Molecular Ecology Resources最新文献

{"title":"Too Far From Relatives? Impact of the Genetic Distance on the Success of Exon Capture in Phylogenomics.","authors":"Lemarcis Thomas, Blin Amandine, Cariou Marie, Derzelle Alessandro, Farhat Sarah, Fedosov Alexander, Zaharias Paul, Zuccon Dario, Puillandre Nicolas","doi":"10.1111/1755-0998.14064","DOIUrl":"https://doi.org/10.1111/1755-0998.14064","url":null,"abstract":"<p><p>The exon capture approach allows for sequencing a large number of loci to reconstruct phylogenetic relationships at varying taxonomic levels. In order to efficiently recover the targeted loci, the probes designed to capture the exons need to be genetically sufficiently similar to bind to the DNA, with a proposed limit of 10% of divergence. However, this threshold has never been tested with a specific protocol. We have designed a set of probes to capture 1125 exons in the Neogastropoda (Mollusca, Gastropoda), processed with the same protocol from the field to the DNA sequencing to control for potential bias in DNA quantity and quality. We sequenced 30 different species, including 14 species of Neogastropoda and 16 species of Caenogastropoda non-Neogastropoda. Each species includes five specimens, for a total of 150 specimens, and for four specimens among the 150, DNA extracts were aliquoted in four samples, sequenced separately, to estimate the intraspecific and intraspecimen variability in capture success. Our results confirm the impact of genetic distance on the success of exon capture with a negative linear correlation between the genetic distance and the number of exons captured for each sample. Consequently, designing new capture probes would allow for capturing exons in genetically more distant groups without the need to redesign a new set of exons.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14064"},"PeriodicalIF":5.5,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941880","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chromosome-Level Genome Assembly of Five Emberiza Species Reveals the Genomic Characteristics and Intrinsic Drivers of Adaptive Radiation.","authors":"Tingli Hu, Haohao Ma, Yongxuan Xiao, Ruolei Sun, Chunlin Li, Lei Shan, Baowei Zhang","doi":"10.1111/1755-0998.14063","DOIUrl":"https://doi.org/10.1111/1755-0998.14063","url":null,"abstract":"<p><p>Emberiza buntings (Aves: Emberizidae) exhibit extensive diversity and rapid diversification within the Old World, particularly in the eastern Palearctic, making them valuable models for studying rapid radiation among sympatric species. Despite their ecological and morphological diversity, there remains a significant gap in understanding the genomic underpinnings driving their rapid speciation. To fill this gap, we assembled high-quality chromosome-level genomes of five representative Emberiza species (E. aureola, E. pusilla, E. rustica, E. rutila and E. spodocephala). Comparative genomic analysis revealed distinct migration-related evolutionary adaptations in their genomes, including variations in lipid metabolism, oxidative stress response, locomotor ability and circadian regulation. These changes may facilitate the rapid occupation of emerging ecological niches and provide opportunities for species diversification. Additionally, these five species exhibited abnormal abundances of long terminal repeat retrotransposons (LTRs), comprising over 20% of their genomes, with insertion times corresponding to their divergence (~2.5 million years ago). The presence of LTRs influenced genome size, chromosomal structure and single-gene expression, suggesting their role in promoting the rapid diversification of Emberiza species. These findings offer valuable insights into the adaptive radiation of Emberiza and establish a robust theoretical foundation for further exploration of the patterns and mechanisms underlying their diversification.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14063"},"PeriodicalIF":5.5,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Post-Mortem Molecular Damage Profile in the Ancient Human Mitochondrial DNA.","authors":"Daniel R Cuesta-Aguirre, Cristina Amor-Jimenez, Assumpció Malgosa, Cristina Santos","doi":"10.1111/1755-0998.14061","DOIUrl":"https://doi.org/10.1111/1755-0998.14061","url":null,"abstract":"<p><p>Mitochondrial DNA (mtDNA) analysis is crucial for understanding human population structure and genetic diversity. However, post-mortem DNA damage poses challenges, that make analysis difficult. DNA preservation is affected by environmental conditions which, among other factors, complicates the differentiation of endogenous variants from artefacts in ancient mtDNA mix profiles. This study aims to develop a molecular damage profile for ancient mtDNA that can become a useful tool in analysing mtDNA from ancient remains. A dataset of 427 whole genomes or capture of mtDNA sequences from individuals representing different historical periods and climatic regions was compiled from the ENA database. Present-day and UDG-treated ancient samples were also included and used to establish levels of damaged reads. Results indicated that samples from cold regions exhibited the lowest percentage of damaged reads, followed by arid, cold, tropical and temperate regions, with significant differences observed between cold and temperate regions. A global damage profile was generated, identifying 2933 positions (25% of the positions considered) with damage in more than 23.8% of the samples analysed, deemed as damage hotspots. Notably, 2856 of these hotspots had never been reported as damage or mutational hotspots, or heteroplasmic positions. Damage hotspot frequency by position was slightly higher in the non-coding region compared with the coding region. In conclusion, this study provides a molecular damage profile for ancient mtDNA analysis that is expected to be a valuable tool in the interpretation of mtDNA variation in ancient samples.