S2P3-R v2.0: computationally efficient modelling of shelf seas on regional to global scales

This is the final version. Available on open access from the European Geosciences Union via the DOI in this recordCode availability: S2P3Rv2.0 is available on GitHub: https://github.com/PaulHalloran/S2P3Rv2.0 (last access: 21 September 2021). The release associated with this paper (https://github.com/PaulHalloran/S2P3Rv2.0/releases/tag/v1.0.1, last access: 21 September 2021​​​​​​​) has been archived on Zenodo with the following DOI: https://doi.org/10.5281/zenodo.4147559 (Halloran, 2020a). The readme file available on GitHub or via the DOI link provides step-by-step instructions for how to install, set up and run the model, and it provides a basic script for analysing the model output. At the bottom of the readme, a worked example is provided to help the user go through the full process from generating model forcing files, running the model and displaying the output with some example data.Data availability: The model minus satellite SST data from the global (65∘ S–65∘ N) simulation averaged between 2006 and 2016, from which the global validation has been undertaken in this paper, is archived as NetCDF and csv files to allow potential users to undertake bespoke assessment of the model http://doi.org/10.5281/zenodo.4018815 (Halloran, 2020b).The marine impacts of climate change on our societies will be largely felt through coastal waters and shelf seas. These impacts involve sectors as diverse as tourism, fisheries and energy production. Projections of future marine climate change come from global models. Modelling at the global scale is required to capture the feedbacks and large-scale transport of physical properties such as heat, which occur within the climate system, but global models currently cannot provide detail in the shelf seas. Version 2 of the regional implementation of the Shelf Sea Physics and Primary Production (S2P3-R v2.0) model bridges the gap between global projections and local shelf-sea impacts. S2P3-R v2.0 is a highly simplified coastal shelf model, computationally efficient enough to be run across the shelf seas of the whole globe. Despite the simplified nature of the model, it can display regional skill comparable to state-of-the-art models, and at the scale of the global (excluding high latitudes) shelf seas it can explain >50 % of the interannual sea surface temperature (SST) variability in ∼60 % of grid cells and >80 % of interannual variability in ∼20 % of grid cells. The model can be run at any resolution for which the input data can be supplied, without expert technical knowledge, and using a modest off-the-shelf computer. The accessibility of S2P3-R v2.0 places it within reach of an array of coastal managers and policy makers, allowing it to be run routinely once set up and evaluated for a region under expert guidance. The computational efficiency and relative scientific simplicity of the tool make it ideally suited to educational applications. S2P3-R v2.0 is set up to be driven directly with output from reanalysis products or daily atmospheric output from climate models such as those which contribute to the sixth phase of the Climate Model Intercomparison Project, making it a valuable tool for semi-dynamical downscaling of climate projections. The updates introduced into version 2.0 of this model are primarily focused around the ability to geographical relocate the model, model usability and speed but also scientific improvements. The value of this model comes from its computational efficiency, which necessitates simplicity. This simplicity leads to several limitations, which are discussed in the context of evaluation at regional and global scales.Natural Environment Research Council (NERC)European Union Horizon 2020NOA

Historic landscape management: a validation of quantitative soil thin-section analyses

The archaeological interpretation of past land management practices can be greatly enhanced through examination of soil thin sections. Features relating to manuring practice are among those key to interpreting agricultural practices. The sources and the pro¬cesses leading to the distribution of these manure materials may further improve knowledge of the past landscape utilisation. The use of quantitative analyses to examine soil thin sections opens the possibility of considering these relationships between manured areas in greater detail and to extract more subtle spatial and temporal changes in past management. In this study the validation of this methodology has been tested with quantitative image analysis methods used to examine manure inputs to a well-documented historical landscape of Papa Stour, Shetland, where intensive manuring has been practised until the 1960s. By using both historic and ethnographic evidence to validate the image analysis protocol, differences in spatial and temporal distribution are examined for the practices of manuring with both fuel residues and with turf. The validation of the hypotheses expected from ethnographic and historical data that quantitative soils-based evidence allows the definition of variations in manuring strategies and provides a more secure basis from which to interpret manuring management strategies in archaeological landscapes

Caribbean Corals in Crisis: Record Thermal Stress, Bleaching, and Mortality in 2005

