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Rapid DNA/eDNA-Based ID Tools for Improved Chondrichthyan Monitoring and Management. 改进软骨鱼监测和管理的快速DNA/ edna ID工具。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-09-19 DOI: 10.1111/1755-0998.70044
Marcela Maki Alvarenga, Ingrid Vasconcellos Bunholi, Aisni Mayumi C L Adachi, Marcelo Merten Cruz, Leonardo Manir Feitosa, Eduarda Valério de Jesus, Maria Eduarda Leda Lopes, Cintia Povill, Daniela Souza, Yan Torres, Antonio Mateo Solé-Cava, Rodrigo Rodrigues Domingues, Patricia Charvet, Vanessa Paes da Cruz
{"title":"Rapid DNA/eDNA-Based ID Tools for Improved Chondrichthyan Monitoring and Management.","authors":"Marcela Maki Alvarenga, Ingrid Vasconcellos Bunholi, Aisni Mayumi C L Adachi, Marcelo Merten Cruz, Leonardo Manir Feitosa, Eduarda Valério de Jesus, Maria Eduarda Leda Lopes, Cintia Povill, Daniela Souza, Yan Torres, Antonio Mateo Solé-Cava, Rodrigo Rodrigues Domingues, Patricia Charvet, Vanessa Paes da Cruz","doi":"10.1111/1755-0998.70044","DOIUrl":"https://doi.org/10.1111/1755-0998.70044","url":null,"abstract":"<p><p>Rapid DNA/eDNA-based ID tools, which detect specific genetic patterns without requiring sequencing, are essential for biodiversity and wildlife trade monitoring, particularly for species of conservation concern. However, the practical application of these methods remains limited by the availability of standardised protocols, accessibility of resources, and coverage across diverse taxa. This challenge is especially pronounced for Chondrichthyes, a group heavily overexploited due to fishing and illegal trade, and with data scarcity for conservation assessments. Despite their ecological and economic importance, many species lack reference sequences in databases, as well as other molecular data and tools, hindering the development of molecular tools for species identification and trade regulation. This review synthesises the current state of rapid DNA/eDNA-based ID tools for the detection of chondrichthyan species, including established and emerging methods. It also compiles available taxon-specific primers to facilitate efficient species identification and recommends the most suitable methods. We identify key gaps in taxonomic and geographic coverage, emphasising the need for further research to expand these tools to under-represented species and regions. Additionally, we highlight the importance of integrating genetic approaches into enforcement frameworks to enhance conservation strategies and regulatory compliance. By providing an accessible reference for time- and cost-effective genetic monitoring, this work will support evidence-based decision-making and improve the practical application of rapid DNA/eDNA-based ID tools in the conservation and management of Chondrichthyes species worldwide.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70044"},"PeriodicalIF":5.5,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145084708","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}
引用次数: 0
BOLDistilled: Automated Construction of Comprehensive but Compact DNA Barcode Reference Libraries. 全面而紧凑的DNA条形码参考文库的自动构建。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-09-14 DOI: 10.1111/1755-0998.70043
S W J Prosser, R M Floyd, K A Thompson, S K Monckton, P D N Hebert
{"title":"BOLDistilled: Automated Construction of Comprehensive but Compact DNA Barcode Reference Libraries.","authors":"S W J Prosser, R M Floyd, K A Thompson, S K Monckton, P D N Hebert","doi":"10.1111/1755-0998.70043","DOIUrl":"https://doi.org/10.1111/1755-0998.70043","url":null,"abstract":"<p><p>Advances in DNA sequencing technology have stimulated the rapid uptake of protocols-such as eDNA analysis and metabarcoding-that infer the species composition of environmental samples from DNA sequences. DNA barcode reference libraries play a critical role in the interpretation of sequences gathered through such protocols, but many of these libraries lack a taxonomic consensus, include redundant records, do not support end-user analytical pipelines, and are not permanently archived. Furthermore, because DNA sequencers are outpacing Moore's Law and reference libraries are growing, the computational power required to assign sequences to source taxa is rapidly increasing. This paper introduces an algorithmic approach to construct DNA barcode reference libraries that addresses these issues. Hosted online, 'BOLDistilled' libraries are comprehensive but compact, because the algorithm distills genetic variation into a minimal set of records. We provide a BOLDistilled library for the barcode region of the cytochrome c oxidase 1 gene (COI) based on data in the Barcode of Life Data System (BOLD). It contains 1.7 M records versus the 15.7 M in the complete library, a compression that reduced the time required for sequence analysis of metabarcoded samples by ≥ 98% with no reduction in the accuracy of taxonomic placements. BOLDistilled libraries will be updated regularly, with current and previous versions available at https://boldsystems.org/data/boldistilled. By providing access to persistent, comprehensive, and high-quality reference data, these libraries strengthen the capacity of DNA-based identification systems to advance biodiversity science.