Molecular Ecology Resources最新文献_第8页

Benchmarking kinship estimation tools for ancient genomes using pedigree simulations 利用血统模拟为古代基因组的亲缘关系估算工具设定基准

IF 7.7 1区生物学

Molecular Ecology Resources Pub Date : 2024-04-27 DOI: 10.1111/1755-0998.13960

Şevval Aktürk, Igor Mapelli, Merve N. Güler, Kanat Gürün, Büşra Katırcıoğlu, Kıvılcım Başak Vural, Ekin Sağlıcan, Mehmet Çetin, Reyhan Yaka, Elif Sürer, Gözde Atağ, Sevim Seda Çokoğlu, Arda Sevkar, N. Ezgi Altınışık, Dilek Koptekin, Mehmet Somel

{"title":"Benchmarking kinship estimation tools for ancient genomes using pedigree simulations","authors":"Şevval Aktürk, Igor Mapelli, Merve N. Güler, Kanat Gürün, Büşra Katırcıoğlu, Kıvılcım Başak Vural, Ekin Sağlıcan, Mehmet Çetin, Reyhan Yaka, Elif Sürer, Gözde Atağ, Sevim Seda Çokoğlu, Arda Sevkar, N. Ezgi Altınışık, Dilek Koptekin, Mehmet Somel","doi":"10.1111/1755-0998.13960","DOIUrl":"10.1111/1755-0998.13960","url":null,"abstract":"There is growing interest in uncovering genetic kinship patterns in past societies using low-coverage palaeogenomes. Here, we benchmark four tools for kinship estimation with such data: lcMLkin, NgsRelate, KIN, and READ, which differ in their input, IBD estimation methods, and statistical approaches. We used pedigree and ancient genome sequence simulations to evaluate these tools when only a limited number (1 to 50 K, with minor allele frequency ≥0.01) of shared SNPs are available. The performance of all four tools was comparable using ≥20 K SNPs. We found that first-degree related pairs can be accurately classified even with 1 K SNPs, with 85% F1 scores using READ and 96% using NgsRelate or lcMLkin. Distinguishing third-degree relatives from unrelated pairs or second-degree relatives was also possible with high accuracy (F1 > 90%) with 5 K SNPs using NgsRelate and lcMLkin, while READ and KIN showed lower success (69 and 79% respectively). Meanwhile, noise in population allele frequencies and inbreeding (first-cousin mating) led to deviations in kinship coefficients, with different sensitivities across tools. We conclude that using multiple tools in parallel might be an effective approach to achieve robust estimates on ultra-low-coverage genomes.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"24 5","pages":""},"PeriodicalIF":7.7,"publicationDate":"2024-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13960","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140805597","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

SEGUL: Ultrafast, memory-efficient and mobile-friendly software for manipulating and summarizing phylogenomic datasets SEGUL：超快、内存效率高、移动友好型软件，用于处理和汇总系统组数据集。

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2024-04-26 DOI: 10.1111/1755-0998.13964

Heru Handika, Jacob A. Esselstyn

{"title":"SEGUL: Ultrafast, memory-efficient and mobile-friendly software for manipulating and summarizing phylogenomic datasets","authors":"Heru Handika, Jacob A. Esselstyn","doi":"10.1111/1755-0998.13964","DOIUrl":"10.1111/1755-0998.13964","url":null,"abstract":"Phylogenetic studies now routinely require manipulating and summarizing thousands of data files. For most of these tasks, currently available software requires considerable computing resources and substantial knowledge of command-line applications. We develop an ultrafast and memory-efficient software, SEGUL, that performs common phylogenomic dataset manipulations and calculates statistics summarizing essential data features. Our software is available as standalone command-line interface (CLI) and graphical user interface (GUI) applications, and as a library for Rust, R and Python, with possible support of other languages. The CLI and library versions run native on Windows, Linux and macOS, including Apple ARM Macs. The GUI version extends support to include mobile iOS, iPadOS and Android operating systems. SEGUL leverages the high performance of the Rust programming language to offer fast execution times and low memory footprints regardless of dataset size and platform choice. The inclusion of a GUI minimizes bioinformatics barriers to phylogenomics while SEGUL's efficiency reduces economic barriers by allowing analysis on inexpensive hardware. Our support for mobile operating systems further enables teaching phylogenomics where access to computing power is limited.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"24 7","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140652800","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

ProSeq4: A user-friendly multiplatform program for preparation and analysis of large-scale DNA polymorphism datasets ProSeq4：用于准备和分析大规模 DNA 多态性数据集的用户友好型多平台程序。

