Admixture, the interbreeding of individuals from differentiated source populations, is now known to be a widespread phenomenon. Genomic studies of natural hybridisation can help to answer many questions on the impacts of admixture on adaptive evolution, reproductive isolation, and speciation. When a large variety of admixture proportions between two source populations exist, both geographic and genomic cline analysis are suitable methods for inferring biased, restricted or excessive gene flow at individual loci into the foreign genomic background, providing evidence for reproductive isolation, selection across an environmental transition, balancing selection, and adaptive introgression. Genomic cline analysis replaces geographic location with genome-wide hybrid index and is therefore useable in circumstances that violate geographic cline assumptions. Here, I introduce gghybrid, an R package for simple and flexible Bayesian estimation of Buerkle's hybrid index and Fitzpatrick's logit-logistic genomic clines using bi-allelic data, suitable for both small and large datasets. gghybrid allows any ploidy and uses Structure input file format. It has separate functions for hybrid index and cline estimation, treating each individual and locus respectively as an independent analysis, making it highly parallelisable. Admixture proportions from other software can alternatively be used in cline analysis, alongside parental allele frequencies. Parameters can be fixed and samples pooled for statistical model comparison with AIC or waic. Here, I describe the functions, pipeline, and statistical properties of gghybrid. Simulations reveal that model comparison with waic is preferred, and use of Bayesian posterior distributions and p values to select candidate non-null loci is problematic and should be avoided.
众所周知,混血(admixture),即来自不同来源种群的个体之间的杂交,是一种普遍现象。对自然杂交的基因组研究有助于回答许多关于混杂对适应性进化、生殖隔离和物种形成的影响的问题。当两个来源种群之间存在大量不同的混杂比例时,地理和基因组系谱分析都是合适的方法,可用于推断单个基因位点进入外来基因组背景的有偏差、受限制或过度的基因流动,为生殖隔离、跨越环境转变的选择、平衡选择和适应性引种提供证据。基因组克隆分析用全基因组杂交指数取代了地理位置,因此可用于违反地理克隆假设的情况。在这里,我介绍一个 R 软件包 gghybrid,它可以使用双等位基因数据,简单灵活地用贝叶斯方法估计 Buerkle 的杂合指数和 Fitzpatrick 的 logit-logistic 基因组克线,适用于小型和大型数据集。它有独立的杂交指数和克隆估计功能,将每个个体和位点分别视为独立的分析,因此具有很高的并行性。其他软件中的混杂比例也可与亲代等位基因频率一起用于克隆分析。参数可以固定,样本可以汇集,以便用 AIC 或 waic 进行统计模型比较。在此,我将介绍 gghybrid 的功能、管道和统计特性。模拟结果表明,使用 waic 进行模型比较更可取,而使用贝叶斯后验分布和 p 值来选择候选非空位点则有问题,应避免使用。
{"title":"Bayesian hybrid index and genomic cline estimation with the R package gghybrid","authors":"Richard Ian Bailey","doi":"10.1111/1755-0998.13910","DOIUrl":"10.1111/1755-0998.13910","url":null,"abstract":"<p>Admixture, the interbreeding of individuals from differentiated source populations, is now known to be a widespread phenomenon. Genomic studies of natural hybridisation can help to answer many questions on the impacts of admixture on adaptive evolution, reproductive isolation, and speciation. When a large variety of admixture proportions between two source populations exist, both geographic and genomic cline analysis are suitable methods for inferring biased, restricted or excessive gene flow at individual loci into the foreign genomic background, providing evidence for reproductive isolation, selection across an environmental transition, balancing selection, and adaptive introgression. Genomic cline analysis replaces geographic location with genome-wide hybrid index and is therefore useable in circumstances that violate geographic cline assumptions. Here, I introduce <i>gghybrid</i>, an R package for simple and flexible Bayesian estimation of Buerkle's hybrid index and Fitzpatrick's logit-logistic genomic clines using bi-allelic data, suitable for both small and large datasets. <i>gghybrid</i> allows any ploidy and uses <i>Structure</i> input file format. It has separate functions for hybrid index and cline estimation, treating each individual and locus respectively as an independent analysis, making it highly parallelisable. Admixture proportions from other software can alternatively be used in cline analysis, alongside parental allele frequencies. Parameters can be fixed and samples pooled for statistical model comparison with AIC or waic. Here, I describe the functions, pipeline, and statistical properties of <i>gghybrid</i>. Simulations reveal that model comparison with waic is preferred, and use of Bayesian posterior distributions and <i>p</i> values to select candidate non-null loci is problematic and should be avoided.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2023-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138561805","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}
Adam A. Pérez, Abigail Tobin, John V. Stechly, Jason A. Ferrante, Margaret E. Hunter
