Flurin Leugger, Michel Schmidlin, Martina Lüthi, Zacharias Kontarakis, Loïc Pellissier
More efficient methods for extensive biodiversity monitoring are required to support rapid measures to address the biodiversity crisis. While environmental DNA (eDNA) metabarcoding and quantitative PCR (qPCR) methods offer advantages over traditional monitoring approaches, their large-scale application is limited by the time and labour required for developing assays and/or for analysis. CRISPR (clustered regularly interspaced short palindromic repeats) diagnostic technologies (Dx) may overcome some of these limitations, but they have been used solely with species-specific primers, restricting their versatility for biodiversity monitoring. Here, we demonstrate the feasibility of designing species-specific CRISPR-Dx assays in silico within a short metabarcoding fragment using a general primer set, a methodology we term 'ampliscanning', for 18 of the 22 amphibian species in Switzerland. We sub-selected nine species, including three classified as regionally endangered, to test the methodology using eDNA sampled from ponds at nine sites. We compared the ampliscanning detections to data from traditional monitoring at these sites. Ampliscanning was successful at detecting target species with different prevalences across the landscape. With only one visit, we detected more species per site than three traditional monitoring visits (visual and acoustic detections by trained experts), in particular more elusive species and previously undocumented but expected populations. Ampliscanning detected 25 species/site combinations compared to 12 with traditional monitoring. Sensitivity analyses showed that larger numbers of field visits and PCR replicates are more important for reliable detection than many technical replicates at the CRISPR-Dx assay level. Given the reduced sampling and analysis effort, our results highlight the benefits of eDNA and CRISPR-Dx combined with universal primers for large-scale monitoring of multiple endangered species across landscapes to inform conservation measures.
{"title":"Scanning amplicons with CRISPR-Dx detects endangered amphibians in environmental DNA.","authors":"Flurin Leugger, Michel Schmidlin, Martina Lüthi, Zacharias Kontarakis, Loïc Pellissier","doi":"10.1111/1755-0998.14009","DOIUrl":"https://doi.org/10.1111/1755-0998.14009","url":null,"abstract":"<p><p>More efficient methods for extensive biodiversity monitoring are required to support rapid measures to address the biodiversity crisis. While environmental DNA (eDNA) metabarcoding and quantitative PCR (qPCR) methods offer advantages over traditional monitoring approaches, their large-scale application is limited by the time and labour required for developing assays and/or for analysis. CRISPR (clustered regularly interspaced short palindromic repeats) diagnostic technologies (Dx) may overcome some of these limitations, but they have been used solely with species-specific primers, restricting their versatility for biodiversity monitoring. Here, we demonstrate the feasibility of designing species-specific CRISPR-Dx assays in silico within a short metabarcoding fragment using a general primer set, a methodology we term 'ampliscanning', for 18 of the 22 amphibian species in Switzerland. We sub-selected nine species, including three classified as regionally endangered, to test the methodology using eDNA sampled from ponds at nine sites. We compared the ampliscanning detections to data from traditional monitoring at these sites. Ampliscanning was successful at detecting target species with different prevalences across the landscape. With only one visit, we detected more species per site than three traditional monitoring visits (visual and acoustic detections by trained experts), in particular more elusive species and previously undocumented but expected populations. Ampliscanning detected 25 species/site combinations compared to 12 with traditional monitoring. Sensitivity analyses showed that larger numbers of field visits and PCR replicates are more important for reliable detection than many technical replicates at the CRISPR-Dx assay level. Given the reduced sampling and analysis effort, our results highlight the benefits of eDNA and CRISPR-Dx combined with universal primers for large-scale monitoring of multiple endangered species across landscapes to inform conservation measures.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141994889","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}
Rapid biodiversity loss threatens many species with extinction. Captive populations of species of conservation concern (such as those housed in zoos and dedicated breeding centres) act as an insurance should wild populations go extinct or need supplemental individuals to boost populations. Limited resources mean that captive populations are almost always small and started from few founding individuals. As a result, captive populations require careful management to minimize negative genetic impacts, with decisions about which individuals to breed together often guided by the principle of minimizing relatedness. Typically this strategy aims to retain 90% of genetic diversity over 200 years (Soulé et al., Zoo Biology, 1986, 5, 101), but it has a weakness in that it does not directly manage for genetic load. In this issue of Molecular Ecology Resources, Speak et al. (Molecular Ecology Resources, 2024, e13967) present a novel proof-of-concept study for taking this next step and incorporating estimates of individual genetic load into the planning of captive breeding, using an approach that is likely to be widely applicable to many captive populations.