IF 7.7 1区生物学

Molecular Ecology Resources Pub Date : 2024-04-22 DOI: 10.1111/1755-0998.13962

Dmitry A. Filatov

{"title":"ProSeq4: A user-friendly multiplatform program for preparation and analysis of large-scale DNA polymorphism datasets","authors":"Dmitry A. Filatov","doi":"10.1111/1755-0998.13962","DOIUrl":"10.1111/1755-0998.13962","url":null,"abstract":"Preparation of DNA polymorphism datasets for analysis is an important step in evolutionary genetic and molecular ecology studies. Ever-growing dataset sizes make this step time consuming, but few convenient software tools are available to facilitate processing of large-scale datasets including thousands of sequence alignments. Here I report “processor of sequences v4” (proSeq4)—a user-friendly multiplatform software for preparation and evolutionary genetic analyses of genome- or transcriptome-scale sequence polymorphism datasets. The program has an easy-to-use graphic user interface and is designed to process and analyse many thousands of datasets. It supports over two dozen file formats, includes a flexible sequence editor and various tools for data visualization, quality control and most commonly used evolutionary genetic analyses, such as NJ-phylogeny reconstruction, DNA polymorphism analyses and coalescent simulations. Command line tools (e.g. vcf2fasta) are also provided for easier integration into bioinformatic pipelines. Apart of molecular ecology and evolution research, proSeq4 may be useful for teaching, e.g. for visual illustration of different shapes of phylogenies generated with coalescent simulations in different scenarios. ProSeq4 source code and binaries for Windows, MacOS and Ubuntu are available from https://sourceforge.net/projects/proseq/.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"24 5","pages":""},"PeriodicalIF":7.7,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13962","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140672187","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

Testing and optimizing metabarcoding of iDNA from dung beetles to sample mammals in the hyperdiverse Neotropics 测试并优化蜣螂 iDNA 的代谢标码，以对多样性极高的新热带地区的哺乳动物进行采样。

IF 7.7 1区生物学

Molecular Ecology Resources Pub Date : 2024-04-22 DOI: 10.1111/1755-0998.13961

Bruno H. Saranholi, Filipe M. França, Alfried P. Vogler, Jos Barlow, Fernando Z. Vaz de Mello, Maria E. Maldaner, Edrielly Carvalho, Carla C. Gestich, Benjamin Howes, Cristina Banks-Leite, Pedro M. Galetti Jr

{"title":"Testing and optimizing metabarcoding of iDNA from dung beetles to sample mammals in the hyperdiverse Neotropics","authors":"Bruno H. Saranholi, Filipe M. França, Alfried P. Vogler, Jos Barlow, Fernando Z. Vaz de Mello, Maria E. Maldaner, Edrielly Carvalho, Carla C. Gestich, Benjamin Howes, Cristina Banks-Leite, Pedro M. Galetti Jr","doi":"10.1111/1755-0998.13961","DOIUrl":"10.1111/1755-0998.13961","url":null,"abstract":"Over the past few years, insects have been used as samplers of vertebrate diversity by assessing the ingested-derived DNA (iDNA), and dung beetles have been shown to be a good mammal sampler given their broad feeding preference, wide distribution and easy sampling. Here, we tested and optimized the use of iDNA from dung beetles to assess the mammal community by evaluating if some biological and methodological aspects affect the use of dung beetles as mammal species samplers. We collected 403 dung beetles from 60 pitfall traps. iDNA from each dung beetle was sequenced by metabarcoding using two mini-barcodes (12SrRNA and 16SrRNA). We assessed whether dung beetles with different traits related to feeding, nesting and body size differed in the number of mammal species found in their iDNA. We also tested differences among four killing solutions in preserving the iDNA and compared the effectiveness of each mini barcode to recover mammals. We identified a total of 50 mammal OTUs (operational taxonomic unit), including terrestrial and arboreal species from 10 different orders. We found that at least one mammal-matching sequence was obtained from 70% of the dung beetle specimens. The number of mammal OTUs obtained did not vary with dung beetle traits as well as between the killing solutions. The 16SrRNA mini-barcode recovered a higher number of mammal OTUs than 12SrRNA, although both sets were partly non-overlapping. Thus, the complete mammal diversity may not be achieved by using only one of them. This study refines the methodology for routine assessment of tropical mammal communities via dung beetle ‘samplers’ and its universal applicability independently of the species traits of local beetle communities.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"24 5","pages":""},"PeriodicalIF":7.7,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140673023","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