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70043"},"PeriodicalIF":5.5,"publicationDate":"2025-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145063059","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}
引用次数: 0
MITE Annotation and Landscape in 207 Plant Genomes Reveal Their Evolutionary Dynamics and Functional Roles. 207个植物基因组的MITE注释与景观分析:进化动态与功能作用
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-09-09 DOI: 10.1111/1755-0998.70041
Jie Gao, Long-Long Yang, Yi-Ran Wang, Yue-Yan Zhao, Yu Shi, Shuai-Jie Wei, Ning Chen, Yu-Lan Zhang, Wu-Jun Gao, Shu-Fen Li
{"title":"MITE Annotation and Landscape in 207 Plant Genomes Reveal Their Evolutionary Dynamics and Functional Roles.","authors":"Jie Gao, Long-Long Yang, Yi-Ran Wang, Yue-Yan Zhao, Yu Shi, Shuai-Jie Wei, Ning Chen, Yu-Lan Zhang, Wu-Jun Gao, Shu-Fen Li","doi":"10.1111/1755-0998.70041","DOIUrl":"https://doi.org/10.1111/1755-0998.70041","url":null,"abstract":"<p><p>Miniature inverted-repeat transposable elements (MITEs) are short, non-autonomous class II transposable elements prevalent in eukaryotic genomes, contributing to various genomic and genic functions in plants. However, research on MITEs mainly targets a few species, limiting a comprehensive understanding and systematic comparison of MITEs in plants. Here, we developed a highly sensitive MITE annotation pipeline with a low false positive rate and applied it to 207 high-quality plant genomes. We found over a 20,000-fold variation in MITE copy numbers among species. The Mutator superfamily accounted for 41.5% of MITEs, whereas the Tc1/Mariner and PIF/Harbinger superfamilies expanded rapidly in monocots, particularly in Poaceae. Insertion time analysis revealed a general pattern of a single amplification wave, with initial insertions occurring around 30 million years ago (Mya) and peaking at 0-9 Mya. In addition, some species exhibited evidence of another ancient, slower expansion phase. In three representative families, we identified many more species-specific MITE loci than shared MITE loci, underscoring MITEs' significant role in genome diversity. Phylogenomic analyses indicate that MITEs accumulated gradually and specifically during speciation, primarily through recent insertions rather than the retention of ancient elements. MITEs preferentially insert near genes and are often associated with enhanced gene expression. Furthermore, we identified 985 MITE-derived miRNAs from 392 families across 56 species, mainly from Mutator, Tc1/Mariner, and PIF/Harbinger, targeting a variety of gene functions. This study enhances our understanding of the evolution and functional roles of MITEs in plants and provides a basis for exploring their function in further research.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70041"},"PeriodicalIF":5.5,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145022563","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}
引用次数: 0
Robust, Open-Source and Automation-Friendly DNA Extraction Protocol for Hologenomic Research. 用于全基因组研究的健壮、开源和自动化的DNA提取协议。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-09-09 DOI: 10.1111/1755-0998.70042
Jonas G Lauritsen, Christian Carøe, Nanna Gaun, Garazi Martin-Bideguren, Aoife Leonard, Raphael Eisenhofer, Iñaki Odriozola, M Thomas P Gilbert, Ostaizka Aizpurua, Antton Alberdi, Carlotta Pietroni
{"title":"Robust, Open-Source and Automation-Friendly DNA Extraction Protocol for Hologenomic Research.","authors":"Jonas G Lauritsen, Christian Carøe, Nanna Gaun, Garazi Martin-Bideguren, Aoife Leonard, Raphael Eisenhofer, Iñaki Odriozola, M Thomas P Gilbert, Ostaizka Aizpurua, Antton Alberdi, Carlotta Pietroni","doi":"10.1111/1755-0998.70042","DOIUrl":"https://doi.org/10.1111/1755-0998.70042","url":null,"abstract":"<p><p>Global efforts to standardise methodologies benefit greatly from open-source procedures that enable the generation of comparable data. Here, we present a modular, high-throughput nucleic acid extraction protocol standardised within the Earth Hologenome Initiative to generate both genomic and microbial metagenomic data from faecal