Molecular Ecology Resources最新文献

{"title":"A Molecular Survey of the Occurrence of Coffee Berry Disease Resistant Coffee Cultivars Near the Wild Gene Pool of Arabica Coffee in Its Region of Origin in Southwest Ethiopia.","authors":"Yves Bawin, Beyene Zewdie, Biruk Ayalew, Isabel Roldán-Ruiz, Steven B Janssens, Ayco J M Tack, Sileshi Nemomissa, Kassahun Tesfaye, Kristoffer Hylander, Olivier Honnay, Tom Ruttink","doi":"10.1111/1755-0998.14085","DOIUrl":"https://doi.org/10.1111/1755-0998.14085","url":null,"abstract":"<p><p>Cultivation of crops close to their wild relatives may jeopardise the integrity of wild genetic resources. Detecting cultivars among wild plants is necessary to characterise crop-wild gene flow, but can be challenging if cultivars and wild plants are phenotypically highly similar. Genomics tools can be used instead, but the selection of diagnostic loci for cultivar identification can be difficult if the wild and cultivated genepools are closely related. In Ethiopia, Arabica coffee cultivars resistant to coffee berry disease (CBD) occur near wild Coffea arabica plants and local landraces. However, the abundance and distribution of these cultivars across coffee sites remains unclear. Here, we present a new module of the SMAP package called SMAP relatedness pairwise to characterise pairwise genetic relationships between individuals based on haplotype calls and to identify diagnostic loci that distinguish (sets of) individuals from each other. Next, we estimate the relative abundance of CBD-resistant cultivars across 60 Ethiopian Arabica coffee sites using a genome-wide fingerprinting approach. We confirm the presence of these cultivars in around 75% of the coffee sites with a high agreement between a field survey and our DNA fingerprinting approach. At least 20 out of 60 sites with supposedly wild C. arabica individuals contain signatures of the cultivated genepool. Overall, we conclude that CBD-resistant cultivars are widespread in Ethiopian coffee sites. The development of SMAP relatedness pairwise opens opportunities to assess the distribution of coffee cultivars in other regions in Ethiopia and to apply similar screenings near wild relatives from other crops.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14085"},"PeriodicalIF":5.5,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466406","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":"Navigating Past Oceans: Comparing Metabarcoding and Metagenomics of Marine Ancient Sediment Environmental DNA.","authors":"Luke E Holman, Giulia Zampirolo, Richard Gyllencreutz, James Scourse, Tobias Frøslev, Christian Carøe, Shyam Gopalakrishnan, Mikkel Winther Pedersen, Kristine Bohmann","doi":"10.1111/1755-0998.14086","DOIUrl":"https://doi.org/10.1111/1755-0998.14086","url":null,"abstract":"<p><p>The condition of ancient marine ecosystems provides context for contemporary biodiversity changes in human-impacted oceans. Sequencing sedimentary ancient DNA (sedaDNA) is an emerging method for generating high-resolution biodiversity time-series data, offering insights into past ecosystems. However, few studies directly compare the two predominant sedaDNA sequencing approaches: metabarcoding and shotgun-metagenomics, and it remains unclear if these methodological differences affect diversity metrics. We compared these methods using sedaDNA from an archived marine sediment record sampled in the Skagerrak, North Sea, spanning almost 8000 years. We performed metabarcoding of a eukaryotic 18S rRNA region (V9) and sequenced 153-229 million metagenomic reads per sample. Our results show limited overlap between metabarcoding and metagenomics, with only three metazoan genera detected by both methods. For overlapping taxa, metabarcoding detections became inconsistent for samples older than 2000 years, while metagenomics detected taxa throughout the time series. We observed divergent patterns of alpha diversity, with metagenomics indicating decreased richness towards the present and metabarcoding showing an increase. However, beta diversity patterns were similar between methods, with discrepancies only in metazoan data comparisons. Our findings demonstrate that the choice of sequencing method significantly impacts detected biodiversity in an ancient marine sediment record. While we stress that studies with limited variation in DNA degradation among samples may not be strongly affected, researchers should exonerate methodological explanations for observed biodiversity changes in marine sediment cores, particularly when considering alpha diversity, before making ecological interpretations.