Molecular Ecology Resources最新文献

{"title":"Individual Identification of Prey in Carnivore Scats","authors":"Charlotte E. Eriksson,&nbsp;Marcus Bianco,&nbsp;Joel Ruprecht,&nbsp;Darren A. Clark,&nbsp;Taal Levi","doi":"10.1111/1755-0998.70164","DOIUrl":"10.1111/1755-0998.70164","url":null,"abstract":"<p>Noninvasive genetic sampling is widely used in ecology and conservation to identify predators and their diets but recovering individual-level information from consumed prey remains largely unexplored. We evaluated whether individual prey can be reliably genotyped from carnivore scats and assessed limitations associated with degraded and mixed DNA sources. We developed a 31-locus SNP panel optimized for genotyping degraded elk (<i>Cervus canadensis</i>) DNA using amplicon sequencing. We validated prey genotyping by matching elk genotypes recovered from carnivore scats (‘carcass scats’) collected at cougar (<i>Puma concolor</i>) kill sites to genotypes from corresponding elk carcasses. We also genotyped scats collected throughout the study area, identified as containing elk using DNA metabarcoding (‘survey scats’). To avoid misidentifying multiple individuals in a scat as a unique genotype, we evaluated artificial mixtures of prey DNA to assess the ability to detect and filter samples containing mixed DNA. Elk genotypes recovered from carcass scats matched associated carcass genotypes, confirming accurate recovery of individual prey DNA from carnivore scats. Genotyping success was 88% in fresh carcass scats and 74% in survey scats of unknown age. Heterozygosity excess filtering removed most mixed samples, although one of 24 mixtures with equal DNA contributions from two individuals produced a false unique genotype. Our results demonstrate that carnivore scats can serve as a reliable source of individual-level prey DNA under appropriate conditions. This method provides a new data stream on individual prey mortality, predation rates, and scavenging dynamics, processes that have previously been difficult to quantify without invasive capture and collaring techniques.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 5","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70164","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148300480","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":"Integrating Megabarcoding and Metabarcoding to Unlock Diversity and Distribution Data Shortfalls in Dark Taxa","authors":"I. Santos-Perdomo,&nbsp;A. Salces-Castellano,&nbsp;M. L. Moraza,&nbsp;E. Mateos,&nbsp;A. Muñoz-Barrera,&nbsp;R. González-Montelongo,&nbsp;D. Suárez,&nbsp;N. Vega-Pita,&nbsp;L. Falcón-López,&nbsp;J. M. Lorenzo-Salazar,&nbsp;C. Flores,&nbsp;P. Arribas,&nbsp;C. Andújar","doi":"10.1111/1755-0998.70166","DOIUrl":"10.1111/1755-0998.70166","url":null,"abstract":"<p>Persistent biodiversity data shortfalls undermine our capacity to detect species, map their distributions and characterize their spatial genetic structure, limiting robust biogeographic analyses and the development of effective conservation strategies. This particularly affects hyperdiverse invertebrate groups where hidden diversity remains largely undocumented. This study develops and demonstrates the potential of an integrated high-throughput sequencing (HTS) framework to improve the representation of hidden diversity in regional species inventories and to help close critical gaps in our understanding of species distributions and genetic diversity from a conservation biogeography perspective. Focusing on the Canary Islands (Spain), the workflow combines megabarcoding of more than 4000 mesofauna specimens to generate a curated species-level molecular reference library with community DNA metabarcoding of 168 soil samples. This approach enables consistent taxonomic assignment across insular landscapes and increases the spatial and genetic resolution of occurrence data. We identified 145 species of mites and springtails, including 49 species newly recorded for the archipelago and numerous genetically distinct lineages likely representing undescribed taxa, highlighting all the biodiversity that remains to be described. Integration of the barcode library with metabarcoding data produced 1440 species occurrences, revealing extensive distributional gaps, multiple range expansions and strong within-island phylogeographic structuring, indicating prevalent diversification at fine spatial scales. These results highlight a deep, taxonomically broad underestimation of soil biodiversity and demonstrate that this integrative approach provides a transferable model for advancing the biogeography, evolutionary understanding and conservation of dark and cryptic taxa across broad taxonomic and conservation-relevant contexts.