The accessibility to CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein) genetic tools has given rise to applications beyond site-directed genome editing for the detection of DNA and RNA. These tools include precise diagnostic detection of human disease pathogens, such as SARS-CoV-2 and Zika virus. Despite the technology being rapid and cost-effective, the use of CRISPR/Cas tools in the surveillance of the causative agents of wildlife diseases has not been prominent. This study presents the development of a minimally invasive, field-applicable and user-friendly CRISPR/Cas-based biosensor for the detection of Pseudogymnoascus destructans (Pd), the causative fungal agent of white-nose syndrome (WNS), an infectious disease that has killed more than five million bats in North America since its discovery in 2006. The biosensor assay combines a recombinase polymerase amplification (RPA) step followed by CRISPR/Cas12a nuclease cleavage to detect Pd DNA from bat dermal swab and guano samples. The biosensor had similar detection results when compared to quantitative PCR in distinguishing Pd-positive versus negative field samples. Although bat dermal swabs could be analysed with the biosensor without nucleic acid extraction, DNA extraction was needed when screening guano samples to overcome inhibitors. This assay can be applied to help with more rapid delineation of Pd-positive sites in the field to inform management decisions. With further optimization, this technology has broad translation potential to wildlife disease-associated pathogen detection and monitoring applications.
CRISPR/Cas(Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein)基因工具的出现,使 DNA 和 RNA 的检测应用超越了定点基因组编辑。这些工具包括对 SARS-CoV-2 和寨卡病毒等人类疾病病原体的精确诊断检测。尽管该技术快速且具有成本效益,但将 CRISPR/Cas 工具用于监测野生动物疾病致病因子的情况并不突出。自 2006 年发现白鼻综合征(WNS)以来,这种传染病已导致北美 500 多万只蝙蝠死亡。该生物传感器测定结合了重组酶聚合酶扩增(RPA)步骤和 CRISPR/Cas12a 核酸酶裂解,以检测蝙蝠皮肤拭子和鸟粪样本中的 Pd DNA。与定量 PCR 相比,该生物传感器在区分 Pd 阳性和阴性现场样本方面具有相似的检测结果。虽然使用生物传感器分析蝙蝠皮肤拭子无需提取核酸,但在筛选鸟粪样本时需要提取 DNA 以克服抑制剂。这种检测方法可用于帮助更快速地划分钯阳性的实地地点,为管理决策提供信息。经过进一步优化,该技术有望广泛应用于野生动物疾病相关病原体的检测和监测。
{"title":"A minimally invasive, field-applicable CRISPR/Cas biosensor to aid in the detection of Pseudogymnoascus destructans, the causative fungal agent of white-nose syndrome in bats","authors":"Adam A. Pérez, Abigail Tobin, John V. Stechly, Jason A. Ferrante, Margaret E. Hunter","doi":"10.1111/1755-0998.13902","DOIUrl":"10.1111/1755-0998.13902","url":null,"abstract":"<p>The accessibility to CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein) genetic tools has given rise to applications beyond site-directed genome editing for the detection of DNA and RNA. These tools include precise diagnostic detection of human disease pathogens, such as SARS-CoV-2 and Zika virus. Despite the technology being rapid and cost-effective, the use of CRISPR/Cas tools in the surveillance of the causative agents of wildlife diseases has not been prominent. This study presents the development of a minimally invasive, field-applicable and user-friendly CRISPR/Cas-based biosensor for the detection of <i>Pseudogymnoascus destructans</i> (<i>Pd</i>), the causative fungal agent of white-nose syndrome (WNS), an infectious disease that has killed more than five million bats in North America since its discovery in 2006. The biosensor assay combines a recombinase polymerase amplification (RPA) step followed by CRISPR/Cas12a nuclease cleavage to detect <i>Pd</i> DNA from bat dermal swab and guano samples. The biosensor had similar detection results when compared to quantitative PCR in distinguishing <i>Pd-</i>positive versus negative field samples. Although bat dermal swabs could be analysed with the biosensor without nucleic acid extraction, DNA extraction was needed when screening guano samples to overcome inhibitors. This assay can be applied to help with more rapid delineation of <i>Pd-</i>positive sites in the field to inform management decisions. With further optimization, this technology has broad translation potential to wildlife disease-associated pathogen detection and monitoring applications.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2023-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13902","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138561806","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}
My-Hanh Le, Brett Morgan, Mei-Yeh Lu, Victor Moctezuma, Oscar Burgos, Jen-Pan Huang