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14086"},"PeriodicalIF":5.5,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466409","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 Short-Read Amplicon Sequencing Protocol and Bioinformatic Pipeline for Ecological Surveillance of Dipteran Disease Vectors.","authors":"Raquel Lima-Cordón, Jason Travis Mohabir, Mohini Sooklall, Aina Martinez Zurita, Meg Shieh, Cheyenne Knox, Sabrina Gobran, Zachary Johnson, Margaret Laws, Ruchit Panchal, Reza Niles-Robin, Horace Cox, Maria Eugenia Grillet, Jorge E Moreno, Socrates Herrera, Martha Quinones, Angela M Early, Jacob A Tennessen, Daniel E Neafsey","doi":"10.1111/1755-0998.14088","DOIUrl":"10.1111/1755-0998.14088","url":null,"abstract":"<p><p>Vector control remains an important strategy worldwide to prevent human infection with pathogens transmitted by arthropods. Vector control strategies rely on accurate identification of vector taxa along with vector-specific biological indicators such as feeding ecology, infection prevalence and insecticide resistance. Multiple 'DNA barcoding' protocols have been published over the past several decades to support these applications, generally relying on informal manual approaches such as BLAST to assign taxonomic identity to the resulting sequences. We present a standardised informatic pipeline for analysis of DNA barcoding data from dipteran vectors, VecTreeID, that uses short-read amplicon sequencing (AmpSeq) coupled with sequence similarity assessment (BLAST) and an evolutionary placement algorithm (EPA-ng) to achieve vector taxonomic identification, capture bionomic features (blood and plant meal sources), determine Plasmodium infection status (for anopheline mosquitoes) and detect target-site insecticide resistance mutations. The VecTreeID pipeline provides uncertainty in assignment through identifications at varying levels of taxonomic rank, a feature missing from many approaches to DNA barcoding, but important given gaps and labelling problems in public sequence databases. We validated an Illumina-based implementation of VecTreeID on laboratory and field samples, and find that the blood meal amplicons can detect vertebrate DNA sequences up to 36 h post-feeding, and that short-read sequencing data are capable of sensitively detecting minor sequences in DNA mixtures representing multi-species blood or nectar meals. This high-throughput VecTreeID approach empowers researchers and public health professionals to survey and control arthropod disease vectors consistently and effectively.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14088"},"PeriodicalIF":5.5,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143439439","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":"detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data.","authors":"Nadja Brait, Thomas Hackl, Sebastian Lequime","doi":"10.1111/1755-0998.14083","DOIUrl":"https://doi.org/10.1111/1755-0998.14083","url":null,"abstract":"<p><p>Endogenous viral elements (EVEs) are fragments of viral genomic material embedded within the host genome. Retroviruses contribute to the majority of EVEs because of their genomic integration during their life cycle; however, the latter can also arise from non-retroviral RNA or DNA viruses, then collectively known as non-retroviral (nr) EVEs. Detecting nrEVEs poses challenges because of their sequence and genomic structural diversity, contributing to the scarcity of specific tools designed for nrEVEs detection. Here, we introduce detectEVE, a user-friendly and open-source tool designed for the accurate identification of nrEVEs in genomic assemblies. detectEVE deviates from other nrEVE detection pipelines, which usually classify sequences in a more rigid manner as either virus-associated or not. Instead, we implemented a scaling system assigning confidence scores to hits in protein sequence similarity searches, using bit score distributions and search hints related to various viral characteristics, allowing for higher sensitivity and specificity. Our benchmarking shows that detectEVE is computationally efficient and accurate, as well as considerably faster than existing approaches, because of its resource-efficient parallel execution. Our tool can help to fill current gaps in both host-associated fields and virus-related studies. This includes (i) enhancing genome annotations with metadata for EVE loci, (ii) conducting large-scale paleo-virological studies to explore deep viral evolutionary histories, and (iii) aiding in the identification of actively expressed EVEs in transcriptomic data, reducing the risk of misinterpretations between exogenous viruses and EVEs.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14083"},"PeriodicalIF":5.5,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143397585","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":"Correction to “Quantifying Mitochondrial Heteroplasmy Diversity: A Computational Approach”","authors":"","doi":"10.1111/1755-0998.14089","DOIUrl":"10.1111/1755-0998.14089","url":null,"abstract":"<p>Liu, K., N. Xie, and Y. Wang. 2024. “Quantifying Mitochondrial Heteroplasmy Diversity: A Computational Approach.” <i>Molecular Ecology Resources</i> 24, no. 1: e13874. https://doi.org/10.1111/1755-0998.13874.</p><p>The authors reported the Pearson correlation coefficient but incorrectly used the symbol <i>R</i>² instead of <i>R</i> for the correlation coefficient. Consequently, the relevant text and figures (Figures 3 and 4) need to be revised accordingly. Additionally, the phrase ‘exceeding the reported <i>R</i>² value for allele frequency correlations’ should be deleted from the abstract. In the discussion section, the phrase ‘higher than the reported <i>R</i>² value of 0.29 for allele frequency between mothers and children in Rebolledo-Jaramillo et al. (2014)’ should also be deleted.