{"title":"Leveraging genomic load estimates to optimize captive breeding programmes","authors":"Evelyn L. Jensen, Rachel Gray, Joshua M. Miller","doi":"10.1111/1755-0998.14007","DOIUrl":"10.1111/1755-0998.14007","url":null,"abstract":"<p>Rapid biodiversity loss threatens many species with extinction. Captive populations of species of conservation concern (such as those housed in zoos and dedicated breeding centres) act as an insurance should wild populations go extinct or need supplemental individuals to boost populations. Limited resources mean that captive populations are almost always small and started from few founding individuals. As a result, captive populations require careful management to minimize negative genetic impacts, with decisions about which individuals to breed together often guided by the principle of minimizing relatedness. Typically this strategy aims to retain 90% of genetic diversity over 200 years (Soulé et al., <i>Zoo Biology</i>, 1986, 5, 101), but it has a weakness in that it does not directly manage for genetic load. In this issue of Molecular Ecology Resources, Speak et al. (<i>Molecular Ecology Resources</i>, 2024, e13967) present a novel proof-of-concept study for taking this next step and incorporating estimates of individual genetic load into the planning of captive breeding, using an approach that is likely to be widely applicable to many captive populations.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141974648","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}
In the context of looming global biodiversity loss, effective species detection represents a critical concern for ecological research and management. Environmental DNA (eDNA) analysis, which refers to the collection and taxonomic identification of genetic fragments that are shed from an organism into its surroundings, emerged approximately 15 years ago as a sensitive tool for species detection. Today, one of the frontiers of eDNA research concerns the collection and analysis of genetic material in dust and other airborne materials, termed airborne eDNA analysis. As the study of airborne eDNA matures, it is an appropriate time to review the foundational and emerging studies that make up the current literature, and use the reviewed literature to summarize, synthesize, and forecast the major challenges and opportunities for this advancing research front. Specifically, we use the “ecology of eDNA” framework to organize our findings across the origin, state, transport, and fate of airborne genetic materials in the environment, and summarize what is so far known of their interactions with surrounding abiotic and biotic factors, including population and community ecologies and ecosystem processes. Within this work we identify key challenges, opportunities, and future directions associated with the application of airborne eDNA development. Lastly, we discuss the development of applications, partnerships, and messaging that promote development and growth of the field. Together, the broad potential of eDNA analysis and the rate at which research is accelerating in this field suggest that the sky's the limit for airborne eDNA science.
{"title":"Macrobial airborne environmental DNA analysis: A review of progress, challenges, and recommendations for an emerging application","authors":"Mark Johnson, Matthew A. Barnes","doi":"10.1111/1755-0998.13998","DOIUrl":"10.1111/1755-0998.13998","url":null,"abstract":"<p>In the context of looming global biodiversity loss, effective species detection represents a critical concern for ecological research and management. Environmental DNA (eDNA) analysis, which refers to the collection and taxonomic identification of genetic fragments that are shed from an organism into its surroundings, emerged approximately 15 years ago as a sensitive tool for species detection. Today, one of the frontiers of eDNA research concerns the collection and analysis of genetic material in dust and other airborne materials, termed airborne eDNA analysis. As the study of airborne eDNA matures, it is an appropriate time to review the foundational and emerging studies that make up the current literature, and use the reviewed literature to summarize, synthesize, and forecast the major challenges and opportunities for this advancing research front. Specifically, we use the “ecology of eDNA” framework to organize our findings across the origin, state, transport, and fate of airborne genetic materials in the environment, and summarize what is so far known of their interactions with surrounding abiotic and biotic factors, including population and community ecologies and ecosystem processes. Within this work we identify key challenges, opportunities, and future directions associated with the application of airborne eDNA development. Lastly, we discuss the development of applications, partnerships, and messaging that promote development and growth of the field. Together, the broad potential of eDNA analysis and the rate at which research is accelerating in this field suggest that the sky's the limit for airborne eDNA science.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13998","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141900298","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}
Aurélien Delaval, Kevin A. Glover, Monica F. Solberg, John B. Taggart, François Besnier, Anne Grete Eide Sørvik, Johanne Øyro, Sofie Nordaune Garnes-Gutvik, Per Gunnar Fjelldal, Tom Hansen, Alison Harvey
Polyploidy occurs naturally across eukaryotic lineages and has been harnessed in the domestication of many crops and vertebrates. In aquaculture, triploidy can be induced as a biocontainment strategy, as it creates a reproductive barrier preventing farm-to-wild introgression, which is currently a major conservation issue for the industry. However, recent work suggests that triploidisation protocols may, on occasion, produce ‘failed triploids’ displaying diploidy, aneuploidy and aberrant inheritance. The potentially negative consequences for conservation and animal welfare motivate the need for methods to evaluate the success of ploidy-manipulation protocols early in the production process. We developed a semi-automated version of the MAC-PR (microsatellite DNA allele counting – peak ratios) method to resolve the allelic configuration of large numbers of individuals across a panel of microsatellite markers that can be used to infer ploidy, pedigree and inheritance aberrations. We demonstrate an application of the approach using material from a series of Atlantic salmon (Salmo salar) breeding experiments where ploidy was manipulated using a hydrostatic pressure treatment. We validated the approach to infer ploidy against blood smears, finding a > 99% agreement between these methods, and demonstrate its potential utility to infer ploidy as early as the embryonic stage. Furthermore, we present tools to assign diploid and triploid progeny to families and to detect aberrant inheritance, which may be useful for breeding programmes that utilise ploidy manipulation techniques. The approach adds to the ploidy verification toolbox. The increased precision in detecting ploidy and inheritance aberrations will facilitate the ability of triploidisation programmes to prevent farm-to-wild introgression.