Beetles, despite their remarkable biodiversity and a long history of research, remain lacking in reference genomes annotated with structural variations in loci of adaptive significance. We sequenced and assembled high-quality chromosome-level genomes of four Hercules beetles which exhibit divergence in male horn size and shape and body colouration. The four Hercules beetle genomes were assembled to 11 pseudo-chromosomes, where the three genomes assembled using Nanopore data (Dynastes grantii, D. hyllus and D. tityus) were mapped to the genome assembled using PacBio + Hi-C data (D. maya). We demonstrated a striking similarity in genome structure among the four species. This conservative genome structure may be attributed to our use of the D. maya assembly as the reference; however, it is worth noting that such a conservative genome structure is a recurring phenomenon among scarab beetles. We further identified homologues of nine and three candidate-gene families that may be associated with the evolution of horn structure and body colouration respectively. Structural variations in Scr and Ebony2 were detected and discussed for their putative impacts on generating morphological diversity in beetles. We also reconstructed the demographic histories of the four Hercules beetles using heterozygosity information from the diploid genomes. We found that the demographic histories of the beetles closely recapitulated historical changes in suitable forest habitats driven by climate shifts.
{"title":"The genomes of Hercules beetles reveal putative adaptive loci and distinct demographic histories in pristine North American forests","authors":"My-Hanh Le, Brett Morgan, Mei-Yeh Lu, Victor Moctezuma, Oscar Burgos, Jen-Pan Huang","doi":"10.1111/1755-0998.13908","DOIUrl":"10.1111/1755-0998.13908","url":null,"abstract":"<p>Beetles, despite their remarkable biodiversity and a long history of research, remain lacking in reference genomes annotated with structural variations in loci of adaptive significance. We sequenced and assembled high-quality chromosome-level genomes of four Hercules beetles which exhibit divergence in male horn size and shape and body colouration. The four Hercules beetle genomes were assembled to 11 pseudo-chromosomes, where the three genomes assembled using Nanopore data (<i>Dynastes grantii</i>, <i>D. hyllus</i> and <i>D. tityus</i>) were mapped to the genome assembled using PacBio + Hi-C data (<i>D. maya</i>). We demonstrated a striking similarity in genome structure among the four species. This conservative genome structure may be attributed to our use of the <i>D. maya</i> assembly as the reference; however, it is worth noting that such a conservative genome structure is a recurring phenomenon among scarab beetles. We further identified homologues of nine and three candidate-gene families that may be associated with the evolution of horn structure and body colouration respectively. Structural variations in <i>Scr</i> and <i>Ebony2</i> were detected and discussed for their putative impacts on generating morphological diversity in beetles. We also reconstructed the demographic histories of the four Hercules beetles using heterozygosity information from the diploid genomes. We found that the demographic histories of the beetles closely recapitulated historical changes in suitable forest habitats driven by climate shifts.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2023-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138567712","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}
Javier Tamames, Diego Jiménez-Lalana, Álvaro Redondo, Sandra Martínez-García, Asunción de los Rios
We present here a complete system for metagenomic analysis that allows performing the sequencing and analysis of a medium-size metagenome in less than one day. This unprecedented development was possible due to the conjunction of state-of-the-art experimental and computational advances: a portable laboratory suitable for DNA extraction and sequencing with nanopore technology; the powerful metagenomic analysis pipeline SqueezeMeta, capable to provide a complete analysis in a few hours and using scarce computational resources; and tools for the automatic inspection of the results via a graphical user interface, that can be coupled to a web server to allow remote visualization of data (SQMtools and SQMxplore). We have tested the feasibility of our approach in the sequencing of the microbiota associated to volcanic rocks in La Palma, Canary Islands. Also, we did a two-day sampling campaign of marine waters in which the results obtained on the first day guided the experimental design of the second day. We demonstrate that it is possible to generate metagenomic information in less than one day, making it feasible to obtain taxonomic and functional profiles fast and efficiently, even in field conditions. This capacity can be used in the further to perform real-time functional and taxonomic monitoring of microbial communities in remote areas.
