":"https://doi.org/10.1002/edn3.70081","url":null,"abstract":"<p>Oceanic islands are among the most unique and vulnerable ecosystems in the world. Biodiversity monitoring is crucial for the sustainable management of resources; however, the isolation of many islands makes routine assessment challenging. Environmental DNA (eDNA) provides a promising approach to enhance traditional marine biodiversity assessments, reducing the logistical and financial challenges of monitoring. This study employed eDNA to characterize marine vertebrate biodiversity at the world's most remote inhabited islands of Tristan da Cunha. Two 12 s rRNA gene metabarcoding assays targeting marine fish and vertebrates were applied to seawater samples from 18 sites across the archipelago. This multi-assay approach detected 51 Operational Taxonomic Units (OTUs) encompassing 24 families, 28 genera, and 13 species. Comparison with existing results from traditional survey methods (SCUBA, pelagic BRUVS, and deep-water camera drops) and fisheries by-catch showed eDNA to successfully resolve the islands characteristic diversity profile. In addition, eDNA reported rare and vulnerable taxa underrepresented by the traditional surveys and detected species previously unrecorded at the islands. eDNA resolved greater species richness in kelp versus non-kelp habitats. Dominant Tristanian taxa had the highest number of reads, adding to evidence linking reads and abundance. eDNA detection was robust to sampling technique, volume filtered, time between collection, filtration, and sequencing of samples, demonstrating the effectiveness of this technique for use in challenging remote locations. Community composition varied significantly between metabarcoding assays, with unique OTUs detected by each marker, highlighting the importance of assay selection for capturing the full depth and breadth of diversity. 23%–40% of OTUs were resolved to species level, emphasizing the need for the expansion of taxonomic and sequence databases for this region. The study demonstrates the potential of eDNA as a high-resolution tool that can provide new insights into biodiversity around Tristan and can be operationalized to monitor future changes at these isolated islands.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70081","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143698918","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Persistent Gaps and Errors in Reference Databases Impede Ecologically Meaningful Taxonomy Assignments in 18S rRNA Studies: A Case Study of Terrestrial and Marine Nematodes","authors":"Alejandro De Santiago,&nbsp;Tiago José Pereira,&nbsp;Timothy John Ferrero,&nbsp;Natalie Barnes,&nbsp;Delphine Lallias,&nbsp;Simon Creer,&nbsp;Holly M. Bik","doi":"10.1002/edn3.70080","DOIUrl":"https://doi.org/10.1002/edn3.70080","url":null,"abstract":"<p>In metabarcoding studies, Linnaean taxonomy assignments of Operational Taxonomic Units (OTUs) or Amplicon Sequence Variants (ASVs) underpin many downstream bioinformatics analyses and ecological interpretations of environmental DNA (eDNA) datasets. However, public molecular databases (i.e., SILVA, EUKARYOME, BOLD) for most microbial metazoan phyla (nematodes, tardigrades, kinorhynchs, etc.) are sparsely populated, negatively impacting our ability to assign ecologically meaningful taxonomy to these understudied groups. Additionally, the choice of bioinformatics parameters and computational algorithms can further affect the accuracy of eDNA taxonomy assignments. Here, we use two <i>in silico</i> datasets to show that taxonomy assignments using the 18S rRNA gene can be dramatically improved by curating Linnaean taxonomy strings associated with each reference sequence and closing phylogenetic gaps by improving taxon sampling. Using free-living nematodes as a case study, we applied two commonly used taxonomy assignment algorithms (BLAST+ and the QIIME2 Naïve Bayes classifier) across six iterations of the SILVA 138 reference database to evaluate the precision and accuracy of taxonomy assignments. The BLAST+ top hit with a 90% sequence similarity cutoff often returned the highest percentage of correctly assigned taxonomy at the genus level, and the QIIME2 Naïve Bayes classifier performed similarly well when paired with a reference database containing corrected taxonomy strings. Our results highlight the urgent need for phylogenetically informed expansions of public reference databases (encompassing both genomes and common gene markers), focused on poorly sampled lineages that are now robustly recovered via eDNA metabarcoding approaches. Additional taxonomy curation efforts should be applied to popular reference databases such as SILVA, and taxon sampling could be rapidly improved by more frequent incorporation of newly published GenBank sequences linked to genus- and/or species-level identifications.