Changes in global methylation patterns of Mytilus galloprovincialis exposed to microplastics

Aquatic Toxicology, Год журнала: 2024, Номер 276, С. 107115 - 107115

Опубликована: Окт. 3, 2024

Язык: Английский

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Developmental stress does not induce genome‐wide DNA methylation changes in wild great tit (Parus major) nestlings

Molecular Ecology, Год журнала: 2023, Номер 32(14), С. 3960 - 3974

Опубликована: Май 8, 2023

Abstract The environment experienced during early life is a crucial factor in the of many organisms. This has been shown to have profound effects on morphology, physiology and fitness. However, molecular mechanisms that mediate these are largely unknown, even though they essential for our understanding processes induce phenotypic variation natural populations. DNA methylation an epigenetic mechanism suggested explain such environmentally induced changes life. To investigate whether associated with experimentally developmental effects, we cross‐fostered great tit ( Parus major ) nestlings manipulated their brood sizes study population. We assessed experimental size pre‐fledging biometry behaviour. linked this genome‐wide levels CpG sites erythrocyte DNA, using 122 individuals improved epiGBS2 laboratory protocol. Brood enlargement caused stress negatively affected nestling condition, predominantly second half breeding season, when conditions harsher. enlargement, however, only one site if hatch date was taken into account. In conclusion, shows nutritional enlarged broods does not associate direct methylation. Future studies should assess may arise later as consequence development.

Язык: Английский

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Epigenetic changes to gene pathways linked to male fertility in ex situ black‐footed ferrets

Evolutionary Applications, Год журнала: 2024, Номер 17(1)

Опубликована: Янв. 1, 2024

Abstract Environmental variation can influence the reproductive success of species managed under human care and in wild, yet mechanisms underlying this phenomenon remain largely mysterious. Molecular such as epigenetic modifiers are important mediating timing progression reproduction humans model organisms, but few studies have linked to fitness wildlife. Here, we investigated black‐footed ferrets ( Mustela nigripes ), an endangered North American mammal reliant on ex situ management for survival persistence wild. Despite similar levels genetic diversity human‐managed wild‐born populations, individuals facilities exhibit problems, poor sperm quality. Differences across these settings suggest that environmentally driven decline capacity may be occurring species. We examined role DNA methylation, one well‐studied modifier, emergent condition. leveraged blood, testes, semen samples from male bred found tissue‐type specificity methylation genome, although 1360 Gene Ontology terms associated with average litter size shared functions tissues. then constructed gene networks differentially methylated genomic sites three different phenotypes explore putative biological impact methylation. Sperm count were functionally enriched candidate genes involved reproduction, development, its regulation through transcriptional repression. propose plays regulating phenotypes, thereby impacting fertility individuals. Our results provide information into how function alteration pathways artificial environments. These findings early insights conservation hurdles faced protection rare

Язык: Английский

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Immune gene regulation is associated with age and environmental adversity in a nonhuman primate

Molecular Ecology, Год журнала: 2024, Номер 33(21)

Опубликована: Июль 20, 2024

Abstract Phenotypic aging is ubiquitous across mammalian species, suggesting shared underlying mechanisms of aging. Aging linked to molecular changes DNA methylation and gene expression, environmental factors, such as severe external challenges or adversities, can moderate these age‐related changes. Yet, it remains unclear whether adversities affect regulation via the same pathways chronological, ‘primary’, Investigating in naturalistic animal populations fill this gap by providing insight into effects a greater diversity – particularly those that be challenging study humans laboratory organisms. Here, we characterised specifically, CpG sample free‐ranging rhesus macaques living off coast Puerto Rico ( n samples = 571, individuals 499), which endured major hurricane during our study. Age was associated with at 78,661 sites (31% all tested). Age‐associated hypermethylation occurred more frequently areas active regulation, while hypomethylation enriched regions show less activity immune cells, may become de‐repressed older individuals. also co‐occurred increased chromatin accessibility showed opposite trend, hinting coordinated, multi‐level loss epigenetic stability We detected 32,048 significantly exposure hurricane, overlapped age‐associated sites, most strongly regulatory weakly quiescent regions. Together, results suggest adversity contribute aging‐related phenotypes transcription, but primary has specific signatures non‐regulatory

Язык: Английский

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Environmental DNA Epigenetics Accurately Predicts the Age of Cultured Fish Larvae

Ecology and Evolution, Год журнала: 2025, Номер 15(2)

Опубликована: Фев. 1, 2025

ABSTRACT While acquiring age information is crucial for efficient stock management and biodiversity conservation, traditional aging methods fail to offer a universal, non‐invasive, precise way of estimating wild animal's age. DNA methylation from tissue (tDNA) was recently proposed as method overcome these issues showed more accurate results than telomere‐length‐based assessments. Here, we used environmental (eDNA) the first time template estimation, focusing on larval phase (10–24 days post‐hatch) cultured Dicentrarchus labrax (seabass), species major economic conservation interest. Using third‐generation sequencing, were able directly detect various modification types (e.g., cytosine adenosine in all contexts) across whole genome using amplification‐free nanopore sequencing. However, sites only present mitogenome, which could be specific feature eDNA or consequence better protection within mitochondria. By considering qualitative quantitative about according an objective model selection framework, our epigenetic clock reached cross‐validated accuracy 2.6 (Median Absolute Error). Such performances are higher those previous clocks, notably adult seabass even when scaling MAE range, linked dynamic epigenome during early life stages. Overall, pilot study proposes new determine potential simultaneous assessments, although robust validation preliminary along with methodological developments needed before field applications can envisaged.