多倍体在真核生物系中自然存在,并在许多作物和脊椎动物的驯化过程中得到利用。在水产养殖业中,三倍体可作为一种生物控制策略进行诱导,因为它能建立一个生殖屏障,防止养殖场向野外的引种,而这正是目前水产养殖业的一个主要保护问题。然而,最近的研究表明,三倍体化方案有时会产生 "失败的三倍体",表现出二倍体、非整倍体和异常遗传。这可能会对动物保护和动物福利造成负面影响,因此需要在生产过程的早期就找到评估倍性操纵方案成功与否的方法。我们开发了一种半自动版本的 MAC-PR(微卫星 DNA 等位基因计数-峰值比)方法,以解决大量个体的微卫星标记的等位基因配置问题,该方法可用于推断倍性、血统和遗传畸变。我们利用一系列大西洋鲑(Salmo salar)育种实验的材料展示了该方法的应用,在这些实验中,倍性是通过静水压处理来操控的。我们根据血液涂片验证了推断倍性的方法,发现这些方法之间的一致性> 99%,并证明了该方法在推断胚胎阶段的倍性方面的潜在用途。此外,我们还提出了将二倍体和三倍体后代分配到家系和检测畸变遗传的工具,这可能对利用倍性操作技术的育种计划有用。这种方法为倍性验证工具箱增添了新的内容。提高检测倍性和遗传畸变的精确度将有助于三倍体化计划防止从农场到野外的引种。
{"title":"A genetic method to infer ploidy and aberrant inheritance in triploid organisms","authors":"Aurélien Delaval, Kevin A. Glover, Monica F. Solberg, John B. Taggart, François Besnier, Anne Grete Eide Sørvik, Johanne Øyro, Sofie Nordaune Garnes-Gutvik, Per Gunnar Fjelldal, Tom Hansen, Alison Harvey","doi":"10.1111/1755-0998.14004","DOIUrl":"10.1111/1755-0998.14004","url":null,"abstract":"<p>Polyploidy occurs naturally across eukaryotic lineages and has been harnessed in the domestication of many crops and vertebrates. In aquaculture, triploidy can be induced as a biocontainment strategy, as it creates a reproductive barrier preventing farm-to-wild introgression, which is currently a major conservation issue for the industry. However, recent work suggests that triploidisation protocols may, on occasion, produce ‘failed triploids’ displaying diploidy, aneuploidy and aberrant inheritance. The potentially negative consequences for conservation and animal welfare motivate the need for methods to evaluate the success of ploidy-manipulation protocols early in the production process. We developed a semi-automated version of the MAC-PR (microsatellite DNA allele counting – peak ratios) method to resolve the allelic configuration of large numbers of individuals across a panel of microsatellite markers that can be used to infer ploidy, pedigree and inheritance aberrations. We demonstrate an application of the approach using material from a series of Atlantic salmon (<i>Salmo salar</i>) breeding experiments where ploidy was manipulated using a hydrostatic pressure treatment. We validated the approach to infer ploidy against blood smears, finding a > 99% agreement between these methods, and demonstrate its potential utility to infer ploidy as early as the embryonic stage. Furthermore, we present tools to assign diploid and triploid progeny to families and to detect aberrant inheritance, which may be useful for breeding programmes that utilise ploidy manipulation techniques. The approach adds to the ploidy verification toolbox. The increased precision in detecting ploidy and inheritance aberrations will facilitate the ability of triploidisation programmes to prevent farm-to-wild introgression.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141892461","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}
João C. Sequeira, Vítor Pereira, M. Madalena Alves, M. Alcina Pereira, Miguel Rocha, Andreia F. Salvador
The analysis of meta-omics data requires the utilization of several bioinformatics tools and proficiency in informatics. The integration of multiple meta-omics data is even more challenging, and the outputs of existing bioinformatics solutions are not always easy to interpret. Here, we present a meta-omics bioinformatics pipeline, Meta-Omics Software for Community Analysis (MOSCA), which aims to overcome these limitations. MOSCA was initially developed for analysing metagenomics (MG) and metatranscriptomics (MT) data. Now, it also performs MG and metaproteomics (MP) integrated analysis, and MG/MT analysis was upgraded with an additional iterative binning step, metabolic pathways mapping, and several improvements regarding functional annotation and data visualization. MOSCA handles raw sequencing data and mass spectra and performs pre-processing, assembly, annotation, binning and differential gene/protein expression analysis. MOSCA shows taxonomic and functional analysis in large tables, performs metabolic pathways mapping, generates Krona plots and shows gene/protein expression results in heatmaps, improving omics data visualization. MOSCA is easily run from a single command while also providing a web interface (MOSGUITO). Relevant features include an extensive set of customization options, allowing tailored analyses to suit specific research objectives, and the ability to restart the pipeline from intermediary checkpoints using alternative configurations. Two case studies showcased MOSCA results, giving a complete view of the anaerobic microbial communities from anaerobic digesters and insights on the role of specific microorganisms. MOSCA represents a pivotal advancement in meta-omics research, offering an intuitive, comprehensive, and versatile solution for researchers seeking to unravel the intricate tapestry of microbial communities.