Collecting baleen whale blow samples by drone: A minimally intrusive tool for conservation genetics 用无人机采集须鲸吹气样本：用于保护遗传学的侵入性最小的工具

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2024-04-04 DOI: 10.1111/1755-0998.13957

Éadin N. O'Mahony, Angela L. Sremba, Eric M. Keen, Nicole Robinson, Archie Dundas, Debbie Steel, Janie Wray, C. Scott Baker, Oscar E. Gaggiotti

{"title":"Collecting baleen whale blow samples by drone: A minimally intrusive tool for conservation genetics","authors":"Éadin N. O'Mahony, Angela L. Sremba, Eric M. Keen, Nicole Robinson, Archie Dundas, Debbie Steel, Janie Wray, C. Scott Baker, Oscar E. Gaggiotti","doi":"10.1111/1755-0998.13957","DOIUrl":"10.1111/1755-0998.13957","url":null,"abstract":"In coastal British Columbia, Canada, marine megafauna such as humpback whales (Megaptera novaeangliae) and fin whales (Balaenoptera physalus velifera) have been subject to a history of exploitation and near extirpation. While their populations have been in recovery, significant threats are posed to these vulnerable species by proposed natural resource ventures in this region, in addition to the compounding effects of anthropogenic climate change. Genetic tools play a vital role in informing conservation efforts, but the associated collection of tissue biopsy samples can be challenging for the investigators and disruptive to the ongoing behaviour of the targeted whales. Here, we evaluate a minimally intrusive approach based on collecting exhaled breath condensate, or respiratory ‘blow’ samples, from baleen whales using an unoccupied aerial system (UAS), within Gitga'at First Nation territory for conservation genetics. Minimal behavioural responses to the sampling technique were observed, with no response detected 87% of the time (of 112 UAS deployments). DNA from whale blow (n = 88 samples) was extracted, and DNA profiles consisting of 10 nuclear microsatellite loci, sex identification and mitochondrial (mt) DNA haplotypes were constructed. An average of 7.5 microsatellite loci per individual were successfully genotyped. The success rates for mtDNA and sex assignment were 80% and 89% respectively. Thus, this minimally intrusive sampling method can be used to describe genetic diversity and generate genetic profiles for individual identification. The results of this research demonstrate the potential of UAS-collected whale blow for conservation genetics from a remote location.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"24 8","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13957","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140569086","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

Metagenomic-based discovery and comparison of the lignin degrading potential of microbiomes in aquatic and terrestrial ecosystems via the LCdb database 通过 LCdb 数据库，基于元基因组发现并比较水生和陆生生态系统中微生物群的木质素降解潜力

IF 7.7 1区生物学

Molecular Ecology Resources Pub Date : 2024-04-03 DOI: 10.1111/1755-0998.13950

Jiyu Chen, Lu Lin, Qichao Tu, Qiannan Peng, Xiaopeng Wang, Congying Liang, Jiayin Zhou, Xiaoli Yu

{"title":"Metagenomic-based discovery and comparison of the lignin degrading potential of microbiomes in aquatic and terrestrial ecosystems via the LCdb database","authors":"Jiyu Chen, Lu Lin, Qichao Tu, Qiannan Peng, Xiaopeng Wang, Congying Liang, Jiayin Zhou, Xiaoli Yu","doi":"10.1111/1755-0998.13950","DOIUrl":"10.1111/1755-0998.13950","url":null,"abstract":"Lignin, as an abundant organic carbon, plays a vital role in the global carbon cycle. However, our understanding of the global lignin-degrading microbiome remains elusive. The greatest barrier has been absence of a comprehensive and accurate functional gene database. Here, we first developed a curated functional gene database (LCdb) for metagenomic profiling of lignin degrading microbial consortia. Via the LCdb, we draw a clear picture describing the global biogeography of communities with lignin-degrading potential. They exhibit clear niche differentiation at the levels of taxonomy and functional traits. The terrestrial microbiomes showed the highest diversity, yet the lowest correlations. In particular, there were few correlations between genes involved in aerobic and anaerobic degradation pathways, showing a clear functional redundancy property. In contrast, enhanced correlations, especially closer inter-connections between anaerobic and aerobic groups, were observed in aquatic consortia in response to the lower diversity. Specifically, dypB and dypA, are widespread on Earth, indicating their essential roles in lignin depolymerization. Estuarine and marine consortia featured the laccase and mnsod genes, respectively. Notably, the roles of archaea in lignin degradation were revealed in marine ecosystems. Environmental factors strongly influenced functional traits, but weakly shaped taxonomic groups. Null mode analysis further verified that composition of functional traits was deterministic, while taxonomic composition was highly stochastic, demonstrating that the environment selects functional genes rather than taxonomic groups. Our study not only develops a useful tool to study lignin degrading microbial communities via metagenome sequencing but also advances our understanding of ecological traits of these global microbiomes.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"24 5","pages":""},"PeriodicalIF":7.7,"publicationDate":"2024-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140568992","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

