Molecular Ecology Resources最新文献

A Possible More Precise Management Unit Delineation Based on Epigenomic Differentiation of a Long-Distance-Migratory Marine Fish Scomberomorus niphonius.

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2025-03-14 DOI: 10.1111/1755-0998.14103

Sailan Liu, Yan Gao, Xinrui Long, Kunhuan Li, Qilin Gutang, Huiying Xie, Jingzhen Wang, Jiashen Tian, Bo Liang, Jianqing Lin, Wenhua Liu

{"title":"A Possible More Precise Management Unit Delineation Based on Epigenomic Differentiation of a Long-Distance-Migratory Marine Fish Scomberomorus niphonius.","authors":"Sailan Liu, Yan Gao, Xinrui Long, Kunhuan Li, Qilin Gutang, Huiying Xie, Jingzhen Wang, Jiashen Tian, Bo Liang, Jianqing Lin, Wenhua Liu","doi":"10.1111/1755-0998.14103","DOIUrl":"https://doi.org/10.1111/1755-0998.14103","url":null,"abstract":"Understanding population structure and adaptive history is critical for designing appropriate management regulations for fisheries and conserving adaptive potential for the future. However, this is not easy for marine fish, especially those with long-distance migration abilities. In this study, we constructed a high-quality reference genome for Japanese Spanish mackerel (Scomberomorus niphonius) and explored its population structure using whole genomic and epigenomic data. Despite the high depth of the sequence data, we failed to identify geographical genetic differentiation of Japanese Spanish mackerel across Chinese coastal waters. However, whole-genome bisulphite sequencing can classify this species into the Bohai-Yellow Sea group and the East China Sea-South China Sea group. Genes involved in embryonic skeletal system development, limb morphogenesis functions, and adult locomotory behaviour were differentially methylated in the southern (Zhanjiang, ZJ) and northern (Western Dalian, WDL) populations and may play important roles as drivers of population structure in Japanese Spanish mackerel. Our study not only provides the first reference genome of the Japanese Spanish mackerel and sheds light on population differentiation at the epigenomic level, but also provides a methylome-based framework for population structure analyses of marine fish with long-distance migration ability. These findings are expected to facilitate the development of scientific programmes for the successful conservation of marine fishery resources.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14103"},"PeriodicalIF":5.5,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143623052","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

Short Read Lengths Recover Ecological Patterns in 16S rRNA Gene Amplicon Data.

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2025-03-13 DOI: 10.1111/1755-0998.14102

Stephanie D Jurburg

{"title":"Short Read Lengths Recover Ecological Patterns in 16S rRNA Gene Amplicon Data.","authors":"Stephanie D Jurburg","doi":"10.1111/1755-0998.14102","DOIUrl":"https://doi.org/10.1111/1755-0998.14102","url":null,"abstract":"16S rRNA gene metabarcoding, the study of amplicon sequences of the 16S rRNA gene from mixed environmental samples, is an increasingly popular and accessible method for assessing bacterial communities across a wide range of environments. As metabarcoding sequence data archives continue to grow, data reuse will likely become an important source of novel insights into the ecology of microbes. While recent work has demonstrated the benefits of longer read lengths for the study of microbial communities from 16S rRNA gene segments, no studies have explored the use of shorter (< 200 bp) read lengths in the context of data reuse. Nevertheless, this information is essential to improve the reuse and comparability of metabarcoding data across existing datasets. This study reanalyzed nine 16S rRNA datasets targeting aquatic, animal-associated and soil microbiomes, and evaluated how processing the sequence data across a range of read lengths affected the resulting taxonomic assignments, biodiversity metrics and differential (i.e., before-after treatment) analyses. Short read lengths successfully recovered ecological patterns and allowed for the use of more sequences. Limited increases in resolution were observed beyond 150 bp reads across environments. Furthermore, abundance-weighted diversity metrics (e.g., Inverse Simpson index, Morisita-Horn dissimilarities or weighted Unifrac distances) were more robust to variation in read lengths. Read lengths alone contributed to consistent increases in the total number of ASVs detected, highlighting the need to consider metabarcoding-derived diversity estimates within the context of the bioinformatics parameters selected. This study provides evidence-based guidelines for the processing of short reads.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14102"},"PeriodicalIF":5.5,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143623053","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

Beware of Plant DNA in Animal Dietary Metabarcoding: Lessons From a Strictly Insectivorous Bat.