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 5","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70166","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148292598","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":"BeeGees: A High-Throughput Protein-Coding DNA Barcode Recovery Pipeline Tailored for Genome Skims of Museum Specimens","authors":"Daniel A. J. Parsons,&nbsp;Rutger A. Vos,&nbsp;Benjamin W. Price","doi":"10.1111/1755-0998.70170","DOIUrl":"10.1111/1755-0998.70170","url":null,"abstract":"<p>Natural history collections are unparalleled archives of global biodiversity, yet most specimens remain molecularly uncharacterised due to the technical challenges of historical DNA (hDNA), including degradation, low endogenous content and contamination. Genome skimming offers a scalable alternative to PCR-based barcoding, but existing bioinformatic workflows are not optimised for the heterogeneous, metagenomic nature of museum-derived data. Here we present BeeGees (Barcode Extraction and Evaluation from Genome Skims), a high-performance computing (HPC) integrated, Snakemake-based workflow designed for protein-guided recovery and validation of mitochondrial and plastid barcode genes from degraded short-read genome sequences. BeeGees integrates dual read pre-processing, systematic per-sample parameter sweeps, sequential consensus cleaning to remove contaminant sequences and rigorous structural and taxonomic validation against curated reference databases. We benchmarked BeeGees on 1518 museum specimen-derived genome skims spanning eight phyla. The workflow completed in approximately 120 h (&lt; 5 min per sample) on HPC infrastructure. When excluding sequencing failures (&lt; 1 M reads), validated COI barcodes were recovered for 73.2% of specimens (1050/1435). Barcode recovery success was influenced by endogenous content, preservation quality and parameter choice rather than raw read count alone, highlighting the importance of systematic parameter optimisation. Sequential consensus cleaning eliminated ambiguous bases and reduced chimeric artefacts, proving essential for robust museomic analyses. BeeGees provides a reproducible, scalable framework for high-throughput barcode recovery and biodiversity genomics and reference gap-filling initiatives from natural history collections. The BeeGees pipeline is available at: https://github.com/bge-barcoding/BeeGees/.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 5","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70170","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148275313","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":"De Novo Genome Assemblies of Four Rainbow Trout Genetic Lines Reveal Structural Variants in Pursuit of a Pangenome Reference","authors":"Ali Ali,&nbsp;Geoffrey C. Waldbieser,&nbsp;Ramey C. Youngblood,&nbsp;Paul A. Wheeler,&nbsp;Brian E. Scheffler,&nbsp;Stuart Willis,&nbsp;Shawn R. Narum,&nbsp;Gary H. Thorgaard,&nbsp;Mohamed Salem,&nbsp;Yniv Palti","doi":"10.1111/1755-0998.70167","DOIUrl":"10.1111/1755-0998.70167","url":null,"abstract":"<p>Rainbow trout (<i>Oncorhynchus mykiss</i>) exhibit extensive genomic diversity shaped by domestication, life history and geographic origin. To advance the development of a comprehensive pangenome reference, we present new de novo genome assemblies of two genetically and ecologically distinct lines: Whale Rock (WR; wild, landlocked, Central California) and Keithley Creek (KC; wild, resident, interior Columbia Basin), along with the previously published assemblies of the Arlee (domesticated, Northern California) and Swanson (semi-domesticated, resident, Alaska) lines. All assemblies provide nearly complete coverage of known genes (BUSCO 95.8%–99.7%) and are similar in genome size (~2.3 Gb), with scaffold N50 values between 3.4 Mb (KC) and 52.4 Mb (Swanson). Comparative whole-genome alignments revealed high sequence conservation (97%–98% identity) among assemblies, but also evidence of extensive structural variation of at least 50 bp in length. Structural variant (SV) profiling identified tens of thousands of deletions, insertions and complex rearrangements largely in noncoding sequences. In an initial assessment of the utility of having multiple de novo genome assemblies for rainbow trout, we found that two strains (Arlee and Swanson; domesticated) share SVs enriched in genes linked with growth, reproduction and adaptation to domestication, such as GTP binding and ECM-receptor interaction. In comparison, the other two strains (WR and KC; wild origin) share SVs associated with reproductive timing, such as the GnRH signalling pathway. Both Arlee and WR also have unique SVs potentially related to their geographic origin and unique life history. Additionally, we identified SVs in key regions, such as a QTL for fillet yield on Omy17 and the maturation-associated <i>six6</i>/<i>erβ</i>-<i>gphb5</i> locus on Omy25q, suggesting the importance of considering SVs when investigating the genomics of complex traits. Together, these assemblies and comparative analyses establish a foundation for a rainbow trout pangenome reference, illuminating how they can be utilized to reveal the structural genomic basis of domestication, adaptation, and other complex traits in <i>O. mykiss</i>.