Evolution of olfactory receptor superfamily in bats based on high throughput molecular modelling 基于高通量分子建模的蝙蝠嗅觉受体超家族的进化

IF 7.7 1区生物学

Molecular Ecology Resources Pub Date : 2024-04-03 DOI: 10.1111/1755-0998.13958

Tianmin Zhang, Haohao Jing, Jinhong Wang, Le Zhao, Yang Liu, Stephen J. Rossiter, Huimeng Lu, Gang Li

{"title":"Evolution of olfactory receptor superfamily in bats based on high throughput molecular modelling","authors":"Tianmin Zhang, Haohao Jing, Jinhong Wang, Le Zhao, Yang Liu, Stephen J. Rossiter, Huimeng Lu, Gang Li","doi":"10.1111/1755-0998.13958","DOIUrl":"10.1111/1755-0998.13958","url":null,"abstract":"The origin of flight and laryngeal echolocation in bats is likely to have been accompanied by evolutionary changes in other aspects of their sensory biology. Of all sensory modalities in bats, olfaction is perhaps the least well understood. Olfactory receptors (ORs) function in recognizing odour molecules, with crucial roles in evaluating food, as well as in processing social information. Here we compare OR repertoire sizes across taxa and apply a new pipeline that integrates comparative genome data with protein structure modelling and then we employ molecular docking techniques with small molecules to analyse OR functionality based on binding energies. Our results suggest a sharp contraction in odorant recognition of the functional OR repertoire during the origin of bats, consistent with a reduced dependence on olfaction. We also compared bat lineages with contrasting different ecological characteristics and found evidence of differences in OR gene expansion and contraction, and in the composition of ORs with different tuning breadths. The strongest binding energies of ORs in non-echolocating fruit-eating bats were seen to correspond to ester odorants, although we did not detect a quantitative advantage of functional OR repertoires in these bats compared with echolocating insectivorous species. Overall, our findings based on molecular modelling and computational docking suggest that bats have undergone olfactory evolution linked to dietary adaptation. Our results from extant and ancestral bats help to lay the groundwork for targeted experimental functional tests in the future.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"24 5","pages":""},"PeriodicalIF":7.7,"publicationDate":"2024-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140568995","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

Epigenetic clocks, sex markers and age-class diagnostics in three harvested large mammals 三种收获的大型哺乳动物的表观遗传时钟、性别标记和年龄段诊断。

IF 7.7 1区生物学

Molecular Ecology Resources Pub Date : 2024-03-30 DOI: 10.1111/1755-0998.13956

Natalie Czajka, Joseph M. Northrup, Meaghan J. Jones, Aaron B. A. Shafer

{"title":"Epigenetic clocks, sex markers and age-class diagnostics in three harvested large mammals","authors":"Natalie Czajka, Joseph M. Northrup, Meaghan J. Jones, Aaron B. A. Shafer","doi":"10.1111/1755-0998.13956","DOIUrl":"10.1111/1755-0998.13956","url":null,"abstract":"The development of epigenetic clocks, or the DNA methylation-based inference of age, is an emerging tool for ageing in free ranging populations. In this study, we developed epigenetic clocks for three species of large mammals that are the focus of extensive management throughout their range in North America: white-tailed deer, black bear and mountain goat. We quantified differential DNA methylation patterns at over 30,000 cytosine-guanine sites (CpGs) from tissue samples of all three species (black bear n = 49; white-tailed deer n = 47; mountain goat n = 45). We used a penalized regression model (elastic net) to build explanatory (black bear r = .95; white-tailed deer r = .99; mountain goat r = .97) and robust (black bear Median Absolute Error or MAE = 1.33; white-tailed deer MAE = 0.29; mountain goat MAE = 0.61) models of age or clocks. We also characterized individual CpG sites within each species that demonstrated clear differences in methylation levels between age classes and sex, which can be used to develop a suite of accessible diagnostic markers. This tool has the potential to contribute to wildlife monitoring by providing easily obtainable representations of age structure in managed populations.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"24 5","pages":""},"PeriodicalIF":7.7,"publicationDate":"2024-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13956","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140326110","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