我们在此介绍一套完整的元基因组分析系统,它可以在一天之内完成中等规模元基因组的测序和分析。这一史无前例的发展之所以成为可能,是因为结合了最先进的实验和计算技术:适合 DNA 提取和纳米孔技术测序的便携式实验室;功能强大的元基因组分析管道 SqueezeMeta,能够在几小时内利用稀缺的计算资源提供完整的分析;以及通过图形用户界面自动检测结果的工具,可与网络服务器连接,实现数据的远程可视化(SQMtools 和 SQMxplore)。我们已经在加那利群岛拉帕尔马火山岩相关微生物群的测序中测试了我们方法的可行性。此外,我们还对海水进行了为期两天的采样活动,第一天获得的结果为第二天的实验设计提供了指导。我们证明,在不到一天的时间里就能生成元基因组信息,即使在野外条件下也能快速有效地获得分类和功能概况。这种能力可进一步用于对偏远地区的微生物群落进行实时功能和分类监测。
{"title":"In situ metagenomics: A platform for rapid sequencing and analysis of metagenomes in less than one day","authors":"Javier Tamames, Diego Jiménez-Lalana, Álvaro Redondo, Sandra Martínez-García, Asunción de los Rios","doi":"10.1111/1755-0998.13909","DOIUrl":"10.1111/1755-0998.13909","url":null,"abstract":"<p>We present here a complete system for metagenomic analysis that allows performing the sequencing and analysis of a medium-size metagenome in less than one day. This unprecedented development was possible due to the conjunction of state-of-the-art experimental and computational advances: a portable laboratory suitable for DNA extraction and sequencing with nanopore technology; the powerful metagenomic analysis pipeline SqueezeMeta, capable to provide a complete analysis in a few hours and using scarce computational resources; and tools for the automatic inspection of the results via a graphical user interface, that can be coupled to a web server to allow remote visualization of data (SQMtools and SQMxplore). We have tested the feasibility of our approach in the sequencing of the microbiota associated to volcanic rocks in La Palma, Canary Islands. Also, we did a two-day sampling campaign of marine waters in which the results obtained on the first day guided the experimental design of the second day. We demonstrate that it is possible to generate metagenomic information in less than one day, making it feasible to obtain taxonomic and functional profiles fast and efficiently, even in field conditions. This capacity can be used in the further to perform real-time functional and taxonomic monitoring of microbial communities in remote areas.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2023-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13909","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138561339","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}
Felipe M. G. Mattos, Niklas Dreyer, Chia-Ling Fong, Yung-Hui Victoria Wen, Dharmesh Jain, Mattia De Vivo, Yu-Sin Huang, John Karichu Mwihaki, Tzi-Yuan Wang, Ming-Jay Ho, Isheng Jason Tsai, John Wang, Benny K. K. Chan, Ryuji J. Machida
PCR-based high-throughput sequencing has permitted comprehensive resolution analyses of zooplankton diversity dynamics. However, significant methodological issues still surround analyses of complex bulk community samples, not least as in prevailing PCR-based approaches. Marine drifting animals—zooplankton—play essential ecological roles in the pelagic ecosystem, transferring energy and elements to higher trophic levels, such as fishes, cetaceans and others. In the present study, we collected 48 size-fractionated zooplankton samples in the vicinity of a coral reef island with environmental gradients. To investigate the spatiotemporal dynamics of zooplankton diversity patterns and the effect of PCR amplification biases across these complex communities, we first took metatranscriptomics approach. Comprehensive computational analyses revealed a clear pattern of higher/lower homogeneity in smaller/larger zooplankton compositions across samples respectively. Our study thus suggests changes in the role of dispersal across the sizes. Next, we applied in silico PCR to the metatranscriptomics datasets, in order to estimate the extent of PCR amplification bias. Irrespective of stringency criteria, we observed clear separations of size fraction sample clusters in both metatranscriptomics and in silico datasets. In contrast, the pattern—smaller-fractioned communities had higher compositional homogeneity than larger ones—was observed in the metatranscriptomics data but not in the in silico datasets. To investigate this discrepancy further, we analysed the mismatches of widely used mitochondrial CO1 primers and identified priming site mismatches likely driving PCR-based biases. Our results suggest the use of metatranscriptomics or, although less ideal, redesigning the CO1 primers is necessary to circumvent these issues.
