Biology subjects

Munday, P. L.

Publications and source records attributed to Munday, P. L..

9 recordsLinked to original sources

bioRxiv2026

MicroRNA-mediated transgenerational plasticity reveals pathways for ocean warming resilience

With anthropogenic climate change driving unprecedented ocean warming and posing a major threat to marine organisms, phenotypic plasticity mediated by epigenetic mechanisms may enable acclimation and persistence across generations. MicroRNAs (miRNAs) are epigenetic regulators that have long been associated with maladaptive stress responses across generations, yet their role in facilitating transgenerational acclimation remains unexplored. To examine miRNAs role in transgenerational thermal plasticity, we conducted a fully factorial split-clutch design experiment in the coral reef fish Acanthochromis polyacanthus. Parents and offspring were exposed throughout development to control (+0{degrees}C) or elevated (+1.5{degrees}C) temperatures, and offspring hepatic miRNA and mRNA were profiled. We identified 678 miRNAs in A. polyacanthus, including 226 conserved and 452 novel sequences. Direct (developmental) and parental (transgenerational) warming caused similar numbers of miRNAs to alter expression, while mRNA expression was more strongly influenced by parental effects. The two parents had distinct effects on offspring miRNA-mRNA networks, with paternal warming mainly altering offspring metabolism and stress responses, while maternal exposure predominantly influencing immunity and tissue organization. Overall, mismatched parental temperatures created trade-offs in offspring, whereas congruent (biparental) warming led to a unique, non-additive, response with fewer miRNA changes and lack of stress pathway activation. Our findings reveal that miRNAs mediate both developmental and transgenerational plasticity, highlighting the capacity of transgenerational effects to influence climate resilience, while also emphasizing the necessity of accounting for both maternal and paternal contributions when predicting species adaptability to ocean warming.

evolutionary biology↗

bioRxiv2023

Cross-talk between tissues is critical for intergenerational acclimation to environmental change

An organisms reaction to environmental changes is mediated by coordinated responses of multiple tissues. Additionally, parental priming may increase offsprings acclimation potential to changing environmental conditions. As the effects of human-induced climate change, such as ocean acidification (OA), continue to intensify it is critical to assess the acclimation potential of species at the whole organismal scale. For this we need to understand the cross-talk between tissues in regulating and responding to pH changes. Here by using a multi-tissue approach we determine the influence of 1) variation in parental behavioural tolerance and 2) parental environment, on molecular responses of their offspring in a coral reef fish. The gills and liver showed the highest transcriptional response to OA conditions in juvenile fish regardless of the parental environment, while the brain and liver showed the greatest signal of intergenerational acclimation. Key functional pathways that were altered in the brain upon within-generational CO2 exposure were restored to control levels when parents were exposed to OA conditions. Furthermore, the expression of a new complement of genes involved in key functions was altered in the offspring only when parents were previously exposed to OA conditions. Therefore, previous parental conditioning to OA can reprogram tissue transcriptomic profiles of the offspring enabling them to better cope in an environment with elevated CO2 levels. Overall, our results reveal tissue-specific transcriptional changes underlying intergenerational plastic responses to elevated CO2 exposure and highlight the integration of these changes in promoting organismal acclimation to OA.

ecology↗

bioRxiv2023

Matching maternal and paternal experiences underpin molecular thermal acclimation

The environment experienced by one generation has the potential to affect the subsequent one through non-genetic inheritance of parental effects. Since both mothers and fathers can influence their offspring, questions arise regarding how the maternal, paternal and offspring experiences integrate into the resulting phenotype. We aimed to disentangle the maternal and paternal contributions to transgenerational thermal acclimation in a reef fish, Acanthochromis polyacanthus, by exposing two generations to elevated temperature (+1.5{degrees}C) in a full factorial design and analyzing the F2 hepatic gene expression. Paternal and maternal effects showed common but also parent-specific components, with the father having the largest influence in shaping the offspring transcriptomic profile. Fathers contributed to transgenerational response to warming through transfer of epigenetically controlled stress-response mechanisms while mothers influenced increased lipid metabolism regulation. However, the key to acclimation potential was matching thermal experiences of the parents. When both parents were exposed to the same condition, offspring showed increased structural RNA production and transcriptional regulation, whereas environmental mismatch in parents resulted in maladaptive parental condition-transfer, revealed by translation suppression and endoplasmic reticulum stress. Interestingly, the offsprings own environmental experience had the smallest influence on their hepatic transcription profiles. Taken together, our results show the complex nature of the interplay between paternal, maternal and offspring cue integration, and reveal that acclimation potential to ocean warming depends not only on maternal and paternal contributions, but importantly on congruent parental thermal experiences.

