Molecular Ecology Resources最新文献

{"title":"MitoNumt: A Workflow for Recovering Mitochondrial Genomes From Long-Read Data and Detecting NUMT Contamination in Mitochondrial Genome Assemblies","authors":"Ruidong Cao,&nbsp;Tong Xin,&nbsp;Yubo Hao,&nbsp;Yibo Hu","doi":"10.1111/1755-0998.70211","DOIUrl":"10.1111/1755-0998.70211","url":null,"abstract":"<p>Nuclear mitochondrial DNA segments (NUMTs) are genomic DNA fragments that originate from historical insertions of mitochondrial DNA sequences into the nuclear genome. During mitochondrial genome (mtgenome) assembly from short-read genome sequencing data, NUMT fragments may be misidentified and incorporated into mtgenome assemblies, leading to NUMT contamination. Although some assembly programs include steps to filter NUMTs, these approaches are not always effective. Here, we present MitoNumt, a multifunctional workflow. Using this pipeline, we recovered mtgenomes, complete NUMT (coexistence with the mtgenomes), and incomplete NUMT fragments from PacBio HiFi long-read sequencing data for five species of the genus <i>Panthera</i> and <i>Puma concolor</i>. We then used these sequences to check mtgenomes available in the NCBI database. NUMT contamination was detected in mtgenomes from all <i>Panthera</i> species examined, with 23 contaminated mtgenomes identified and contamination lengths ranging from 3 to 416 bp. In addition, phylogenetic trees reconstructed from NUMT fragments of at least 5000 bp consistently recovered a topology congruent with the currently accepted <i>Panthera</i> phylogeny. Overall, this workflow enables the identification of HiFi-supported mtgenomes and complete NUMTs, and the detection of NUMT contamination in assembled mtgenomes, thereby improving the reliability of mtgenome-based evolutionary and genetic studies.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 7","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13643347/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149101601","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":"Simplifying Macroinvertebrate Biodiversity Assessment: A Standardised Metabarcoding Method for Invertebrate Samples With High Volumes of Debris","authors":"Melissa Carew,&nbsp;Jessica Chung,&nbsp;Geneveive Hehir,&nbsp;Ary Hoffmann,&nbsp;Rhys Coleman","doi":"10.1111/1755-0998.70213","DOIUrl":"10.1111/1755-0998.70213","url":null,"abstract":"<p>DNA metabarcoding of freshwater macroinvertebrate samples can provide rapid and accurate identification of species diversity. Processing samples where macroinvertebrates are not separated from net contents can substantially reduce time and cost. We devised and tested a standardised method for processing combined kick/sweep samples using DNA metabarcoding to provide accurate estimates of macroinvertebrate species diversity. Kick and sweep samples were collected from 10 sites across Greater Melbourne known to vary in catchment land use, macroinvertebrate abundance and diversity as well as the type and volume of sampling debris. A sieving, blending and DNA extraction protocol was developed to reduce large debris, rocks and sand in samples, and to concentrate macroinvertebrates for metabarcoding. Variable percentages of the dry weight of samples from each site were used as a source of DNA for metabarcoding. We found that the macroinvertebrate species diversity recovered was mostly consistent when processing different percentages (20%–40%) of dry weight, but a minimum dry weight would be recommended for samples with low total dry weight. We present a method with a laboratory and bioinformatic workflow that enables the cost-effective and reliable processing of large volume samples, like those encountered in freshwater bioassessment. This metabarcoding approach has potential to be applied to any invertebrate biodiversity analysis where invertebrates are not separated from sampling debris, regardless of volume and composition, and used on samples varying in species abundance, diversity and density.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 7","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13635761/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149101522","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":"Car-Mounted Airborne eDNA Sampling Detects Landscape Scale Biodiversity Turnover Along Environmental Gradients.","authors":"Joshua P Newton, Morten E Allentoft, Philip W Bateman, Simon Ferrier, Philip F Thomsen, Paul Nevill","doi":"10.1111/1755-0998.70217","DOIUrl":"10.1111/1755-0998.70217","url":null,"abstract":"<p><p>Documenting accelerating global biodiversity decline requires monitoring tools that can operate across large spatial scales and repeated timeframes. Analysis of airborne environmental DNA (eDNA) is an emerging method used to track species distributions, but it is unknown whether airborne eDNA retains coherent ecological signals across terrestrial landscapes, or