{"title":"Potential PCR amplification bias in identifying complex ecological patterns: Higher species compositional homogeneity revealed in smaller-size coral reef zooplankton by metatranscriptomics","authors":"Felipe M. G. Mattos, Niklas Dreyer, Chia-Ling Fong, Yung-Hui Victoria Wen, Dharmesh Jain, Mattia De Vivo, Yu-Sin Huang, John Karichu Mwihaki, Tzi-Yuan Wang, Ming-Jay Ho, Isheng Jason Tsai, John Wang, Benny K. K. Chan, Ryuji J. Machida","doi":"10.1111/1755-0998.13911","DOIUrl":"10.1111/1755-0998.13911","url":null,"abstract":"<p>PCR-based high-throughput sequencing has permitted comprehensive resolution analyses of zooplankton diversity dynamics. However, significant methodological issues still surround analyses of complex bulk community samples, not least as in prevailing PCR-based approaches. Marine drifting animals—zooplankton—play essential ecological roles in the pelagic ecosystem, transferring energy and elements to higher trophic levels, such as fishes, cetaceans and others. In the present study, we collected 48 size-fractionated zooplankton samples in the vicinity of a coral reef island with environmental gradients. To investigate the spatiotemporal dynamics of zooplankton diversity patterns and the effect of PCR amplification biases across these complex communities, we first took metatranscriptomics approach. Comprehensive computational analyses revealed a clear pattern of higher/lower homogeneity in smaller/larger zooplankton compositions across samples respectively. Our study thus suggests changes in the role of dispersal across the sizes. Next, we applied in silico PCR to the metatranscriptomics datasets, in order to estimate the extent of PCR amplification bias. Irrespective of stringency criteria, we observed clear separations of size fraction sample clusters in both metatranscriptomics and in silico datasets. In contrast, the pattern—smaller-fractioned communities had higher compositional homogeneity than larger ones—was observed in the metatranscriptomics data but not in the in silico datasets. To investigate this discrepancy further, we analysed the mismatches of widely used mitochondrial <i>CO1</i> primers and identified priming site mismatches likely driving PCR-based biases. Our results suggest the use of metatranscriptomics or, although less ideal, redesigning the <i>CO1</i> primers is necessary to circumvent these issues.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2023-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13911","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138561322","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}
Genfu Yagi, Huiyuan Qi, Kana Arai, Yuki F. Kita, Kazunobu Kogi, Tadamichi Morisaka, Motoi Yoshioka, Miho Inoue-Murayama
Age is necessary information for the study of life history of wild animals. A general method to estimate the age of odontocetes is counting dental growth layer groups (GLGs). However, this method is highly invasive as it requires the capture and handling of individuals to collect their teeth. Recently, the development of DNA-based age estimation methods has been actively studied as an alternative to such invasive methods, of which many have relied on used biopsy samples. However, if DNA-based age estimation can be developed from faecal samples, age estimation can be performed entirely non-invasively. We developed an age estimation model using the methylation rate of two gene regions, GRIA2 and CDKN2A, measured through methylation-sensitive high-resolution melting (MS-HRM) from faecal samples of wild Indo-Pacific bottlenose dolphins (Tursiops aduncus). The age of individuals was known through conducting longitudinal individual identification surveys underwater. Methylation rates were quantified from 36 samples collected from 30 individuals. Both gene regions showed a significant correlation between age and methylation rate. The age estimation model was constructed based on the methylation rates of both genes which achieved sufficient accuracy (after LOOCV: MAE = 5.08, R2 = 0.33) for the ecological studies of the Indo-Pacific bottlenose dolphins, with a lifespan of 40–50 years. This is the first study to report the use of non-invasive faecal samples to estimate the age of marine mammals.
