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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Calcification Accretion Units (CAUS): A standardized approach for quantifying recruitment and calcium carbonate accretion in marine habitatsJohnson, Maggie D.; Price, Nichole N; Smith, Jennifer E (Methods in Ecology and Evolution, Wiley, 2022-04-11) [Article]1. Standardized metrics that quantify a component of ecosystem functioning are essential for evaluating the current status of coastal marine habitats and for monitoring how ecologically important ecosystems are changing in response to global and local environmental change. Calcification Accretion Units (CAUs) are a standardized tool for quantifying net calcium carbonate accretion, early successional community structure, recruitment of algae and sessile invertebrates, and other response metrics that can be determined from image analyses in coastal marine habitats. 2. CAUs are comprised of paired settlement tiles that are separated by a spacer. This design mimics the presence of different representative habitats that are common in most marine systems such as exposed benthic surfaces, cryptic spaces inaccessible to grazers, and shaded overhangings. The protected space between the tiles facilitates recruitment and inclusion of cryptic taxa in community assemblage estimates. After a period of deployment, CAUs are photographed for image analysis and then decalcified to quantify calcium carbonate accretion rates. 3. The CAU methodology provides a cost-effective, standardized protocol for evaluating structure and function in marine benthic habitats. We show illustrate how CAU data can be used to compare accretion rates and the relative proportion of carbonate polymorphs in ecosystems across the globe. 4. Here we provide a comprehensive standard operating procedure for building, deploying, and processing CAUs, to ensure that a consistent protocol is used for accurate data collection and cross-system comparative studies.
Deviations from Vegard’s law in ternary III-V alloysMurphy, S. T.; Chroneos, Alexander; Grimes, R. W.; Jiang, C.; Schwingenschlögl, Udo (Physical Review B, American Physical Society (APS), 2010-08-03) [Article]Vegard’s law states that, at a constant temperature, the volume of an alloy can be determined from a linear interpolation of its constituent’s volumes. Deviations from this description occur such that volumes are both greater and smaller than the linear relationship would predict. Here we use special quasirandom structures and density functional theory to investigate such deviations for MxN1−xAs ternary alloys, where M and N are group III species (B, Al, Ga, and In). Our simulations predict a tendency, with the exception of AlxGa1−xAs, for the volume of the ternary alloys to be smaller than that determined from the linear interpolation of the volumes of the MAs and BAs binary alloys. Importantly, we establish a simple relationship linking the relative size of the group III atoms in the alloy and the predicted magnitude of the deviation from Vegard’s law.
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.