Molecular Ecology Resources最新文献

{"title":"Seeing the Forest Despite the Trees in Repeat-Rich Genomic Regions","authors":"Amanda M. Larracuente,&nbsp;John S. Sproul","doi":"10.1111/1755-0998.70008","DOIUrl":"10.1111/1755-0998.70008","url":null,"abstract":"<p>Technological advances are producing genome assemblies of increasing quality at steadily decreasing costs. These assemblies enable the extraction of rich biological information from previously inaccessible genomic regions (e.g., repeat-rich regions) and from diverse organisms underrepresented in genomic research. Gaining functional insights from new assemblies often requires generating additional data sets, experimental approaches and complex analysis. Novel analytical methods that substantially shorten the path to biological insights are valuable, particularly if they draw conclusions from the direct analysis of assemblies. In this issue of <i>Molecular Ecology Resources</i>, Elphinstone et al. (<span>2025</span>) present RepeatOBserver—a tool to visualise repeat organisation through direct analysis of chromosome-scale assemblies. This tool facilitates the summary and visualisation of large- and fine-scale patterns of repetitive DNA sequence structure across assemblies. Their approach borrows metrics from information theory, which have found uses in ecology (i.e., the Shannon Diversity Index), to help infer functional regions within repetitive sequences including putative centromeres. Importantly, RepeatOBserver does not require annotations, repeat libraries or functional genomic data—just a high-quality assembly. This type of tool addresses ongoing challenges in mapping the structure and functions of repeat-rich chromosomal regions, which remain the least well-understood components of genomes.</p><p>The availability of chromosome-scale genome assemblies is growing rapidly, as advances in long-read sequencing technology make assembly-based approaches accessible to more taxa. These genome assemblies can reveal important insights into genome biology, biomedicine and biodiversity. Our ability to extract these insights from assemblies is built on decades of hard-won work in early genomic model organisms. For example, early work on gene structure, regulation and evolution provided a knowledge base for ab initio gene prediction from nothing more than a DNA sequence. While annotation tools for non-coding sequences like the abundant repetitive DNAs found in most eukaryotic genomes are now accessible, the methods to extract insights from these regions are less mature. Repetitive DNAs evolve rapidly: their composition, organisation and abundance varies across species (Yunis and Yasmineh <span>1971</span>), making predictions based on sequence conservation difficult. Many insights require functional genomic data (e.g., ChIP-seq, methylation and ATAC-seq), which may be challenging to access in non-model systems. Despite recent progress in resolving repeats in chromosome-scale assemblies, their assembly and annotation remain non-trivial problems (Lower et al. <span>2018</span>).</p><p>Some genome regions with critical functions are enriched in, or entirely composed of, repeated DNA sequences. Centromeres—the essential structures that guide chromosome segr","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 7","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70008","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144551534","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":"Accelerating Moss Identification Through the Development of Specific DNA Barcodes Based on the Whole Chloroplast Genome","authors":"Yanlei Liu,&nbsp;Fengjiao Shen,&nbsp;Lu Wang,&nbsp;Jiancong Dou,&nbsp;Tao Dong,&nbsp;Min Li,&nbsp;Qinghua Wang,&nbsp;Shang Dong,&nbsp;Gengchi Zhang,&nbsp;Jiancheng Zhao,&nbsp;Lin Li,&nbsp;Shuo Shi","doi":"10.1111/1755-0998.70004","DOIUrl":"10.1111/1755-0998.70004","url":null,"abstract":"<div>\u0000 \u0000 <p>Mosses represent the most species-diverse clade of bryophytes and are among the earliest land plants. These diminutive organisms hold substantial ecological importance and have significant applications in horticulture and medicine. However, their study, development and utilisation are impeded by the complex identification process and scarcity of researchers specialising in moss taxonomy. The advancement of DNA barcoding technology presents an opportunity for precise moss identification. Present molecular markers primarily originate from angiosperm research and may not be optimal for moss species. This study aims to identify suitable DNA barcodes for mosses at the chloroplast genome level. Utilising 61 complete chloroplast genome datasets of mosses, including 14 orders, 23 families and 60 species, this research presented the first construction of a reliable phylogenetic tree at the family level of mosses using whole chloroplast genomes, enabling accurate