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14061"},"PeriodicalIF":5.5,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941630","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MaxTemp: A Method to Maximise Precision of the Temporal Method for Estimating N_e in Genetic Monitoring Programs.","authors":"Robin S Waples, Michele M Masuda, Melanie E F LaCava, Amanda J Finger","doi":"10.1111/1755-0998.14057","DOIUrl":"https://doi.org/10.1111/1755-0998.14057","url":null,"abstract":"<p><p>We introduce a new software program, MaxTemp, that increases precision of the temporal method for estimating effective population size (N_e) in genetic monitoring programs, which are increasingly used to systematically track changes in global biodiversity. Scientists and managers are typically most interested in N_e for individual generations, either to match with single-generation estimates of census size (N) or to evaluate consequences of specific management actions or environmental events. Systematically sampling every generation produces a time series of single-generation estimates of temporal F ( <math> <semantics> <mrow><mover><mi>F</mi> <mo>̂</mo></mover> <mo>)</mo></mrow> <annotation>$$ hat{F}Big) $$</annotation></semantics> </math> , which can then be used to estimate N_e; however, these estimates have relatively low precision because each reflects just a single episode of genetic drift. Systematic sampling also produces an array of multigenerational temporal estimates that collectively contain a great deal of information about genetic drift that, however, can be difficult to interpret. Here, we show how additional information contained in multigenerational temporal estimates can be leveraged to increase precision of <math> <semantics> <mrow><mover><mi>F</mi> <mo>̂</mo></mover> </mrow> <annotation>$$ hat{F} $$</annotation></semantics> </math> for individual generations. Using information from one additional generation before and after a target generation can reduce the standard deviation of <math> <semantics> <mrow><mover><mi>F</mi> <mo>̂</mo></mover> </mrow> <annotation>$$ hat{F} $$</annotation></semantics> </math> ( <math> <semantics> <mrow><msub><mi>σ</mi> <mover><mi>F</mi> <mo>̂</mo></mover> </msub> </mrow> <annotation>$$ {sigma}_{hat{F}} $$</annotation></semantics> </math> ) by up to 50%, which not only tightens confidence intervals around <math> <semantics> <mrow> <msub><mover><mi>N</mi> <mo>̂</mo></mover> <mi>e</mi></msub> </mrow> <annotation>$$ {hat{N}}_e $$</annotation></semantics> </math> but also reduces the incidence of extreme estimates, including infinite estimates of N_e. Practical application of MaxTemp is illustrated with data for a long-term genetic monitoring program for California delta smelt. A second feature of MaxTemp, which allows one to estimate N_e in an unsampled generation using a combination of temporal and single-sample estimates of N_e from sampled generations, is also described and evaluated.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14057"},"PeriodicalIF":5.5,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Insect Cytochrome P450 Database: An Integrated Resource of Genetic Diversity, Evolution and Function.","authors":"Hongxin Wu, Zhongsheng Li, Zichun Zhong, Yujing Guo, Liuyan He, Xiaoxia Xu, Yijun Mao, Deyu Tang, Wenqing Zhang, Fengliang Jin, Rui Pang","doi":"10.1111/1755-0998.14070","DOIUrl":"https://doi.org/10.1111/1755-0998.14070","url":null,"abstract":"<p><p>Insects, the most numerous and diverse group of animal species on Earth, have important interactions with humans through providing resources, transmitting diseases and damaging agricultural cultivars. Cytochrome P450 monooxygenases (P450s) are one of the most important protein families in insects implicated in the endogenous metabolism and detoxification of xenobiotics, including allelochemicals, insecticides and environmental pollutants. To better understand the evolution and function of insect P450s and support the development and application of insecticides for pest control, an integrated bioinformatics platform is highly desirable. Here, we present the Insect Cytochrome P450 database (ICPD, http://www.insectp450.net/), which contains 66,477 P450s collected from public databases and predicted from the genomes of 682 insect species using a standardised bioinformatics protocol. Phylogenetic relationships between P450 genes are constructed for each species. The structures of all P450 proteins in the database are predicted using ESMFold, then visualised using WeView. Web services, such as BLAST, homogeneous modelling and molecular docking, are provided for determining the catalytic activities of P450 proteins. The ICPD will facilitate systematic investigations of the evolution and functions of the complete insect P450 complement, and represents a powerful tool for guiding insecticide design and application.