Posts Tagged 'individualmodeling'

Blue mussel (Genus Mytilus) transcriptome response to simulated climate change in the Gulf of Maine

The biogeochemistry of the Gulf of Maine (GOM) is rapidly changing in response to the changing climate, including rising temperatures, acidification, and declining primary productivity. These impacts are projected to worsen over the next 100 y and will apply selective pressure on populations of marine calcifiers. This study investigates the transcriptome expression response to these changes in ecologically and economically important marine calcifiers, blue mussels. Wild mussels (Mytilus edulis and Mytilus trossulus) were sampled from sites spanning the GOM and exposed to two different biogeochemical water conditions: (1) present-day conditions in the GOM and (2) simulated future conditions, which included elevated temperature, increased acidity, and decreased food supply. Patterns of gene expression were measured using RNA sequencing from 24 mussel samples and contrasted between ambient and future conditions. The net calcification rate, a trait predicted to be under climate-induced stress, was measured for each individual over a 2-wk exposure period and used as a covariate along with gene expression patterns. Generalized linear models, with and without the calcification rate, were used to identify differentially expressed transcripts between ambient and future conditions. The comparison revealed transcripts that likely comprise a core stress response characterized by the induction of molecular chaperones, genes involved in aerobic metabolism, and indicators of cellular stress. Furthermore, the model contrasts revealed transcripts that may be associated with individual variation in calcification rate and suggest possible biological processes that may have downstream effects on calcification phenotypes, such as zinc-ion binding and protein degradation. Overall, these findings contribute to the understanding of blue mussel adaptive responses to imminent climate change and suggest metabolic pathways are resilient in variable environments.

Continue reading ‘Blue mussel (Genus Mytilus) transcriptome response to simulated climate change in the Gulf of Maine’

Ocean acidification does not impair the behaviour of coral reef fishes

The partial pressure of CO2 in the oceans has increased rapidly over the past century, driving ocean acidification and raising concern for the stability of marine ecosystems1,2,3. Coral reef fishes are predicted to be especially susceptible to end-of-century ocean acidification on the basis of several high-profile papers4,5 that have reported profound behavioural and sensory impairments—for example, complete attraction to the chemical cues of predators under conditions of ocean acidification. Here, we comprehensively and transparently show that—in contrast to previous studies—end-of-century ocean acidification levels have negligible effects on important behaviours of coral reef fishes, such as the avoidance of chemical cues from predators, fish activity levels and behavioural lateralization (left–right turning preference). Using data simulations, we additionally show that the large effect sizes and small within-group variances that have been reported in several previous studies are highly improbable. Together, our findings indicate that the reported effects of ocean acidification on the behaviour of coral reef fishes are not reproducible, suggesting that behavioural perturbations will not be a major consequence for coral reef fishes in high CO2 oceans.

Continue reading ‘Ocean acidification does not impair the behaviour of coral reef fishes’

Coccolithophore growth and calcification in an acidified ocean: insights from community earth system model simulations

Anthropogenic CO2 emissions are inundating the upper ocean, acidifying the water, and altering the habitat for marine phytoplankton. These changes are thought to be particularly influential for calcifying phytoplankton, namely, coccolithophores. Coccolithophores are widespread and account for a substantial portion of open ocean calcification; changes in their abundance, distribution, or level of calcification could have far‐reaching ecological and biogeochemical impacts. Here, we isolate the effects of increasing CO2 on coccolithophores using an explicit coccolithophore phytoplankton functional type parameterization in the Community Earth System Model. Coccolithophore growth and calcification are sensitive to changing aqueous CO2. While holding circulation constant, we demonstrate that increasing CO2 concentrations cause coccolithophores in most areas to decrease calcium carbonate production relative to growth. However, several oceanic regions show large increases in calcification, such the North Atlantic, Western Pacific, and parts of the Southern Ocean, due to an alleviation of carbon limitation for coccolithophore growth. Global annual calcification is 6% higher under present‐day CO2 levels relative to preindustrial CO2 (1.5 compared to 1.4 Pg C/year). However, under 900 μatm CO2, global annual calcification is 11% lower than under preindustrial CO2 levels (1.2 Pg C/year). Large portions of the ocean show greatly decreased coccolithophore calcification relative to growth, resulting in significant regional carbon export and air‐sea CO2 exchange feedbacks. Our study implies that coccolithophores become more abundant but less calcified as CO2 increases with a tipping point in global calcification (changing from increasing to decreasing calcification relative to preindustrial) at approximately ∼600 μatm CO2.