年龄是研究野生动物生活史的必要资料。估计牙胚年龄的一般方法是计算牙生长层组(GLGs)。然而,这种方法是高度侵入性的,因为它需要捕获和处理个体来收集他们的牙齿。最近,基于dna的年龄估计方法的发展已经被积极研究,作为这种侵入性方法的替代方法,其中许多方法依赖于使用过的活检样本。然而,如果基于dna的年龄估计可以从粪便样本中发展出来,年龄估计可以完全无创地进行。我们通过甲基化敏感高分辨率熔融(MS-HRM)从野生印度太平洋宽吻海豚(Tursiops aduncus)的粪便样本中测量两个基因区域GRIA2和CDKN2A的甲基化率,建立了一个年龄估计模型。个体的年龄是通过在水下进行纵向个体识别调查来确定的。从30个个体中收集36个样本,对甲基化率进行了量化。这两个基因区域在年龄和甲基化率之间显示出显著的相关性。基于两个基因的甲基化率构建的年龄估计模型对于寿命为40-50年的印度太平洋宽吻海豚的生态学研究具有足够的准确性(经LOOCV: MAE = 5.08, R2 = 0.33)。这是第一个报告使用非侵入性粪便样本来估计海洋哺乳动物年龄的研究。
{"title":"Non-invasive age estimation based on faecal DNA using methylation-sensitive high-resolution melting for Indo-Pacific bottlenose dolphins","authors":"Genfu Yagi, Huiyuan Qi, Kana Arai, Yuki F. Kita, Kazunobu Kogi, Tadamichi Morisaka, Motoi Yoshioka, Miho Inoue-Murayama","doi":"10.1111/1755-0998.13906","DOIUrl":"10.1111/1755-0998.13906","url":null,"abstract":"<p>Age is necessary information for the study of life history of wild animals. A general method to estimate the age of odontocetes is counting dental growth layer groups (GLGs). However, this method is highly invasive as it requires the capture and handling of individuals to collect their teeth. Recently, the development of DNA-based age estimation methods has been actively studied as an alternative to such invasive methods, of which many have relied on used biopsy samples. However, if DNA-based age estimation can be developed from faecal samples, age estimation can be performed entirely non-invasively. We developed an age estimation model using the methylation rate of two gene regions, <i>GRIA2</i> and <i>CDKN2A</i>, measured through methylation-sensitive high-resolution melting (MS-HRM) from faecal samples of wild Indo-Pacific bottlenose dolphins (<i>Tursiops aduncus</i>). The age of individuals was known through conducting longitudinal individual identification surveys underwater. Methylation rates were quantified from 36 samples collected from 30 individuals. Both gene regions showed a significant correlation between age and methylation rate. The age estimation model was constructed based on the methylation rates of both genes which achieved sufficient accuracy (after LOOCV: MAE = 5.08, <i>R</i><sup>2</sup> = 0.33) for the ecological studies of the Indo-Pacific bottlenose dolphins, with a lifespan of 40–50 years. This is the first study to report the use of non-invasive faecal samples to estimate the age of marine mammals.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2023-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13906","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138469546","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}
Claudio S Quilodrán, Mathias Currat, Juan I Montoya-Burgos
Testing the association between objects is central in ecology, evolution, and quantitative sciences in general. Two types of variables can describe the relationships between objects: point variables (measured on individual objects), and distance variables (measured between pairs of objects). The Mantel test and derived methods have been extensively used for distance variables. Yet, these methods have been criticized due to low statistical power and inflated type I error when spatial autocorrelation is present. Here, we assessed the statistical power between different types of tested variables and the type I error rate over a wider range of autocorrelation intensities than previously assessed, both on univariate and multivariate data. We also illustrated the performance of distance matrix statistics through computational simulations of genetic diversity. We show that the Mantel test and derived methods are not affected by inflated type I error when spatial autocorrelation affects only one variable when investigating correlations, or when either the response or the explanatory variable(s) is affected by spatial autocorrelation while investigating causal relationships. As previously noted, with autocorrelation affecting more variables, inflated type I error could be reduced by modifying the significance threshold. Additionally, the Mantel test has no problem of statistical power when the hypothesis is formulated in terms of distance variables. We highlight that transformation of variable types should be avoided because of the potential information loss and modification of the tested hypothesis. We propose a set of guidelines to help choose the appropriate method according to the type of variables and defined hypothesis.