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14070"},"PeriodicalIF":5.5,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mind the Gap: A Neural Network Framework for Imputing Genotypes in Non-Model Species","authors":"Katia Bougiouri","doi":"10.1111/1755-0998.14066","DOIUrl":"10.1111/1755-0998.14066","url":null,"abstract":"<p>Reduced representation sequencing (RRS) has proven to be a cost-effective solution for sequencing subsets of the genome in non-model species for large-scale studies. However, the targeted nature of RRS approaches commonly introduces large amounts of missing data, leading to reduced statistical power and biased estimates in downstream analyses. Genotype imputation, the statistical inference of missing sites across the genome, is a powerful alternative to overcome the caveats associated with missing sites. Typically, genotype imputation requires the presence of a reference panel of haplotypes, however, this is not always feasible for non-model species. In this issue of Molecular Ecology Resources, Mora-Márquez et al. (2024) develop <span>gtImputation</span>, an unsupervised machine learning imputation tool with an interactive GUI, which leverages information from the underlying data structure itself, without the need for a reference panel. They showcase that their method performs equally well and even surpasses existing haplotype-clustering and unsupervised machine learning algorithms, particularly for sites with low minor allele frequency (MAF) and for data sets with strong underlying population structure. This innovative framework adds to the ongoing efforts to expand the applicability of imputation to non-model species, offering the opportunity to apply varied types of analyses requiring dense sets of markers, while also maintaining lower sequencing costs.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142918745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reframing Formalin: A Molecular Opportunity Enabling Historical Epigenomics and Retrospective Gene Expression Studies","authors":"Clare E. Holleley,&nbsp;Erin E. Hahn","doi":"10.1111/1755-0998.14065","DOIUrl":"10.1111/1755-0998.14065","url":null,"abstract":"<p>Formalin preservation of museum specimens has long been considered a barrier to molecular research due to extensive crosslinking and chemical modification. However, recent optimisation of hot alkaline lysis and proteinase K digestion DNA extraction methods have enabled a growing number of studies to overcome these challenges and conduct genome-wide re-sequencing and targeted locus-specific sequencing. The newest, and perhaps most unexpected utility of formalin preservation in archival samples is its ability to preserve in situ DNA-protein interactions at a molecular level. Retrieving this signal provides information about the relative compaction or accessibility of the genome to the transcriptional machinery required for gene expression. Thus, exposure to formalin essentially corresponds to taking a snapshot of organism-wide gene expression at the time of death. While DNA methylation and RNA-Seq analyses of dried tissues have provided glimpses into historical gene regulation, these techniques were previously limited to skeletal or desiccated remains, offering only partial insights. By examining fluid-preserved specimens, molecular tools can now be applied to a broader range of tissues, enabling more detailed tissue-specific gene regulation profiling across vertebrates. In this review, we chronicle the historical use of formaldehyde in collections and discuss how targeted chromatin profiling with assays like MNase-seq and FAIRE-seq are surmounting fixation challenges and unlocking invaluable insights into historical genomes and gene expression profiles. The deeper integration of molecular genetics with museum collections bridges the gap between past and present and provides a vital tool that could help us predict and mitigate some of the impacts of future environmental change, novel pathogens, or invasive species.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14065","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142918746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Teknonaturalist: A Snakemake Pipeline for Assessing Fungal Diversity From Plant Genome Bycatch","authors":"Nicholas W. Bard,&nbsp;T. Jonathan Davies,&nbsp;Quentin C. B. Cronk","doi":"10.1111/1755-0998.14056","DOIUrl":"10.1111/1755-0998.14056","url":null,"abstract":"<p>Relatively little is known of the host associations and compatibility of fungal plant pathogens and endophytes. Publicly available plant genomic DNA can be mined to detect incidental fungal DNA, but taxonomic assignment can be challenging due to short lengths and variable discriminative power among different genomic regions and taxa. Here, we introduce a computationally lightweight and accessible Snakemake pipeline for rapid detection and classification (identification and assignment to taxonomic rank) of pathogenic and endophytic fungi (and other fungi associated with plants) that targets the internal transcribed spacer (ITS) region, a fungal barcode standard. We include methods for maximising query sequence length, which gives higher support for ITS1 and ITS2 taxonomic classifications by extending to other fragments of the ITS region and providing taxon-specific local cut-off and confidence scores. We demonstrate our