identification of most samples. Based on nucleotide polymorphism in the complete chloroplast genome, 12 highly variable regions were selected as candidate DNA barcodes for mosses. Experimental validation of the newly designed primers demonstrated high universality (&gt; 90%). The resolution verification experiment, employing DNA barcodes from 103 samples representing 21 families and 48 genera, confirmed the efficacy of <i>atpB-rbcL</i>, <i>psaI-accD</i>, <i>ycf2</i>, <i>ycf1</i>, <i>matK</i>, <i>rpoB-trnC</i> and <i>clpP</i> as reliable DNA barcodes for mosses. The study also revealed inconsistencies in the chloroplast genome structures of mosses submitted to public databases, which hinder subsequent research. Consequently, we recommend that researchers upload data with a designated reference genome in future submissions.</p>\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 7","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144525641","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":"InsectTFDB: A Comprehensive Database and Analysis Platform for Insect Transcription Factors","authors":"Hang Zhou,&nbsp;Jiejing Tang,&nbsp;Ziqi Cheng,&nbsp;Yang Mei","doi":"10.1111/1755-0998.70006","DOIUrl":"10.1111/1755-0998.70006","url":null,"abstract":"<div>\u0000 \u0000 <p>Transcription factors (TFs) are key regulators of gene expression, driving diverse biological processes in insects. Despite their importance, a dedicated and comprehensive database for insect TFs has been lacking. To address this gap, we developed InsectTFDB (http://www.insecttfdb.com/), a specialised resource encompassing 1796 insect species across 21 orders, 258 families and 1034 genera. From 59,491,033 predicted proteins, we identified 1,570,627 TFs, systematically classified into six structural groups and annotated using multiple approaches. Approximately 87% of these TFs were successfully annotated to known proteins, enhancing their functional interpretability. InsectTFDB offers a user-friendly interface with four functional modules, including tools for species retrieval, TF exploration, sequence alignment and predictive analysis of novel sequences. These features make it a versatile platform for diverse research applications, from evolutionary studies to functional genomics and pest management. By providing unprecedented taxonomic coverage and reliable annotations, InsectTFDB serves as a critical resource for advancing our understanding of transcriptional regulation and gene regulatory networks across the insects.</p>\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 7","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144525701","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":"Arthropod: A Tool for Phylogenomic Research in Arthropods","authors":"Jiajia Wang,&nbsp;Shichen Gao,&nbsp;Renfeng Chen,&nbsp;Yunfei Wu,&nbsp;Yan Dong","doi":"10.1111/1755-0998.70003","DOIUrl":"10.1111/1755-0998.70003","url":null,"abstract":"<div>\u0000 \u0000 <p>Arthropods account for 80% of the species diversity in the animal kingdom, yet many challenges remain in studying their evolutionary history. With advancements in genome sequencing technologies, it has become possible to obtain large quantities of genome skimming or transcriptomic data at low costs. However, the lack of a standardised analytical pipeline for arthropods has created inconveniences for many researchers. This study addresses this gap by extensively collecting representative (high-quality) genomic and transcriptomic data from 49 orders and 306 families of arthropods, as well as constructing a low-copy gene set comprising 694 low-copy nuclear genes. Furthermore, we developed the Arthropod analysis tool (https://github.com/Wangjiajia-1111/Arthropod-v1), which takes raw data from genome skimming and transcriptomic sequencing as input. This tool facilitates the automated analysis of phylogenetic trees for newly sequenced species through data filtering, alignment, assembly, and tree construction. These efforts provide new resources for the evolutionary study of arthropods.</p>\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 7","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144525642","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-Scale Genome Assembly Provides Insights Into Condor Evolution and Conservation","authors":"Diego De Panis,&nbsp;François Le Dily,&nbsp;Sergio A. Lambertucci,&nbsp;Guillermo Wiemeyer,&nbsp;Hernán Dopazo,&nbsp;Marta Gut,&nbsp;Tyler S. Alioto,&nbsp;Camila J. Mazzoni,&nbsp;Ivo Gut,&nbsp;Marc Martí-Renom,&nbsp;Julián Padró","doi":"10.1111/1755-0998.70000","DOIUrl":"10.1111/1755-0998.70000","url":null,"abstract":"<div>\u0000 \u0000 <p>Rare species are highly vulnerable to anthropogenic threats due to their unique life-history traits and specialised adaptations. The Andean condor (<i>Vultur gryphus</i>), the world's largest soaring bird, exemplifies these