Molecular Ecology Resources最新文献

{"title":"PopGenHelpR: An R Package to Streamline and Facilitate Informed Population Genomic Analyses and Visualization of Genetic Ancestry, Diversity and Differentiation.","authors":"Keaka Farleigh, Mason O Murphy, Christopher Blair, Tereza Jezkova","doi":"10.1111/1755-0998.70142","DOIUrl":"10.1111/1755-0998.70142","url":null,"abstract":"<p><p>Analysing large population genomic datasets requires an interdisciplinary skillset. Beyond a knowledge base in genetics and population biology, population genomic analyses involve computer science and statistics, representing a barrier for researchers without experience in those fields. PopGenHelpR seeks to lower this barrier by enabling researchers to perform population genomic analyses and generate near-publication quality figures in a streamlined and informed fashion. PopGenHelpR allows users to estimate genetic diversity within populations as well as differentiation among populations and individuals from single nucleotide polymorphism data. PopGenHelpR includes commonly used measures such as observed heterozygosity and F_ST. PopGenHelpR also provides five previously unavailable measures of heterozygosity, including the proportion of heterozygous loci and homozygosity by locus. Additionally, PopGenHelpR integrates widely used visualization tools in population genomics that normally require additional software packages, such as ancestry bar charts, piechart maps, and genetic differentiation heatmaps. Moreover, PopGenHelpR is minimally dependent on other R packages, reducing its chance of being removed from public networks. The PopGenHelpR website also provides tutorials and educational resources. Altogether, PopGenHelpR provides resources for informed analyses and effective visualization, making PopGenHelpR a valuable tool for many researchers. PopGenHelpR is available on the Comprehensive R Archive Network and GitHub (https://github.com/kfarleigh/PopGenHelpR).</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 4","pages":"e70142"},"PeriodicalIF":5.9,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148012813","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 Scalable and Cost-Effective In-Line Barcoding Strategy for Standardized 16S rRNA Gene Amplicon Sequencing: Performance Evaluation and Bias Assessment.","authors":"Lisa Jourdain, Pierre Rossi, Aline Charpagne, Emmanuelle Chevalier, Viviane Praz, Julien Marquis, Johann Weber, Wenyu Gu","doi":"10.1111/1755-0998.70138","DOIUrl":"10.1111/1755-0998.70138","url":null,"abstract":"<p><p>In-line barcoding offers a streamlined and scalable alternative to two-step PCR library preparation for 16S rRNA gene amplicon sequencing, enabling cost-effective, high-throughput profiling of microbial communities. Here, we tested 136 and 156 in-line barcoded primer pairs for bacterial and archaeal communities for their performance across environmental samples and a mock standard community. The primers were designed by combining widely used universal 16S rRNA gene primers with existing barcode sets from Illumina kits. The designed primer pairs produced efficient and consistent amplification with minimal dropout and no systematic taxonomic bias. Through clustering and performance-based filtering, we selected final sets of 96 pairs for both bacterial and archaeal communities that work efficiently and well together for direct further use. This in-line tagging strategy is easy to adopt with fewer processing steps and PCR-associated artefacts, allows straightforward sample tracking, and supports reliable large-scale microbiome studies. We also present a framework for evaluating barcode- or primer-induced biases. More broadly, the proposed in-line barcoding strategy can be adapted to any amplicon-sequencing application, as well as targeted sequencing, highlighting its relevance beyond 16S rRNA gene surveys. All validation datasets, open-source processing scripts, and barcode design resources are provided to promote reproducibility and community-wide adoption.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 4","pages":"e70138"},"PeriodicalIF":5.9,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13159520/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147865964","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":"Hybrid Horizons: Screening Hybridisation Through Nuclear Environmental DNA.","authors":"Daniel Zumel, Emilie Didaskalou, Tijana Vučić, Milena Cvijanović, Ana Ivanović, Maja Ajduković, Ben Wielstra, Anagnostis Theodoropoulos, Kathryn Stewart","doi":"10.1111/1755-0998.70134","DOIUrl":"10.1111/1755-0998.70134","url":null,"abstract":"<p><p>Effective monitoring of hybrid zones is essential for understanding evolutionary dynamics and mitigating species loss caused by human-mediated hybridisation. Conventional methods rely on sampling numerous individuals, which is costly, time-consuming and often impractical for rare or elusive species. Environmental DNA (eDNA) offers a promising alternative for locating hybrid zones but requires the detection of nuclear eDNA, which is typically scarce in natural ecosystems. While a few recent studies have successfully recovered sufficient nuclear eDNA to assess intraspecific variation, its application in hybridisation studies remains untested. This study provides the first empirical validation that nuclear eDNA can screen for hybrid populations. We present an eDNA-based toolkit that employs Kompetitive