Molecular Ecology Resources最新文献

{"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}

{"title":"Separating Faces in ARMS Metabarcoding Improves Marine Biodiversity Monitoring: A Comparison Across Protocols, Experimental Designs and Photographic Surveys","authors":"Anne Chenuil,&nbsp;Elyna Bouchereau,&nbsp;Térence Legrand,&nbsp;Virgile Calvert,&nbsp;Cécile Chemin,&nbsp;Sandrine Chenesseau,&nbsp;Dorian Guillemain,&nbsp;José Miguel Gutiérrez Ortega,&nbsp;Anne Haguenauer,&nbsp;Michèle Leduc,&nbsp;Frédéric Legendre,&nbsp;Florent Marschal,&nbsp;Christian Marschal,&nbsp;Fatma Mirleau,&nbsp;Marjorie Selva,&nbsp;Laurent Vanbostal,&nbsp;Frédéric Zuberer,&nbsp;Pascal Mirleau,&nbsp;Laetitia Plaisance,&nbsp;Vincent Rossi,&nbsp;Sandrine Ruitton,&nbsp;Emese Meglécz,&nbsp;Vincent Dubut","doi":"10.1111/1755-0998.70188","DOIUrl":"https://doi.org/10.1111/1755-0998.70188","url":null,"abstract":"<p>Monitoring marine biodiversity requires approaches capable of capturing its spatial and temporal complexity. DNA metabarcoding coupled with Autonomous Reef Monitoring Structures (ARMS) is increasingly used for this purpose, yet most applications still pool all sessile fractions and rarely benchmark molecular outputs against photographic observations. Here, we combined photographic analysis with cytochrome <i>c</i> oxidase I (COI) metabarcoding across 10 north-western Mediterranean sites to compare and refine ARMS-based monitoring protocols. We first optimized laboratory procedures (DNA extraction and polymerase choice) and applied the control-driven, replicate-aware VTAM pipeline to minimize false positives and ensure traceability. We then conducted the first face-by-face comparison of α- and β-diversity between imaging and eDNA, metabarcoding each ARMS face separately rather than pooling samples. Metabarcoding detected ~15× higher site-level richness and revealed stronger correlations with geographic distance and environmental gradients—which stemmed from its finer taxonomic resolution—whereas photography provided complementary information on macro-taxa and surface cover. For metabarcoding, processing each face separately yielded much higher richness and stronger β-diversity–distance correlations than with the NOAA pooling protocol, demonstrating that pooling inflates sampling variance, weakening ecological signal. Grouping the 17 faces into five structural categories offered a more operational alternative while further increasing α-diversity and strengthening β-diversity correlations. Overall, our results show that retaining ARMS microhabitat structure is critical for maximizing metabarcoding performance. Using five structural sessile fractions per ARMS combined with a control-driven bioinformatic workflow provides a reproducible, scalable framework for long-term eDNA monitoring and early detection of biodiversity change.</p>","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/10.1111/1755-0998.70188","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148943188","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":"Combining Annotation Software to Identify Orthologous Genes (CASIO) Provides a New Dataset of Orthologous Genes for Swallowtail Butterflies","authors":"Gwenaelle Vigo,&nbsp;Benjamin Penaud,&nbsp;Eliette L. Reboud,&nbsp;Fabien L. Condamine,&nbsp;Benoit Nabholz","doi":"10.1111/1755-0998.70161","DOIUrl":"10.1111/1755-0998.70161","url":null,"abstract":"<p>With the massive increase in genomic resources, it is becoming increasingly popular to analyse thousands of loci across many species. However, many of the available genomes are not annotated, which hinders an efficient search for orthologous protein-coding genes. Here, we aim to develop a semi-automated pipeline and compare four genomic annotation methods (BRAKER2, BUSCO, Miniprot and Scipio). Our results highlight the importance of integrating multiple annotation tools to optimise ortholog detection and improve genomic studies. Each annotation method showed different strengths. BRAKER2 annotated a substantial number of genes. BUSCO, despite limitations inherent to its reference database, identified a higher number of orthologs. Miniprot exhibited notable flexibility in accommodating diverse protein datasets, whereas Scipio successfully recovered a considerable set of genes that were not detected by the other tools. The combination of these tools allowed for more comprehensive ortholog detection. Taking advantage of this pipeline, we developed a comprehensive dataset of orthologous genes for swallowtail butterflies (Lepidoptera: Papilionidae), called <i>Papilionidae_odb</i>, which will facilitate future studies, especially for a non-model group with abundant genomic data and few transcriptomic resources. We tested <i>Papilionidae_odb</i> by inferring a robust phylogenetic framework for Leptocircini using 142 complete genomes, which improved branch support for some phylogenetic relationships, although challenges remained in resolving relationships within certain species groups, likely due to rapid radiations. Our results highlight the complementary nature of the annotation methods and suggest that combining these tools can yield more accurate results in genomic research. This approach was implemented in a Snakemake workflow called CASIO (Combining Annotation Software to Identify Orthologous genes) and can easily be applied to other non-model groups to improve genomic datasets in diverse taxa where transcriptomic resources are still limited.