Molecular Ecology Resources最新文献

{"title":"The Long and the Short of It: Nanopore-Based eDNA Metabarcoding of Marine Vertebrates Works; Sensitivity and Species-Level Assignment Depend on Amplicon Lengths","authors":"Karlijn Doorenspleet,&nbsp;Lara Jansen,&nbsp;Saskia Oosterbroek,&nbsp;Pauline Kamermans,&nbsp;Oscar Bos,&nbsp;Erik Wurz,&nbsp;Albertinka Murk,&nbsp;Reindert Nijland","doi":"10.1111/1755-0998.14079","DOIUrl":"10.1111/1755-0998.14079","url":null,"abstract":"<p>To monitor the effect of nature restoration projects in North Sea ecosystems, accurate and intensive biodiversity assessments are vital. DNA-based techniques and especially environmental (e)DNA metabarcoding is becoming a powerful monitoring tool. However, current approaches rely on genetic target regions under 500 bp, offering limited taxonomic resolution. We developed a method for long-read eDNA metabarcoding, using Nanopore sequencing of a longer amplicon and present DECONA, a read processing pipeline to enable improved identification of marine vertebrate species. We designed a universal primer pair targeting a 2 kb region of fish mitochondrial DNA and compared it to the commonly used MiFish primer pair targeting a ~ 170 bp region. In silico testing showed that 2 kb fragments improved accurate identification of closely related species. Analysing eDNA from a North Sea aquarium showed that sequences from both primer pairs could be assigned to most species, and additional species level assignments could be made through the 2 kb primer pair. Interestingly, this difference was opposite in eDNA from the North Sea, where not the 2 kb but the MiFish primer pair detected more species. This study demonstrates the feasibility of using long-read metabarcoding for eDNA vertebrate biodiversity assessments. However, our findings suggests that longer fragments are less abundant in environmental settings, but not in aquarium settings, suggesting that longer fragments may provide a more recent snapshot of the community. Thus, long-read metabarcoding can expand the molecular toolbox for biodiversity assessments by improving species-level identification and may be especially useful when the temporal origin of the eDNA signal is better understood.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 4","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14079","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143389725","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Strategy of Assessing Gene Copy Number Differentiation Between Populations Using Ultra-Fast De Novo Assembly of Next-Generation Sequencing Data","authors":"Tao Shi,&nbsp;Zhiyan Gao,&nbsp;Yue Zhang,&nbsp;Mark D. Rausher,&nbsp;Jinming Chen","doi":"10.1111/1755-0998.14080","DOIUrl":"10.1111/1755-0998.14080","url":null,"abstract":"<div>\u0000 \u0000 <p>Gene duplication and loss play pivotal roles in the evolutionary dynamics of genomes, contributing to species phenotypic diversity and adaptation. However, detecting copy number variations (CNVs) in homoploid populations and newly-diverged species using short reads from next-generation sequencing (NGS) with traditional methods can often be challenging due to uneven read coverage caused by variations in GC content and the presence of repetitive sequences. To address these challenges, we developed a novel pipeline, ST4gCNV, which leverages ultra-fast de novo assemblies of NGS data to detect gene-specific CNVs between populations. The pipeline effectively reduces the variance of read coverage due to technical factors such as GC bias, providing a reliable CNV detection with a minimum sequencing depth of 10. We successfully apply ST4gCNV to the resequencing analysis of homoploid species <i>Nelumbo nucifera</i> and <i>Nelumbo lutea</i> (lotus). We reveal significant CNV-driven differentiation between these species, particularly in genes related to petal colour diversity such as those involved in the anthocyanin pathway. By highlighting the extensive gene duplication and loss events in <i>Nelumbo</i>, our study demonstrates the utility of ST4gCNV in population genomics and underscores its potential of integrating genomic CNV analysis with traditional SNP-based resequencing analysis.