{"title":"MOSCA 2.0: A bioinformatics framework for metagenomics, metatranscriptomics and metaproteomics data analysis and visualization","authors":"João C. Sequeira, Vítor Pereira, M. Madalena Alves, M. Alcina Pereira, Miguel Rocha, Andreia F. Salvador","doi":"10.1111/1755-0998.13996","DOIUrl":"10.1111/1755-0998.13996","url":null,"abstract":"<p>The analysis of meta-omics data requires the utilization of several bioinformatics tools and proficiency in informatics. The integration of multiple meta-omics data is even more challenging, and the outputs of existing bioinformatics solutions are not always easy to interpret. Here, we present a meta-omics bioinformatics pipeline, Meta-Omics Software for Community Analysis (MOSCA), which aims to overcome these limitations. MOSCA was initially developed for analysing metagenomics (MG) and metatranscriptomics (MT) data. Now, it also performs MG and metaproteomics (MP) integrated analysis, and MG/MT analysis was upgraded with an additional iterative binning step, metabolic pathways mapping, and several improvements regarding functional annotation and data visualization. MOSCA handles raw sequencing data and mass spectra and performs pre-processing, assembly, annotation, binning and differential gene/protein expression analysis. MOSCA shows taxonomic and functional analysis in large tables, performs metabolic pathways mapping, generates Krona plots and shows gene/protein expression results in heatmaps, improving omics data visualization. MOSCA is easily run from a single command while also providing a web interface (MOSGUITO). Relevant features include an extensive set of customization options, allowing tailored analyses to suit specific research objectives, and the ability to restart the pipeline from intermediary checkpoints using alternative configurations. Two case studies showcased MOSCA results, giving a complete view of the anaerobic microbial communities from anaerobic digesters and insights on the role of specific microorganisms. MOSCA represents a pivotal advancement in meta-omics research, offering an intuitive, comprehensive, and versatile solution for researchers seeking to unravel the intricate tapestry of microbial communities.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141887732","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}
Juan Li, Tingting Chen, Kai Gao, Yinxuan Xue, Ruqian Wu, Bin Guo, Zhong Chen, Shanwen Li, Ren-Gang Zhang, Kai-Hua Jia, Jian-Feng Mao, Xinmin An
Populus tomentosa, an indigenous tree species, is widely distributed and cultivated over 1,000,000 km2 in China, contributing significantly to forest production, ecological conservation and urban–rural greening. Although a reference genome is available for P. tomentosa, the intricate interspecific hybrid origins, chromosome structural variations (SVs) and sex determination mechanisms remain confusion and unclear due to its broad and even overlapping geographical distribution, extensive morphological variations and cross infiltration among white poplar species. We conducted a haplotype-resolved de novo assembly of P. tomentosa elite individual GM107, which comprises subgenomes a and b with a total genome size of 714.9 Mb. We then analysed the formation of hybrid species and the phylogenetic evolution and sex differentiation across the entire genus. Phylogenomic analyses suggested that GM107 likely originated from a hybridisation event between P. alba (♀) and P. davidiana (♂) which diverged at approximately 3.8 Mya. A total of 1551 chromosome SVs were identified between the two subgenomes. More noteworthily, a distinctive inversion structure spanning 2.15–2.95 Mb was unveiled among Populus, Tacamahaca, Turaga, Aigeiros poplar species and Salix, highlighting a unique evolutionary feature. Intriguingly, a novel sex genotype of the ZY type, which represents a crossover between XY and ZW systems, was identified and confirmed through both natural and artificial hybrids populations. These novel insights offer significant theoretical value for the study of the species' evolutionary origins and serve as a valuable resource for ecological genetics and forest biotechnology.