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 7","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70161","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148910268","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":"Benchmarking of Reference-Based Tools for Strain-Level Resolution of Plant Microbiome","authors":"Rishav Sahil,&nbsp;Mukesh Jain","doi":"10.1111/1755-0998.70197","DOIUrl":"10.1111/1755-0998.70197","url":null,"abstract":"<p>Strain-level identification of each microbe is crucial for understanding its role in the host. Most of the existing tools have primarily been evaluated on human metagenomic datasets, whereas the plant microbiome exhibits greater diversity and complexity and thus poses a challenge in the strain-level resolution of individual microbes. In this study, we conducted a comprehensive benchmarking of available reference-based tools for strain-level resolution of the plant microbiome. We evaluated seven tools on various performance parameters, like computational requirements, F1-score and relative abundances using synthetic datasets comprising microbes known to have strong associations with plants as well as real plant microbiome datasets. Our results demonstrated a better performance of StrainScan on the synthetic data, achieving higher F1-score and more accurate relative abundance estimates as compared to other tools, but its performance declined gradually with increasing strain diversity. However, StrainGE and StrainScan exhibited competitive performance on real plant metagenome data. Overall, though StrainGE exhibited better performance, it was more computationally expensive. However, StrainScan performed better in detecting low-abundance strains. Our findings suggest the comparative suitability of the available tools for the strain-level analysis of plant metagenome data and highlight the need for the development of more efficient and accurate taxonomic classifiers capable of handling the complex plant metagenome data while maintaining computational efficiency.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 7","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13550808/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148904702","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":"Upscaling Genotyping by Amplicon Sequencing With GBAS-GUI","authors":"Sebastian Sonnenberg,&nbsp;Thapasya Vijayan,&nbsp;Christina Rupprecht,&nbsp;Yoko Philipina Krenn,&nbsp;Melissa Gruber,&nbsp;Hannah Dorfer,&nbsp;Gerald Kwikiriza,&nbsp;Harald Meimberg,&nbsp;Manuel Curto","doi":"10.1111/1755-0998.70198","DOIUrl":"10.1111/1755-0998.70198","url":null,"abstract":"<p>Genotyping by amplicon sequencing (GBAS) is a relatively low-cost approach for generating genotypic data compared with established genomic methods, making it highly scalable and particularly suitable for large-scale genetic monitoring projects. However, most existing analytical pipelines are either marker-specific, insufficiently scalable, or lacking efficient data management systems for the long-term integration of genotypic information, limiting the full potential of GBAS. Here, we address this gap by introducing GBAS-GUI (https://github.com/sonnenbe-dot/GBAS-GUI), a pipeline capable of generating GBAS-based genotypic data for a wide variety of loci at scale. GBAS-GUI integrates a graphical user interface with multiple checkpoints to improve accessibility and robustness. It implements multiprocessing architecture and a relational database that links genotypic data with associated sample metadata to enhance scalability and data management. The pipeline further enables marker screening through automated calculation of polymorphism information content (PIC) and implements a strategy to recover homologous genotypic information from paralogous loci with non-overlapping amplicon length ranges. Using multiple empirical datasets, we demonstrate substantial improvements in processing speed, database management and handling artefacts related to co-amplification of unspecific regions and duplicates of the same genomic region. We further show that incorporating the full sequence information captured by an amplicon increases marker information content beyond what is achievable with length-based genotyping alone and expands the analytical versatility of GBAS. Overall, GBAS-GUI provides a robust, scalable and versatile framework that unlocks the potential of GBAS for large-scale population genetic and phylogeographic studies.