</p>\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 4","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143381391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integration of De Novo Chromosome-Level Genome and Population Resequencing of Peganum (Nitrariaceae): A Case Study of Speciation and Evolutionary Trajectories in Arid Central Asia","authors":"Hao Xu,&nbsp;Yun Han,&nbsp;Xiaofeng Chi,&nbsp;Jingya Yu,&nbsp;Mingze Xia,&nbsp;Shuang Han,&nbsp;Yu Niu,&nbsp;Faqi Zhang,&nbsp;Shilong Chen","doi":"10.1111/1755-0998.14078","DOIUrl":"10.1111/1755-0998.14078","url":null,"abstract":"<div>\u0000 \u0000 <p>Natural hybridization is a significant driving force in plant evolution and speciation. Understanding the genetic mechanism and dynamic evolutionary trajectories of divergence between species and hybrids remains a central goal in evolutionary biology. Here, we examined the genetic divergence of <i>Peganum</i> and their intermittent and hybrid entities (IHEs) from large-scale sympatric and allopatric regions. We sequenced the genomes of <i>Peganum</i> from the Arid Central Asia (ACA) region and its surrounding areas, discovering that the origin of <i>Peganum</i> could be traced to the Hexi Corridor in eastern Central Asia, where migration led to geographic and environmental isolation, giving rise to new species based on natural selection. Different <i>Peganum</i> species, exhibiting excellent dispersal abilities, migrated to the same regions and underwent hybridization. The descendant species of <i>Peganum</i> inherited and developed adaptive traits from parent species through gene flow and introgression, particularly in DNA repair and wax layer formation, leading to the speciation of the IHEs. This study clarified the transition stages in hybrid speciation and identified the Mixing-Isolation-Mixing cycles (MIM) model as a speciation framework suitable for <i>Peganum</i>, marking the initial identification of this unique evolutionary model in the ACA region.</p>\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 4","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143381400","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cgsim: An R Package for Simulation of Population Genetics for Conservation and Management Applications","authors":"Shawna J. Zimmerman,&nbsp;Sara J. Oyler-McCance","doi":"10.1111/1755-0998.14081","DOIUrl":"10.1111/1755-0998.14081","url":null,"abstract":"<p>Wildlife conservation and management increasingly considers genetic information to plan, understand and evaluate implemented population interventions. These actions commonly include conservation translocation and population reductions through removals. Change in genetic variation in response to management actions can be unintuitive due to the influence of multiple interacting drivers (e.g. genetic drift, life history traits, environmental stochasticity). Simulation is an excellent tool to understand the predicted consequences of different proposed or implemented actions. However, the genetic simulators that are robust to a wide variety of life history traits also have a steep learning curve to appropriately parameterize common management actions. To fill this gap, we have developed cgsim, an R package for simulating the genetic consequences of common management interventions for populations of wildlife species. We developed a set of functions to specifically understand the effects of four main aspects of managing small, declining or isolated populations: loss of genetic diversity to drift, augmenting existing populations (e.g. translocation), population reduction through targeted removals and population catastrophes driven by stochastic extrinsic forces. Our single population simulation model is individual-based, and flexible to a range of life history traits. Here we validate cgsim through comparison of simulations to theoretical expectations of genetic diversity loss and illustrate its applied utility by focusing on a recently published empirical example for the Greater Sage-Grouse. Cgsim is available as an R package at: https://doi.org/10.5066/P1BXBEXJ.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 4","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14081","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143381396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Estimation of Species Abundance Based on the Number of Segregating Sites Using Environmental DNA (eDNA).","authors":"Qiaoyun Ai, Hao Yuan, Ying Wang, Chenhong Li","doi":"10.1111/1755-0998.14076","DOIUrl":"https://doi.org/10.1111/1755-0998.14076","url":null,"abstract":"<p><p>The advance of environmental DNA (eDNA) has enabled rapid and non-invasive species detection in aquatic environments. While most studies focus on species detection, recent works explored using eDNA concentration