Molecular Ecology Resources最新文献

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 4","pages":""},"PeriodicalIF":5.5,"publicationDate":"2026-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148091685","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":"2026-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148091684","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":"SPrUCE: Utilizing Ultraconserved Elements of DNA for Population-Level Genetic Diversity Estimation.","authors":"Daira Melendez, Ali Osman Berk Şapcı, Vineet Bafna, Siavash Mirarab","doi":"10.1111/1755-0998.70145","DOIUrl":"10.1111/1755-0998.70145","url":null,"abstract":"<p><p>Ultraconserved elements (UCEs) provide ideal candidates for targeted sequencing and cost-effective acquisition of genome-wide data. While UCEs have been widely used in phylogenetic studies to reconstruct evolutionary relationships, their use in population-level research has been limited. This limited application stems from uncertainty over whether UCEs can capture the levels of genetic variation needed to answer population genomic questions central to ecology and biodiversity research. The concern is that, by definition, UCEs are highly conserved and may therefore lack sufficient within-species variation. The more variable flanking regions (400-750 bp from the UCE core) contain informative polymorphisms, though diversity decreases near the core. Thus, any naive estimator of genetic diversity that ignores this conservation will have an underestimation bias. In this paper, we introduce SPrUCE: Sigmoid Pi requiring UCEs, a reference-free method that estimates nucleotide diversity <math> <semantics><mrow><mi>π</mi></mrow> <annotation>$$ pi $$</annotation></semantics> </math> from aligned UCE data. SPrUCE corrects underestimation bias by modelling the change in diversity away from the UCE core using a Gompertz function. The model accounts for the bias introduced by the conserved core and allows for more accurate per-site diversity estimates. We tested SPrUCE on UCE alignments from a range of taxa, including invertebrates and vertebrates (finches, honeybees, sheep and smelt). SPrUCE produces diversity values consistent with whole-genome derived estimates that require an assembled reference. It is fast, scalable, and effective even with missing data. Its modelling approach enables accurate population-level assessments of genetic diversity, offering a new and reliable option for conservation and population genetics.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 3","pages":"e70145"},"PeriodicalIF":5.9,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13106921/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147758530","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":"Navigating Cetacean Mitochondrial Genome Data: Identifying Coverage and Deficiencies in Public Repositories.","authors":"Luís Afonso, Alessandro Lagrotteria, Ana Sofia Lavrador, Paula Suarez-Bregua, Miguel Álvarez-González, Raul Valente, Mads Reinholdt Jensen, Camilo Saavedra, Daniel Kumazawa Morais, Isabel Sousa-Pinto, Graham J Pierce, Catarina Magalhães, Ana Mafalda Correia","doi":"10.1111/1755-0998.70141","DOIUrl":"10.1111/1755-0998.70141","url":null,"abstract":"<p><p>Genetic reference databases underpin a wide range of molecular approaches used to study cetacean biodiversity, including environmental DNA (eDNA), yet their reliability depends critically on data completeness, taxonomic accuracy, and metadata quality. Here, we present the first global assessment of mitochondrial sequence availability for cetaceans, evaluating taxonomic coverage, geographic representation, metadata completeness, and the distribution of five commonly targeted mitochondrial markers (12S rRNA, 16S rRNA, D-loop, cytochrome oxidase I, and cytochrome b). We retrieved 17,569 cetacean accessions from the NCBI Nucleotide database and an additional 259 COI-only records from BOLD Systems. Sequence availability was strongly biased toward Delphinidae and Balaenopteridae, whereas several families, notably Ziphiidae, were markedly underrepresented. We also identified discrepancies between database records and currently accepted cetacean taxonomy (e.g., outdated genera, non-accepted species, and collapsed higher-level taxa). Among markers, the D-loop dominated database representation, largely as standalone sequences (12,437 records), reflecting historical and current sequencing priorities and underscoring its continued relevance for population-level studies and eDNA marker development. Only 38% of accessions included geographic metadata, with georeferenced records concentrated primarily in the Americas and the Northwest Pacific, while large regions, including much of Africa, remained poorly represented. Although broad geographic patterns mirrored known family distributions, pronounced regional and taxonomic gaps persist. Our results highlight critical deficiencies in mitochondrial reference databases for cetaceans and emphasise the need for improved metadata standards, targeted sequencing of underrepresented taxa and regions, and open data sharing to enhance the effectiveness and global applicability of eDNA-based cetacean monitoring.