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 7","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13544635/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148890492","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":"Getting to the Core of the Matter—Assessing the Role of Replication in Metabarcoding-Based sedaDNA","authors":"Elena Baños,&nbsp;Clara Ras Segura,&nbsp;Erik J. De Boer,&nbsp;Andrew B. Cundy,&nbsp;Xavier Turon Barrera,&nbsp;Sandra Nogué,&nbsp;Luke E. Holman,&nbsp;Marc Rius","doi":"10.1111/1755-0998.70200","DOIUrl":"10.1111/1755-0998.70200","url":null,"abstract":"<p>Replication is central to most experimental and sampling designs, increasing inferential power and capturing fine-scale data heterogeneity. However, its importance remains poorly evaluated in some ecological and evolutionary settings. This is the case of metabarcoding studies using DNA recovered from sedimentary archives, in which biological signals integrate ecological information through depositional and burial processes, yet are commonly inferred from a single sediment core per site. Here, we evaluated the effect of different types of replication using sedimentary DNA metabarcoding data from two genetic markers (mitochondrial COI and nuclear 18S) using a nested sampling design. The design included three intertidal sites, three spatially separated sediment cores per site (biological replicates), two sediment horizons per core, and eight PCR (technical) replicates per sediment sample. Variance partitioning showed that site identity and sediment age group together explained &gt; 70% of the variation in beta diversity, indicating that among-site spatial and stratigraphic differences were the dominant drivers of community composition. PERMANOVA likewise identified non-significant effects of biological replication. Among PCR replicates from the same sediment sample, richness varied substantially, whereas Shannon diversity was more consistent. Despite this variability, differences in community composition among technical replicates remained smaller than those associated with biological replication or site identity, indicating a limited influence on broader ecological patterns. Community composition was highly similar among replicate cores within sites, consistent with stratigraphic coherence. These results indicate limited within-site heterogeneity and suggest that, under stratigraphically coherent conditions, increasing biological replication may provide little additional information, whereas enhancing technical replication and stratigraphic resolution can improve ecological inference from sedimentary DNA metabarcoding datasets.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 7","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13542785/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148885668","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":"Target Capture of Ancient Shell DNA Enables Phylogenetic Reconstruction of Deep-Sea Molluscs","authors":"Yi-Xuan Li,&nbsp;Yanjie Zhang,&nbsp;Qi Dai,&nbsp;Chong Chen,&nbsp;Crispin T. S. Little,&nbsp;Moriaki Yasuhara,&nbsp;Yusuke Yokoyama,&nbsp;Jack Chi-Ho Ip,&nbsp;Jian-Wen Qiu","doi":"10.1111/1755-0998.70199","DOIUrl":"https://doi.org/10.1111/1755-0998.70199","url":null,"abstract":"<p>Target capture is widely used to enrich endogenous DNA from calcium phosphate skeletal material in vertebrates, but its performance on calcium carbonate hard parts widely produced by invertebrates remains poorly understood. Here, we compared DNA recovery from four fresh and 12 ancient (eight radiocarbon-dated to 1671–1135 years old before present) deep-sea vesicomyid clam shells, including species <i>Archivesica marissinica</i>, <i>A. nanshaensis</i> and <i>A. okutanii</i>, using whole-genome sequencing (WGS) or target capture of ultraconserved elements (UCEs). WGS achieved 16.65% on-target read recovery of UCEs from fresh soft tissue, but &lt; 1% from shell specimens. By contrast, UCE capture in the same specimen increased on-target reads by up to 155-fold, reaching 29.84% in fresh shells and up to 72-fold, reaching 19.89% in ancient shells. Target capture of UCEs recovered 142–1001 loci per sample compared to 0–230 with WGS alone. Ancient shells of <i>A. marissinica</i> and <i>A. okutanii</i>, based on reads mapped with bwa-mem2 and bbmap, exhibited characteristic post-mortem DNA damage signals, with average 5′-end C-to-T misincorporation rates of 3.46% and 15.97%, respectively, exceeding the levels observed in fresh <i>A. marissinica</i> shells (maximum 1.24%). UCE-based phylogenetic reconstructions incorporating shell ancient DNA recovered two major clades within Pliocardiinae, consistent with published phylogenomic trees. Together, these findings demonstrate that target-capture enrichment enables effective recovery of highly degraded DNA from ancient mollusc shells and supports robust phylogenetic inference at the intrageneric scale, expanding the utility of shells—one of the most abundant invertebrate remains—for evolutionary, biogeographic and conservation studies.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 7","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70199","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148860197","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}