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RETRACTION: Age Prediction of Green Turtles With an Epigenetic Clock 用表观遗传时钟预测绿海龟的年龄。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-07-17 DOI: 10.1111/1755-0998.70016
{"title":"RETRACTION: Age Prediction of Green Turtles With an Epigenetic Clock","authors":"","doi":"10.1111/1755-0998.70016","DOIUrl":"10.1111/1755-0998.70016","url":null,"abstract":"<p><b>RETRACTION</b>: B. Mayne, W. Mustin, V. Baboolal, F. Casella, K. Ballorain, M. Barret, M. A. Vanderklift, A. D. Tucker, D. Korbie, S. Jarman and O. Berry, “Age Prediction of Green Turtles With an Epigenetic Clock,” <i>Molecular Ecology Resources</i> 22, no. 6 (2022): 2275-2284, https://doi.org/10.1111/1755-0998.13621.</p><p>The above article, published online on 15 April 2022 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the journal Editors-in-Chief, Shawn Narum and Ben Sibbett; and John Wiley &amp; Sons Ltd. The retraction has been agreed upon following an alert from one of the authors, S. Jarman, identifying that the results shown in Figure 2 are inaccurate and do not represent a real relationship between age and DNA methylation. Consequently, the editors consider the results and conclusions invalid. The authors, S. Jarman, B. Mayne, M. A. Vanderklift, O. Berry, K. Ballorain and M. Barret agree with the decision to retract this article.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 7","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70016","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144648082","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}
引用次数: 0
Historical Collections of Tropical Marine Mammals Are an Excellent Resource for Ancient DNA 热带海洋哺乳动物的历史收藏是古代DNA的优秀资源。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-07-17 DOI: 10.1111/1755-0998.70015
Lydia Hildebrand Furness, Richard Sabin, Marianne Strand Torvanger, Oliver Kersten, James H. Barrett, Bastiaan Star
{"title":"Historical Collections of Tropical Marine Mammals Are an Excellent Resource for Ancient DNA","authors":"Lydia Hildebrand Furness,&nbsp;Richard Sabin,&nbsp;Marianne Strand Torvanger,&nbsp;Oliver Kersten,&nbsp;James H. Barrett,&nbsp;Bastiaan Star","doi":"10.1111/1755-0998.70015","DOIUrl":"10.1111/1755-0998.70015","url":null,"abstract":"<div>\u0000 \u0000 <p>The ability to predict ancient DNA sequencing success in natural history collections is critical to reducing the amount of destructive sampling of a finite resource. So far, studies investigating such success have predominantly focused on taxa with ranges restricted to temperate or cold environments at northern latitudes, which likely aids DNA preservation. Here, we report remarkably high aDNA sequencing success in <i>Sirenia</i>, herbivorous marine mammals of which the distribution is currently constrained to the global tropics. We investigate 91 samples from 85 specimens comprising all four contemporary species and one extinct species, comparing different sample types (cranial/post-cranial bone, skin and cartilage), species, collections, and material age. We obtained remarkably high (e.g., &gt; 20%) endogenous DNA preservation for the majority (e.g., ~57% percent) of samples. Sequencing success was linked to sample type, with cranial bones (including petrous and tympanic bones) yielding significantly higher endogenous DNA. Additionally, we obtained variable, but potentially superior DNA results for preserved cartilage and hide samples that can be associated with historical bone. Although such tissue is not always present, this type of material is easy to sample, with very limited destructive impacts on the associated bones, and we therefore highlight its untapped potential as a source of DNA. Overall, our results show the high success of ancient DNA retrieval from historical collections of species with a tropical distribution, expanding on the types of specimens that are available for temporal genomic analyses.</p>\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 7","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144648080","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
Multi-Tool Marine Metabarcoding Bioassessment for Baselining and Monitoring Species and Communities in Kelp Habitats 多工具海洋元条形码生物评价在海带生境的基线和监测物种和群落。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-07-17 DOI: 10.1111/1755-0998.70010
Giulia Maiello, Marilla R. Lippert, Erika F. Neave, Erik A. Hanson, Stephen R. Palumbi, Stefano Mariani