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 3","pages":"e70141"},"PeriodicalIF":5.9,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13087493/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147697008","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":"OligoN-Design: A Simple and Versatile Tool to Design Specific Probes and Primers From Large Heterogeneous Datasets.","authors":"Miguel M Sandin, Marie Walde, Nicolas Henry, Irene Forn, Nathalie Simon, Cédric Berney, Ramon Massana, Daniel J Richter","doi":"10.1111/1755-0998.70140","DOIUrl":"10.1111/1755-0998.70140","url":null,"abstract":"<p><p>High-throughput environmental DNA sequencing has ushered ecological and evolutionary studies into the big data era. With thousands to millions of DNA sequences, designing taxon-specific oligonucleotides is a current bottleneck of molecular studies that rely on primers for Polymerase Chain Reactions (PCRs) or probes for Fluorescence in situ Hybridization (FISH). No software currently exists to design specific oligonucleotides starting from a custom set of sequences. Existing tools rely on specific databases, alignments or phylogenetic trees, or cannot accommodate increasingly large molecular environmental datasets. Here we present oligoN-design, a versatile tool to design oligonucleotides specific to a set of target sequences while minimizing predicted binding to non-target sequences. OligoN-design is simple, reproducible and adaptable to high-throughput sequencing data analyses. It requires only two fasta files as input, one containing target taxa and the other containing non-target taxa. Using standard bioinformatic formats, it integrates easily with other tools such as BLAST, VSEARCH or MAFFT. OligoN-design allows a range of strategies that we present in detail, from an unsupervised end-to-end usage all the way to a detailed and thorough expert usage. Starting with large, comprehensive ribosomal databases that are widely used by the community (i.e., PR2, SILVA) and the unsupervised function, we were able to replicate known taxa-specific oligonucleotides in under 30 min and up to 6 GB of RAM on a personal laptop. OligoN-design, available at github.com/MiguelMSandin/oligoN-design under GNU General Public Licence version 3.0, is easily installed via bioconda bioconda.github.io/recipes/oligon-design/README.html.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 3","pages":"e70140"},"PeriodicalIF":5.9,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13071497/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147669414","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":"DNA Barcode Reference Library for European Ants: A Roadmap for Phylogeography and Species Discovery.","authors":"Mattia Menchetti, Enrico Schifani, Fede García, Sämi Schär, Elisabetta Sbrega, Nikola Balević, Bonnie B Blaimer, Lech Borowiec, Dario Cioppa, Cecilia Corbella, Vlad Dincă, Vincenzo Gentile, Irakleitos Giotis, Kiko Gómez, José María Gómez Durán, Konstantinos Kalaentzis, Albena Lapeva-Gjonova, Emiliano Mori, Gerard Talavera, Alberto Tinaut, Francisca Ruano, Sebastian Salata, Eduardo Sequeira, Maria Serracanta, Tomasz Suchan, Paul D N Hebert, Leonardo Dapporto, Roger Vila","doi":"10.1111/1755-0998.70135","DOIUrl":"10.1111/1755-0998.70135","url":null,"abstract":"<p><p>DNA barcode reference libraries provide useful tools for specimen identification, highlighting potential new species and detecting introduced ones. Here, we present a comprehensive DNA barcode library for European ants and, in order to tackle the Linnean, Wallacean and Darwinian shortfalls of this group, we provide an updated checklist, distribution data, mitochondrial genetic diversity maps and mitochondrial gene trees. The European ant fauna is here established to include 55 genera and 650 species (587 of which are native), including one species newly recorded for Europe and novel citations for 26 species from 11 countries. Our genetic dataset includes 6530 georeferenced COI sequences (62.1% de novo) for 506 species (77.8%) across all genera. On average, 12.9 sequences were obtained per species, and 209 species were sequenced for the first time. We generated intra- and interspecific genetic distance estimates, 52 genus-level trees, mitochondrial genetic diversity and specimen maps for 384 species, as well as haplotype networks for 289 species, available in the Atlas V1.0 'The Mitochondrial Genetic Diversity Maps of European Ants'. We estimate that 56.3% of European ants are monophyletic with respect to the COI gene and can be unambiguously identified by DNA barcoding, though performance varies widely among genera. We observed moderate levels of barcode sharing (19.3%) and of barcode gap presence (47.6%), as well as high levels of intraspecific divergences (up to 17.9%). These findings likely reflect both biological and operational factors and highlight the existence of potential cryptic taxa and the need for taxonomic revisions. The framework presented here aims to facilitate future research, species discovery and conservation of European ants.