Allele-Specific PCR (KASP) to genotype a panel of species-diagnostic unlinked nuclear SNPs without sequencing, mapping end-point fluorescence to a hybrid index that reflects ancestry levels at the population scale. In mesocosms housing different combinations of individuals from two crested newt species (Triturus ivanbureschi and T. macedonicus) and their captive-bred F1 hybrids, we compared eDNA-derived ancestry estimates with genotypes obtained from skin swabs of the same individuals placed in the mesocosms. eDNA-based ancestry estimates showed strong concordance with individual genotypes across two eDNA sampling concentrations. This approach represents a promising non-invasive, fast and cost-efficient screening tool, qualities that make it well suited to locate and track putative hybrid zones and a scalable complement to conventional sampling for biodiversity monitoring and conservation.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 4","pages":"e70134"},"PeriodicalIF":5.9,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13137079/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147808933","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":"Champuru 2: Improved Scoring of Alignments and a User-Friendly Graphical Interface.","authors":"Yann Spöri, Jean-François Flot","doi":"10.1111/1755-0998.70110","DOIUrl":"10.1111/1755-0998.70110","url":null,"abstract":"<p><p>Champuru is a web-based software tool that helps determine the two sequences present in mixed Sanger chromatograms obtained by simultaneously sequencing two DNA templates of unequal lengths. A previous version (Champuru 1.0) was published as a simple Perl CGI (Common Gateway Interface) application, but the server hosting it was decommissioned, which prompted us to update Champuru and develop it further. The new Champuru 2, implemented in Haxe and hosted at GitHub Pages, offers an improved graphical user interface as well as more sophisticated algorithms to compute alignment scores, making it more efficient at detecting the most likely alignment positions between forward and reverse traces. It also compares the distribution of alignment scores to the theoretical expectation for the comparison of two random sequences and uses this comparison to calculate p-values for the offset pairs it detects. Moreover, Champuru 2 now makes it possible to analyse other offset pairs than the one detected as most likely by the selected algorithm. Champuru 2 is freely accessible at https://eeg-ebe.github.io/Champuru/, including both a graphical user interface (running a JavaScript version transpiled from the Haxe source code) and a compiled command-line version (obtained by transpiling the Haxe source code into C++).</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 4","pages":"e70110"},"PeriodicalIF":5.9,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13111972/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147758458","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":"Optimising Zooplankton DNA Metabarcoding: Methodological Considerations for Large-Scale Monitoring.","authors":"Elizaveta Ershova-Menze, Jon-Ivar Westgaard, Helene Hjellnes, Tone Falkenhaug","doi":"10.1111/1755-0998.70149","DOIUrl":"10.1111/1755-0998.70149","url":null,"abstract":"<p><p>DNA metabarcoding is becoming an increasingly common approach in ecological monitoring of marine and freshwater planktonic communities, yet methodological choices along the metabarcoding workflow and data post-processing approaches remain highly inconsistent across studies, limiting the ability to track biodiversity trends, detect range shifts, or integrate datasets across monitoring programs. This study addresses this methodological bottleneck by combining controlled experimental comparisons with a comprehensive literature synthesis to identify how protocol decisions-from sample preservation and DNA extraction to sequencing platforms and taxonomic assignments-affect the results of COI metabarcoding and its interpretation. Overall biodiversity and community patterns were recovered by all combinations of tested methods, supporting the notion that patterns identified through DNA metabarcoding are robust and comparable across studies. We identify TES (Tris-EDTA-SDS) buffer, optionally paired with at-sea homogenisation, as a practical alternative to ethanol preservation for large-scale monitoring surveys. We show that integrating several classification methods and reference databases for taxonomic assignment improves diversity estimates and confidence in the assignments, and advocate for increased use of tools like BOLDigger that facilitate manual curation of ambiguous/erroneous references. Finally, we demonstrate that introducing stricter filtering thresholds reduces the effect of false positives, pseudogenes and lab-specific contamination, and make comparisons of data generated by different laboratories and methodological configurations more robust, although potentially at the expense of excluding rare taxa. While we intentionally refrain from recommending a universal best practices protocol, this study aims to provide a practical roadmap to help enhance the reliability and reproducibility of marine zooplankton monitoring via DNA metabarcoding.