evolutionary biology↗

bioRxiv2023

Timing specific parental effects of ocean warming in a coral reef fish

Population and species persistence in a rapidly warming world will be determined by an organisms ability to acclimate to warmer conditions, especially across generations. There is potential for transgenerational acclimation, but the importance of ontogenetic timing in the transmission of environmentally induced parental effects remains mostly unknown. We aimed to disentangle the contributions of two critical ontogenetic stages (juvenile development and adult reproduction) to transgenerational plasticity, by exposing the coral reef fish Acanthochromis polyacanthus to simulated ocean warming with natural diel thermal fluctuations across two generations. By using hepatic transcriptomics, we discovered that the developmental environment of the offspring themselves had little effect on their acclimation potential at 2.5 months of life. Instead, the developmental experience of parents increased regulatory RNA production and protein synthesis, which could improve the offsprings response to warming. Conversely, reproduction in warmer water elicited stress response mechanisms, with suppression of translation and mitochondrial respiration. Mismatches between temperatures in the parental ontogenetic thermal experience deeply affected offspring gene expression profiles, and detrimental effects were also evident when warming occurred both during parents development and reproduction. This study reveals that the previous generations developmental temperature contributes substantially to thermal acclimation potential during early life, however prolonged heat stress will likely have adverse effects on the species persistence.

evolutionary biology↗

bioRxiv2022

Genetic architecture of behavioural resilience to ocean acidification

Genetic variation is essential for adaptation to rapid environmental changes. Identifying genetic variation associated with climate-change related phenotypes is therefore the necessary first step towards predictive models of genomic vulnerability. Here we used a whole-genome scan to identify candidate genetic variants associated with differences in behavioural resilience to ocean acidification in a coral reef fish. We identified three genomic regions that differ between individuals that are behaviourally tolerant compared with behaviourally sensitive to elevated CO2. These include a dopamine receptor (drd4rs), cadherin related family member 5-like (cdhr5l), Synapse-associated protein 1 (syap1), and GRB2 Associated Regulator of MAPK1 Subtype 2 (garem2), which have previously been found to modify behaviour related to boldness, novelty seeking, and learning in other species, and differ between behaviourally tolerant and sensitive individuals. Consequently, the identified genes are promising candidates in the search of the genetic underpinnings and adaptive potential of behavioural resilience to ocean acidification in fishes.

ecology↗

bioRxiv2022

Reanalysis shows the extreme decline effect does not exist in fish ocean acidification studies

A meta-analysis published in PLoS Biology by Clements et al. (2022) claims there is an extreme decline effect in studies published between 2009-2019 on the impacts of ocean acidification (OA) on fish behaviour. Here I show that the extreme decline effect reported by Clements et al. is a statistical artifact caused by the way they corrected for zero values in percentage data, which was more common in the earliest experiments compared with later studies. Furthermore, selective choices for excluding or including data, along with serious errors in the compilation of data and missing studies with strong effects, weakened the effect sizes reported for papers after 2010, further exacerbating the decline effect reported by Clements et al. When the data is reanalyzed using appropriate corrections for zero values in percentage and proportional data, and using a complete, corrected and properly screened data set, the extreme decline effect reported by Clements et al. no longer exists.

animal behavior and cognition↗

bioRxiv2021

Diel CO2 fluctuations alter the molecular response of coral reef fishes to ocean acidification conditions

