Seawater carbonate chemistry and gene expression of a reef fish Acanthochromis polyacanthus, supplement to: Schunter, Celia; Welch, Megan J; Nilsson, Göran E; Rummer, Jodie L; Munday, Philip L; Ravasi, Timothy (2018): An interplay between plasticity and parental phenotype determines impacts of ocean acidification on a reef fish. Nature Ecology & Evolution, 2(2), 334-342
AuthorsSchunter, Celia Marei
Welch, Megan J.
Nilsson, Göran E.
Rummer, Jodie L.
Munday, Philip L.
KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Integrative Systems Biology Lab
Permanent link to this recordhttp://hdl.handle.net/10754/663946
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AbstractThe impacts of ocean acidification will depend on the ability of marine organisms to tolerate, acclimate and eventually adapt to changes in ocean chemistry. Here, we use a unique transgenerational experiment to determine the molecular response of a coral reef fish to short-term, developmental and transgenerational exposure to elevated CO2, and to test how these responses are influenced by variations in tolerance to elevated CO2 exhibited by the parents. Within-generation responses in gene expression to end-of-century predicted CO2 levels indicate that a self-amplifying cycle in GABAergic neurotransmission is triggered, explaining previously reported neurological and behavioural impairments. Furthermore, epigenetic regulator genes exhibited a within-generation specific response, but with some divergence due to parental phenotype. Importantly, we find that altered gene expression for the majority of within-generation responses returns to baseline levels following parental exposure to elevated CO2 conditions. Our results show that both parental variation in tolerance and cross-generation exposure to elevated CO2 are crucial factors in determining the response of reef fish to changing ocean chemistry.
CitationSchunter, C., Welch, M. J., Nilsson, G. E., Rummer, J. L., Munday, P. L., & Ravasi, T. (2019). Seawater carbonate chemistry and gene expression of a reef fish Acanthochromis polyacanthus, supplement to: Schunter, Celia; Welch, Megan J; Nilsson, Göran E; Rummer, Jodie L; Munday, Philip L; Ravasi, Timothy (2018): An interplay between plasticity and parental phenotype determines impacts of ocean acidification on a reef fish. Nature Ecology & Evolution, 2(2), 334-342 [Data set]. PANGAEA - Data Publisher for Earth & Environmental Science. https://doi.org/10.1594/PANGAEA.900202
RelationsIs Supplement To:
Schunter C, Welch MJ, Nilsson GE, Rummer JL, Munday PL, et al. (2017) An interplay between plasticity and parental phenotype determines impacts of ocean acidification on a reef fish. Nature Ecology & Evolution. Available: http://dx.doi.org/10.1038/s41559-017-0428-8.. DOI: 10.1038/s41559-017-0428-8 HANDLE: 10754/626399
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Community-level sensitivity of a calcifying ecosystem to acute in situ CO2 enrichment, supplement to: Burdett, H L; Perna, G; McKay, Lucy; Broomhead, Gemma; Kamenos, N A (2018): Community-level sensitivity of a calcifying ecosystem to acute in situ CO2 enrichment. Marine Ecology Progress Series, 587, 73-80Burdett, HL; Perna, Gabriela; McKay, L; Broomhead, G; Kamenos, NA (PANGAEA - Data Publisher for Earth & Environmental Science, 2019) [Dataset]The rate of change in ocean carbonate chemistry is a vital determinant in the magnitude of effects observed. Benthic marine ecosystems are facing an increasing risk of acute CO2 exposure that may be natural or anthropogenically derived (e.g. engineering and industrial activities). However, our understanding of how acute CO2 events impact marine life is restricted to individual organisms, with little understanding for how this manifests at the community level. Here, we investigated in situ the effect of acute CO2 enrichment on the coralline algal ecosystem—a globally ubiquitous, ecologically and economically important habitat, but one which is likely to be sensitive to CO2 enrichment due to its highly calcified reef-like structures engineered by coralline algae. Most notably, we observed a rapid community-level shift to favour net dissolution rather than net calcification. Smaller changes from net respiration to net photosynthesis were also observed. There was no effect on the net flux of DMS/DMSP (algal secondary metabolites), nor on the nutrients nitrate and phosphate. Following return to ambient CO2 levels, only a partial recovery was seen within the monitoring timeframe. This study highlights the sensitivity of biogenic carbonate marine communities to acute CO2 enrichment and raises concerns over the capacity for the system to 'bounce back' if subjected to repeated acute high-CO2 events.
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Codon Deviation Coefficient: A novel measure for estimating codon usage bias and its statistical significanceZhang, Zhang; Li, Jun; Cui, Peng; Ding, Feng; Li, Ang; Townsend, Jeffrey P; Yu, Jun (BMC Bioinformatics, Springer Nature, 2012-03-23) [Article]Background: Genetic mutation, selective pressure for translational efficiency and accuracy, level of gene expression, and protein function through natural selection are all believed to lead to codon usage bias (CUB). Therefore, informative measurement of CUB is of fundamental importance to making inferences regarding gene function and genome evolution. However, extant measures of CUB have not fully accounted for the quantitative effect of background nucleotide composition and have not statistically evaluated the significance of CUB in sequence analysis.Results: Here we propose a novel measure--Codon Deviation Coefficient (CDC)--that provides an informative measurement of CUB and its statistical significance without requiring any prior knowledge. Unlike previous measures, CDC estimates CUB by accounting for background nucleotide compositions tailored to codon positions and adopts the bootstrapping to assess the statistical significance of CUB for any given sequence. We evaluate CDC by examining its effectiveness on simulated sequences and empirical data and show that CDC outperforms extant measures by achieving a more informative estimation of CUB and its statistical significance.Conclusions: As validated by both simulated and empirical data, CDC provides a highly informative quantification of CUB and its statistical significance, useful for determining comparative magnitudes and patterns of biased codon usage for genes or genomes with diverse sequence compositions. 2012 Zhang et al; licensee BioMed Central Ltd.