{"title":"Multi-Tool Marine Metabarcoding Bioassessment for Baselining and Monitoring Species and Communities in Kelp Habitats","authors":"Giulia Maiello,&nbsp;Marilla R. Lippert,&nbsp;Erika F. Neave,&nbsp;Erik A. Hanson,&nbsp;Stephen R. Palumbi,&nbsp;Stefano Mariani","doi":"10.1111/1755-0998.70010","DOIUrl":"10.1111/1755-0998.70010","url":null,"abstract":"<p>The astonishing biological diversity found in Californian kelp forests requires efficient and robust monitoring tools to better understand ecological trends and mitigate against loss or disruption of ecosystem services due to human pressure and climate changes. With environmental DNA (eDNA) metabarcoding becoming a popular biodiversity assessment approach, we set out to evaluate a combination of powerful, rapid and sustainable eDNA solutions for characterising marine community composition in kelp-dominated habitats along the central California coast, in the newly proposed Chumash Heritage National Marine Sanctuary. We employed and compared the efficiency of several eDNA collection approaches, including ‘traditional’ surface water filtration, the collection of organisms encrusting cobble rocks and various deployments of an artificial passive sampler, the metaprobe (i.e., attached to divers, dangled from a boat and cast from the shore using a fishing rod). By combining the information from fish specific (Tele02 12S) and universal metazoan (COI) markers, we ‘captured’ 501 unique marine taxa, belonging to at least 36 phyla, over 400 of which were identified to genus/species level, and including 52 vertebrate species typical of Californian kelp forest ecosystems. Despite differences in the type of biodiversity returned by the tested sampling methods, the overall community structure of the surveyed area was highly spatially structured and strongly influenced by the biogeographic break around Point Conception (<i>Humqaq</i>). We discuss the benefits of integrating eDNA metabarcoding in existing monitoring programs and devising a reproducible approach to monitor faunal changes in kelp forest habitats and beyond.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 7","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70010","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144648081","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}
引用次数: 0
Conserved Sequence Identification Within Large Genomic Datasets Using ‘Unikseq2’: Application in Environmental DNA Assay Development 使用“Unikseq2”的大型基因组数据集中的保守序列鉴定:在环境DNA分析开发中的应用。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-07-11 DOI: 10.1111/1755-0998.70014
Mark Louie D. Lopez, René L. Warren, Michael J. Allison, Lauren Coombe, Jacob J. Imbery, Inanc Birol, Caren C. Helbing
{"title":"Conserved Sequence Identification Within Large Genomic Datasets Using ‘Unikseq2’: Application in Environmental DNA Assay Development","authors":"Mark Louie D. Lopez,&nbsp;René L. Warren,&nbsp;Michael J. Allison,&nbsp;Lauren Coombe,&nbsp;Jacob J. Imbery,&nbsp;Inanc Birol,&nbsp;Caren C. Helbing","doi":"10.1111/1755-0998.70014","DOIUrl":"10.1111/1755-0998.70014","url":null,"abstract":"<p>Identification of conserved genomic sequences and their utilisation as anchor points for clade detection and/or characterisation is a mainstay in ecological studies. For environmental DNA (eDNA) assays, effective processing of large genomic datasets is crucial for reliable species detection in biodiversity monitoring. While considerable focus has been on developing robust species-targeted assays, eDNA assays with broader taxonomic coverage (e.g., detecting any species within a taxonomic group such as fish), can significantly streamline environmental monitoring, especially when detecting individual species' DNA proves challenging. Designing such assays requires identifying conserved regions representing the target taxonomic group, a chiefly manual task that is often labor-intensive and error-prone, particularly when working with large sequence datasets. To address these challenges, we present <i>unikseq2</i>, an enhanced, alignment-free, k-mer-based tool for identifying unique and conserved sequences. It introduces a new functionality to identify sequence conservation among target species, enabling more informed marker selection for applications such as universal primer design. This automates sequence selection in large-scale mitochondrial genome datasets eliminating the need for manual inspection of computationally costly multiple sequence alignments. Herein, we demonstrate <i>unikseq2</i>'s capabilities by developing and validating eDNA assays for various taxa, including Osteichthyes (bony fishes), the Salmonidae family (salmon and trout), <i>Myotis</i> bats and <i>Cervus</i> deer. <i>Unikseq2</i>-based eDNA assays allow for accurate detection across multiple taxonomic levels, from genus to class, enhancing the flexibility, scalability and reliability of eDNA tools in environmental monitoring. By leveraging genomic data from public repositories, <i>unikseq2</i> supports efficient, reproducible assay design, making it an invaluable tool for a wide range of ecological and biodiversity research applications.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 7","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70014","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144606956","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}
引用次数: 0