{"title":"Unravelling the novel sex determination genotype with ‘ZY’ and a distinctive 2.15–2.95 Mb inversion among poplar species through haplotype-resolved genome assembly and comparative genomics analysis","authors":"Juan Li, Tingting Chen, Kai Gao, Yinxuan Xue, Ruqian Wu, Bin Guo, Zhong Chen, Shanwen Li, Ren-Gang Zhang, Kai-Hua Jia, Jian-Feng Mao, Xinmin An","doi":"10.1111/1755-0998.14002","DOIUrl":"10.1111/1755-0998.14002","url":null,"abstract":"<p><i>Populus tomentosa</i>, an indigenous tree species, is widely distributed and cultivated over 1,000,000 km<sup>2</sup> in China, contributing significantly to forest production, ecological conservation and urban–rural greening. Although a reference genome is available for <i>P. tomentosa</i>, the intricate interspecific hybrid origins, chromosome structural variations (SVs) and sex determination mechanisms remain confusion and unclear due to its broad and even overlapping geographical distribution, extensive morphological variations and cross infiltration among white poplar species. We conducted a haplotype-resolved de novo assembly of <i>P. tomentosa</i> elite individual GM107, which comprises subgenomes a and b with a total genome size of 714.9 Mb. We then analysed the formation of hybrid species and the phylogenetic evolution and sex differentiation across the entire genus. Phylogenomic analyses suggested that GM107 likely originated from a hybridisation event between <i>P. alba</i> (♀) and <i>P. davidiana</i> (♂) which diverged at approximately 3.8 Mya. A total of 1551 chromosome SVs were identified between the two subgenomes. More noteworthily, a distinctive inversion structure spanning 2.15–2.95 Mb was unveiled among <i>Populus</i>, <i>Tacamahaca</i>, <i>Turaga</i>, <i>Aigeiros</i> poplar species and <i>Salix</i>, highlighting a unique evolutionary feature. Intriguingly, a novel sex genotype of the ZY type, which represents a crossover between XY and ZW systems, was identified and confirmed through both natural and artificial hybrids populations. These novel insights offer significant theoretical value for the study of the species' evolutionary origins and serve as a valuable resource for ecological genetics and forest biotechnology.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141873699","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}
Jan-Niklas Macher, Alejandro Martínez, Sude Çakir, Pierre-Etienne Cholley, Eleni Christoforou, Marco Curini Galletti, Lotte van Galen, Marta García-Cobo, Ulf Jondelius, Daphne de Jong, Francesca Leasi, Michael Lemke, Iñigo Rubio Lopez, Nuria Sánchez, Martin Vinther Sørensen, M. Antonio Todaro, Willem Renema, Diego Fontaneto
Molecular techniques like metabarcoding, while promising for exploring diversity of communities, are often impeded by the lack of reference DNA sequences available for taxonomic annotation. Our study explores the benefits of combining targeted DNA barcoding and morphological taxonomy to improve metabarcoding efficiency, using beach meiofauna as a case study. Beaches are globally important ecosystems and are inhabited by meiofauna, microscopic animals living in the interstitial space between the sand grains, which play a key role in coastal biodiversity and ecosystem dynamics. However, research on meiofauna faces challenges due to limited taxonomic expertise and sparse sampling. We generated 775 new cytochrome c oxidase I DNA barcodes from meiofauna specimens collected along the Netherlands' west coast and combined them with the NCBI GenBank database. We analysed alpha and beta diversity in 561 metabarcoding samples from 24 North Sea beaches, a region extensively studied for meiofauna, using both the enriched reference database and the NCBI database without the additional reference barcodes. Our results show a 2.5-fold increase in sequence annotation and a doubling of species-level Operational Taxonomic Units (OTUs) identification when annotating the metabarcoding data with the enhanced database. Additionally, our analyses revealed a bell-shaped curve of OTU richness across the intertidal zone, aligning more closely with morphological analysis patterns, and more defined community dissimilarity patterns between supralittoral and intertidal sites. Our research highlights the importance of expanding molecular reference databases and combining morphological taxonomy with molecular techniques for biodiversity assessments, ultimately improving our understanding of coastal ecosystems.