{"title":"Benchmarking the Mantel test and derived methods for testing association between distance matrices.","authors":"Claudio S Quilodrán, Mathias Currat, Juan I Montoya-Burgos","doi":"10.1111/1755-0998.13898","DOIUrl":"https://doi.org/10.1111/1755-0998.13898","url":null,"abstract":"<p><p>Testing the association between objects is central in ecology, evolution, and quantitative sciences in general. Two types of variables can describe the relationships between objects: point variables (measured on individual objects), and distance variables (measured between pairs of objects). The Mantel test and derived methods have been extensively used for distance variables. Yet, these methods have been criticized due to low statistical power and inflated type I error when spatial autocorrelation is present. Here, we assessed the statistical power between different types of tested variables and the type I error rate over a wider range of autocorrelation intensities than previously assessed, both on univariate and multivariate data. We also illustrated the performance of distance matrix statistics through computational simulations of genetic diversity. We show that the Mantel test and derived methods are not affected by inflated type I error when spatial autocorrelation affects only one variable when investigating correlations, or when either the response or the explanatory variable(s) is affected by spatial autocorrelation while investigating causal relationships. As previously noted, with autocorrelation affecting more variables, inflated type I error could be reduced by modifying the significance threshold. Additionally, the Mantel test has no problem of statistical power when the hypothesis is formulated in terms of distance variables. We highlight that transformation of variable types should be avoided because of the potential information loss and modification of the tested hypothesis. We propose a set of guidelines to help choose the appropriate method according to the type of variables and defined hypothesis.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2023-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138469545","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}
Mesozooplankton is a very diverse group of small animals ranging in size from 0.2 to 20 mm not able to swim against ocean currents. It is a key component of pelagic ecosystems through its roles in the trophic networks and the biological carbon pump. Traditionally studied through microscopes, recent methods have been however developed to rapidly acquire large amounts of data (morphological, molecular) at the individual scale, making it possible to study mesozooplankton using a trait-based approach. Here, combining quantitative imaging with metabarcoding time-series data obtained in the Sargasso Sea at the Bermuda Atlantic Time-series Study (BATS) site, we showed that organisms' transparency might be an important trait to also consider regarding mesozooplankton impact on carbon export, contrary to the common assumption that just size is the master trait directing most mesozooplankton-linked processes. Three distinct communities were defined based on taxonomic composition, and succeeded one another throughout the study period, with changing levels of transparency among the community. A co-occurrences' network was built from metabarcoding data revealing six groups of taxa. These were related to changes in the functioning of the ecosystem and/or in the community's morphology. The importance of Diel Vertical Migration at BATS was confirmed by the existence of a group made of taxa known to be strong migrators. Finally, we assessed if metabarcoding can provide a quantitative approach to biomass and/or abundance of certain taxa. Knowing more about mesozooplankton diversity and its impact on ecosystem functioning would allow to better represent them in biogeochemical models.