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 5","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70167","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148262510","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":"Fragmentation of Long Reads Enables Reliable Mitogenome Assembly From Whole-Genome Amplification Data With Pervasive Palindromic Reads","authors":"Matteo Vecchi,&nbsp;Bartłomiej Surmacz,&nbsp;Ingemar K. Jönsson,&nbsp;Daniel Stec","doi":"10.1111/1755-0998.70165","DOIUrl":"10.1111/1755-0998.70165","url":null,"abstract":"<p>Whole genome amplification (WGA), and in particular multiple displacement amplification (MDA), has become a key technique for genomic sequencing of microscopic organisms, yet it introduces artefacts such as palindromic (inverted chimeric) reads that may compromise downstream analyses. We assessed how pervasive palindromic reads generated by MDA impact the assembly of tardigrade (<i>Acutuncus giovanniniae</i> and <i>A. mecnuffi</i>) mitogenomes sequenced with Oxford Nanopore technology. We show that the MDA produces a high proportion of palindromic reads, often exceeding one-third of mitochondrial reads and frequently exhibiting complex multi-inversion structures. These artefacts severely impair long-read assembly, leading to low success rates and inconsistent genome reconstruction. To solve this issue, a strategy based on in silico fragmentation of long reads into short, high-quality fragments, followed by short-read assembly, consistently produced complete and accurate circularised mitochondrial genomes. Our results demonstrate that palindromic read formation can be, in some cases, a limitation of MDA coupled with long-read sequencing, but this issue can be mitigated through read fragmentation. This approach provides a simple, robust and scalable solution for mitogenome assembly from data heavily affected by amplification artefacts, particularly in microscopic taxa where whole genome amplification is often unavoidable.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 5","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70165","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148248471","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":"Treeline Provides a Unified Strategy for Optimising Phylogenetic Trees Under Alternative Criteria","authors":"Erik S. Wright","doi":"10.1111/1755-0998.70163","DOIUrl":"10.1111/1755-0998.70163","url":null,"abstract":"<p>The choice of optimality criterion is a key consideration in phylogenetic studies. Recent work challenges the notion that more computationally demanding optimisation objectives result in better phylogenetic trees. This finding underscores the importance of comparing trees across optimisation objectives in addition to different models of evolution and data partitions. It is currently cumbersome to optimise trees for alternative objectives because multiple programmes must be used, each with its own optimisation framework. Here, I introduce Treeline for optimising balanced minimum evolution, maximum likelihood and maximum parsimony trees. Treeline explores the optimisation landscape using a new strategy based on perturbing the patristic distance matrix used to initialize candidate trees, which is shown to be particularly effective for the balanced minimum evolution objective. Tests suggest Treeline can be more accurate, memory efficient or faster than existing programmes designed for a single optimisation objective. Treeline's unified nature facilitates comparison of phylogenetic trees across distinct optimisation objectives and models of sequence evolution. Consistent with prior studies, the balanced minimum evolution objective resulted in gene trees that were more consistent with species trees than maximum likelihood or maximum parsimony objectives. With a case study of species from the family Hominidae, including <i>Homo sapiens</i>, I show how Treeline simplifies the process of constructing trees under alternative optimisation objectives and models of evolution. Treeline is part of the DECIPHER package for R and is available from Bioconductor and online (https://DECIPHER.codes/).