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2025-03-12 DOI: 10.1111/1755-0998.14100

Luis P da Silva, Miguel Porto, Francisco Amorim, Pedro Beja, Vanessa A Mata

{"title":"Beware of Plant DNA in Animal Dietary Metabarcoding: Lessons From a Strictly Insectivorous Bat.","authors":"Luis P da Silva, Miguel Porto, Francisco Amorim, Pedro Beja, Vanessa A Mata","doi":"10.1111/1755-0998.14100","DOIUrl":"https://doi.org/10.1111/1755-0998.14100","url":null,"abstract":"DNA metabarcoding is increasingly used in dietary studies, but it has limitations, such as detecting nonfood taxa. This issue is frequently mentioned in the literature but poorly understood, limiting interpretation of results and mitigation strategies. We evaluate the extent and sources of nonfood plant DNA in dietary metabarcoding, based on 281 faecal samples of a strictly insectivorous bat. We modelled plant taxa detections in relation to pollination syndromes, flowering and fruiting phenology and habitat associations, and we estimated co-occurrences between plants and arthropods. The bat arthropod diet was consistent with previous studies. Plants were detected in 82.9% of samples, representing 148 taxa, and all pollination syndromes evaluated. Plant detections were more frequent during their flowering periods, particularly for those with mixed pollination syndromes, suggesting a relationship between flowering and detectability. Fruiting had a positive, albeit weaker, effect. There was a tendency for more frequent detection of forest plants and less frequent detection of plants associated with riparian and agricultural habitats. Co-occurrences between arthropods and plants were weak and inconsistent. Our results highlight the potential for widespread detection of nonfood plant DNA in metabarcoding studies, calling for great care when analysing the plant component of diets. Specifically, we recommend: (i) implementing strategies for reducing plant contamination during field sampling; (ii) using multiple field and lab negative controls; and (iii) using ancillary information (e.g., sample visual inspection and literature review) to aid interpretation of metabarcoding results. Moreover, we recommend that studies reporting plant consumption results greatly diverging from dietary patterns obtained through other methods should include detailed explanations of methodological steps taken to exclude the confounding effects of nonfood plant DNA.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14100"},"PeriodicalIF":5.5,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143603277","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

EntoSieve: Automated Size-Sorting of Insect Bulk Samples to Aid Accurate Megabarcoding and Metabarcoding.

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2025-03-11 DOI: 10.1111/1755-0998.14097

Aleida Ascenzi, Lorenz Wührl, Vivian Feng, Nathalie Klug, Christian Pylatiuk, Pierfilippo Cerretti, Rudolf Meier

{"title":"EntoSieve: Automated Size-Sorting of Insect Bulk Samples to Aid Accurate Megabarcoding and Metabarcoding.","authors":"Aleida Ascenzi, Lorenz Wührl, Vivian Feng, Nathalie Klug, Christian Pylatiuk, Pierfilippo Cerretti, Rudolf Meier","doi":"10.1111/1755-0998.14097","DOIUrl":"https://doi.org/10.1111/1755-0998.14097","url":null,"abstract":"Widespread insect decline necessitates the development and use of standardized protocols for regular monitoring. These methods have to be rapid, efficient and cost-effective to allow for large-scale implementation. Many insect sampling and molecular methods have been developed. These include Malaise trapping, high-throughput DNA barcoding ('megabarcoding') and metabarcoding. The latter allows for assessing the species diversity in whole samples using few steps, but sample heterogeneity in terms of body size remains a challenge since large insects contribute disproportionately more mtDNA than small ones. This can potentially overwhelm the template DNA from small species that then go undetected. Size-sorting can mitigate this problem, but no satisfying automated, rapid and non-destructive solutions are available. We introduce the EntoSieve, a low-cost and DIY motorized instrument that disentangles and sorts abundant insect bulk samples into several body size fractions while minimizing damage to specimens, thus reducing the risk of DNA contamination across size fractions (e.g. legs of large specimens in small body size fraction). EntoSieve utilizes readily available components, 3D-printed parts and customizable meshes, thus enabling parallelization at low cost. We here show the efficiency of the EntoSieve for three samples with more than 10,000 specimens using three sieving protocols and assess the impact on specimen integrity. Efficiency ranged from 92% to 99%, achieved within 18-60 min, and specimen damage was not significant for subsamples. By facilitating rapid pre-processing, the device contributes to producing morphologically valuable vouchers for megabarcoding and is likely to improve compositional diversity accuracy across size classes when using metabarcoding.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14097"},"PeriodicalIF":5.5,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143595905","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