{"title":"Morphological and taxonomic diversity of mesozooplankton is an important driver of carbon export fluxes in the ocean","authors":"Margaux Perhirin, Hannah Gossner, Jessica Godfrey, Rodney Johnson, Leocadio Blanco-Bercial, Sakina-Dorothée Ayata","doi":"10.1111/1755-0998.13907","DOIUrl":"10.1111/1755-0998.13907","url":null,"abstract":"<p>Mesozooplankton is a very diverse group of small animals ranging in size from 0.2 to 20 mm not able to swim against ocean currents. It is a key component of pelagic ecosystems through its roles in the trophic networks and the biological carbon pump. Traditionally studied through microscopes, recent methods have been however developed to rapidly acquire large amounts of data (morphological, molecular) at the individual scale, making it possible to study mesozooplankton using a trait-based approach. Here, combining quantitative imaging with metabarcoding time-series data obtained in the Sargasso Sea at the Bermuda Atlantic Time-series Study (BATS) site, we showed that organisms' transparency might be an important trait to also consider regarding mesozooplankton impact on carbon export, contrary to the common assumption that just size is the master trait directing most mesozooplankton-linked processes. Three distinct communities were defined based on taxonomic composition, and succeeded one another throughout the study period, with changing levels of transparency among the community. A co-occurrences' network was built from metabarcoding data revealing six groups of taxa. These were related to changes in the functioning of the ecosystem and/or in the community's morphology. The importance of Diel Vertical Migration at BATS was confirmed by the existence of a group made of taxa known to be strong migrators. Finally, we assessed if metabarcoding can provide a quantitative approach to biomass and/or abundance of certain taxa. Knowing more about mesozooplankton diversity and its impact on ecosystem functioning would allow to better represent them in biogeochemical models.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2023-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13907","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138456706","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}
Sven Weber, Manuel Stothut, Lisa Mahla, Alanah Kripp, Lena Hirschler, Nina Lenz, Anneke Junker, Sven Künzel, Henrik Krehenwinkel
Our limited knowledge about the ecological drivers of global arthropod decline highlights the urgent need for more effective biodiversity monitoring approaches. Monitoring of arthropods is commonly performed using passive trapping devices, which reliably recover diverse communities, but provide little ecological information on the sampled taxa. Especially the manifold interactions of arthropods with plants are barely understood. A promising strategy to overcome this shortfall is environmental DNA (eDNA) metabarcoding from plant material on which arthropods leave DNA traces through direct or indirect interactions. However, the accuracy of this approach has not been sufficiently tested. In four experiments, we exhaustively test the comparative performance of plant-derived eDNA from surface washes of plants and homogenized plant material against traditional monitoring approaches. We show that the recovered communities of plant-derived eDNA and traditional approaches only partly overlap, with eDNA recovering various additional taxa. This suggests eDNA as a useful complementary tool to traditional monitoring. Despite the differences in recovered taxa, estimates of community α- and β-diversity between both approaches are well correlated, highlighting the utility of eDNA as a broad scale tool for community monitoring. Last, eDNA outperforms traditional approaches in the recovery of plant-specific arthropod communities. Unlike traditional monitoring, eDNA revealed fine-scale community differentiation between individual plants and even within plant compartments. Especially specialized herbivores are better recovered with eDNA. Our results highlight the value of plant-derived eDNA analysis for large-scale biodiversity assessments that include information about community-level interactions.
{"title":"Plant-derived environmental DNA complements diversity estimates from traditional arthropod monitoring methods but outperforms them detecting plant–arthropod interactions","authors":"Sven Weber, Manuel Stothut, Lisa Mahla, Alanah Kripp, Lena Hirschler, Nina Lenz, Anneke Junker, Sven Künzel, Henrik Krehenwinkel","doi":"10.1111/1755-0998.13900","DOIUrl":"10.1111/1755-0998.13900","url":null,"abstract":"<p>Our limited knowledge about the ecological drivers of global arthropod decline highlights the urgent need for more effective biodiversity monitoring approaches. Monitoring of arthropods is commonly performed using passive trapping devices, which reliably recover diverse communities, but provide little ecological information on the sampled taxa. Especially the manifold interactions of arthropods with plants are barely understood. A promising strategy to overcome this shortfall is environmental DNA (eDNA) metabarcoding from plant material on which arthropods leave DNA traces through direct or indirect interactions. However, the accuracy of this approach has not been sufficiently tested. In four experiments, we exhaustively test the comparative performance of plant-derived eDNA from surface washes of plants and homogenized plant material against traditional monitoring approaches. We show that the recovered communities of plant-derived eDNA and traditional approaches only partly overlap, with eDNA recovering various additional taxa. This suggests eDNA as a useful complementary tool to traditional monitoring. Despite the differences in recovered taxa, estimates of community α- and β-diversity between both approaches are well correlated, highlighting the utility of eDNA as a broad scale tool for community monitoring. Last, eDNA outperforms traditional approaches in the recovery of plant-specific arthropod communities. Unlike traditional monitoring, eDNA revealed fine-scale community differentiation between individual plants and even within plant compartments. Especially specialized herbivores are better recovered with eDNA. Our results highlight the value of plant-derived eDNA analysis for large-scale biodiversity assessments that include information about community-level interactions.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2023-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13900","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138443311","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}