whether atmospheric mixing and DNA transport make it too spatially diffuse to resolve meaningful macroecological patterns. To address this question, we conducted a biodiversity survey using car-mounted airborne eDNA sampling along a repeated 1155 km route across south-western Western Australia, spanning the Southwest Australian biodiversity hotspot and adjacent inland regions. This extensive and environmentally heterogeneous region faces ongoing pressures from habitat loss, invasive species and climate change, highlighting the need for scalable biodiversity monitoring approaches. Samples were collected at ~26 km intervals and analysed using metabarcoding assays targeting plants, vertebrates and arthropods, with generalised dissimilarity modelling used to assess environmental drivers of community turnover. We detected a broad range of plants and animals, including species of ecological and biosecurity importance. Different taxonomic groups showed distinct spatial scales of airborne eDNA community similarity and beta diversity was structured primarily by habitat and environmental gradients rather than geographic distance alone. This indicates that airborne eDNA did not simply reflect spatially homogenised biological material but retained ecological structure informative of macroecological patterns. Together, these findings demonstrate that car-mounted airborne eDNA can recover ecologically meaningful patterns of community turnover across heterogeneous terrestrial landscapes and support landscape-scale biodiversity assessment.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 7","pages":"e70217"},"PeriodicalIF":5.9,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13680127/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149222874","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":"Distinct Environmental DNA States Reveal Biodiversity and Transport Patterns Across Alpine Watersheds","authors":"Anish Kirtane,&nbsp;Enrico van der Loo,&nbsp;Zora Doppmann,&nbsp;Kristy Deiner","doi":"10.1111/1755-0998.70207","DOIUrl":"10.1111/1755-0998.70207","url":null,"abstract":"<p>Environmental DNA (eDNA) exists in three states: membrane-bound, adsorbed and dissolved. These states differ in persistence and degradation, strongly influencing the interpretation of eDNA data. Despite this, they have rarely been separated and analyzed independently from environmental samples. We developed a state-sorting workflow to isolate and analyze them, applying it to samples from 221 sites from 58 streams across eight lake watersheds with COI and ITS metabarcoding, targeting metazoans and plants, respectively, to reveal differences in biodiversity content and transport dynamics. Our results show that all three states contain both shared and unique taxonomic diversity of metazoan eDNA. However, the plant eDNA was only detected in the membrane-bound state. For metazoans, membrane-bound eDNA contained 87.8% of observed ASVs, far exceeding the adsorbed (37.2%) and dissolved (20.5%) states. Only membrane-bound eDNA showed evidence of downstream transport, but its extent varied among watersheds due to local hydrology. While upstream eDNA was transported to stream–lake confluences, lake surface samples showed a turnover in community composition. Clarifying the fate of membrane-bound eDNA within lakes will enhance catchment-level detection from lake samples and understanding of lake hydrodynamics. Of the environmental parameters assessed, water temperature was most strongly aligned with changes in community composition between sites. Most previous studies have likely captured the majority of the eDNA diversity within their samples by inadvertently targeting the membrane-bound state. This study demonstrates the utility of eDNA state-sorting, but the methods require further refinement. Analyzing states independently improves the interpretation of eDNA data and elucidates the processes governing eDNA fate and transport.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 7","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13618895/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149073028","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":"Simultaneous Inference of Flora-Wide Nuclear and Plastid Phylogenies Using Angiosperms353 Sequence Capture Data","authors":"Sébastien Miche,&nbsp;Charles Pouchon,&nbsp;Camille Christe,&nbsp;Anna Marcionetti,&nbsp;Maya Wells,&nbsp;Yamama Naciri,&nbsp;Nicolas Wyler,&nbsp;Mathieu Perret","doi":"10.1111/1755-0998.70202","DOIUrl":"10.1111/1755-0998.70202","url":null,"abstract":"<p>Accurate knowledge of phylogenetic relationships and divergence time among plant species composing a regional flora is crucial for understanding the origin of the biodiversity patterns we observe today. Despite advances in phylogenomics, resources available for reconstructing regional phylogenies are still largely incomplete and poorly