challenges with exceptional flight efficiency, delayed maturity, long lifespan, extreme sexual dimorphism and a critical scavenging role. The species faces significant threats, including habitat loss, persecution and poisoning. Meanwhile, conservation efforts have been hindered by knowledge gaps, including limited genetic data. Herein, we present the first chromosome-scale reference genome for the species, a key resource for investigating its evolution and ecology, as well as informing conservation measures. The assembly spans 1.19 Gb with 97.4% completeness, including 29 autosomes and the Z chromosome. High synteny with the California condor (<i>Gymnogyps californianus</i>) genome reflects their close evolutionary relationship. Genomic diversity in Andean condors (~0.65He/Kbp; π: 6.73^e-4) was lower than in California condors (~0.97 He/Kbp; π: 1.09^e−3). Runs of Homozygosity (RoH) analyses revealed a smaller genomic proportion (~15%) with shorter elements in Andean condors (&gt; 5 Mb covering 1.43% of the genome). In contrast, California condors showed a higher genomic proportion (~40%), with longer RoH segments (&gt; 5 Mb covering 7.3% of the genome). Analyses of gene family evolution revealed divergent patterns of expansion and contraction between Andean and California condors, including genes linked to detoxification metabolism, high-altitude adaptation and immune response. Shared genomic trends among avian scavengers highlight convergent evolution in stress response and metabolic pathways. This study provides a key genomic resource for advancing avian research and guiding conservation strategies for threatened vultures.</p>\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 7","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144332215","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":"Needle in a Haystack: A Droplet Digital Polymerase Chain Reaction Assay to Detect Rare Helminth Parasites Infecting Natural Host Populations","authors":"Chloe A. Fouilloux,&nbsp;Eric Neeno-Eckwall,&nbsp;Ipsita Srinivas,&nbsp;Jonathan S. Compton,&nbsp;Josh Sampson,&nbsp;Jesse Weber,&nbsp;Cole Wolf,&nbsp;Amanda Hund,&nbsp;John Berini III,&nbsp;Heather Alexander,&nbsp;Emma Choi,&nbsp;Daniel I. Bolnick,&nbsp;Jessica L. Hite","doi":"10.1111/1755-0998.14131","DOIUrl":"10.1111/1755-0998.14131","url":null,"abstract":"<p>Helminths infect humans, livestock, and wildlife, yet remain understudied despite their significant impact on public health and agriculture. Because many of the most prevalent helminth-borne diseases are zoonotic, understanding helminth transmission among wildlife could improve predictions and management of infection risks across species. A key challenge to understanding helminth transmission dynamics in wildlife is accurately and quantitatively tracking parasite load across hosts and environments. Traditional methods, such as visual parasite identification from environmental samples or infected hosts, are time-consuming, while standard molecular techniques (e.g., PCR and qPCR) often lack the sensitivity to reliably detect lower parasite burdens. These limitations can underestimate the prevalence and severity of infection, hindering efforts to manage infectious diseases. Here, we developed a multiplexed droplet digital PCR (ddPCR) assay to quantify helminth loads in aquatic habitats using 18S rRNA target genes. Using <i>Schistocephalus solidus</i> and their copepod hosts as a case study, we demonstrate ddPCR's sensitivity and precision. The assay is highly reproducible, reliably detecting target genes at concentrations as low as 1 pg of DNA in lab standards and field samples (multi-species and eDNA). Thus, we provide a toolkit for quantifying parasite load in intermediate hosts and monitoring infection dynamics across spatio-temporal scales in multiple helminth systems of concern for public health, agriculture, and conservation biology.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 7","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12230807/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144264957","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":"Scaling Up Species Delimitation From DNA Barcodes to Whole Organelle Genomes: Strong Evidence for Discordance Among Genes and Methods for the Red Alga Dasyclonium","authors":"Heroen Verbruggen,&nbsp;Kavitha Uthanumallian,&nbsp;Felix Powrie,&nbsp;Tara Jalali,&nbsp;Chiela Cremen,&nbsp;Maren Preuss,&nbsp;Sebastian Duchene,&nbsp;Pilar Diaz-Tapia","doi":"10.1111/1755-0998.14132","DOIUrl":"10.1111/1755-0998.14132","url":null,"abstract":"<p>Molecular sequence data have become a ubiquitous tool for delimiting species and are particularly important in organisms where morphological traits are not informative about species boundaries. A range of statistical methods have been developed to derive species limits from molecular data, for example, by quantifying