</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 5","pages":""},"PeriodicalIF":5.5,"publicationDate":"2026-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70163","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148209479","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":"Using Metabarcoding Techniques to Map Multiple Dung Beetle-Vertebrate iDNA Networks in a Southeast Asian Forest","authors":"Xin Rui Ong,&nbsp;Rosie Drinkwater,&nbsp;Samuel K. S. Cheong,&nbsp;Rebecca Ker Loh,&nbsp;Hie Lim Kim,&nbsp;Adriana Lopes dos Santos,&nbsp;Nalini Puniamoorthy,&nbsp;Eleanor M. Slade","doi":"10.1111/1755-0998.70151","DOIUrl":"10.1111/1755-0998.70151","url":null,"abstract":"<p>Given the high levels of endemism, diversity, and increasing anthropogenic impacts in tropical regions, studies on species interactions and ecological networks are urgently needed to understand community responses to environmental change. Increasingly, molecular methods are used to monitor biodiversity and identify species interactions. In this study, we developed an optimised DNA metabarcoding protocol to construct quantitative dung beetle-vertebrate trophic networks in a heterogenous tropical forest. We show that while the highest probability of detection is within 3 h of feeding, vertebrate DNA can still be detected in most beetles after 24 h, including around 50% of beetles with visually empty guts. Using the vertebrate taxa detected from DNA in the gut contents, we constructed dung beetle-vertebrate networks across 50 forest sites. Our networks displayed high trophic generalism and nestedness. By using group-specific primers, we documented interactions between dung beetles and multiple vertebrate species, including amphibians, birds, and rare mammals, such as the Sunda slow loris and Sunda pangolin. Our optimised molecular techniques contribute towards the development of new methods for comprehensive biodiversity assessments and ecological network studies that are urgently needed to monitor biodiversity in the hyper-diverse tropics.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 5","pages":""},"PeriodicalIF":5.5,"publicationDate":"2026-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70151","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148203559","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 Roadmap for Using Hybridisation Capture–Based Target Enrichment of Ancient Environmental DNA in Palaeoecology","authors":"Nicole R. Foster,&nbsp;Luke E. Holman,&nbsp;Linda Armbrecht,&nbsp;Jérémy Courtin,&nbsp;Theis Jensen,&nbsp;Mikkel Winther Pedersen,&nbsp;Lennart Schreiber,&nbsp;Hannes Schroeder,&nbsp;Frederik V. Seersholm,&nbsp;Giulia Zampirolo,&nbsp;Kristine Bohmann,&nbsp;Heike H. Zimmermann","doi":"10.1111/1755-0998.70152","DOIUrl":"10.1111/1755-0998.70152","url":null,"abstract":"<p>Recovering ancient DNA from environmental samples is transforming the way we understand historical ecosystems. While high-throughput sequencing of the total DNA in environmental samples (shotgun metagenomic sequencing) reveals the taxonomic contents of these samples, the genetic signals of some taxa (e.g., eukaryotes) can be weak compared to the background levels of DNA from organisms such as bacteria, requiring deep sequencing approaches that are costly. Thus, to increase cost-effectiveness, pre-sequencing enrichment of target DNA can be advantageous. One technique to enrich this target DNA is hybridisation capture, where short RNA or DNA baits are designed to match, bind and isolate specific stretches of DNA. Hybridisation capture has previously been applied to recover DNA from ancient skeletal remains, but it is only beginning to emerge as an approach to characterise organisms from ancient environmental samples. Thus, there is limited information on establishing hybridisation capture workflows for ancient environmental DNA applications, including the limitations and advantages. This mini review focuses on establishing a roadmap for the applications of hybridisation capture to ancient environmental DNA samples.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 5","pages":""},"PeriodicalIF":5.5,"publicationDate":"2026-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70152","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148203418","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":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 4","pages":""},"PeriodicalIF":5.5,"publicationDate":"2026-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148095126","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":"2026-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148094937","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}