Genomes of Two Monophagous Weevils and Their Host Plant Provide Insights Into Evolution of Plant Defence and Insect Counter-Defence 两种单食象鼻虫及其寄主植物的基因组为植物防御和昆虫反防御的进化提供了新的见解。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-07-11 DOI: 10.1111/1755-0998.70009
Wei Song, Li-Jun Cao, Jin-Cui Chen, Wen-Juan Guo, Hui-Juan Li, Xue-Wen Sun, Ary Anthony Hoffmann, Jun-Bao Wen, Shu-Jun Wei
{"title":"Genomes of Two Monophagous Weevils and Their Host Plant Provide Insights Into Evolution of Plant Defence and Insect Counter-Defence","authors":"Wei Song,&nbsp;Li-Jun Cao,&nbsp;Jin-Cui Chen,&nbsp;Wen-Juan Guo,&nbsp;Hui-Juan Li,&nbsp;Xue-Wen Sun,&nbsp;Ary Anthony Hoffmann,&nbsp;Jun-Bao Wen,&nbsp;Shu-Jun Wei","doi":"10.1111/1755-0998.70009","DOIUrl":"10.1111/1755-0998.70009","url":null,"abstract":"<div>\u0000 \u0000 <p>Plant secondary metabolites play important roles in defence against herbivorous insects. However, many insects can overcome plant defences even when they produce a rich toxin load, and an arms race between plants evolving new toxins and insects evolving to counter them is expected. Here, we deciphered genomic features linked to a potential race between the tree of heaven and two monophagous weevils that only feed on this tree species, with the tree of heaven producing a rich set of secondary metabolites involving about 745 compounds. We first assembled chromosome-level genomes for the tree of heaven and the two weevils. Comparative genomics showed an expansion of genes related to synthesising secondary metabolites in the tree, while in the weevils, genes related to detoxification and chemosensing expanded. The expansion of core genes involved in quassinoid biosynthesis in the tree was linked to tandem duplication and whole genome duplication, while the expansion of detoxifying <i>GST</i> and chemosensing <i>SNMP</i> genes in the two weevils was linked to tandem duplication and novel genes, respectively. The results indicate that plants and insect herbivores both reshaped their genomes through gene expansion, while the host tree also underwent whole genome duplication and the two weevils evolved novel genes. These changes likely reflect an arms race of defence and counter-defence, providing an understanding of genome evolution driven by trophic interactions.</p>\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 7","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144606957","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
‘Highly-Informative’ Genetic Markers Can Bias Conclusions: Examples and General Solutions “高信息量”的遗传标记可能导致结论偏差:示例和一般解决方案。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-07-11 DOI: 10.1111/1755-0998.70011
Andy Lee, William Hemstrom, Natalie Molea, Gordon Luikart, Mark R. Christie
{"title":"‘Highly-Informative’ Genetic Markers Can Bias Conclusions: Examples and General Solutions","authors":"Andy Lee,&nbsp;William Hemstrom,&nbsp;Natalie Molea,&nbsp;Gordon Luikart,&nbsp;Mark R. Christie","doi":"10.1111/1755-0998.70011","DOIUrl":"10.1111/1755-0998.70011","url":null,"abstract":"<p>High-grading bias is the overestimation power in a subset of loci caused by model overfitting. Using both empirical and simulated datasets, we show that high-grading bias can cause severe overestimation of population structure, and thus mislead investigators, whenever highly informative or high-<i>F</i><sub><i>ST</i></sub> markers are chosen (i.e., ascertained) and used for subsequent assessments, a common practice in population genetic studies. This problem can occur in panmictic populations with no local adaptation<i>.</i> Biased results from choosing high-<i>F</i><sub><i>ST</i></sub> markers may have severe downstream implications for management and conservation, such as erroneous conservation unit delineation, which could squander limited conservation resources to protect incorrectly defined ‘populations’. Furthermore, we caution that high-grading is not limited to <i>F</i><sub><i>ST</i></sub> approaches; high-grading bias is a concern whenever a small subset of markers are first chosen to explain differences among groups based on their degree of difference and are subsequently reused to estimate the degree of difference among those groups. For example, selecting high <i>F</i><sub><i>ST</i></sub> loci for use in a GT-seq panel or using differentially expressed genes to plot sample membership in multivariate space can both result in spurious structure when none exists. We illustrate that using statistically based outlier tests in place of arbitrary <i>F</i><sub><i>ST</i></sub> cut-offs can reduce bias. Alternatively, permutation tests or cross-evaluation can be used to detect high-grading bias. We provide an R package, PCAssess, to help researchers detect and prevent high-grading bias in genetic datasets by automating permutation tests and principal component analyses (https://github.com/hemstrow/PCAssess).</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 7","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70011","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144606958","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}