changes in branching patterns in phylogenetic trees. We aim to investigate how such methods scale up from single genes to whole organelle genomes. We gathered chloroplast genome data from 38 samples of the red algal genus <i>Dascyclonium</i> and analysed them with the popular species delimitation methods Assemble Species by Automatic Partitioning (ASAP), General Mixed Yule Coalescent (GMYC), and Poisson Tree Processes (PTP). We show extensive variation in inferred species boundaries depending on the method and dataset used. Genome-scale analyses differed substantially between methods, with ASAP predicting the fewest species, PTP intermediate, and GMYC inferring many species. Based on a series of simulations, we identify a tendency of GMYC to overestimate species numbers as alignments increase in length, while the other two methods are not sensitive to this scaling. Gene-by-gene analyses show strong differences in predicted species limits, which is unexpected seeing that all genes are on a single uniparentally inherited chromosome, and highlight that choosing a particular gene as a DNA barcode has significant consequences for species diversity estimates. We show extensive cryptic diversity in the genus <i>Dasyclonium</i> and propose a consensus solution for species limits based on our combined results, enriched with biogeographic and morphological interpretations. Finally, we make recommendations for interpreting the results and improving the inferences drawn from species delimitation methods.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 7","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14132","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144256984","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":"Advancing Species Conservation and Management Through Omics Tools","authors":"Sophie von der Heyden,&nbsp;Luciano B. Beheregaray,&nbsp;Sarah Fitzpatrick,&nbsp;Catherine E. Grueber,&nbsp;Yibo Hu,&nbsp;Alison G. Nazareno","doi":"10.1111/1755-0998.14123","DOIUrl":"https://doi.org/10.1111/1755-0998.14123","url":null,"abstract":"&lt;p&gt;The conservation of biological resources has become a priority worldwide, exacerbated by the negative effects of a growing human population and related impacts on the structure, function and composition of ecosystems. A plethora of species and populations across terrestrial, freshwater and marine environments are experiencing reductions in population sizes, some of which are more susceptible to demographic and genetic stochasticity than others (Exposito-Alonso et al. &lt;span&gt;2022&lt;/span&gt;). The era of omics has inspired thought-provoking possibilities in the field of conservation biology. Access to and application of large-scale omics datasets (e.g., genomics, epigenomics, transcriptomics, proteomics, metabolomics, metagenomics) can shed novel insights on and resolve aspects of wildlife species biology and demography relevant to conservation assessments, management actions and monitoring (Allendorf et al. &lt;span&gt;2010&lt;/span&gt;; Schweizer et al. &lt;span&gt;2021&lt;/span&gt;; Zamudio &lt;span&gt;2023&lt;/span&gt;). The compilation and analysis of omics datasets can also inform management strategies for threatened wild and captive populations by, for example, identifying genetically vulnerable populations, adaptive loci, or uncovering interactions between host and symbiotic microbiota. These approaches contribute to a better understanding of local adaptation, introgression, inbreeding depression and genetic mechanisms of disease susceptibility and resistance. To this extent, the use of omics data to maximise effective actions for conservation and management is critical, particularly for species on the verge of extinction.&lt;/p&gt;&lt;p&gt;Halting climate change and the ongoing anthropogenic pressures that impact biodiversity is mandatory to curb the extinction crisis, but the loss of species and populations requires additional novel approaches for their conservation and management. To this end, the Special Issue ‘Advancing species conservation and management through omics tools’ was launched to bring attention to scientists interested in demonstrating how innovative techniques are useful to safeguard and manage biodiversity. In this editorial, we highlight how omics tools can help preserve biological diversity across space and time and across a wide range of biodiversity, encompassing authors from across the globe (Figure 1). Topics in this Special Issue include conservation surveys using genomics, epigenomics, metagenomics, transcriptomics, the development of computational models, novel pipelines related to best practices for sampling design and wet lab procedures, as well as genomic resources for wildlife species and their applicability to guide conservation and management strategies. Overall, our special issue provides a timely collection of research across