元条码等分子技术虽然有望探索群落的多样性,但往往因缺乏可用于分类注释的参考 DNA 序列而受阻。我们的研究以海滩小型底栖生物为例,探讨了将有针对性的 DNA 条形码和形态学分类相结合以提高元标码效率的益处。海滩是全球重要的生态系统,生活着小型底栖生物(生活在沙粒间隙中的微小动物),它们在沿海生物多样性和生态系统动态中发挥着关键作用。然而,由于分类学专业知识有限和取样稀少,对小型底栖动物的研究面临挑战。我们从荷兰西海岸采集的小型底栖生物标本中生成了 775 个新的细胞色素 c 氧化酶 I DNA 条形码,并将其与 NCBI GenBank 数据库相结合。我们分析了来自 24 个北海海滩的 561 个代谢条码样本中的α和β多样性,该地区的小型底栖生物已被广泛研究,我们同时使用了丰富的参考数据库和不含额外参考条码的 NCBI 数据库。我们的结果表明,使用增强型数据库注释元条码数据时,序列注释量增加了 2.5 倍,物种级的操作分类单元(OTUs)鉴定量增加了一倍。此外,我们的分析揭示了整个潮间带 OTU 丰富度的钟形曲线,与形态分析模式更加吻合,而且滨上和潮间带之间的群落差异模式更加明确。我们的研究强调了扩大分子参考数据库以及将形态分类学与分子技术结合起来进行生物多样性评估的重要性,从而最终提高我们对沿海生态系统的认识。
{"title":"Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: A case study on beach meiofauna","authors":"Jan-Niklas Macher, Alejandro Martínez, Sude Çakir, Pierre-Etienne Cholley, Eleni Christoforou, Marco Curini Galletti, Lotte van Galen, Marta García-Cobo, Ulf Jondelius, Daphne de Jong, Francesca Leasi, Michael Lemke, Iñigo Rubio Lopez, Nuria Sánchez, Martin Vinther Sørensen, M. Antonio Todaro, Willem Renema, Diego Fontaneto","doi":"10.1111/1755-0998.13997","DOIUrl":"10.1111/1755-0998.13997","url":null,"abstract":"<p>Molecular techniques like metabarcoding, while promising for exploring diversity of communities, are often impeded by the lack of reference DNA sequences available for taxonomic annotation. Our study explores the benefits of combining targeted DNA barcoding and morphological taxonomy to improve metabarcoding efficiency, using beach meiofauna as a case study. Beaches are globally important ecosystems and are inhabited by meiofauna, microscopic animals living in the interstitial space between the sand grains, which play a key role in coastal biodiversity and ecosystem dynamics. However, research on meiofauna faces challenges due to limited taxonomic expertise and sparse sampling. We generated 775 new cytochrome c oxidase I DNA barcodes from meiofauna specimens collected along the Netherlands' west coast and combined them with the NCBI GenBank database. We analysed alpha and beta diversity in 561 metabarcoding samples from 24 North Sea beaches, a region extensively studied for meiofauna, using both the enriched reference database and the NCBI database without the additional reference barcodes. Our results show a 2.5-fold increase in sequence annotation and a doubling of species-level Operational Taxonomic Units (OTUs) identification when annotating the metabarcoding data with the enhanced database. Additionally, our analyses revealed a bell-shaped curve of OTU richness across the intertidal zone, aligning more closely with morphological analysis patterns, and more defined community dissimilarity patterns between supralittoral and intertidal sites. Our research highlights the importance of expanding molecular reference databases and combining morphological taxonomy with molecular techniques for biodiversity assessments, ultimately improving our understanding of coastal ecosystems.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13997","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141858460","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}
Lauren Roman, Benjamin Mayne, Chloe Anderson, Yuna Kim, Terence O'Dwyer, Nicholas Carlile
Understanding the demography of wildlife populations is a key component for ecological research, and where necessary, supporting the conservation and management of long-lived animals. However, many animals lack phenological changes with which to determine individual age; therefore, gathering this fundamental information presents difficulties. More so for species that are rare, highly mobile, migratory and those that reside in inaccessible habitats. Until recently, the primary method to measure demography is through labour intensive mark-recapture approaches, necessitating decades of effort for long-lived species. Gadfly petrels (genus: Pterodroma) are one such taxa that are overrepresented with threatened and declining species, and for which numerous aspects of their ecology present challenges for research, monitoring and recovery efforts. To overcome some of these challenges, we developed the first DNA methylation (DNAm) demography technique to estimate the age of petrels, using the epigenetic clock of Gould's petrels (Pterodroma leucoptera). We collected reference blood samples from known-aged Gould's petrels at a long-term monitored population on Cabbage Tree Island, Australia. Epigenetic ages were successfully estimated for 121 individuals ranging in age from zero (fledgling) to 30 years of age, showing a mean error of 2.24 ± 0.17 years between the estimated and real age across the population. This is the first development of an epigenetic clock using multiplex PCR sequencing in a bird. This method enables demography to be measured with relative accuracy in a single sampling trip. This technique can provide information for emerging demographic risks that can mask declines in long-lived seabird populations and be applied to other Pterodroma populations.