引用次数: 0
Enrichment of Helminth Mitochondrial Genomes From Faecal Samples Using Hybridisation Capture. 利用杂交捕获技术富集粪便样本中的蠕虫线粒体基因组。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-07-09 DOI: 10.1111/1755-0998.70005
Marina Papaiakovou, Andrea Waeschenbach, Roy M Anderson, Piet Cools, Zeleke Mekonnen, D Timothy J Littlewood, Cinzia Cantacessi, Stephen R Doyle
{"title":"Enrichment of Helminth Mitochondrial Genomes From Faecal Samples Using Hybridisation Capture.","authors":"Marina Papaiakovou, Andrea Waeschenbach, Roy M Anderson, Piet Cools, Zeleke Mekonnen, D Timothy J Littlewood, Cinzia Cantacessi, Stephen R Doyle","doi":"10.1111/1755-0998.70005","DOIUrl":"https://doi.org/10.1111/1755-0998.70005","url":null,"abstract":"<p><p>New approaches are urgently needed to enrich rare or low-abundant DNA in complex samples. Soil-transmitted helminths (STHs) inhabit heterogeneous environments, including the gastrointestinal tract of their host as adults and are excreted as eggs and larvae in faeces, complicating our understanding of their biology and the use of genetic tools for species monitoring and population tracking. We have developed a hybridisation capture approach to enrich mitochondrial genome sequences of two STH species, the roundworm Ascaris lumbricoides and whipworm Trichuris trichiura, from extracted DNA from faecal material and worm specimens. Employing ~1000 targeted probes, we achieved > 6000 and > 12,000 fold enrichment for A. lumbricoides and T. trichiura, respectively, relative to direct whole genome shotgun (WGS) sequencing. Sequencing coverage was highly concordant with probe targets and correlated with the number of eggs per gram (EPG) of parasites present, from which DNA from as few as 336 EPG for Ascaris and 48 EPG for Trichuris were efficiently captured and sufficient to provide effective mitochondrial genome data. Finally, allele frequencies were highly concordant between WGS and hybridisation capture, suggesting little genetic information is lost with additional sample processing required for enrichment. Our hybridisation capture design and approach enable sensitive and flexible STH mitochondrial genome sampling from faecal DNA extracts and pave the way for broader hybridisation capture-based genome-wide applications and molecular epidemiology studies of STHs.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70005"},"PeriodicalIF":5.5,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144590044","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
Pan-Genome of Jasminum sambac Reveals the Genetic Diversity of Different Petal Morphology and Aroma-Related Genes 茉莉泛基因组揭示了不同花瓣形态和香气相关基因的遗传多样性。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-07-09 DOI: 10.1111/1755-0998.70013
Wenmin Fan, Zhenyang Liao, Mengya Gu, Yuhang Zhang, Wenlong Lei, Yingao Zhang, Huike Li, Jiawei Yan, Yezi Xiao, Hongzheng Lin, Shan Jin, Youben Yu, Jingping Fang, Naixing Ye, Pengjie Wang
{"title":"Pan-Genome of Jasminum sambac Reveals the Genetic Diversity of Different Petal Morphology and Aroma-Related Genes","authors":"Wenmin Fan,&nbsp;Zhenyang Liao,&nbsp;Mengya Gu,&nbsp;Yuhang Zhang,&nbsp;Wenlong Lei,&nbsp;Yingao Zhang,&nbsp;Huike Li,&nbsp;Jiawei Yan,&nbsp;Yezi Xiao,&nbsp;Hongzheng Lin,&nbsp;Shan Jin,&nbsp;Youben Yu,&nbsp;Jingping Fang,&nbsp;Naixing Ye,&nbsp;Pengjie Wang","doi":"10.1111/1755-0998.70013","DOIUrl":"10.1111/1755-0998.70013","url":null,"abstract":"<div>\u0000 \u0000 <p>Jasmine (<i>Jasminum sambac</i>) is globally renowned for its distinct fragrance and ornamental appeal, existing primarily in three floral morphologies: single-petal, double-petal and multi-petal. De novo sequencing and chromosome-level genome assembly were performed on two distinct jasmine varieties: ‘Yuanye’ double-petal and ‘Bijian’ multi-petal jasmines. These assemblies, along with three previously published genomes, were integrated to construct a pan-genome framework that comprehensively encompasses both the core and variable genomic components of jasmine. A substantial number of structural variations (SVs) and single nucleotide polymorphisms (SNPs) had been identified, of which 89.5% were insertions/deletions (size ≥ 50 bp), whereas gene families also exhibited significant contractions and expansions, revealing the high complexity and dynamics of the jasmine genomes. Comparative genomic approaches further revealed multiple transcription factor families associated with aromatic biosynthesis, floral organogenesis and environmental adaptability. Key genes involved in the formation of jasmine scent, with a particular focus on the variation in copy number and expression levels of critical enzyme genes responsible for the production of four major volatile terpenoids and benzyl acetate, thereby elucidating the genetic basis of jasmine aroma diversity. Additionally, within the MADS-box gene family, the PI and AP3 subfamilies are hypothesized to play crucial roles in the development of floral organs. Through the integration of these comprehensive data, a pan-genome website for jasmine was developed to facilitate data download and visualise genomic variations via a genome browser (https://www.pan-jasmine.cn/). In summary, this work provides valuable genomic resources for the genetic enhancement and marker-assisted breeding of jasmine.</p>\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 7","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144590045","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