broad themes that expand the application of omics tools across the tree of life. In doing so, we not only showcase contemporary development of the field but also provide an opportunity for engagement with stakeholders interested in","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 5","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14123","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144220414","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":"A Practical Comparison of Short- and Long-Read Metabarcoding Sequencing: Challenges and Solutions for Plastid Read Removal and Microbial Community Exploration of Seaweed Samples","authors":"Coralie Rousseau,&nbsp;Nicolas Henry,&nbsp;Sylvie Rousvoal,&nbsp;Gwenn Tanguy,&nbsp;Erwan Legeay,&nbsp;Catherine Leblanc,&nbsp;Simon M. Dittami","doi":"10.1111/1755-0998.14129","DOIUrl":"10.1111/1755-0998.14129","url":null,"abstract":"<p>Short-read metabarcoding analysis is the gold standard for accessing partial 16S and ITS genes with high read quality. With the advent of long-read sequencing, the amplification of full-length target genes is possible, but with low read accuracy. Moreover, 16S rRNA gene amplification in seaweed results in a large proportion of plastid reads, which are directly or indirectly derived from cyanobacteria. Primers designed not to amplify plastid sequences are available for short-read sequencing, while Oxford Nanopore Technology (ONT) offers adaptive sampling, a unique way to remove reads in real time. In this study, we compare three options to address the issue of plastid reads: deleting plastid reads with adaptive sampling, using optimised primers with Illumina MiSeq technology, and sequencing large numbers of reads with Illumina NovaSeq technology with universal primers. We show that adaptive sampling using the default settings of the MinKNOW software was ineffective for plastid depletion. NovaSeq sequencing with universal primers stood out with its deep coverage, low error rate, and ability to include both eukaryotes and bacteria in the same sequencing run, but it had limitations regarding the identification of fungi. The ONT sequencing helped us explore the fungal diversity and allowed for the retrieval of taxonomic information for genera poorly represented in the sequence databases. We also demonstrated with a mock community that the SAMBA workflow provided more accurate taxonomic assignment at the bacterial genus level than the IDTAXA and KRAKEN2 pipelines, but many false positives were generated at the species level.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 7","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14129","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144214415","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":"Independent Avian Epigenetic Clocks for Ageing and Development","authors":"Ayke Haller,&nbsp;Judith Risse,&nbsp;Bernice Sepers,&nbsp;Kees van Oers","doi":"10.1111/1755-0998.14128","DOIUrl":"10.1111/1755-0998.14128","url":null,"abstract":"<p>Information on individual age is a fundamental aspect in many ecological and evolutionary studies. However, accurate and non-lethal methods that can be applied to estimate the age of wild animals are often absent. Furthermore, since the process of ageing is accompanied by a physical decline and the deterioration of biological functions, the biological age often deviates from the chronological age. Epigenetic marks are widely suggested to be associated with this age-related physical decline, and especially changes in DNA methylation are suggested to be reliable age-predictive biomarkers. Here, we developed separate epigenetic clocks for ageing and development in a small passerine bird, the great tit (<i>Parus major</i>). The ageing clock was constructed and evaluated using erythrocyte DNA methylation data of 122 post-fledging individuals, and the developmental clock using 67 pre-fledging individuals from a wild population. Using a leave-one-out cross-validation approach, we were able to accurately predict the ages of individuals with median absolute deviations of 0.40 years for the ageing and 1.06 days for the development clock. Moreover, using existing data from a brood-size manipulation, we show that nestlings from reduced broods are estimated to be biologically older compared to control nestlings, while they are expected to have higher fitness. These epigenetic clocks provide further evidence that, as observed in mammals, changes in DNA methylation of certain CpG sites are highly correlated with chronological age in birds and this opens up new avenues for broad applications in behavioural and evolutionary ecology.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 7","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14128","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144207288","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}