to quantify species abundance. However, the differential individual DNA contribution to eDNA samples could easily obscure the eDNA concentration-species abundance relationship. We propose using the number of segregating sites as a proxy for estimating species abundance. Segregating sites reflect the genetic diversity of the population, which is less sensitive to differential individual DNA contribution than eDNA concentration. We examined the relationship between the number of segregating sites and species abundance in silico, in vitro, and in situ experiments, using two brackish goby species, Acanthogobius hasta and Tridentiger bifasciatus. Analyses of the simulated and in vitro data with DNA mixed from a known number of individuals showed a strong correlation between the number of segregating sites and species abundance (R² > 0.9; p < 0.01). In the in situ experiments, we analysed eDNA samples collected from mesocosm. The results further validated that the correlation (R² = 0.70, p < 0.01) was not affected by biotic factors, including body size and feeding behaviour (p > 0.05). The cross-validation test results also showed that the number of segregating sites predicted species abundance with less bias and variability than the eDNA concentration. Overall, the number of segregating sites is less affected by differential DNA contribution among individuals compared to eDNA concentration. This advancement can significantly enhance the proficiency of estimating species abundance using eDNA.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14076"},"PeriodicalIF":5.5,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143253985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A High-Throughput Ancient DNA Extraction Method for Large-Scale Sample Screening","authors":"Alexandre Gilardet,&nbsp;Edana Lord,&nbsp;Gonzalo Oteo García,&nbsp;Georgios Xenikoudakis,&nbsp;Katerina Douka,&nbsp;Matthew J. Wooller,&nbsp;Timothy Rowe,&nbsp;Michael D. Martin,&nbsp;Mathilde Le Moullec,&nbsp;Michail Anisimov,&nbsp;Peter D. Heintzman,&nbsp;Love Dalén","doi":"10.1111/1755-0998.14077","DOIUrl":"10.1111/1755-0998.14077","url":null,"abstract":"<p>Large-scale DNA screening of palaeontological and archaeological collections remains a limiting and costly factor for ancient DNA studies. Several DNA extraction protocols are routinely used in ancient DNA laboratories and have even been automated on robotic platforms. Robots offer a solution for high-throughput screening but the costs, as well as necessity for trained technicians and engineers, can be prohibitive for some laboratories. Here, we present a high-throughput alternative to robot-based ancient DNA extraction using a 96-column plate. When compared to routine single MinElute columns, we retrieved highly similar endogenous DNA contents, an important metric in ancient DNA screening. Mitogenomes with a coverage depth greater than 0.1× could be generated and allowed for taxonomic assignment. However, average fragment lengths, DNA damage and library complexities significantly differed between methods but these differences became nonsignificant after modification of our library purification protocol. Our high-throughput extraction method allows generation of 96 extracts within approximately 4 hours of laboratory work while bringing the cost down by ~39% compared to using single columns. Additionally, we formally demonstrate that the addition of Tween-20 during the elution step results in higher complexity libraries, thereby enabling higher genome coverage for the same sequencing effort.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 4","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14077","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143253979","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bamboozle: A Bioinformatic Tool for Identification and Quantification of Intraspecific Barcodes","authors":"Matthew I. M. Pinder,&nbsp;Björn Andersson,&nbsp;Hannah Blossom,&nbsp;Marie Svensson,&nbsp;Karin Rengefors,&nbsp;Mats Töpel","doi":"10.1111/1755-0998.14067","DOIUrl":"10.1111/1755-0998.14067","url":null,"abstract":"<p>Evolutionary changes in populations of microbes, such as microalgae, cannot be traced using conventional metabarcoding loci as they lack intraspecific resolution. Consequently, selection and competition processes among strains of the same species cannot be resolved without elaborate isolation, culturing, and genotyping efforts. Bamboozle, a new bioinformatic tool introduced here, scans