The life cycle of many benthic macro-invertebrates is characterised by a planktonic life stage where larvae are transported by ocean currents and mixing and after some time they reach a stage where they settle onto the ocean bottom and, provided a suitable habitat is available, initiate their benthic life stage as juvenile organisms and complete their life cycle when they mature and spawn as adults. Such age-specific behaviour is in general difficult to include in large scale ocean models unless dispersal is considered on an individual basis, i.e. individual based model coupled with a Lagrangian description of the flow field. However, here we address this issue in an Eulerian framework and develop and apply a new life cycle and population dynamical model of benthic fauna and implement the model in a high-resolution three-dimensional circulation model of the North Sea/Baltic Sea transition zone. The model explicitly describes specific life stages of the population and considers the different processes affecting the organisms during their life cycle, e.g. spawning, dispersion and settling. The model considers different life stages of an idealised marine organism, representing a typical benthic macro-invertebrate species in the area. Populations of juvenile and adult benthic organisms are maintained by spawning, occurring regularly every spring, and subsequent settling of larvae. The pelagic larval stages are simulated by a larval concentration distribution function, i.e. discrete age-classes of the total larval concentration, and age-specific physiological processes, as the onset of their settling behaviour, is explicitly accounted for in the model. Model simulations show, in general, a large connectivity between habitats in the northern and southern part of the area but also that self-recruitment is sufficient to sustain the two populations independently. A sensitivity study were carried out with the spawning rate as a control parameter and two non-trivial quasi-stationary steady states of benthic biomass distributions were identified, characterised by a high and low distribution of organisms in the area, respectively. A stability diagram identifies a bifurcation point when the spawning rate is reduced by 65% and where lower spawning rates implies two different stable equilibria. The existence of multiple quasi-stationary steady states can be explained by the general circulation in the area: when spawning into the surface layer takes place from recruitment areas close to the North Sea where the out-flowing Baltic Sea surface water hinder the southward transport of pelagic larvae. The existence of multiple equilibria support the hypothesis of regime shifts in coupled physical-biological systems where modest changes in critical processes causes rapid and extensive structural changes in the ecosystem. Such changes could occur if a system is close to a bifurcation point such that small changes in critical internal biotic dynamics or in environmental conditions force the system into a new equilibria, for example due to hypoxia or changes in temperature or salinity. Finally, it is shown that model simulations of periods with hypoxic bottom water masses reduces the total benthic biomass distribution in the area significantly.
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