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14089","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143397661","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":"The Long and the Short of It: Nanopore-Based eDNA Metabarcoding of Marine Vertebrates Works; Sensitivity and Species-Level Assignment Depend on Amplicon Lengths.","authors":"Karlijn Doorenspleet, Lara Jansen, Saskia Oosterbroek, Pauline Kamermans, Oscar Bos, Erik Wurz, Albertinka Murk, Reindert Nijland","doi":"10.1111/1755-0998.14079","DOIUrl":"https://doi.org/10.1111/1755-0998.14079","url":null,"abstract":"<p><p>To monitor the effect of nature restoration projects in North Sea ecosystems, accurate and intensive biodiversity assessments are vital. DNA-based techniques and especially environmental (e)DNA metabarcoding is becoming a powerful monitoring tool. However, current approaches rely on genetic target regions under 500 bp, offering limited taxonomic resolution. We developed a method for long-read eDNA metabarcoding, using Nanopore sequencing of a longer amplicon and present DECONA, a read processing pipeline to enable improved identification of marine vertebrate species. We designed a universal primer pair targeting a 2 kb region of fish mitochondrial DNA and compared it to the commonly used MiFish primer pair targeting a ~ 170 bp region. In silico testing showed that 2 kb fragments improved accurate identification of closely related species. Analysing eDNA from a North Sea aquarium showed that sequences from both primer pairs could be assigned to most species, and additional species level assignments could be made through the 2 kb primer pair. Interestingly, this difference was opposite in eDNA from the North Sea, where not the 2 kb but the MiFish primer pair detected more species. This study demonstrates the feasibility of using long-read metabarcoding for eDNA vertebrate biodiversity assessments. However, our findings suggests that longer fragments are less abundant in environmental settings, but not in aquarium settings, suggesting that longer fragments may provide a more recent snapshot of the community. Thus, long-read metabarcoding can expand the molecular toolbox for biodiversity assessments by improving species-level identification and may be especially useful when the temporal origin of the eDNA signal is better understood.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14079"},"PeriodicalIF":5.5,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143389725","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 Strategy of Assessing Gene Copy Number Differentiation Between Populations Using Ultra-Fast De Novo Assembly of Next-Generation Sequencing Data.","authors":"Tao Shi, Zhiyan Gao, Yue Zhang, Mark D Rausher, Jinming Chen","doi":"10.1111/1755-0998.14080","DOIUrl":"https://doi.org/10.1111/1755-0998.14080","url":null,"abstract":"<p><p>Gene duplication and loss play pivotal roles in the evolutionary dynamics of genomes, contributing to species phenotypic diversity and adaptation. However, detecting copy number variations (CNVs) in homoploid populations and newly-diverged species using short reads from next-generation sequencing (NGS) with traditional methods can often be challenging due to uneven read coverage caused by variations in GC content and the presence of repetitive sequences. To address these challenges, we developed a novel pipeline, ST4gCNV, which leverages ultra-fast de novo assemblies of NGS data to detect gene-specific CNVs between populations. The pipeline effectively reduces the variance of read coverage due to technical factors such as GC bias, providing a reliable CNV detection with a minimum sequencing depth of 10. We successfully apply ST4gCNV to the resequencing analysis of homoploid species Nelumbo nucifera and Nelumbo lutea (lotus). We reveal significant CNV-driven differentiation between these species, particularly in genes related to petal colour diversity such as those involved in the anthocyanin pathway. By highlighting the extensive gene duplication and loss events in Nelumbo, our study demonstrates the utility of ST4gCNV in population genomics and underscores its potential of integrating genomic CNV analysis with traditional SNP-based resequencing analysis.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14080"},"PeriodicalIF":5.5,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143381391","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":"Integration of De Novo Chromosome-Level Genome and Population Resequencing of Peganum (Nitrariaceae): A Case Study of Speciation and Evolutionary Trajectories in Arid Central Asia.","authors":"Hao Xu, Yun Han, Xiaofeng Chi, Jingya Yu, Mingze Xia, Shuang Han, Yu Niu, Faqi Zhang, Shilong Chen","doi":"10.1111/1755-0998.14078","DOIUrl":"https://doi.org/10.1111/1755-0998.14078","url":null,"abstract":"<p><p>Natural hybridization is a significant driving force in plant evolution and speciation. Understanding the genetic mechanism and dynamic evolutionary trajectories of divergence between species and hybrids remains a central goal in evolutionary biology. Here, we examined the genetic divergence of Peganum and their intermittent and hybrid entities (IHEs) from large-scale sympatric and allopatric regions. We sequenced the genomes of Peganum from the Arid Central Asia (ACA) region and its surrounding areas, discovering that the origin of Peganum could be traced to the Hexi Corridor in eastern Central Asia, where migration led to geographic and environmental isolation, giving rise to new species based on natural selection. Different Peganum species, exhibiting excellent dispersal abilities, migrated to the same regions and underwent hybridization. The descendant species of Peganum inherited and developed adaptive traits from parent species through gene flow and introgression, particularly in DNA repair and wax layer formation, leading to the speciation of the IHEs. This study clarified the transition stages in hybrid speciation and identified the Mixing-Isolation-Mixing cycles (MIM) model as a speciation framework suitable for Peganum, marking the initial identification of this unique evolutionary model in the ACA region.