Environmental CO2 variation can modify the responses of marine organisms to ocean acidification, yet the underlying mechanisms for this effect remain unclear. On coral reefs, environmental CO2 fluctuates on a regular day-night cycle. Effects of future ocean acidification on coral reef fishes might therefore depend on their response to this diel cycle of CO2. To evaluate the effects on the brain molecular response, we exposed two common reef fishes (Acanthochromis polyacanthus and Amphiprion percula) to two projected future CO2 levels (750 and 1,000 atm) under both stable and diel fluctuating conditions. We found a common signature to stable elevated pCO2 for both species, which included the downregulation of immediate early genes, indicating lower brain activity. The transcriptional program was more strongly affected by higher average CO2 in a stable treatment than for fluctuating treatments, however, the largest difference in molecular response was between stable and fluctuating CO2 treatments. This indicates that a response to a change in environmental CO2 conditions is different for organisms living in a fluctuating than in stable environments. The differential regulation was related to steroid hormones and circadian rhythm (CR). Both species exhibited a marked difference in the expression of CR genes among CO2 treatments, possibly accommodating a more flexible adaptive approach to acid-base control, which could explain reduced impairment. Our results suggest that environmental CO2 fluctuations might enable reef fishes to phase shift their clocks and anticipate CO2 changes, thereby avoiding impairments and more successfully adjust to ocean acidification conditions.

ecology↗

bioRxiv2020

Proteomic responses to ocean acidification in the brain of juvenile coral reef fish

Elevated CO2 levels predicted to occur by the end of the century can affect the physiology and behaviour of marine fishes. For one important survival mechanism, the response to chemical alarm cues from conspecifics, substantial among-individual variation in the extent of behavioural impairment when exposed to elevated CO2 has been observed in previous studies. Whole brain transcriptomic data has further emphasized the importance of parental phenotypic variation in the response of juvenile fish to elevated CO2. In this study, we investigate the genome-wide proteomic responses of this variation in the brain of 5-week old spiny damselfish, Acanthochromis polyacanthus. We compared the expression of proteins in the brains of juvenile A. polyacanthus from two different parental behavioural phenotypes (sensitive and tolerant) that had been experimentally exposed to short-term, long-term and inter-generational elevated CO2. Our results show differential expression of key proteins related to stress response and epigenetic markers with elevated CO2 exposure. Proteins related to neurological development were also differentially expressed particularly in the long-term developmental treatment, which might be critical for juvenile development. By contrast, exposure to elevated CO2 in the parental generation resulted in only three differentially expressed proteins in the offspring, revealing potential for inter-generational acclimation. Lastly, we found a distinct proteomic pattern in juveniles due to the behavioural sensitivity of parents to elevated CO2, even though the behaviour of the juvenile fish was impaired regardless of parental phenotype. Our data shows that developing juveniles are affected in their brain protein expression by elevated CO2, but the effect varies with the length of exposure as well as due to variation of parental phenotypes in the population.

ecology↗

bioRxiv2018

Finding Nemo’s Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula

The iconic orange clownfish, Amphiprion percula, is a model organism for studying the ecology and evolution of reef fishes, including patterns of population connectivity, sex change, social organization, habitat selection and adaptation to climate change. Notably, the orange clownfish is the only reef fish for which a complete larval dispersal kernel has been established and was the first fish species for which it was demonstrated that anti-predator responses of reef fishes could be impaired by ocean acidification. Despite its importance, molecular resources for this species remain scarce and until now it lacked a reference genome assembly. Here we present a de novo chromosome-scale assembly of the genome of the orange clownfish Amphiprion percula. We utilized single-molecule real-time sequencing technology from Pacific Biosciences to produce an initial polished assembly comprised of 1,414 contigs, with a contig N50 length of 1.86 Mb. Using Hi-C based chromatin contact maps, 98% of the genome assembly were placed into 24 chromosomes, resulting in a final assembly of 908.8 Mb in length with contig and scaffold N50s of 3.12 and 38.4 Mb, respectively. This makes it one of the most contiguous and complete fish genome assemblies currently available. The genome was annotated with 26,597 protein coding genes and contains 96% of the core set of conserved actinopterygian orthologs. The availability of this reference genome assembly as a community resource will further strengthen the role of the orange clownfish as a model species for research on the ecology and evolution of reef fishes.

genomics↗