Genome and Metagenome Skimming: Future Sequencing Methods for Environmental DNA (eDNA) Studies.

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2025-03-07 DOI: 10.1111/1755-0998.14095

Yiqiu Lu, Yuran Dong, Min Zhang, Lingfeng Mao

引用次数: 0

Popfinder: A Highly Effective Artificial Neural Network Package for Genetic Population Assignment.

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2025-03-07 DOI: 10.1111/1755-0998.14096

K Birchard, C Boccia, H Lounder, L Colston-Nepali, V L Friesen

{"title":"Popfinder: A Highly Effective Artificial Neural Network Package for Genetic Population Assignment.","authors":"K Birchard, C Boccia, H Lounder, L Colston-Nepali, V L Friesen","doi":"10.1111/1755-0998.14096","DOIUrl":"https://doi.org/10.1111/1755-0998.14096","url":null,"abstract":"The ability to assign biological samples to source populations with high accuracy and precision based on genetic variation is important for numerous applications from ecological studies through wildlife conservation to epidemiology. However, population assignment when genetic differentiation is low is challenging, and methods to address this problem are lacking. The application of artificial neural networks to population assignment using genomic data is highly promising. Here we present popfinder: a new, easy-to-use Python-based artificial neural network pipeline for genetic population assignment. We tested popfinder both with simulated genetic data from populations connected by varying levels of gene flow and with reduced-representation sequence data for three species of seabirds with weak to no population genetic structure. Popfinder was able to assign individuals to their source populations with high accuracy, precision and recall in most cases, including both simulated and empirical data sets, except in the empirical data set with the weakest population structure, where the comparator programs also performed poorly. Compared to other available software, popfinder was slower on the simulated data sets due to hyperparameter tuning and the fact that it does not reduce the dimensionality of the data set; however, all programs ran in seconds on empirical data sets. Additionally, popfinder provides a perturbation ranking method to help develop optimised SNP panels for genetic population assignment and is designed to be user-friendly. Finally, we caution users of all assignment programs to watch both for leakage of data during model training, which can lead to overfitting and inflation of performance metrics, and for unequal detection probabilities.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14096"},"PeriodicalIF":5.5,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143571622","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

RepeatOBserver: Tandem Repeat Visualisation and Putative Centromere Detection.

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2025-03-04 DOI: 10.1111/1755-0998.14084