{"title":"A novel technique for estimating age and demography of long-lived seabirds (genus Pterodroma) using an epigenetic clock for Gould's petrel (Pterodroma leucoptera)","authors":"Lauren Roman, Benjamin Mayne, Chloe Anderson, Yuna Kim, Terence O'Dwyer, Nicholas Carlile","doi":"10.1111/1755-0998.14003","DOIUrl":"10.1111/1755-0998.14003","url":null,"abstract":"<p>Understanding the demography of wildlife populations is a key component for ecological research, and where necessary, supporting the conservation and management of long-lived animals. However, many animals lack phenological changes with which to determine individual age; therefore, gathering this fundamental information presents difficulties. More so for species that are rare, highly mobile, migratory and those that reside in inaccessible habitats. Until recently, the primary method to measure demography is through labour intensive mark-recapture approaches, necessitating decades of effort for long-lived species. Gadfly petrels (genus: <i>Pterodroma</i>) are one such taxa that are overrepresented with threatened and declining species, and for which numerous aspects of their ecology present challenges for research, monitoring and recovery efforts. To overcome some of these challenges, we developed the first DNA methylation (DNAm) demography technique to estimate the age of petrels, using the epigenetic clock of Gould's petrels (<i>Pterodroma leucoptera</i>). We collected reference blood samples from known-aged Gould's petrels at a long-term monitored population on Cabbage Tree Island, Australia. Epigenetic ages were successfully estimated for 121 individuals ranging in age from zero (fledgling) to 30 years of age, showing a mean error of 2.24 ± 0.17 years between the estimated and real age across the population. This is the first development of an epigenetic clock using multiplex PCR sequencing in a bird. This method enables demography to be measured with relative accuracy in a single sampling trip. This technique can provide information for emerging demographic risks that can mask declines in long-lived seabird populations and be applied to other <i>Pterodroma</i> populations.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141791404","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}
Hans Recknagel, Luka Močivnik, Valerija Zakšek, Yonglun Luo, Rok Kostanjšek, Peter Trontelj
High-density genotyping methods have revolutionized the field of population and conservation genetics in the past decade. To exploit the technological and analytical advances in the field, access to high-quality genetic material is a key component. However, access to such samples in endangered and rare animals is often challenging or even impossible. Here, we used a minimally invasive sampling method (MIS) in the endangered cave salamander Proteus anguinus, the olm, to generate thousands of genetic markers using ddRADseq for population and conservation genomic analyses. Using tail clips and MIS skin swabs taken from the same individual, we investigated genotyping data properties of the two different sampling types. We found that sufficient DNA can be extracted from swab samples to generate up to 200,000 polymorphic SNPs in divergent Proteus lineages. Swab and tissue samples were highly reproducible exhibiting low SNP genotyping error rates. We found that SNPs were most frequently (~50%) located within genic regions, while the rest mapped to mostly flanking regions of repetitive DNA. The vast majority of DNA recovered from swabbing was host DNA. However, a fraction of DNA recovered from swabs contained additional ecological information on the species, including eDNA from the surrounding environment and bacterial skin fauna. Most exogenous DNA recovered from swabs were bacteria (~80%), followed by vertebrates (~20%). Our results demonstrate that MIS can be used to (i) generate tens of thousands of ddRADseq markers for conservation and population genomic analyses and (ii) inform on the species health status and ecology from exogenous DNA.
过去十年间,高密度基因分型方法彻底改变了种群和保护遗传学领域。要利用该领域的技术和分析进步,获取高质量的遗传材料是关键要素。然而,在濒危和珍稀动物中获取此类样本往往具有挑战性,甚至是不可能的。在这里,我们在濒危洞螈(Proteus anguinus,olm)中使用了一种微创取样方法(MIS),利用 ddRADseq 生成了数千个遗传标记,用于种群和保护基因组分析。我们使用从同一个体身上采集的尾夹和 MIS 皮肤拭子,研究了两种不同取样类型的基因分型数据特性。我们发现,从拭子样本中提取的 DNA 足以在不同的变形杆菌系中产生多达 200,000 个多态 SNP。拭子和组织样本的重复性很高,SNP 基因分型错误率很低。我们发现,SNPs 最常(约 50%)位于基因区域内,而其余的大多位于重复 DNA 的侧翼区域。从拭子中回收的 DNA 绝大多数是宿主 DNA。不过,从拭子中回收的部分DNA含有物种的额外生态信息,包括来自周围环境和细菌皮肤动物群的eDNA。从拭子中回收的外源 DNA 大部分是细菌(约占 80%),其次是脊椎动物(约占 20%)。我们的研究结果表明,MIS 可用于:(i) 生成数以万计的 ddRADseq 标记,用于保护和种群基因组分析;(ii) 从外源 DNA 中获取物种健康状况和生态学信息。
{"title":"Generation of genome-wide SNP markers from minimally invasive sampling in endangered animals and applications in species ecology and conservation","authors":"Hans Recknagel, Luka Močivnik, Valerija Zakšek, Yonglun Luo, Rok Kostanjšek, Peter Trontelj","doi":"10.1111/1755-0998.13995","DOIUrl":"10.1111/1755-0998.13995","url":null,"abstract":"<p>High-density genotyping methods have revolutionized the field of population and conservation genetics in the past decade. To exploit the technological and analytical advances in the field, access to high-quality genetic material is a key component. However, access to such samples in endangered and rare animals is often challenging or even impossible. Here, we used a minimally invasive sampling method (MIS) in the endangered cave salamander <i>Proteus anguinus</i>, the olm, to