Benchmarking Imputed Low Coverage Genomes in a Human Population Genetics Context. 在人类群体遗传学背景下对标估算低覆盖率基因组。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-07-08 DOI: 10.1111/1755-0998.70007
Gludhug A Purnomo, João C Teixeira, Herawati Sudoyo, Bastien Llamas, Raymond Tobler
{"title":"Benchmarking Imputed Low Coverage Genomes in a Human Population Genetics Context.","authors":"Gludhug A Purnomo, João C Teixeira, Herawati Sudoyo, Bastien Llamas, Raymond Tobler","doi":"10.1111/1755-0998.70007","DOIUrl":"https://doi.org/10.1111/1755-0998.70007","url":null,"abstract":"<p><p>Ongoing advances in population genomic methodologies have recently enabled the study of millions of loci across hundreds of genomes at a relatively low cost, by leveraging a combination of low-coverage shotgun sequencing and innovative genotype imputation methods. This approach has the potential to provide abundant genotype information at low costs comparable to another widely used cost-effective genotyping approach-that is, SNP panels-while avoiding potential issues related to loci being ascertained in distantly related populations. Nonetheless, the wide adoption of imputation methods in humans and other species is currently constrained by the lack of publicly available reference panels that capture diversity representative of the target genomes-though the recent development of 'joint' imputation approaches, which allow genetic information from the target population to be used in genotype calling, may potentially mitigate this shortcoming. Here, we assess the performance of multiple genotyping approaches on eight low coverage genomes (range ~3× to ~5×) sourced from different Indonesian populations-including a joint imputation approach that leverages 248 additional low coverage genomes (mean ~2.4×) from related populations. The inclusion of these related genomes in the joint imputation process resulted in more accurate genotype calls and produced population genetic inferences with similar accuracy but improved precision compared to pseudohaploid calls-even though the reference panel was only weakly representative of the target genomes. These results highlight the enormous potential of joint imputation to enable economical population genetic research for taxa that are currently poorly represented in publicly available reference panels.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70007"},"PeriodicalIF":5.5,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144582696","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
RDAforest: Identifying Environmental Drivers of Polygenic Adaptation. 森林:确定多基因适应的环境驱动因素。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-07-04 DOI: 10.1111/1755-0998.70002
Mikhail V Matz, Kristina L Black
{"title":"RDAforest: Identifying Environmental Drivers of Polygenic Adaptation.","authors":"Mikhail V Matz, Kristina L Black","doi":"10.1111/1755-0998.70002","DOIUrl":"https://doi.org/10.1111/1755-0998.70002","url":null,"abstract":"<p><p>Identifying environmental gradients driving genetic adaptation is one of the major goals of ecological genomics. We present RDAforest, a methodology that leverages the predominantly polygenic nature of adaptation and harnesses the versatility of random forest regression to solve this problem. Instead of computing individual SNP-environment associations, RDAforest seeks to explain the overall genetic covariance structure based on multiple environmental predictors. By relying on random forest instead of linear regression, this method can detect non-linear and non-monotonous dependencies as well as all possible interactions between predictors. It also incorporates a novel procedure to select the best predictor out of several correlated ones, and uses jackknifing to model uncertainty of genetic structure determination. Lastly, our methodology incorporates delineation and plotting of \"adaptive neighbourhoods\"-areas on the landscape that are predicted to harbour differentially adapted individuals. Such maps can be used as a guide for planning conservation and ecological restoration efforts. We demonstrate the use of RDAforest in two simulated scenarios and one real dataset (North American grey wolves).</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70002"},"PeriodicalIF":5.5,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144566863","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
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