resolved at the species level. We developed a workflow to assemble a phylogenetic dataset for a regional flora using Angiosperms353 target-enrichment and high-throughput genome sequencing. We sampled tissues from freshly collected plants and herbarium specimens representing the angiosperm diversity of the Geneva canton in Switzerland (1098 species). We used ORTHOSKIM to recover targeted nuclear genes and plastid loci from off-target reads, estimated relationships and time divergence using IQTREE, weighted-ASTRAL and treePL, and compared the results obtained from nuclear and plastid genes. We recovered a mean of 289 nuclear and 54 plastid genes for 1316 taxa, representing 92% of the species native to the Geneva canton. We demonstrate that nuclear genes provide increased resolution and phylogenetic support, but similar divergence time estimates compared to plastomes. Our workflow based on Angiosperms353 data provides a phylogenetic framework for an entire regional flora that is consistent with current systematic knowledge and more resolved and complete at the infrageneric level than trees obtained from phylogenetic resources available for angiosperms. This type of genomic data opens perspectives for fine-scale biodiversity and conservation research that integrates evolutionary history.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 7","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13618893/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149072995","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 Genomic Tool to Tackle Cryptic Diversity Demonstrates the Potential for Off-Target Use of GT-Seq Panels","authors":"Amanda S. Ackiss,&nbsp;Mark R. Vinson,&nbsp;Ann J. Ropp,&nbsp;Kristen M. Gruenthal,&nbsp;Trevor J. Krabbenhoft,&nbsp;Joseph V. Siegel,&nbsp;Wendylee Stott,&nbsp;Daniel L. Yule,&nbsp;Wesley A. Larson","doi":"10.1111/1755-0998.70203","DOIUrl":"10.1111/1755-0998.70203","url":null,"abstract":"<p>A comprehensive understanding of life history is vital to successful species conservation and management. When different life history stages are accompanied by considerable morphological or cryptic variation, such as the egg and larval phases exhibited by most fishes, genomic tools are essential for identifying species so that early-life ecology questions can be studied. Genotyping-in-thousands by sequencing (GT-seq) has recently emerged as a targeted and efficient approach for species identification. We leveraged existing genomic and transcriptomic data to develop a GT-seq panel capable of differentiating the members of the <i>Coregonus artedi</i> complex, a radiation of salmonids in the Laurentian Great Lakes whose members are indistinguishable with mitochondrial DNA barcoding loci and are the focus of bi-national conservation initiatives. Our panel of 494 loci was able to assign fishes in the <i>C. artedi</i> complex to species and lake. We examined cross-amplification in other coregonines with overlapping distributions and found that congeneric Lake Whitefish (<i>C. clupeaformis</i>) cross-amplified at 94% of loci and confamilial Round and Pygmy Whitefish (<i>Prosopium</i> spp.) cross-amplified at 42% and 38% of loci, respectively. We adapted bioinformatic probes to account for <i>Prosopium</i>-specific variants including 22 new SNPs and developed a whitelist of 428 SNPs capable of distinguishing these whitefishes. Finally, we demonstrated performance by identifying 3066 coregonine larvae and juveniles collected in spring 2019–2021 from Lake Superior. These results hold promise for future insights into the species-specific ecology of early life coregonines and demonstrate the flexibility of GT-seq panels, which may cross-amplify hundreds of informative genome-wide loci in related taxa.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 7","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70203","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149035792","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":"Substrate-Dependent Variation in Environmental DNA Persistence and Degradation From a Small Mammal","authors":"Austin M. Guthrie,&nbsp;Christine E. Cooper,&nbsp;Philip W. Bateman,&nbsp;Mieke van der Heyde,&nbsp;Morten E. Allentoft,&nbsp;Paul Nevill","doi":"10.1111/1755-0998.70205","DOIUrl":"10.1111/1755-0998.70205","url":null,"abstract":"<p>Environmental DNA (eDNA) analyses have been applied to terrestrial environments for over a decade, yet knowledge of the dynamics of eDNA deposition, movement and degradation remains limited. To address this, we conducted a controlled experiment over 1 year to assess the persistence of eDNA from an arboreal mammal across four substrates (water, sediment, sheltered nest-box surfaces, and exposed nest-box surfaces). Environmental DNA deposited by captive individuals was sampled repeatedly following removal of animals and analysed using both species-specific qPCR and