DNA barcoding insufficiently identifies European wild bees (Hymenoptera, Anthophila) due to undefined species diversity, genus-specific barcoding gaps and database errors 由于未确定的物种多样性、特定属的条形码缺口和数据库错误，DNA 条形码无法充分识别欧洲野生蜜蜂（膜翅目，Anthophila）。

IF 7.7 1区生物学

Molecular Ecology Resources Pub Date : 2024-03-25 DOI: 10.1111/1755-0998.13953

Šet Janko, Šturm Rok, Koderman Blaž, Bevk Danilo, Gogala Andrej, Kutnjak Denis, Čandek Klemen, Gregorič Matjaž

{"title":"DNA barcoding insufficiently identifies European wild bees (Hymenoptera, Anthophila) due to undefined species diversity, genus-specific barcoding gaps and database errors","authors":"Šet Janko, Šturm Rok, Koderman Blaž, Bevk Danilo, Gogala Andrej, Kutnjak Denis, Čandek Klemen, Gregorič Matjaž","doi":"10.1111/1755-0998.13953","DOIUrl":"10.1111/1755-0998.13953","url":null,"abstract":"Recent declines in insect abundances, especially populations of wild pollinators, pose a threat to many natural and agricultural ecosystems. Traditional species monitoring relies on morphological character identification and is inadequate for efficient and standardized surveys. DNA barcoding has become a standard approach for molecular identification of organisms, aiming to overcome the shortcomings of traditional biodiversity monitoring. However, its efficacy depends on the completeness of reference databases. Large DNA barcoding efforts are (almost entirely) lacking in many European countries and such patchy data limit Europe-wide analyses of precisely how to apply DNA barcoding in wild bee identification. Here, we advance towards an effective molecular identification of European wild bees. We conducted a high-effort survey of wild bees at the junction of central and southern Europe and DNA barcoded all collected morphospecies. For global analyses, we complemented our DNA barcode dataset with all relevant European species and conducted global analyses of species delimitation, general and genus-specific barcoding gaps and examined the error rate in DNA data repositories. We found that (i) a sixth of all specimens from Slovenia could not be reliably identified, (ii) species delimitation methods show numerous systematic discrepancies, (iii) there is no general barcoding gap across all bees and (iv) the barcoding gap is genus specific, but only after curating for errors in DNA data repositories. Intense sampling and barcoding efforts in underrepresented regions and strict curation of DNA barcode repositories are needed to enhance the use of DNA barcoding for the identification of wild bees.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"24 5","pages":""},"PeriodicalIF":7.7,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13953","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140206014","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

Plant mitochondrial genome map (PMGmap): A software tool for the comprehensive visualization of coding, noncoding and genome features of plant mitochondrial genomes 植物线粒体基因组图谱（PMGmap）：全面可视化植物线粒体基因组编码、非编码和基因组特征的软件工具。

IF 7.7 1区生物学

Molecular Ecology Resources Pub Date : 2024-03-24 DOI: 10.1111/1755-0998.13952

Xinyi Zhang, Haimei Chen, Yang Ni, Bin Wu, Jingling Li, Artur Burzyński, Chang Liu

{"title":"Plant mitochondrial genome map (PMGmap): A software tool for the comprehensive visualization of coding, noncoding and genome features of plant mitochondrial genomes","authors":"Xinyi Zhang, Haimei Chen, Yang Ni, Bin Wu, Jingling Li, Artur Burzyński, Chang Liu","doi":"10.1111/1755-0998.13952","DOIUrl":"10.1111/1755-0998.13952","url":null,"abstract":"Tools for visualizing genomes are essential for investigating genomic features and their interactions. Currently, tools designed originally for animal mitogenomes and plant plastomes are used to visualize the mitogens of plants but cannot accurately display features specific to plant mitogenomes, such as nonlinear exon arrangement for genes, the prevalence of functional noncoding features and complex chromosomal architecture. To address these problems, a software package, plant mitochondrial genome map (PMGmap), was developed using the Python programming language. PMGmap can draw genes at exon levels; draw cis- and trans-splicing gene maps, noncoding features and repetitive sequences; and scale genic regions by using the scaling of the genic regions on the mitogenome (SAGM) algorithm. It can also draw multiple chromosomes simultaneously. Compared with other state-of-the-art tools, PMGmap showed better performance in visualizing 405 plant mitogenomes, showing potential as an invaluable tool for plant mitogenome research. The web and container versions and the source code of PMGmap can be accessed through the following link: http://www.1kmpg.cn/pmgmap.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"24 5","pages":""},"PeriodicalIF":7.7,"publicationDate":"2024-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140206015","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