Molecular Ecology Resources最新文献

{"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}

{"title":"MixedUpParents: A New and Improved Method for Genetic Parentage Assignment in Admixed Populations","authors":"Jared A. Grummer,&nbsp;Eric C. Anderson,&nbsp;Gordon Luikart","doi":"10.1111/1755-0998.70194","DOIUrl":"10.1111/1755-0998.70194","url":null,"abstract":"<p>Hybridization is ubiquitous throughout the tree of life. Its presence in genetic datasets often violates model assumptions or leads to erroneous inferences. Nonetheless, few parentage assignment methods have been developed that account for hybridization or admixture, particularly in non-model systems. Here, we describe a novel method of parentage analysis, <i>MixedUpParents</i>, that accounts for hybridization by using species-diagnostic single nucleotide polymorphisms while accounting for mixed ancestry within discrete genomic segments. We test <i>MixedUpParents</i> alongside other parentage assignment programs through simulations to assess assignment accuracy in scenarios with and without hybridization. Our simulations included a range of parameter values, including missing genotypes, migration (hybridization) rates and proportions of un-sampled individuals. Simulation results showed that in all scenarios with admixture, <i>MixedUpParents</i> outperformed the other parentage methods tested and performed well for parent–offspring assignment even when only one parent is sampled. In the best cases, <i>MixedUpParents</i> achieved <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mo>≥</mo>\u0000 </mrow>\u0000 <annotation>$$ ge $$</annotation>\u0000 </semantics></math> 95% true-positive and <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mo>∼</mo>\u0000 </mrow>\u0000 <annotation>$$ sim $$</annotation>\u0000 </semantics></math>5% false-positive rates (i.e., assigning the wrong parent). Accuracy of all parentage methods increased when a higher proportion of the population was sampled, but decreased with higher levels of missing marker data. The most challenging cases for all methods were those with intermediate migration rates, and when full-siblings were included in the parent sample (representing age-agnostic field sampling). Overall, we show that ‘traditional’ methods can yield high false-positive rates when hybridization is present, emphasizing the importance of using appropriate methods in admixed systems. Our results and freely available software should advance population management and research on measures of reproductive success (fitness) in wild and captive populations, and parentage and pedigree reconstruction broadly.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 6","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13508186/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148816830","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":"High-Throughput DNA Barcoding Reveals Multi-Trophic Networks of Plants, Leafminers and Parasitoids in a Tropical Dry Forest","authors":"Ariel H. Muñoz-Sánchez,&nbsp;Gonzalo Contreras-Negrete,&nbsp;Alejandro Zaldívar-Riverón,&nbsp;Rafael Torres Colín,&nbsp;Evgeny V. Zakharov,&nbsp;Carlos López-Vaamonde,&nbsp;Antonio Hernández-López","doi":"10.1111/1755-0998.70183","DOIUrl":"10.1111/1755-0998.70183","url":null,"abstract":"<p>Tropical dry forests host highly diverse insect communities and complex trophic interactions, yet these networks remain difficult to resolve using conventional molecular or rearing-based approaches. Here, we integrate long-read DNA barcoding, non-target sequence co-amplification, and host plant taxonomy to reconstruct tri-trophic interactions among leaf-mining insects, their host plants, and associated parasitoids in a Mexican tropical dry forest. Using Single Molecule, Real-Time (SMRT) sequencing on the PacBio Sequel IIe platform, we generated high-fidelity barcodes from individual leaf-miner larvae and from parasitoid larvae and pupae recovered from leaf mines. From 253 specimens, we obtained 214 sequences, and identified 83 operational taxonomic units including leaf-mining Lepidoptera, Diptera, Coleoptera, and their hymenopteran parasitoids, plus 31 non-target sequences. Of the 214 sequences, 69 were parasitoid wasps (32.2%). Of these, 40 were obtained from parasitoids dissected directly from leaf mines, while 29 were co-amplified from leaf-miner samples, demonstrating that SMRT-based co-amplification allows detection of parasitism without rearing. Our analysis revealed 156 trophic interaction types and 247 interaction events. Network analyses showed a highly modular tripartite network, with module structure primarily driven by host plant identity and a reduced set of influential leaf-miner and parasitoid taxa. Bipartite networks supported the hypothesis that interactions are more strongly compartmentalized between leafminers and host plants than at higher trophic levels. These results demonstrate that long-read DNA barcoding with co-amplification detection provides a scalable framework for reconstructing multi-trophic interactions from individual specimens, overcoming key limitations of rearing-based methods and enabling robust biodiversity and ecological network assessments in species-rich ecosystems.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 6","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13509077/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148816897","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":"Updating the RZooRoH Package for the Analysis of Inbreeding, Identity-By-Descent and Relatedness From Genomic Data","authors":"Natalia S. Forneris,&nbsp;Pierre Faux,&nbsp;Mathieu Gautier,&nbsp;Tom Druet","doi":"10.1111/1755-0998.70186","DOIUrl":"10.1111/1755-0998.70186","url":null,"abstract":"<p>The RZooRoH R package was implemented to characterize individual inbreeding levels. It identifies DNA segments inherited twice from a common ancestor through different paths, which are known as homozygous-by-descent (HBD) segments. The package accepts different data formats and provides multiple outputs: HBD segments, inbreeding rates and genome-wide and locus-specific HBD probabilities. In addition, it partitions HBD levels into multiple HBD classes. The length distribution varies between these classes, which therefore correspond to distinct groups of ancestors that can be traced back to different generations in the past. This provides information about mating structure and recent demographic history. The computational performance of the package has been substantially improved, enabling, for example, computing times to be reduced when working with whole-genome sequence data and more HBD classes to be fitted. It is now possible to fit one class per past generation, which facilitates interpretation of the results. Since we have previously demonstrated that the ZooRoH model can be used to characterize identity-by-descent (IBD) between haploid individuals or phased haplotypes, this option has been included in the new package version. Estimating kinship by characterizing IBD levels between the four possible pairs of haplotypes from two individuals is another feature we added to the package. Finally, new options allow models to be refined, for instance by defining HBD classes as intervals or constant inbreeding rates for neighbouring classes. Overall, the new version of the package offers improved computational efficiency and interpretability when characterizing inbreeding, IBD and relatedness levels.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 6","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13509087/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148816733","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":"Correction to “Quantitative Monitoring of Diverse Fish Communities at a Large Scale Combining eDNA Metabarcoding and qPCR”","authors":"","doi":"10.1111/1755-0998.70193","DOIUrl":"10.1111/1755-0998.70193","url":null,"abstract":"<p>Pont, D., P. Meulenbroek, V. Bammer, et al. 2023. “Quantitative Monitoring of Diverse Fish Communities on a Large Scale Combining eDNA Metabarcoding and qPCR.” <i>Molecular Ecology Resources</i> 23: 396–409. https://doi.org/10.1111/1755-0998.13715.</p><p>Due to an error in the calculation of teleo-eDNA concentrations (real time qPCR), all figures expressing the number of teleo-eDNA copies per litre or per sample must be divided by 100.</p><p>Figures 4, 5 and 7 are corrected (modifications of the axis numerical values and axis labels when necessary). Figures 1, 2, 3 and 6 are unchanged.</p><p>We apologize for this error.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 6","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13504688/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148811622","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}