samples of vertebrates. The procedure enables the purification of either RNA and DNA in separate fractions (DREX1) or as total nucleic acids (DREX2). We demonstrate their effectiveness across faecal samples from amphibians, reptiles and mammals, with reduced performance observed on bird guano. Despite some variation in laboratory performance metrics, both DREX1 and DREX2 yielded highly similar microbial community profiles, as well as comparable depth and breadth of host genome coverages. Benchmarking against a commercial kit widely used in microbiome research showed comparable recovery of host genomic data and microbial community complexity. Our open-source method offers a robust, cost-effective, scalable and automation-friendly nucleic acid extraction procedure to generate high-quality hologenomic data across vertebrate taxa. The method enhances research comparability and reproducibility by providing standardised, high-throughput, open-access protocols with fully transparent reagents. It is designed to integrate automatised pipelines, and its modular structure also supports continuous development and improvement.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70042"},"PeriodicalIF":5.5,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145022607","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}
引用次数: 0
Quaternary Habitat Fluctuations and Demographic Dynamics in Turtles Inferred From Environmental Niche Modelling and Whole Genome Data. 基于环境生态位模型和全基因组数据推断的龟类第四纪栖息地波动和种群动态
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-09-04 DOI: 10.1111/1755-0998.70040
Marcella Sozzoni, Jennifer Balacco, Massimo Bellavita, Anna Brüniche-Olsen, Giulio Formenti, Nivesh Jain, Bonhwang Koo, Jacquelyn Mountcastle, Marc Palmada-Flores, Vladimir Trifonov, Guido Chelazzi, Sara Fratini, Erich D Jarvis, Chiara Natali, Davide Nespoli, Claudio Ciofi, Alessio Iannucci
{"title":"Quaternary Habitat Fluctuations and Demographic Dynamics in Turtles Inferred From Environmental Niche Modelling and Whole Genome Data.","authors":"Marcella Sozzoni, Jennifer Balacco, Massimo Bellavita, Anna Brüniche-Olsen, Giulio Formenti, Nivesh Jain, Bonhwang Koo, Jacquelyn Mountcastle, Marc Palmada-Flores, Vladimir Trifonov, Guido Chelazzi, Sara Fratini, Erich D Jarvis, Chiara Natali, Davide Nespoli, Claudio Ciofi, Alessio Iannucci","doi":"10.1111/1755-0998.70040","DOIUrl":"https://doi.org/10.1111/1755-0998.70040","url":null,"abstract":"<p><p>Quaternary climatic fluctuations had a substantial influence on ecosystems, species distribution, phenology and genetic diversity, driving extinction, adaptation and demographic shifts during glacial periods and postglacial expansions. Integration of genomic data and environmental niche modelling can provide valuable insights on how organisms responded to past environmental variations and contribute to assessing vulnerability and resilience to ongoing climatic challenges. Among vertebrates, turtles are particularly vulnerable to habitat changes because of distinctive life history traits and the effect of environmental conditions on physiology and survival. We estimated contemporary heterozygosity (H) and effective population size (N<sub>e</sub>) using a high-quality chromosome-level reference genome we produced for the European pond turtle (Emys orbicularis) and reference genomes and whole genome sequence data available for 21 species of tortoises and freshwater turtles. We implemented environmental niche modelling (ENM) to estimate past habitat dynamics. We found recurrent cycles of population expansion and contraction over the last 10 Mya in all species, with a general pattern of decrease in N<sub>e</sub> correlated with temperature reduction after the last interglacial period. No correlation was found between habitat fluctuations during the Quaternary and past N<sub>e</sub>. Moreover, neither H nor mean N<sub>e</sub> was correlated to threat status as defined by IUCN Red List categories. Our results add to studies on other vertebrates showing the extent to which genetic parameters can aid the assessment of conservation status, and although genomic data may not always be consistent indicators of the level of threat, investigations of which genomic parameters could best represent essential biodiversity variables should be consistently supported.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70040"},"PeriodicalIF":5.5,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144991051","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}
引用次数: 0
Spider Webs, Soil or Leaf Swabs to Detect Environmental DNA From Terrestrial Vertebrates: What Is the Best Substrate? 用蜘蛛网、土壤或叶子拭子检测陆生脊椎动物的环境DNA:什么是最好的基质?