BACKGROUND The rising temperature of the world's oceans has become a major threat to coral reefs globally as the severity and frequency of mass coral bleaching and mortality events increase. In 2005, high ocean temperatures in the tropical Atlantic and Caribbean resulted in the most severe bleaching event ever recorded in the basin. METHODOLOGY/PRINCIPAL FINDINGS Satellite-based tools provided warnings for coral reef managers and scientists, guiding both the timing and location of researchers' field observations as anomalously warm conditions developed and spread across the greater Caribbean region from June to October 2005. Field surveys of bleaching and mortality exceeded prior efforts in detail and extent, and provided a new standard for documenting the effects of bleaching and for testing nowcast and forecast products. Collaborators from 22 countries undertook the most comprehensive documentation of basin-scale bleaching to date and found that over 80% of corals bleached and over 40% died at many sites. The most severe bleaching coincided with waters nearest a western Atlantic warm pool that was centered off the northern end of the Lesser Antilles. CONCLUSIONS/SIGNIFICANCE Thermal stress during the 2005 event exceeded any observed from the Caribbean in the prior 20 years, and regionally-averaged temperatures were the warmest in over 150 years. Comparison of satellite data against field surveys demonstrated a significant predictive relationship between accumulated heat stress (measured using NOAA Coral Reef Watch's Degree Heating Weeks) and bleaching intensity. This severe, widespread bleaching and mortality will undoubtedly have long-term consequences for reef ecosystems and suggests a troubled future for tropical marine ecosystems under a warming climate.This work was partially supported by salaries from the NOAA Coral Reef Conservation Program to the NOAA Coral Reef Conservation Program authors. NOAA provided funding to Caribbean ReefCheck investigators to undertake surveys of bleaching and mortality. Otherwise, no funding from outside authors' institutions was necessary for the undertaking of this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Connectivity and systemic resilience of the Great Barrier Reef

Australia’s iconic Great Barrier Reef (GBR) continues to suffer from repeated impacts of cyclones, coral bleaching, and outbreaks of the coral-eating crown-of-thorns starfish (COTS), losing much of its coral cover in the process. This raises the question of the ecosystem’s systemic resilience and its ability to rebound after large-scale population loss. Here, we reveal that around 100 reefs of the GBR, or around 3%, have the ideal properties to facilitate recovery of disturbed areas, thereby imparting a level of systemic resilience and aiding its continued recovery. These reefs (1) are highly connected by ocean currents to the wider reef network, (2) have a relatively low risk of exposure to disturbances so that they are likely to provide replenishment when other reefs are depleted, and (3) have an ability to promote recovery of desirable species but are unlikely to either experience or spread COTS outbreaks. The great replenishment potential of these ‘robust source reefs’, which may supply 47% of the ecosystem in a single dispersal event, emerges from the interaction between oceanographic conditions and geographic location, a process that is likely to be repeated in other reef systems. Such natural resilience of reef systems will become increasingly important as the frequency of disturbances accelerates under climate change

Oceanic inflow from the Coral Sea into the Great Barrier Reef

Long-term current meter data from the continental shelf region of the Great Barrier Reef show that there exists a zone of oceanic inflow onto the shelf. This oceanic inflow splits into two branches on meeting the continental shelf slope, resulting in two net longshore currents on the slope, one to the north and the other to the south of the separation point. In 1981 this separation point was located between 17°S and 18°S. This circulation was successfully predicted using a depth-averaged two-dimensional model in which the regional sea level gradient is explicitly added in the momentum equations. The resulting circulation on the continental shelf is controlled by an oceanic inflow of 0·58 Sv, spread over 500 km of the shelf edge both north and south of the separation point. The inflow appears measurably impeded by the presence of coral reefs, with >50% of the inflow occurring in a 150 km long area where reef density is small. Satellite images confirm this spatial variability. Longshore currents on the shelf generated by the inflow are modulated by the wind and tides, which can deflect the mean current away from areas of high reef density and generate localized outflows to the Coral Sea. Oceanic inflow is believed to be important because it flushes the shelf even in the absence of wind; it controls the dominant direction of across-shelf and along-shelf spread of spawn material from reefs; it makes it possible for upwelled water to spread quickly over the GBR shelf; it may also protect coral reefs by preventing river plumes from spreading onto the outer shelf

Early cellular changes are indicators of pre-bleaching thermal stress in the coral host

Thermal stress causes the coral-dinoflagellate symbiosis to disassociate and the coral tissues to whiten. The onset and occurrence of this coral bleaching is primarily defined via the dinoflagellate responses. Here we demonstrate that thermal stress responses occur in the coral host tissues in the days before the onset of coral bleaching. The observed sequence of thermal responses includes reductions in thickness of coral tissue layers and apoptosis of the cells prior to reductions in symbiont density. In the days before the onset of coral bleaching the outer coral tissue layer (epithelium) thickness reduces and apoptosis occurs within the gastrodermis. Two days following this, coinciding with an initial reduction of symbiont density (by approximately 25%), gastrodermal thickness decreased and apoptosis of host cells was identified in the epithelium. This was eventually followed by large reduction in symbiont density (by approximately 50%) consistent with coral bleaching. Both pro-apoptotic and anti-apoptotic genes are identified in the reef building coral Acropora aspera, demonstrating the necessary pathways are present for fine control of host apoptosis. Our study shows that defining periods of host stress based on the responses defined by dinoflagellate symbiont underestimates the importance of early cellular events and the cellular complexity of coral host. (c) 2008 Elsevier B.V. All rights reserved