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 3","pages":"e70135"},"PeriodicalIF":5.9,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13093865/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147721079","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":"Recovering Historical eDNA From Museum-Preserved Filter Feeders via Non-Destructive Metabarcoding.","authors":"Gert-Jan Jeunen, Sadie Mills, Marc Bailie, Quentin Mauvisseau, Miles Lamare, Stefano Mariani, William Pearman, Monika Zavodna, Jackson Treece, Sara Ferreira, Neil J Gemmell","doi":"10.1111/1755-0998.70132","DOIUrl":"10.1111/1755-0998.70132","url":null,"abstract":"<p><p>Recent technical advances have significantly enhanced the value of museum specimens for molecular research, with metagenomic and metabarcoding approaches expanding further the utility of museum collections. However, given the finite number of specimens, there is a critical need to move past destructive DNA extraction approaches and to explore non-destructive techniques. In this proof-of-concept study, we evaluated the feasibility of extracting historical eDNA from the ethanol preservative used to store museum specimens. We compared a variety of extraction methods (centrifugation, evaporation, filtration, and precipitation) using ten replicate samples per treatment for statistical analyses. To assess potential differences in preservative-derived eDNA recovery across different filter-feeding taxonomic groups, we included a bryozoan, a demosponge, and a glass sponge. Comparative analyses with tissue biopsies revealed that 10 mL ethanol filtration performed equal to or, in some instances, outperformed tissue biopsies for all three specimens when examining the historical eDNA of Antarctic fish using a 16S rRNA metabarcoding approach, both for the number of species detected (α-diversity) and community characterisation (β-diversity). This initial study demonstrates the potential of ethanol preservative as a valuable, non-destructive source of historical eDNA from museum-stored filter-feeding specimens. These findings highlight the viability of non-destructive sampling for molecular research on museum collections, preserving specimen integrity while enabling biodiversity assessments. Further refinement of non-destructive eDNA extraction could expand its applicability across taxa, collection types, and preservation methods, ensuring the long-term sustainability of museum-based genomic, metagenomic, and metabarcoding research.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 3","pages":"e70132"},"PeriodicalIF":5.9,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13034409/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147571408","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":"Harnessing Deep Learning in Searching Wild Relatives of Domestic Animals.","authors":"Zheng-Fei Cai, Bei Liu, Ting-Ting Yin, Cheng Ma, Zi-Teng Han, Li-Hong Gu, Chao Zhang, Fei Wu, Li-Sheng Liu, Xian Shi, Xue-Qi Wang, Ru-Nian Wu, Lin-Zhe Xie, Yue Bai, Yun-Chun Zhang, Shu-Run Zhang, Li-Jiao Gu, Ming-Shan Wang, Guo-Li Xie, Wang-Kun Cheng, Jian-Gao Lu, Yan Luo, Shao-Bin Li, Hidayat Ashari, Moch Syamsul Arifin Zein, Jian-Lin Han, Worapong Singchat, Kornsorn Srikulnath, Ya-Ping Zhang, Min-Sheng Peng","doi":"10.1111/1755-0998.70133","DOIUrl":"10.1111/1755-0998.70133","url":null,"abstract":"<p><p>Wild relatives of domestic animals are crucial reservoirs of genetic diversity, yet pervasive hybridization with domestic animals poses significant conservation challenges. Here, we developed a deep learning-based pipeline, consisting of a multi-layer perceptron for SNP panel selection and a Deep & Cross Network for model training, to discern wild relatives from their closely related domestic animals using genomic SNP data. Leveraging the 1960 genomes from 164 red jungle fowl (RJF; Gallus gallus) and 1796 domestic chicken samples, we applied this pipeline to yield the RJF identification model based on a 285-SNP panel. We employed this model to characterize domestic chickens, RJF, and hybrids in the independent genomic datasets from contemporary samples and historical specimens, respectively. The accuracy was 97.8% for historical samples with missing genotypes. The benchmarking multiple hybrid detection tools indicated that the RJF identification model was effective and practical. The further application to the genomic data from wild boar (Sus scrofa), domestic pigs, and their hybrids validated the pipeline. Our method has potential in not only monitoring genetic diversity in wild relatives of domestic animals but also supporting animal genetic resource conservation and management.