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70080","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143698826","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metazoan Diversity and Its Drivers: An eDNA Survey in the Pacific Gateway of a Changing Arctic Ocean","authors":"Gerlien Verhaegen,&nbsp;Tatsuya Kawakami,&nbsp;Ayla Murray,&nbsp;Akihide Kasai,&nbsp;Charlotte Havermans","doi":"10.1002/edn3.70082","DOIUrl":"https://doi.org/10.1002/edn3.70082","url":null,"abstract":"<p>Climate change drives species to adapt or undergo range shifts to survive. The Arctic Ocean, experiencing more drastic environmental changes than any other ocean, has two primary inflow regions that facilitate these shifts: the wide, deep Atlantic Gateway and the narrow, shallow Pacific Gateway. Environmental DNA (eDNA) surveys have proven to be effective in characterizing community composition and understanding its ecological drivers. We conducted the first COI marker-based eDNA survey in the Pacific Gateway that analyzed seawater samples from various geographic regions, depths, and water masses across the Bering Strait, the Chukchi Sea, and the South Beaufort Sea. Metazoan taxa from 15 different phyla and indicator species for various regions and water masses were identified. We characterized a highly diverse neritic fauna in the Bering Strait and Chukchi Sea, aligning with known locations of benthic hotspots. On the slope of the Beaufort Sea, we observed transitions from copepod-dominated epipelagic waters to cnidarian- and sponge-dominated deeper areas. Alpha diversity peaked near the seabed and coastlines and was the highest within the warmest Alaskan Coastal Water mass. We linked metazoan communities to different environmental variables, with the community in the Bering Strait being associated with higher temperatures and fluorescence, and the majority of them with lower salinities. This included mostly <i>Pseudocalanus</i> copepod species and verongiid sponges. While rising temperatures might enhance alpha diversity, we anticipate this will primarily be due to the influx of warmer and fresher water masses. Several benthic taxa, including the bivalve <i>Macoma calcarea</i> and seastar <i>Leptasterias arctica</i>, as well as the jellyfish <i>Chrysaora melanaster</i> and the copepod <i>Triconia borealis</i>, were associated with colder, saltier waters and will likely be negatively impacted by ongoing environmental change. Our study successfully characterized changes in metazoan communities across the geographic regions and water masses within the Pacific Gateway of the rapidly changing Arctic Ocean.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70082","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143689873","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Environmental RNA-Based Surveillance of Viral Hemorrhagic Septicemia Virus (VHSV) in Olive Flounder (Paralichthys olivaceus) Aquaculture: Detection Dynamics and Risk Assessment","authors":"Hyo-Young Kang,&nbsp;Yoonhang Lee,&nbsp;Jiyeon Park,&nbsp;Ju-Yeop Lee,&nbsp;Young-Ung Heo,&nbsp;Nameun Kim,&nbsp;Jae-Ok Kim,&nbsp;Mun-Gyeong Kwon,&nbsp;Chan-Il Park,&nbsp;Do-Hyung Kim","doi":"10.1002/edn3.70083","DOIUrl":"https://doi.org/10.1002/edn3.70083","url":null,"abstract":"<p>Viral hemorrhagic septicemia virus (VHSV) is a major pathogen in aquaculture worldwide, causing significant outbreaks through waterborne transmission. This study aimed to evaluate the effectiveness of environmental RNA (eRNA)-based surveillance for detecting VHSV in aquaculture systems, focusing on the relationship between infection dynamics, water temperature, and fish weight. Over an 8-month period, VHSV prevalence was assessed in fish and outlet water samples from six olive flounder farms in Jeju Island, South Korea. Higher detection rates were observed at lower temperatures (&lt; 18°C) and in smaller fish, with 18.7°C and 158 g identified as critical susceptibility thresholds. Controlled laboratory experiments further confirmed a strong correlation between VHSV shedding and infection intensity, with a qPCR CT value of 23 (~10⁶ copies mg⁻¹) serving as a reliable indicator for high-risk infections. The eRNA method successfully detected VHSV in farms with severe infections, demonstrating its potential for noninvasive disease surveillance, although sensitivity was limited at low infection rates. These findings provide actionable insights for early detection, biosecurity enhancement, and sustainable aquaculture management, particularly in temperature-sensitive regions like Jeju Island. This study supports the integration of eRNA-based surveillance into routine disease monitoring, contributing to both aquaculture sustainability and environmental health.