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14078"},"PeriodicalIF":5.5,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143381400","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":"Cgsim: An R Package for Simulation of Population Genetics for Conservation and Management Applications.","authors":"Shawna J Zimmerman, Sara J Oyler-McCance","doi":"10.1111/1755-0998.14081","DOIUrl":"https://doi.org/10.1111/1755-0998.14081","url":null,"abstract":"<p><p>Wildlife conservation and management increasingly considers genetic information to plan, understand and evaluate implemented population interventions. These actions commonly include conservation translocation and population reductions through removals. Change in genetic variation in response to management actions can be unintuitive due to the influence of multiple interacting drivers (e.g. genetic drift, life history traits, environmental stochasticity). Simulation is an excellent tool to understand the predicted consequences of different proposed or implemented actions. However, the genetic simulators that are robust to a wide variety of life history traits also have a steep learning curve to appropriately parameterize common management actions. To fill this gap, we have developed cgsim, an R package for simulating the genetic consequences of common management interventions for populations of wildlife species. We developed a set of functions to specifically understand the effects of four main aspects of managing small, declining or isolated populations: loss of genetic diversity to drift, augmenting existing populations (e.g. translocation), population reduction through targeted removals and population catastrophes driven by stochastic extrinsic forces. Our single population simulation model is individual-based, and flexible to a range of life history traits. Here we validate cgsim through comparison of simulations to theoretical expectations of genetic diversity loss and illustrate its applied utility by focusing on a recently published empirical example for the Greater Sage-Grouse. Cgsim is available as an R package at: https://doi.org/10.5066/P1BXBEXJ.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14081"},"PeriodicalIF":5.5,"publicationDate":"2025-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143381396","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":"Estimation of Species Abundance Based on the Number of Segregating Sites Using Environmental DNA (eDNA).","authors":"Qiaoyun Ai, Hao Yuan, Ying Wang, Chenhong Li","doi":"10.1111/1755-0998.14076","DOIUrl":"https://doi.org/10.1111/1755-0998.14076","url":null,"abstract":"<p><p>The advance of environmental DNA (eDNA) has enabled rapid and non-invasive species detection in aquatic environments. While most studies focus on species detection, recent works explored using eDNA concentration to quantify species abundance. However, the differential individual DNA contribution to eDNA samples could easily obscure the eDNA concentration-species abundance relationship. We propose using the number of segregating sites as a proxy for estimating species abundance. Segregating sites reflect the genetic diversity of the population, which is less sensitive to differential individual DNA contribution than eDNA concentration. We examined the relationship between the number of segregating sites and species abundance in silico, in vitro, and in situ experiments, using two brackish goby species, Acanthogobius hasta and Tridentiger bifasciatus. Analyses of the simulated and in vitro data with DNA mixed from a known number of individuals showed a strong correlation between the number of segregating sites and species abundance (R² > 0.9; p < 0.01). In the in situ experiments, we analysed eDNA samples collected from mesocosm. The results further validated that the correlation (R² = 0.70, p < 0.01) was not affected by biotic factors, including body size and feeding behaviour (p > 0.05). The cross-validation test results also showed that the number of segregating sites predicted species abundance with less bias and variability than the eDNA concentration. Overall, the number of segregating sites is less affected by differential DNA contribution among individuals compared to eDNA concentration. This advancement can significantly enhance the proficiency of estimating species abundance using eDNA.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14076"},"PeriodicalIF":5.5,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143253985","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}