metabarcoding. We modelled degradation using quantitative decay, detection probability, and conditional decay frameworks, and applied a random breakage model to estimate theoretical fragment persistence. Decay followed first-order exponential kinetics in water and on nest box surfaces but not in sediment, which exhibited high stochasticity. We observed a large difference in degradation rates between substrates, with exponential decay models revealing half-lives ranging from 7.3 days in water to 276 days on sheltered internal surfaces. Rapid decay in water restricted detections to approximately 77 days, while persistence models predicted that sheltered surfaces could retain detectable DNA for more than 4 years (&gt; 1700 days), indicating the potential for prolonged accumulation of legacy DNA in protected environments. While species-specific qPCR offered higher sensitivity than metabarcoding, both methods had parallel decay patterns. Our findings indicate that substrate selection is a critical decision when designing an eDNA survey, as there is a trade-off between maximising detection probability and maintaining temporal resolution.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 7","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13598355/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149023555","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":"Comparing the Performance of Double-Stranded and Single-Stranded DNA Libraries for Ancient Oral Microbiome Reconstruction","authors":"Keri Burge,&nbsp;Irina M. Velsko,&nbsp;Domingo C. Salazar-García,&nbsp;María Haber Uriarte,&nbsp;Joaquín Lomba Maurandi,&nbsp;Christina Warinner","doi":"10.1111/1755-0998.70201","DOIUrl":"10.1111/1755-0998.70201","url":null,"abstract":"<p>DNA library construction methods can affect the recovery of ancient DNA, thus influencing downstream analyses. While single-stranded library preparation (ssLib) has been shown to outperform double-stranded (dsLib) for highly degraded vertebrate host DNA, especially for samples older than 40,000 years, few studies have examined how library protocols shape ancient microbial community reconstruction. Here, we compare the sequencing output of paired ssLib and dsLib dental calculus libraries generated from 12 Neanderthals and two Chalcolithic humans, prepared using implementations of the Gansauge et al. and Meyer and Kircher protocols, respectively, and sequenced with identical Illumina chemistry. We compared read length and GC%, read duplication and taxonomic profiles across normalization strategies to assess protocol-specific biases. Double-stranded libraries retained a significantly higher proportion of sequenced reads throughout data processing (dsLib 72.1%, ssLib 37.9%), a higher proportion of oral reads (dsLib 9.78%, ssLib 6.75%), significantly longer median oral DNA read lengths (dsLib 57.5 bp, ssLib 50.5 bp) and more GC-rich fragments (dsLib 60.5% GC, ssLib 52.5% GC). In contrast, ssLibs exhibited slightly higher Shannon diversity and a greater proportion of unique reads. Despite these differences, species richness and overall community composition was not significantly different between protocols, with individual and preservation status explaining the most variance. Stratifying reads by length (&lt; 50 bp vs. ≥ 50 bp) resulted in different classification rates but only had minor effects on diversity estimates. Together, these results demonstrate that dsLib and ssLib protocols impose distinct trade-offs and library choice should be guided by study-specific goals.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 7","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13593575/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149015030","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":"Surveying Biodiverse Coral Reef Ecosystems Across the Tree of Life With Environmental DNA","authors":"Van Wishingrad,&nbsp;Brian W. Bowen,&nbsp;Robert J. Toonen","doi":"10.1111/1755-0998.70196","DOIUrl":"10.1111/1755-0998.70196","url":null,"abstract":"<p>A central challenge in evaluating biodiversity using environmental DNA (eDNA) metabarcoding is that each primer set has biases resulting in selective amplification of taxonomic diversity. Here we test 11 primer pairs to assess Central Pacific coral reef diversity in the five kingdoms of marine eukaryotes: Chromista, Fungi, Metazoa, Plantae and Protozoa. Zero-width OTUs (ZOTUs) were compared to public sequence databases and resolved to the finest taxonomic rank possible. Across all primers, we recovered 421 distinct taxa from five kingdoms in 35 phyla, comprising 62 classes. The number of taxa and taxonomic groups recovered varied widely. Nearly all primers recovered a large fraction of metazoan taxa, and several also recovered a large portion of taxa belonging to Chromista. Based on our results, most primers we tested here can be clustered into four groups: (1) the ‘fish’ primers, specialized for fishes, (2) the ‘diverse’ primers, which recover the highest number of identifications at lower taxonomic levels, (3) the ‘general’ primers, which perform moderately well across the tree of life, and (4) the algae primers. Taxonomic assignments tended to decrease with taxonomic rank, from 86%–100% at the phylum level to 35%–77% at the species level. Primers specialized for specific groups (i.e., fishes) tended to recover fewer taxa at higher taxonomic resolution, while more general primers tended to recover more taxa, though at lower taxonomic resolution. While each primer set proved uniquely informative for some taxa, the taxon recovery profiles provided here should aid researchers in matching the taxonomic specificity of environmental metabarcoding primers with research questions of interest.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 7","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70196","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148987275","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":"Is There a Fly in My Soup? To What Extent Do Metabarcoding and Individual Barcoding Tell the Same Story?","authors":"Brendan Furneaux,&nbsp;Tomas Roslin,&nbsp;Bess Hardwick,&nbsp;Deirdre Kerdraon,&nbsp;Hannu Autto,&nbsp;Gaia Banelyte,&nbsp;Jeremy R. deWaard,&nbsp;Stephanie L. deWaard,&nbsp;Arielle Farrell,&nbsp;Oula Kalttopää,&nbsp;Erik Kristensen,&nbsp;Hanna M. K. Rogers,&nbsp;Jayme E. Sones,&nbsp;Evgeny V. Zakharov,&nbsp;Otso Ovaskainen","doi":"10.1111/1755-0998.70195","DOIUrl":"https://doi.org/10.1111/1755-0998.70195","url":null,"abstract":"&lt;p&gt;Metabarcoding has become the method of choice for characterizing complex arthropod communities. The extent to which metabarcoded bulk samples will recover the same community composition as individual sequencing of all individuals in the sample remains poorly quantified. Biases such as unequal extraction of DNA from different taxa, primer mismatches and non-random PCR may cause the selective drop-out of species from metabarcoding data. At the same time, DNA metabarcoding may reveal arthropod taxa present not as individuals, but as DNA residues on the surface or in the gut of insects. To quantify the consistency in sample contents established by different means, we metabarcoded 45 bulk insect samples, then extracted all arthropods and sequenced them individually. Metabarcoding targeted 418 bp at the 3′ end of the Folmer barcoding region, while individual barcodes captured the entire 658 bp Folmer region. The metabarcoding workflow, including PCR amplification, sequencing and bioinformatics, was performed in three replicates from three separate lysate aliquots per sample. For the main analyses, sequences were assigned to Barcode Index Numbers (BINs) as identical taxonomic categories across data types, thereby allowing the detection of even rare but biologically true taxa. Since such reference-based validation will be unavailable to any researcher dealing with metabarcoding data alone, we validated our key findings through an alternative workflow, i.e., de novo clustering of sequences. We found that metabarcoding is replicable, as different replicates of the same sample recover similar species richness and composition. Individual barcoding and metabarcoding provide similar impressions of relative differences in community structure: species-rich vs. species-poor samples rank similarly among data types (Spearman's &lt;i&gt;⍴&lt;/i&gt; = 0.88–0.99) as do differences in relative dissimilarity between sample pairs (Spearman's &lt;i&gt;⍴&lt;/i&gt; = 0.55–0.90). Dissimilarity between data types varies with BIN richness in the sample, but this relationship reflects nestedness rather than turnover: metabarcoding recovers the same set of core species as individual barcoding but adds hundreds of species on top. Any BIN recovered as an individual occurred with high probability in the metabarcoding data, and any BIN found in high read abundances by metabarcoding was likely found as an individual (&lt;i&gt;p&lt;/i&gt; &gt; 0.8). In terms of abundances, the number of individual insects per BIN was well predicted by the number of metabarcoding reads (&lt;i&gt;R&lt;/i&gt;&lt;sup&gt;2&lt;/sup&gt; &gt; 0.68 for a model including taxonomy as a random effect). Our analysis suggests that metabarcoding data will be informative of the sample contents in terms of arthropod species richness, composition and taxon-specific abundances. Taxa recovered in low copy numbers in metabarcoding sequence data will likely represent DNA left as residues from past biotic interactions. Barring sequencing errors, both types of data yield biologica","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 7","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70195","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148943199","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}