Probabilistic approach of water residence time and connectivity using Markov Chains with application to tidal embayments

Markov Chain analysis was recently proposed to assess the time scales and preferential pathways into biological or physical networks by computing residence time, first passage time, rates of transfer between nodes and number of passages in a node. We propose to adapt an algorithm already published for simple systems to physical systems described with a high resolution hydrodynamic model. The method is applied to bays and estuaries on the Eastern Coast of Canada for their interest in shellfish aquaculture. Current velocities have been computed by using a 2 dimensional grid of elements and circulation patterns were summarized by averaging Eulerian flows between adjacent elements. Flows and volumes allow computing probabilities of transition between elements and to assess the average time needed by virtual particles to move from one element to another, the rate of transfer between two elements, and the average residence time of each system. We also combined transfer rates and times to assess the main pathways of virtual particles released in farmed areas and the potential influence of farmed areas on other areas. We suggest that Markov chain is complementary to other sets of ecological indicators proposed to analyse the interactions between farmed areas - e.g. depletion index, carrying capacity assessment. Markov Chain has several advantages with respect to the estimation of connectivity between pair of sites. It makes possible to estimate transfer rates and times at once in a very quick and efficient way, without the need to perform long term simulations of particle or tracer concentration.

Mixed Layer formation and restratification in presence of mesoscale and submesoscale turbulence

Recent realistic high resolution modeling studies show a net increase of submesoscale activity in fall and winter when the mixed layer depth is at its maximum. This submesoscale activity increase is associated with a reduced deepening of the mixed layer. Both phenomena can be related to the development of mixed layer instabilities, which convert available potential energy into submesoscale eddy kinetic energy and contribute to a fast restratification by slumping the horizontal density gradient in the mixed layer. In the present work, the mixed layer formation and restratification was studied by uniformly cooling a fully turbulent zonal jet in a periodic channel at different resolutions, from eddy resolving (10 km) to submesoscale permitting (2 km). The effect of the submesoscale activity, highlighted by these different horizontal resolutions, was quantified in terms of mixed layer depth, restratification rate and buoyancy fluxes. Contrary to many idealized studies focusing on the restratification phase only, this study addresses a continuous event of mixed layer formation followed by its complete restratification. The robustness of the present results was established by ensemble simulations. The results show that, at higher resolution, when submesoscale starts to be resolved, the mixed layer formed during the surface cooling is significantly shallower and the total restratification almost three times faster. Such differences between coarse and fine resolution models are consistent with the submesoscale upward buoyancy flux, which balances the convection during the formation phase and accelerates the restratification once the surface cooling is stopped. This submesoscale buoyancy flux is active even below the mixed layer. Our simulations show that mesoscale dynamics also cause restratification, but on longer time scales. Finally, the spatial distribution of the mixed layer depth is highly heterogeneous in the presence of submesoscale activity, prompting the question of whether it is possible to parameterize submesoscale effects and their effects on the marine biology as a function of a spatially-averaged mixed layer depth.

Origin and fate of surface drift in the oceanic convergence zones of the eastern Pacific

This study investigates the structure and intensity of the surface pathways connecting to and from the central areas of the large-scale convergence regions of the eastern Pacific Ocean. Surface waters are traced with numerical Lagrangian particles transported in the velocity field of three different ocean models with horizontal resolutions that range from ¼° to 1/32°. The connections resulting from the large-scale convergent Ekman dynamics agree qualitatively but are strongly modulated by eddy variability that introduces meridional asymmetry in the amplitude of transport. Lagrangian forward-in-time integrations are used to analyze the fate of particles originating from the central regions of the convergence zones and highlight specific outflows not yet reported for the southeastern Pacific when using the currents at the highest resolutions (1/12° and 1/32°). The meridional scales of these outflows are comparable to the characteristic width of the fine-scale striation of mean currents.

Report of the Workshop on Growth-increment Chronologies in Marine Fish: climate-ecosystem interactions in the North Atlantic 2 (WKGIC2). 18-22 April 2016 Esporles, Mallorca, Spain

Over the past several decades, thousands of otoliths, bivalve shells, and scales have been collected for the purposes of age determination and remain archived in European and North American fisheries laboratories. Advances in digital imaging and computer software combined with techniques developed by tree-ring scientists provide a means by which to extract additional levels of information in these calcified structures and generate annually resolved (one value per year), multidecadal time-series of population-level growth anomalies. Chemical and isotopic properties may also be extracted to provide additional information regarding the environmental conditions these organisms experienced.Given that they are exactly placed in time, chronologies can be directly compared to instrumental climate records, chronologies from other regions or species, or time-seriesof other biological phenomena. In this way, chronologies may be used to reconstruct historical ranges of environmental variability, identify climatic drivers of growth, establish linkages within and among species, and generate ecosystem-level indicators. Following the first workshop in Hamburg, Germany, in December 2014, the second workshop on Growth increment Chronologies in Marine Fish: climate-ecosystem interactions in the North Atlantic (WKGIC2) met at the Mediterranean Institute for Advanced Studies headquarters in Esporles, Spain, on 18–22 April 2016, chaired by Bryan Black (USA) and Christoph Stransky (Germany).Thirty-six participants from fifteen different countries attended. Objectives were to i) review the applications of chronologies developed from growth-increment widths in the hard parts (otoliths, shells, scales) of marine fish and bivalve species ii) review the fundamentals of crossdating and chronology development, iii) discuss assumptions and limitations of these approaches, iv) measure otolith growth-increment widths in image analysis software, v) learn software to statistically check increment dating accuracy, vi) generate a growth increment chronology and relate it to climate indices, and vii) initiate cooperative projects or training exercises to commence after the workshop.The workshop began with an overview of tree-ring techniques of chronology development, including a hands-on exercise in cross dating. Next, we discussed the applications of fish and bivalve biochronologies and the range of issues that could be addressed. We then reviewed key assumptions and limitations, especially those associated with short-lived species for which there are numerous and extensive otolith archives in European fisheries labs. Next, participants were provided with images of European plaice otoliths from the North Sea and taught to measure increment widths in image analysis software. Upon completion of measurements, techniques of chronology development were discussed and contrasted to those that have been applied for long-lived species. Plaice growth time-series were then related to environmental variability using the KNMI Climate Explorer. Finally, potential future collaborations and funding opportunities were discussed, and there was a clear desire to meet again to compare various statistical techniques for chronology development using a range existing fish, bivalve, and tree growth-increment datasets. Overall, we hope to increase the use of these techniques, and over the long term, develop networks of biochronologies for integrative analyses of ecosystem functioning and relationships to long-term climate variability and fishing pressure.