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-09-04 DOI: 10.1111/1755-0998.70037
Aloïs Berard, Julien Pradel, Nathalie Charbonnel, Maxime Galan
{"title":"Spider Webs, Soil or Leaf Swabs to Detect Environmental DNA From Terrestrial Vertebrates: What Is the Best Substrate?","authors":"Aloïs Berard, Julien Pradel, Nathalie Charbonnel, Maxime Galan","doi":"10.1111/1755-0998.70037","DOIUrl":"https://doi.org/10.1111/1755-0998.70037","url":null,"abstract":"<p><p>As human activities drive biodiversity decline, effective biomonitoring is more crucial than ever to track species distribution changes and inform conservation and restoration actions. Environmental DNA (eDNA) metabarcoding has emerged as a promising tool for the simultaneous detection of multiple taxa. However, while substrates play a crucial role in eDNA studies, limited research has compared substrate performance for terrestrial vertebrate detection, leaving a critical gap in empirical knowledge for large-scale application. This study evaluates and compares the effectiveness of three easy-to-collect substrates: soil, leaf swabs, and spider webs, for broad terrestrial vertebrate eDNA monitoring. Specifically, we examined taxonomic richness overlaps among substrates, their effects on wild vertebrate detection probabilities, and within-sample PCR repeatability. We analysed 120 samples from the Landes Forest, an intensively managed temperate forest in Western France, and included additional control samples from the Montpellier zoo to validate our detection capabilities. Using metabarcoding with 12S-V5 and 16S mam primers, we identified 63 taxa at the genus or species level. Our findings highlight the advantages of substrates that passively accumulate airborne DNA (leaf swabs and spider webs) over soil, and position spider webs as a suitable choice for maximising detection probabilities in rapid eDNA surveys, emphasising their potential for efficient, scalable biomonitoring. Further research is needed to identify factors affecting eDNA detectability from these substrates, aiming to standardise procedures and move from proof-of-concept to broad use by researchers and managers.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70037"},"PeriodicalIF":5.5,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144999314","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}
引用次数: 0
Host Traits Impact the Outcome of Metagenomic Library Preparation From Dental Calculus Samples Across Diverse Mammals. 宿主性状影响不同哺乳动物牙石样本宏基因组文库制备的结果。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-09-01 DOI: 10.1111/1755-0998.70039
Markella Moraitou, John L Richards, Chanah Bolyos, Konstantina Saliari, Emmanuel Gilissen, Zena Timmons, Andrew C Kitchener, Olivier S G Pauwels, Richard Sabin, Phaedra Kokkini, Roberto Portela Miguez, Katerina Guschanski
{"title":"Host Traits Impact the Outcome of Metagenomic Library Preparation From Dental Calculus Samples Across Diverse Mammals.","authors":"Markella Moraitou, John L Richards, Chanah Bolyos, Konstantina Saliari, Emmanuel Gilissen, Zena Timmons, Andrew C Kitchener, Olivier S G Pauwels, Richard Sabin, Phaedra Kokkini, Roberto Portela Miguez, Katerina Guschanski","doi":"10.1111/1755-0998.70039","DOIUrl":"https://doi.org/10.1111/1755-0998.70039","url":null,"abstract":"<p><p>Dental calculus metagenomics has emerged as a valuable tool for studying the oral microbiomes of humans and a few select mammals. With increasing interest in wild animal microbiomes, it is important to understand how widely this material can be used across the mammalian tree of life, refine the related protocols and understand the expected outcomes and potential challenges of dental calculus sample processing. In this study, we significantly expand the breadth of studied host species, analysing laboratory and bioinformatics metadata of dental calculus samples from 32 ecologically and phylogenetically diverse mammals. Although we confirm the presence of an oral microbiome signature in the metagenomes of all studied mammals, the fraction recognised as oral varies between host species, possibly because of both biological differences and methodological biases. The overall success rate of dental calculus processing, from extractions to sequencing, was ~74%. Although input sample weight was positively associated with the number of produced library molecules, we identify a negative impact of enzymatic inhibition on the library preparation protocol. The inhibition was most prevalent in herbivores and frugivores and is likely diet-derived. In contrast, hosts with an animalivore diet posed fewer challenges during laboratory processing and yielded more DNA relative to sample weight. Our results translate into recommendations for future studies of dental calculus metagenomics from a variety of host species, identifying required sample amounts, and emphasising the utility of dental calculus in exploring the oral microbiome in relation to broader ecological and evolutionary questions.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70039"},"PeriodicalIF":5.5,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144937508","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}
引用次数: 0