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Reduced nitrogenase efficiency dominates response of the globally important nitrogen fixer Trichodesmium to ocean acidification

The response of the prominent marine dinitrogen (N2)-fixing cyanobacteria Trichodesmium to ocean acidification (OA) is critical to understanding future oceanic biogeochemical cycles. Recent studies have reported conflicting findings on the effect of OA on growth and N2fixation of Trichodesmium. Here, we quantitatively analyzed experimental data on how Trichodesmium reallocated intracellular iron and energy among key cellular processes in response to OA, and integrated the findings to construct an optimality-based cellular model. The model results indicate that Trichodesmium growth rate decreases under OA primarily due to reduced nitrogenase efficiency. The downregulation of the carbon dioxide (CO2)-concentrating mechanism under OA has little impact on Trichodesmium, and the energy demand of anti-stress responses to OA has a moderate negative effect. We predict that if anthropogenic CO2 emissions continue to rise, OA could reduce global N2 fixation potential of Trichodesmium by 27% in this century, with the largest decrease in iron-limiting regions.

Continue reading ‘Reduced nitrogenase efficiency dominates response of the globally important nitrogen fixer Trichodesmium to ocean acidification’

Studentized bootstrap model-averaged tail area intervals

In many scientific studies, the underlying data-generating process is unknown and multiple statistical models are considered to describe it. For example, in a factorial experiment we might consider models involving just main effects, as well as those that include interactions. Model-averaging is a commonly-used statistical technique to allow for model uncertainty in parameter estimation. In the frequentist setting, the model-averaged estimate of a parameter is a weighted mean of the estimates from the individual models, with the weights typically being based on an information criterion, cross-validation, or bootstrapping. One approach to building a model-averaged confidence interval is to use a Wald interval, based on the model-averaged estimate and its standard error. This has been the default method in many application areas, particularly those in the life sciences. The MA-Wald interval, however, assumes that the studentized model-averaged estimate has a normal distribution, which can be far from true in practice due to the random, data-driven model weights. Recently, the model-averaged tail area Wald interval (MATA-Wald) has been proposed as an alternative to the MA-Wald interval, which only assumes that the studentized estimate from each model has a N(0, 1) or t-distribution, when that model is true. This alternative to the MA-Wald interval has been shown to have better coverage in simulation studies. However, when we have a response variable that is skewed, even these relaxed assumptions may not be valid, and use of these intervals might therefore result in poor coverage. We propose a new interval (MATA-SBoot) which uses a parametric bootstrap approach to estimate the distribution of the studentized estimate for each model, when that model is true. This method only requires that the studentized estimate from each model is approximately pivotal, an assumption that will often be true in practice, even for skewed data. We illustrate use of this new interval in the analysis of a three-factor marine global change experiment in which the response variable is assumed to have a lognormal distribution. We also perform a simulation study, based on the example, to compare the lower and upper error rates of this interval with those for existing methods. The results suggest that the MATA-SBoot interval can provide better error rates than existing intervals when we have skewed data, particularly for the upper error rate when the sample size is small.

Continue reading ‘Studentized bootstrap model-averaged tail area intervals’

Linking social preferences and ocean acidification impacts in mussel aquaculture

Ocean Acidification (OA) has become one of the most studied global stressors in marine science during the last fifteen years. Despite the variety of studies on the biological effects of OA with marine commercial species, estimations of these impacts over consumers’ preferences have not been studied in detail, compromising our ability to undertake an assessment of market and economic impacts resulting from OA at local scales. Here, we use a novel and interdisciplinary approach to fill this gap. We experimentally test the impact of OA on commercially relevant physical and nutritional attributes of mussels, and then we use economic discrete choice models to assess the marginal effects of these impacts over consumers’ preferences and wellbeing. Results showed that attributes, which were significantly affected by OA, are also those preferred by consumers. Consumers are willing to pay on average 52% less for mussels with evidences of OA and are willing to increase the price they pay to avoid negative changes in attributes due to OA. The interdisciplinary approach developed here, complements research conducted on OA by effectively informing how OA economic impacts can be analyzed under the lens of marginal changes in market price and consumer’ welfare. Thereby, linking global phenomena to consumers’ wellbeing, and shifting the focus of OA impacts to assess the effects of local vulnerabilities in a wider context of people and businesses.

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Particulate inorganic to organic carbon production as a predictor for coccolithophorid sensitivity to ongoing ocean acidification

Ocean acidification (OA) can induce shifts in plankton community composition, with coccolithophores being mostly negatively impacted. This is likely to change particulate inorganic and organic carbon (PIC and POC, respectively) production, with impacts on the biological carbon pump. Hence, assessing and, most importantly, understanding species‐specific sensitivities of coccolithophores is paramount. In a multispecies comparison, spanning more than two orders of magnitude in terms of POC and PIC production rates, among Calcidiscus leptoporus, Coccolithus pelagicus subsp. braarudii, Emiliania huxleyi, Gephyrocapsa oceanica, and Scyphosphaera apsteinii, we found that cellular PIC : POC was a good predictor for a species’ OA sensitivity. This is likely related to the need for cellular pH homeostasis, which is challenged by the process of calcification producing protons internally, especially when seawater pH decreases in an OA scenario. With higher PIC : POC, species and strains being more sensitive to OA coccolithophores may shift toward less calcified varieties in the future.

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Ocean acidification in the IPCC AR5 WG II

OUP book