pipeline with a case study using public genomic sequence data for six diverse plant species, including four species within <i>Betula</i>, an ecologically and economically important broadleaved forest tree genus, a shrub and a grass. Our pipeline classified fungi within minutes to a few hours per host individual, with 204 different fungal genera identified at high confidence (≥ 70%). Our pipeline detected and classified pathogenic and endophytic genera known to associate with <i>Betula</i>, and many others with no prior record of association. Our pipeline, leveraging existing sequence data, has several potential applications, including detecting cryptic fungal pathogens and helping characterise the endophytic fungal microbiome, bioprospecting commercially useful fungal species, and determining the plant host range of fungi.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14056","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142908747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PopCluster: A Population Genetics Model-Based Toolset for Simulating, Inferring and Visualising Individual Admixture and Population Structure.","authors":"Jinliang Wang","doi":"10.1111/1755-0998.14058","DOIUrl":"https://doi.org/10.1111/1755-0998.14058","url":null,"abstract":"<p><p>In this computer note I introduce software, PopCluster, that implements a new likelihood method for unsupervised population structure analysis from marker data. To infer a coarse population structure, it assumes the mixture model and adopts a simulated annealing algorithm to make a maximum likelihood clustering analysis, partitioning the sampled individuals into a predefined number of clusters. To deduce a fine population structure, it further assumes the admixture model and employs an expectation maximisation algorithm to estimate individual admixture proportions. PopCluster has many features. First, it is one of just a couple of model-based methods that can handle both biallelic and multiallelic markers in the same framework. Second, it is the first population structure analysis method that uses both Message Passing Interface (MPI) and openMP to exploit multiple CPUs with both shared and distributed memories and has the capacity to handle genomic data with millions of individuals and millions of loci. Third, the algorithms for both mixture and admixture analyses are fast, rendering PopCluster favourably in computational efficiency over previous methods in analysing genomic data. Fourth, PopCluster is built for Windows, Linux and Mac platforms, and its Windows version has an integrated GUI that can conveniently visualise analysis results and facilitate data input. Fifth, its Windows version has a built-in simulation module designed to simulate genotype data under admixture, hybridization or migration models. PopCluster provides a valuable toolset for researchers to simulate, infer and visualise individual admixture and population genetic structure, hybridization and migration using marker data.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14058"},"PeriodicalIF":5.5,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142890749","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparing eDNA and Transect Methods for Aquatic Biodiversity Assessment in Lakes and Ponds","authors":"Katharina Schwesig,&nbsp;Vera Zizka,&nbsp;Christoph Scherber,&nbsp;Norbert Hölzel","doi":"10.1111/1755-0998.14060","DOIUrl":"10.1111/1755-0998.14060","url":null,"abstract":"<p>Biodiversity monitoring increasingly relies on molecular methods such as eDNA metabarcoding. However, sound applications have so far been only established for a limited number of taxonomic groups. More information on the strengths and weaknesses of eDNA methods, especially for poorly covered groups, is essential for practical applications to achieve the highest possible reliability. We compared amphibian and Odonata data from eDNA metabarcoding and traditional transect walks on <i>N</i> = 56 plots in 38 water bodies distributed over six extraction sites for building materials in Northwest Germany. The traditional amphibian assessment included visual encounters, dip netting and acoustic detection, while Odonata were assessed through exuviae. In total, both methods detected 8 out of 11 amphibian species, while the remaining three species were detected by eDNA only. We did not find differences in amphibian species numbers per plot, but mean detection probabilities were higher with metabarcoding. In contrast, both methods detected 10 out of 29 Odonata species, while the remaining 19 species were detected by exuviae only. Species numbers per plot were higher for exuviae and only 30% of species were detected with metabarcoding. The species identified by eDNA were those with high abundance, and their detection probabilities were similar to transect walks. The results for amphibians show equal suitability and high complementarity of the compared methods. Metabarcoding detected species more efficiently and therefore offers a suitable protocol for biodiversity monitoring. For Odonata, eDNA metabarcoding showed considerable gaps, implying the need for protocol evaluation and improvement in assessment of ecological communities based on eDNA.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14060","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142890747","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}