the entire genome of a species and identifies allele-rich barcodes that enable direct identification of different genetic strains from a population using amplicon sequencing of a single DNA sample. We demonstrate its usefulness by identifying hypervariable barcoding loci (&lt; 500 bp) from genomic data in two microalgal species, the diploid diatom <i>Skeletonema marinoi</i> and the haploid chlorophyte <i>Chlamydomonas reinhardtii</i>. Across the two genomes, four and twenty-two loci, respectively, were identified that could <i>in silico</i> resolve all analysed genotypes. All of the identified loci are within protein-coding genes with various metabolic functions. Single nucleotide polymorphisms (SNPs) provided the most reliable genetic markers, and among 54 strains of <i>S. marinoi,</i> three 500 bp loci contained, on average, 46 SNPs, 103 strain-specific alleles, and displayed 100% heterozygosity. This high level of heterozygosity was identified as a novel opportunity to improve strain quantification and detect false positive artefacts during denoising of amplicon sequences. Finally, we illustrate how metabarcoding of a single genetic locus can be used to track abundances of <i>S. marinoi</i> strains in an artificial selection experiment. As future genomic datasets become available and DNA sequencing technologies develop, Bamboozle has flexible user settings enabling optimal barcodes to be designed for other species and applications.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 4","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14067","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143187519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative Genomics Points to Ecological Drivers of Genomic Divergence Among Intertidal Limpets","authors":"Emily C. Giles,&nbsp;Vanessa L. González,&nbsp;Paulina Carimán,&nbsp;Carlos Leiva,&nbsp;Ana Victoria Suescún,&nbsp;Sarah Lemer,&nbsp;Marie Laure Guillemin,&nbsp;Daniel Ortiz-Barrientos,&nbsp;Pablo Saenz-Agudelo","doi":"10.1111/1755-0998.14075","DOIUrl":"10.1111/1755-0998.14075","url":null,"abstract":"<div>\u0000 \u0000 <p>Comparative genomic studies of closely related taxa are important for our understanding of the causes of divergence on a changing Earth. This being said, the genomic resources available for marine intertidal molluscs are limited and currently, there are few publicly available high-quality annotated genomes for intertidal species and for molluscs in general. Here we report transcriptome assemblies for six species of Patellogastropoda and genome assemblies and annotations for three of these species (<i>Scurria scurra</i>, <i>Scurria viridula</i> and <i>Scurria zebrina</i>). Comparative analysis using these genomic resources suggest that and recently diverging lineages (10–20 Mya) have experienced similar amounts of contractions and expansions but across different gene families. Furthermore, differences among recently diverged species are reflected in variation in the amount of coding and noncoding material in genomes, such as amount of repetitive elements and lengths of transcripts and introns and exons. Additionally, functional ontologies of species-specific and duplicated genes together with demographic inference support the finding that recent divergence among members of the genus <i>Scurria</i> aligns with their unique ecological characteristics. Overall, the resources presented here will be valuable for future studies of adaptation in molluscs and in intertidal habitats as a whole.</p>\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 4","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143062764","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Next-Generation Snow Leopard Population Assessment Tool: Multiplex-PCR SNP Panel for Individual Identification From Faeces","authors":"Katherine A. Solari,&nbsp;Shakeel Ahmad,&nbsp;Ellie E. Armstrong,&nbsp;Michael G. Campana,&nbsp;Hussain Ali,&nbsp;Shoaib Hameed,&nbsp;Jami Ullah,&nbsp;Barkat Ullah Khan,&nbsp;Muhammad A. Nawaz,&nbsp;Dmitri A. Petrov","doi":"10.1111/1755-0998.14074","DOIUrl":"10.1111/1755-0998.14074","url":null,"abstract":"<div>\u0000 \u0000 <p>In recent years, numerous single nucleotide polymorphism (SNP) panel methods to genotype non-invasive faecal samples have been developed. However, none of these existing methods fit all of the criteria necessary to make a SNP panel broadly usable for conservation projects in any country—cost effective, streamlined lab protocol and user-friendly open-source