Evaluation of Preservation and Extraction Methods on eDNA Yield and Detection Probability After Long-Term Storage. 保存和提取方法对长期保存后eDNA产率和检测概率的评价。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-08-26 DOI: 10.1111/1755-0998.70035
Sarah A Tomke, Ethan N Buland, Steven J Price
{"title":"Evaluation of Preservation and Extraction Methods on eDNA Yield and Detection Probability After Long-Term Storage.","authors":"Sarah A Tomke, Ethan N Buland, Steven J Price","doi":"10.1111/1755-0998.70035","DOIUrl":"https://doi.org/10.1111/1755-0998.70035","url":null,"abstract":"<p><p>Establishing best practices for the overall workflow of environmental DNA (eDNA) sampling is necessary to increase reproducibility and precision in estimates of biodiversity across studies. Rigorous comparisons between eDNA sample preservation strategies for long-term storage durations are lacking, and previous studies have primarily evaluated DNA yield rather than detection success, despite detection being of critical importance when studying rare or elusive species. Here, we assessed the efficacy of common preservation media, storage temperatures and DNA extraction methods on eDNA yield and detection probability after one- and four-years of storage. We found that frozen and ethanol-preserved filters had significantly higher DNA concentrations and detection rates than samples preserved in Longmire's lysis buffer when DNA extraction methods differed among the treatment groups. Substantial inhibition was observed in the Longmire's samples when using a phenol-chloroform-isoamyl alcohol (PCI) extraction method, but did not occur when Longmire's samples were extracted using a Qiagen DNeasy Blood & Tissue Kit. PCI extraction also caused reduced yield and detection rates in ethanol-preserved samples, demonstrating its relative inefficiency for eDNA recovery. eDNA yield and detection rates were highly stable over one- and four-years of storage for all preservation strategies except for ethanol samples stored at room temperature, in which concentrations, but not detection rates, declined significantly after 4 years. Overall, frozen and Longmire's preserved samples had higher yield than ethanol-preserved samples, although detections were high across all media. Our study contributes valuable information towards the optimisation and standardisation of long-term storage protocols of filtered eDNA samples.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70035"},"PeriodicalIF":5.5,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144937464","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}
引用次数: 0
Evaluating Kinship Estimation Methods for Reduced-Representation SNP Data in Non-model Species. 评估非模式物种中简化表示SNP数据的亲缘关系估计方法。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-08-26 DOI: 10.1111/1755-0998.70038
Eilish S McMaster, Patricia Lu-Irving, Marlien M van der Merwe, Simon Y W Ho, Maurizio Rossetto
{"title":"Evaluating Kinship Estimation Methods for Reduced-Representation SNP Data in Non-model Species.","authors":"Eilish S McMaster, Patricia Lu-Irving, Marlien M van der Merwe, Simon Y W Ho, Maurizio Rossetto","doi":"10.1111/1755-0998.70038","DOIUrl":"https://doi.org/10.1111/1755-0998.70038","url":null,"abstract":"<p><p>Accurate kinship estimation between close relatives is crucial in conservation and restoration but remains challenging in wild populations due to structure and inbreeding. The efficacy of kinship inference using reduced-representation sequencing data (e.g., DArTseq, RADseq) is also uncertain. We evaluated the sensitivity and precision of six kinship methods (Goudet's beta dosage, KING Homo, KING Robust, PC-Relate, PLINK, RelateAdmix) at detecting parent-offspring and sibling relationships. Analyses were conducted on 3395 individuals and 363 families from six non-model Australian plant species: Acacia terminalis, Acacia suaveolens, Banksia serrata, Banksia aemula, Hakea sericea and Hakea teretifolia. Method performance varied across species and filtering parameters. Goudet's beta dosage and RelateAdmix performed well in low-structure, noninbred species but were less reliable in structured or inbred contexts. PLINK offered a balance of sensitivity and precision but was sensitive to filtering and often underestimated relatedness. KING Robust was highly precise but missed many true relatives. PC-Relate showed high false positives and is not recommended for similar applications. We recommend PLINK for general use, Goudet's beta dosage and RelateAdmix for low-structure species, and KING Robust for high-precision needs. Comparing multiple methods is advisable, as each has different assumptions and complementary strengths. Further theoretical development is needed for species with high inbreeding.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70038"},"PeriodicalIF":5.5,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144937433","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}
引用次数: 0
A Targeted Reference Database for Improved Analysis of Environmental 16S rRNA Oxford Nanopore Sequencing Data. 环境16S rRNA牛津纳米孔测序数据改进分析的目标参考数据库。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-08-25 DOI: 10.1111/1755-0998.70036
Melcy Philip, Tonje Nilsen, Sanna Majaneva, Ragnhild Pettersen, Morten Stokkan, Jessica Louise Ray, Nigel Keeley, Knut Rudi, Lars-Gustav Snipen
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