Язык: Английский

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The interplay between epigenomic and transcriptomic variation during ecotype divergence in stickleback

BMC Biology, Год журнала: 2025, Номер 23(1)

Опубликована: Март 5, 2025

Populations colonizing contrasting environments are likely to undergo adaptive divergence and evolve ecotypes with locally adapted phenotypes. While diverse molecular mechanisms underlying ecotype have been identified, less is known about their interplay degree of divergence. Here we integrated epigenomic transcriptomic data explore the interactions among gene expression, alternative splicing, DNA methylation, microRNA expression gauge extent which patterns at four levels aligned in a case postglacial between marine freshwater nine-spined sticklebacks (Pungitius pungitius). Despite significant genome-wide associations variation, found largely non-parallel across levels, predominantly nonoverlapping (ranging from 43.40 87.98%) sets differentially expressed, spliced methylated genes, candidate genes targeted by expressed miRNA ecotypes. Furthermore, variation different mechanisms, differential methylation splicing showing highest lowest ecotypes, respectively. Finally, enrichment associated methylation. Our results suggest nuanced relationship processes, alignment level masking relatively independent effects on level.

Язык: Английский

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Sample-specific CpG loci are important for accurate long-read methylation analysis

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Май 6, 2025

Abstract Methylated CpG loci mutate at high rates, but it remains challenging to identify sample-specific non-reference for methylation analyses. Here, we present a likelihood-based method that identifies precision in long-read sequencing data from Nanopore and PacBio platforms. Inclusion of increased the number reduced reference bias, is important accurate estimation global levels across samples.

Язык: Английский

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The Mutagenic Consequences of DNA Methylation within and across Generations

Epigenomes, Год журнала: 2022, Номер 6(4), С. 33 - 33

Опубликована: Окт. 4, 2022

DNA methylation is an epigenetic modification with wide-ranging consequences across the life of organism. This can be stable, persisting through development despite changing environmental conditions. However, in other contexts, also flexible, underlying organismal phenotypic plasticity. One underappreciated aspect that it a potent mutagen; methylated cytosines mutate at much faster rate than genetic motifs. mutagenic property has been largely ignored eco-evolutionary literature, its prevalence. Here, we explore how induced by and factors could promote mutation lead to evolutionary change more rapid directed manner stochastic mutations alone. We argue for future research on implications driven both within lifetime organisms, as well timescales.

Язык: Английский

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DNA methylation differences between stick insect ecotypes

Molecular Ecology, Год журнала: 2023, Номер 32(24), С. 6809 - 6823

Опубликована: Окт. 21, 2023

Abstract Epigenetic mechanisms, such as DNA methylation, can influence gene regulation and affect phenotypic variation, raising the possibility that they contribute to ecological adaptation. Beginning address this issue requires high‐resolution sequencing studies of natural populations pinpoint epigenetic regions potential evolutionary significance. However, are still relatively uncommon, especially in insects, mainly restricted a few model organisms. Here, we characterize patterns methylation for Timema cristinae adapted two host plant species (i.e. ecotypes). By integrating results from whole transcriptomes, genomes methylomes, investigate whether environmental, genetic differences these stick insects associated with levels cytosine nucleotides CpG context. We report an overall genome‐wide level T. ~14%, being enriched bodies impoverished repetitive elements. Genome‐wide variation was strongly positively correlated distance (relatedness), but also exhibited significant host‐plant effects. Using methylome‐environment association analysis, pinpointed specific genomic differentially methylated between ecotypes, genes functions membrane processes. The observed relatedness, ecologically important variable plant, suggests role modification To substantiate adaptive significance, future could test be transmitted across generations extent which it responds experimental manipulation field laboratory studies.

Язык: Английский

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Thermal plasticity has higher fitness costs among thermally tolerant genotypes of Tigriopus californicus

Functional Ecology, Год журнала: 2024, Номер 38(7), С. 1562 - 1577

Опубликована: Май 2, 2024

Abstract Under climate change, ectotherms will likely face pressure to adapt novel thermal environments by increasing their upper tolerance and its plasticity, a measure of acclimation. Ectotherm populations with high are often less thermally plastic, trade‐off hypothesized result from (i) phenotypic limit on above which plasticity cannot further increase the trait, (ii) negative genetic correlation or (iii) fitness trade‐offs between two traits. Whether each hypothesis causes associations has implications for evolution trait. We empirically tested hypotheses leveraging experimental tractability biology intertidal copepod Tigriopus californicus . Using four latitudinally distributed sites in coastal California, six lines per population were reared under laboratory common garden generations. Ninety‐six full sibling replicates ( n = 4–5 line) third generation developmentally conditioned 21.5 16.5°C until adulthood. then measured fecundity sibships at temperature. detected significant fecundity, corollary, baseline plasticity. genotypes higher plastic. directional selection ambient temperature evidenced reduced fecundity. These costs significantly among tolerant genotypes, consistent hypothesis. This was evident conditions, but not Observed best explained model incorporating both rather than models parameters associated one Effects family negatively covaried, suggesting that could be ruled as contributing Our study provides empirical test leverages strong inference approach. discuss our results' insights into how adaptation may constrained physiological limits, correlations, Read free Plain Language Summary this article Journal blog.

Язык: Английский

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