bioinformatics protocols for panel design and analysis. Here, we present such a method and display its utility by developing a multiplex PCR SNP panel for conducting individual ID of snow leopards, <i>Panthera uncia</i>, from faecal samples. The SNP panel we present consists of 144 SNPs and utilises next-generation sequencing technology. We validate our SNP panel with paired tissue and faecal samples from zoo individuals, showing a minimum of 96.7% accuracy in allele calls per run. We then generate SNP data from 235 field-collected faecal samples from across Pakistan to show that the panel can reliably identify individuals from low-quality faecal samples of unknown age and is robust to contamination. We also show that our SNP panel has the capability to identify first-order relatives among sampled zoo individuals and provides insights into the geographic origin of samples. This SNP panel will empower the snow leopard research community in their efforts to assess local and global snow leopard population sizes. More broadly, we present a SNP panel development method that can be used for any species of interest for which adequate genomic reference data is available.</p>\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 4","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143062706","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Long-Term Ecological Research Data Set From the Marine Genetic Monitoring Program ARMS-MBON 2018–2020","authors":"Nauras Daraghmeh,&nbsp;Katrina Exter,&nbsp;Justine Pagnier,&nbsp;Piotr Balazy,&nbsp;Ibon Cancio,&nbsp;Giorgos Chatzigeorgiou,&nbsp;Eva Chatzinikolaou,&nbsp;Maciej Chelchowski,&nbsp;Nathan Alexis Mitchell Chrismas,&nbsp;Thierry Comtet,&nbsp;Thanos Dailianis,&nbsp;Klaas Deneudt,&nbsp;Oihane Diaz de Cerio,&nbsp;Markos Digenis,&nbsp;Vasilis Gerovasileiou,&nbsp;José González,&nbsp;Laura Kauppi,&nbsp;Jon Bent Kristoffersen,&nbsp;Piotr Kukliński,&nbsp;Rafał Lasota,&nbsp;Liraz Levy,&nbsp;Magdalena Małachowicz,&nbsp;Borut Mavrič,&nbsp;Jonas Mortelmans,&nbsp;Estefania Paredes,&nbsp;Anita Poćwierz-Kotus,&nbsp;Henning Reiss,&nbsp;Ioulia Santi,&nbsp;Georgia Sarafidou,&nbsp;Grigorios Skouradakis,&nbsp;Jostein Solbakken,&nbsp;Peter A. U. Staehr,&nbsp;Javier Tajadura,&nbsp;Jakob Thyrring,&nbsp;Jesus S. Troncoso,&nbsp;Emmanouela Vernadou,&nbsp;Frederique Viard,&nbsp;Haris Zafeiropoulos,&nbsp;Małgorzata Zbawicka,&nbsp;Christina Pavloudi,&nbsp;Matthias Obst","doi":"10.1111/1755-0998.14073","DOIUrl":"10.1111/1755-0998.14073","url":null,"abstract":"<p>Molecular methods such as DNA/eDNA metabarcoding have emerged as useful tools to document the biodiversity of complex communities over large spatio-temporal scales. We established an international Marine Biodiversity Observation Network (ARMS-MBON) combining standardised sampling using autonomous reef monitoring structures (ARMS) with metabarcoding for genetic monitoring of marine hard-bottom benthic communities. Here, we present the data of our first sampling campaign comprising 56 ARMS units deployed in 2018–2019 and retrieved in 2018–2020 across 15 observatories along the coasts of Europe and adjacent regions. We describe the open-access data set (image, genetic and metadata) and explore the genetic data to show its potential for marine biodiversity monitoring and ecological research. Our analysis shows that ARMS recovered more than 60 eukaryotic phyla capturing diversity of up to ~5500 amplicon sequence variants and ~1800 operational taxonomic units, and up to ~250 and ~50 species per observatory using the cytochrome <i>c</i> oxidase subunit I (COI) and 18S rRNA marker genes, respectively. Further, ARMS detected threatened, vulnerable and non-indigenous species often targeted in biological monitoring. We show that while deployment duration does not drive diversity estimates, sampling effort and sequencing depth across observatories do. We recommend that ARMS should be deployed for at least 3–6 months during the main growth season to use resources as efficiently as possible and that post-sequencing curation is applied to enable statistical comparison of spatio-temporal entities. We suggest that ARMS should be used in biological monitoring programs and long-term ecological research and encourage the adoption of our ARMS-MBON protocols.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 4","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14073","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143062749","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}