Cassandra Elphinstone, Rob Elphinstone, Marco Todesco, Loren H Rieseberg

{"title":"RepeatOBserver: Tandem Repeat Visualisation and Putative Centromere Detection.","authors":"Cassandra Elphinstone, Rob Elphinstone, Marco Todesco, Loren H Rieseberg","doi":"10.1111/1755-0998.14084","DOIUrl":"https://doi.org/10.1111/1755-0998.14084","url":null,"abstract":"Tandem repeats play an important role in centromere structure, subtelomeric regions, DNA methylation, recombination and the regulation of gene activity. Analysis of their distribution in genomes offers a potential means for predicting putative centromere locations, which continues to be a challenge for genome annotation. Here we present RepeatOBserver (https://github.com/celphin/RepeatOBserverV1), a new tool for visualising repeat patterns and identifying putative centromere locations, using a Fourier transform of DNA walks. RepeatOBserver can identify and visualise a broad range of perfect and imperfect repeats (3-5000 bp long) in genome assemblies without any a priori knowledge of repeat sequences or the need for optimising parameters. RepeatOBserver heatmaps can distinguish between tandem and retrotransposon repeats. We analysed 159 chromosomes with experimentally-verified centromere positions from 12 plant and animal species. We find that 93% of experimentally-verified tandem repeat centromeres occur in regions of low sequence diversity and 97% of retrotransposon centromeres occur in regions with a high abundance of repeat lengths. Depending on the centromere type predicted by the heatmaps, putative centromere locations can be predicted using either a genomic Shannon diversity index or a repeat abundance sum. RepeatOBserver can also locate other regions of interest including potential neocentromeres and gene copy variation. Split and inverted tandem repeats at inversion boundaries suggest that chromosomal inversions or mis-assemblies can also be located. RepeatOBserver is a flexible tool for comprehensive characterisation of repeat patterns that can be used to visualise and identify a variety of regions of interest in genome assemblies.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14084"},"PeriodicalIF":5.5,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143539580","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 the Benefits and Limits of Multiple Displacement Amplification With Whole-Genome Oxford Nanopore Sequencing.

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2025-02-28 DOI: 10.1111/1755-0998.14094

Fiifi Agyabeng-Dadzie, Megan S Beaudry, Alex Deyanov, Haley Slanis, Minh Q Duong, Randi Turner, Asis Khan, Cesar A Arias, Jessica C Kissinger, Travis C Glenn, Rodrigo de Paula Baptista

{"title":"Evaluating the Benefits and Limits of Multiple Displacement Amplification With Whole-Genome Oxford Nanopore Sequencing.","authors":"Fiifi Agyabeng-Dadzie, Megan S Beaudry, Alex Deyanov, Haley Slanis, Minh Q Duong, Randi Turner, Asis Khan, Cesar A Arias, Jessica C Kissinger, Travis C Glenn, Rodrigo de Paula Baptista","doi":"10.1111/1755-0998.14094","DOIUrl":"10.1111/1755-0998.14094","url":null,"abstract":"Multiple displacement amplification (MDA) outperforms conventional PCR in long fragment and whole-genome amplification, making it attractive to couple MDA with long-read sequencing of samples with limited quantities of DNA to obtain improved genome assemblies. Here, we explore the efficacy and limits of MDA for efficient low-cost genome sequence assembly using Oxford Nanopore Technologies (ONTs) rapid library preparations and minION sequencing. We successfully generated almost complete genome sequences for all organisms examined, including Gram-positive (Staphylococcus aureus, Enterococcus faecium) and Gram-negative (Escherichia coli) prokaryotes and one challenging eukaryotic pathogen (Cryptosporidium spp) representing a broad spectrum of critical infectious disease pathogens. High-quality data from those samples were generated starting with only 0.025 ng of total DNA. Controlled sheared DNA samples exhibited a distinct pattern of size increase after MDA, which may be associated with the amplification of long, low-abundance fragments present in the assay, as well as generating concatemeric sequences during amplification. To address concatemers, we developed a computational pipeline (CADECT: Concatemer Detection Tool) to identify and remove putative concatemeric sequences. This study highlights the efficacy of MDA in generating high-quality genome assemblies from limited amounts of input DNA. Also, the CADECT pipeline effectively mitigated the impact of concatemeric sequences, enabling the assembly of contiguous sequences even in cases where the input genomic DNA was degraded. These results have significant implications for the study of organisms that are challenging to culture in vitro, such as Cryptosporidium, and for expediting critical results in clinical settings with limited quantities of available genomic DNA.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14094"},"PeriodicalIF":5.5,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143522364","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 Meta-Omics Approach Using eDNA and eRNA for the Assessment of Biotic Communities Associated With Royal Jelly Produced by the Western Honey Bee (Apis mellifera L.).