generate thousands of genetic markers using ddRADseq for population and conservation genomic analyses. Using tail clips and MIS skin swabs taken from the same individual, we investigated genotyping data properties of the two different sampling types. We found that sufficient DNA can be extracted from swab samples to generate up to 200,000 polymorphic SNPs in divergent <i>Proteus</i> lineages. Swab and tissue samples were highly reproducible exhibiting low SNP genotyping error rates. We found that SNPs were most frequently (~50%) located within genic regions, while the rest mapped to mostly flanking regions of repetitive DNA. The vast majority of DNA recovered from swabbing was host DNA. However, a fraction of DNA recovered from swabs contained additional ecological information on the species, including eDNA from the surrounding environment and bacterial skin fauna. Most exogenous DNA recovered from swabs were bacteria (~80%), followed by vertebrates (~20%). Our results demonstrate that MIS can be used to (i) generate tens of thousands of ddRADseq markers for conservation and population genomic analyses and (ii) inform on the species health status and ecology from exogenous DNA.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13995","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141756052","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}
Gert-Jan Jeunen, Sadie Mills, Miles Lamare, Grant A. Duffy, Michael Knapp, Jo-Ann L. Stanton, Stefano Mariani, Jackson Treece, Sara Ferreira, Benjamín Durán-Vinet, Monika Zavodna, Neil J. Gemmell
Marine sponges have recently emerged as efficient natural environmental DNA (eDNA) samplers. The ability of sponges to accumulate eDNA provides an exciting opportunity to reconstruct contemporary communities and ecosystems with high temporal and spatial precision. However, the use of historical eDNA, trapped within the vast number of specimens stored in scientific collections, opens up the opportunity to begin to reconstruct the communities and ecosystems of the past. Here, we define the term ‘heDNA’ to denote the historical environmental DNA that can be obtained from the recent past with high spatial and temporal accuracy. Using a variety of Antarctic sponge specimens stored in an extensive marine invertebrate collection, we were able to recover information on Antarctic fish biodiversity from specimens up to 20 years old. We successfully recovered 64 fish heDNA signals from 27 sponge specimens. Alpha diversity measures did not differ among preservation methods, but sponges stored frozen had a significantly different fish community composition compared to those stored dry or in ethanol. Our results show that we were consistently and reliably able to extract the heDNA trapped within marine sponge specimens, thereby enabling the reconstruction and investigation of communities and ecosystems of the recent past with a spatial and temporal resolution previously unattainable. Future research into heDNA extraction from other preservation methods, as well as the impact of specimen age and collection method, will strengthen and expand the opportunities for this novel resource to access new knowledge on ecological change during the last century.
{"title":"Unlocking Antarctic molecular time-capsules – Recovering historical environmental DNA from museum-preserved sponges","authors":"Gert-Jan Jeunen, Sadie Mills, Miles Lamare, Grant A. Duffy, Michael Knapp, Jo-Ann L. Stanton, Stefano Mariani, Jackson Treece, Sara Ferreira, Benjamín Durán-Vinet, Monika Zavodna, Neil J. Gemmell","doi":"10.1111/1755-0998.14001","DOIUrl":"10.1111/1755-0998.14001","url":null,"abstract":"<p>Marine sponges have recently emerged as efficient natural environmental DNA (eDNA) samplers. The ability of sponges to accumulate eDNA provides an exciting opportunity to reconstruct contemporary communities and ecosystems with high temporal and spatial precision. However, the use of historical eDNA, trapped within the vast number of specimens stored in scientific collections, opens up the opportunity to begin to reconstruct the communities and ecosystems of the past. Here, we define the term ‘heDNA’ to denote the historical environmental DNA that can be obtained from the recent past with high spatial and temporal accuracy. Using a variety of Antarctic sponge specimens stored in an extensive marine invertebrate collection, we were able to recover information on Antarctic fish biodiversity from specimens up to 20 years old. We successfully recovered 64 fish heDNA signals from 27 sponge specimens. Alpha diversity measures did not differ among preservation methods, but sponges stored frozen had a significantly different fish community composition compared to those stored dry or in ethanol. Our results show that we were consistently and reliably able to extract the heDNA trapped within marine sponge specimens, thereby enabling the reconstruction and investigation of communities and ecosystems of the recent past with a spatial and temporal resolution previously unattainable. Future research into heDNA extraction from other preservation methods, as well as the impact of specimen age and collection method, will strengthen and expand the opportunities for this novel resource to access new knowledge on ecological change during the last century.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141756053","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}