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 4","pages":"e70149"},"PeriodicalIF":5.9,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147985490","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":"DIY: A Practical Field-to-Sequencer Workflow for Metabarcoding the Diet of Terrestrial Carnivore Species.","authors":"Francisca A S Virtuoso, Jos Boekhorst, Shasa van Ravenstein, Dora Schouten, Maria Juanpere-Borràs, Femke Broekhuis, Sander Vissia, Richard Mazebedi, Alessandro Araldi, Frank van Langevelde","doi":"10.1111/1755-0998.70144","DOIUrl":"10.1111/1755-0998.70144","url":null,"abstract":"<p><p>Metabarcoding of faecal samples is a powerful, non-invasive approach for investigating the feeding ecology of carnivores, revealing prey diversity and unexpected dietary components with greater resolution than traditional methods. However, the approach remains technically demanding, as challenges and potential biases arise at every stage, from scat collection and DNA extraction to primer selection, sequencing, and data interpretation. Methodological details for these steps are often scattered across studies, limiting reproducibility and accessibility for ecologists. Here, we present a comprehensive field-to-sequencer workflow for dietary metabarcoding of terrestrial carnivores using Oxford Nanopore Technologies (ONT), covering all stages from sample collection to ecological interpretation. Drawing on field-collected scats of brown (Parahyaena brunnea) and spotted hyenas (Crocuta crocuta) across arid and semi-arid savannas in Botswana, we illustrate practical decisions, technical considerations, and common pitfalls encountered throughout the process. By integrating field, laboratory, and bioinformatic components into a single, accessible framework, this paper provides a pragmatic reference for ecologists aiming to design robust, transparent, and comparable studies of carnivore diet composition.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 4","pages":"e70144"},"PeriodicalIF":5.9,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13112516/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147758546","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":"Dietary RNA: Integration of RNA Data Offers a Potential Paradigm Shift for Molecular Dietary Analyses.","authors":"Jordan P Cuff, James J N Kitson, Fredric M Windsor, Daniela Sint, Ben S J Hawthorne, Michael Traugott, Catriona M H Anderson, Veronika Neidel, Angharad M R Gatehouse, David T Thwaites, Martin G Edwards, Darren M Evans","doi":"10.1111/1755-0998.70139","DOIUrl":"10.1111/1755-0998.70139","url":null,"abstract":"<p><p>Just over two decades ago, DNA-based dietary analysis promised to advance the resolution, sensitivity, and speed with which we could detect and identify trophic interactions. Since then, these approaches have generated a paradigm shift in our understanding across a wide range of natural systems. Although decreasing sequencing costs and increased access to sequencing technologies have significantly broadened adoption in recent years, advances in the methods used for dietary analysis have arguably slowed. We stand now, however, at the brink of the next advance, as traditionally DNA-based ecological studies increasingly apply RNA-based methods. To date, this has most commonly taken place in the context of environmental monitoring, and the application to dietary analysis is still underrepresented despite immense potential and relatively straightforward implementation. Given the reduced stability of some RNA types, the detection of consumed resources via RNA alongside DNA can mitigate many longstanding methodological pitfalls of DNA-based dietary analyses alone by (i) differentiating between living and dead resources, (ii) identifying potential false positives, and (iii) providing temporal context to detections, facilitating the construction of weighted or multilayer trophic networks. Detection of functional RNA may also present an opportunity to ascribe functional contexts to both consumers and resources, and contextualise interactions or their impact on wider trophic networks. With the increasing accessibility of RNA-based methods, their application to community and network ecology may significantly advance our ability to analyse and understand trophic interactions in complex natural systems. Here, we summarise RNA-based dietary analysis methods with reference to recent literature in trophic ecology and identify areas that would benefit from additional research. By summarising the immediately identifiable advances and constraints that dietary RNA presents, we hope to stimulate widespread adoption of these approaches and advance integration of RNA-based analyses into trophic ecological research.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 4","pages":"e70139"},"PeriodicalIF":5.9,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147985570","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":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 4","pages":""},"PeriodicalIF":5.5,"publicationDate":"2026-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148095369","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":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 4","pages":""},"PeriodicalIF":5.5,"publicationDate":"2026-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148095439","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":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 4","pages":""},"PeriodicalIF":5.5,"publicationDate":"2026-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148095368","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}