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 3","pages":"e70133"},"PeriodicalIF":5.9,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13094329/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147721066","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":"Genome-Wide Characterization of Sex-Linked Regions in the Sangzhi Horned Toad (Boulenophrys sangzhiensis) Reveals Complex Sex Determination Mechanisms.","authors":"Chun H Huang, Si Y Xie, Jun Li, Wan Y Chen, Fu Y Qiu, Mian Zhao, Wei Liu, Chun L Liao, Hua Wu","doi":"10.1111/1755-0998.70136","DOIUrl":"10.1111/1755-0998.70136","url":null,"abstract":"<p><p>Sex chromosomes in amphibians exhibit substantial variability and often remain largely homomorphic, providing a powerful system for studying sex determination. The Sangzhi horned toad (Boulenophrys sangzhiensis) is an ideal model, but limited genomic resources have hindered insights into sex determination mechanisms. Here, we assembled a 2.8 Gb chromosome-level genome of B. sangzhiensis generated using PacBio HiFi and Hi-C data, achieving a Contig N50 of 30 Mb and identifying 21,775 protein-coding genes. Genome-wide analyses of coverage, F_ST, SNP density, and linkage disequilibrium identified two putative sex-linked regions on chromosome 2 and 6, showing sex-specific coverage and strong genetic differentiation. Within these sex-linked regions, we identified a Y-specific sequence and several candidate sex-determining genes, including Hsd11b2, Nlrp14, and zinc finger genes. Our findings suggest that sex determination in B. sangzhiensis involves a complex, possibly polymorphic mechanism, with multiple Y haplotypes segregating within populations. Additionally, the sex-linked regions exhibit accumulation of repetitive sequences, multi-copy genes, and chromosomal rearrangements, which may contribute to the evolution of sex chromosomes. This chromosome-level genome provides a valuable resource for understanding the dynamic evolution of sex-determining mechanisms in amphibians.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 3","pages":"e70136"},"PeriodicalIF":5.9,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13059060/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147632084","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":"ChloroScan: Recovering Plastid Genome Bins From Metagenomic Data.","authors":"Yuhao Tong, Vanessa Rossetto Marcelino, Robert Turnbull, Heroen Verbruggen","doi":"10.1111/1755-0998.70143","DOIUrl":"10.1111/1755-0998.70143","url":null,"abstract":"<p><p>Genome-resolved metagenomics has contributed greatly to discovering prokaryotic genomes. When applied to microscopic eukaryotes (protists), challenges such as the high number of introns and repeat regions found in nuclear genomes have hampered the mining and discovery of novel protistan lineages. Organellar genomes are simpler, smaller, have higher abundance than their nuclear counterparts and contain valuable phylogenetic information, but are yet to be widely used to identify new protist lineages from metagenomes. Here we present \"ChloroScan\", a new bioinformatics pipeline to extract eukaryotic plastid genomes from metagenomes. It incorporates a deep learning contig classifier to identify putative plastid contigs and an automated binning module to recover bins with guidance from a curated marker gene database. Additionally, ChloroScan summarizes the results in different user-friendly formats, including annotated coding sequences and proteins for each bin. We show that ChloroScan recovers more high-quality plastid bins than MetaBAT2 for simulated metagenomes. The practical utility of ChloroScan is illustrated by recovering 16 medium to high-quality metagenome assembled genomes (MAGs) from four protist-size-fraction metagenomes, with several bins showing high taxonomic novelty. The ChloroScan code (v0.1.7) is available at https://github.com/Andyargueasae/chloroscan/tree/release_v0.1.7 under Apache-2.0 licence.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 3","pages":"e70143"},"PeriodicalIF":5.9,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13093128/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147721305","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}