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70083","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143689115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Squishy and Crunchy Invasive Invertebrates: Environmental DNA Is Not Shed Equally","authors":"Emily Rose Lancaster,&nbsp;Erin Katherine Grey,&nbsp;Damian Coman Brady,&nbsp;Markus Frederich","doi":"10.1002/edn3.70072","DOIUrl":"https://doi.org/10.1002/edn3.70072","url":null,"abstract":"<p>Environmental DNA (eDNA) detection can be a powerful approach to detect organisms in low abundance and can be crucial for early invasive species detection. Despite its potential, the body plan diversity of invertebrates can pose significant challenges, notably arthropods with exoskeletons that may have low eDNA shedding rates. In this study, we validated nine single-species quantitative PCR assays targeting invasive and nuisance species representing various body plans in the Gulf of Maine, an area of rapid ocean warming. Combining visual surveys and molecular analyses in a two-year eDNA time series, we successfully detected eight of nine target species with qPCR. Of the soft-bodied, “squishy” species, four of five exhibited eDNA detection consistent with visual abundances. Of species with an exoskeleton or shell (crunchy), three of four species were not detected consistently in accordance with visual abundance. Our findings demonstrate the effectiveness of eDNA for early invasive species detection but emphasize the need for long-term field and laboratory validation, informed by species' bauplan. It is imperative to recognize that while eDNA is a valuable tool, its applicability varies across taxa. Therefore, interpreting eDNA results requires careful consideration of its limitations and the specific characteristics of the target organisms.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70072","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143689116","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Confidence Scoring Procedure for eDNA Metabarcoding Records and Its Application to a Global Marine Fish Dataset","authors":"Andrea Polanco F.,&nbsp;Romane Rozanski,&nbsp;Virginie Marques,&nbsp;Martin Helmkampf,&nbsp;David Mouillot,&nbsp;Stéphanie Manel,&nbsp;Camille Albouy,&nbsp;Oscar Puebla,&nbsp;Loïc Pellissier","doi":"10.1002/edn3.70077","DOIUrl":"https://doi.org/10.1002/edn3.70077","url":null,"abstract":"<p>Environmental DNA (eDNA) metabarcoding is changing the way biodiversity is surveyed in many types of ecosystems. eDNA surveys are now commonly performed and integrated into biodiversity monitoring programs and public databases. Although it is widely recognized that eDNA records require interpretation in light of taxonomy and biogeography, there remains a range of perceptions about how thoroughly records should be evaluated and which ones should be reported. Here, we present a modular procedure, available as an R script, that uses a set of five steps to assess the confidence of species-level eDNA records by assigning them a score from 0 to 5. This procedure includes evaluations of the known geographic distribution of each taxon, the taxonomic resolution of the marker used, the regional completeness of the reference database, the diversification rate, and the range map of each taxon. We tested the procedure on a large-scale marine fish eDNA dataset (572 samples) covering 15 ecoregions worldwide, from the poles to the tropics, using the <i>teleo</i> marker on the mitochondrial 12S ribosomal gene. Our analysis revealed broad variation in the average confidence score of eDNA records among regions, with the highest scores occurring along the European and Eastern Atlantic coasts. Generalized linear models applied to record covariates highlighted the significant influences of latitude and species richness on low confidence scores (&lt; 2.5). The polar regions notably displayed high proportions of low confidence scores, probably due to the limited completeness of the regional reference databases and the taxonomic resolution of the <i>teleo</i> marker. We conclude that only records with high confidence scores (&gt; 2.5) should be integrated into biodiversity databases. The medium (2.5) to relatively low-confidence (&lt; 2.5) records correspond to species that require further investigation and may be integrated after inspection to ensure high-quality species records.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70077","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143689067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}