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2025-02-27 DOI: 10.1111/1755-0998.14090

Jennifer M Standley, Jose Marcelino, Fahong Yu, James D Ellis

{"title":"A Meta-Omics Approach Using eDNA and eRNA for the Assessment of Biotic Communities Associated With Royal Jelly Produced by the Western Honey Bee (Apis mellifera L.).","authors":"Jennifer M Standley, Jose Marcelino, Fahong Yu, James D Ellis","doi":"10.1111/1755-0998.14090","DOIUrl":"https://doi.org/10.1111/1755-0998.14090","url":null,"abstract":"Royal jelly (RJ) is a glandular secretion fed to developing honey bee larvae by adult worker bees. It is also a potential source of disease transmission in and between honey bee colonies. We endeavored to characterize the microbiome, virome, and other biota present in RJ via an integrated meta-omics approach. Using a magnetic beads-based extraction protocol, we identified eDNA and eRNA fragments from organisms of interest in RJ using high-throughput metagenomics (DNA-seq), metatranscriptomics (total RNA-seq), and parallel sequencing. This allowed us to enhance the detection of Operational Taxonomic Units (OTUs) undetectable by standard 'omics or amplicon protocols'. Using this integrated approach, we detected OTUs present in RJ from honey bee pests and pathogens, including Melissococcus plutonius, Paenibacillus larvae, Varroa destructor, V. jacobsoni, Aethina tumida, Galleria mellonella, Vairimorpha ceranae, Apis mellifera filamentous virus, Black queen cell virus, Acute bee paralysis virus, Sacbrood virus, Deformed wing virus, Israeli acute bee paralysis virus, Kashmir bee virus, and Slow bee paralysis virus, as well as multiple beneficial gut bacteria from the genera Lactobacillus, Actinobacteria, and Gluconobacter. The presence of DNA and RNA from these organisms does not conclusively indicate the presence of live organisms in the RJ, but it does suggest some exposure of the RJ to these organisms. The results present a comprehensive eDNA and eRNA microbial profile of RJ, demonstrating that our novel method is an effective and sensitive molecular tool for high-resolution metagenomic and metatranscriptomic profiling, and is of value for detection of pathogens of concern for the beekeeping industry.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14090"},"PeriodicalIF":5.5,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143514280","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

Dung Beetle iDNA Provides an Effective Way to Detect Diverse Mycological Communities. 蜣螂 iDNA 为检测多样化的真菌群落提供了一种有效方法。

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2025-02-26 DOI: 10.1111/1755-0998.14091

Thilina S Nimalrathna, Huan Fan, Ahimsa Campos-Arceiz, Akihiro Nakamura

{"title":"Dung Beetle iDNA Provides an Effective Way to Detect Diverse Mycological Communities.","authors":"Thilina S Nimalrathna, Huan Fan, Ahimsa Campos-Arceiz, Akihiro Nakamura","doi":"10.1111/1755-0998.14091","DOIUrl":"https://doi.org/10.1111/1755-0998.14091","url":null,"abstract":"Fungi play crucial ecological and economic roles, yet their diversity and distribution remain poorly known and challenging to assess. Using recent advances in invertebrate-derived DNA (iDNA) for biodiversity monitoring, we investigated the potential of dung beetle iDNA for fungal sampling and monitoring. We sampled two habitats (rainforest vs. rubber plantation) and seasons (dry vs. rainy) in tropical Xishuangbanna, southwest China. We extracted, amplified and identified 9259 unique fungi Amplicon Sequence Variants (ASVs) from the gut of three species of dung beetles (Paragymnopleurus sp., telecoprids; Onthophagus diabolicus, paracoprids; and Onthophagus cf. gracilipes, endocoprids). Fungal community composition was different across habitats and seasons, with the highest diversity found in the rainy season rainforest. Our results were consistent with previous eDNA-based studies based on soil samples in the detection of habitat differences (both approaches were able to detect low diversity of Basidiomycota in rubber plantations). However, our approach outperformed soil-based eDNA studies in being able to detect fungal occurrences associated with seasonal precipitation patterns. Our findings highlight the utility of dung beetle iDNA to uncover spatiotemporal dynamics of fungal communities across different habitats. The use of iDNA broadens fungal biodiversity research, strengthens fungal monitoring to assess anthropogenic impacts and presents opportunities to conserve fungal diversity.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14091"},"PeriodicalIF":5.5,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143497735","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