S1 File -

Supporting Information A. The Baltic Sea Atlantis:
File A. Input data of the tracers per box for the Baltic Atlantis
File B. Input data of the tracers per box and layer for the Baltic Atlantis
File C. Input data for the fill values for the tracers for the Baltic Atlantis
Figure A. Schematic diagram illustrating the structure of the coupled HBM-ERGOM model system
Figure B. 120 year simulation run
Figure C. The FISHRENT model diagram, here applied to Kattegat and Western Baltic.
Figure D. One-year cycle of Chl-a in the different polygons
Figure E. Relative biomass–initial condition values compared with simulation outcome
Figure F. Diet composition of all predators
Figure G. Biomass per age group over time for all vertebrates
Figure H. Demography distribution for all vertebrates—the number of individuals for each age group
Figure I. Geographical distribution of all functional groups
Figure J. Geographical distribution of oxygen in the different layers. Panel 1 = top layer, panel 7 = bottom layer
Figure K. Total biomass of Cod for scenario 1 (baseline) compared to scenario 5
Figure L. Relative prey biomass for predator cod, baseline compared to scenario 5
Figure M. One-year cycle of nutrients in the different polygons
Table A. Physical and geochemical parameters used to internally force the Baltic Atlantis model.
Table B. Summary of riverine + direct point source waterborne nitrogen loads applied to the Baltic Atlantis grid based on information from the Review of the Fifth Baltic Sea Pollution Load Compilation for the 2013 HELCOM Ministerial Meeting (HELCOM PLC-5.5). Nitrogen fractionation between DIN and DON based on Savchuk et al. (2012). Bioavailable fraction of DON assumed equal to labile DON as in Savchuk and Wolff (2009). Coastal retention fractions from Savchuk and Wolff (2009).
Table C. Summary of key sources used to inform the biological module of Baltic Atlantis in relation to abundance and biomass, demography, prey-predator interaction and other functions.
Table D. Summary of key biological parameters used for vertebrates in the Baltic Atlantis model.
Table E. Maximum potential growth rates and clearance rates per age class of all vertebrate biological groups.
Table F. Key biological rates calibrated for the invertebrate groups.
Table G. Biological functional group structure of the Baltic Atlantis model. Groups are categorized according to the ecosystem level they represent. Key species aggregated within a functional group are listed. The first species in each list is the representative one for that particular functional group. Groups that are currently “turned off”, and which do not play a role in the biological interactions, are marked with an asterisk (*).
Table H. Summary of basic parameters describing the general behavior of biological groups in the model, used as input to the model.
Table I. Relative cover of each polygon with 3 types of bottom abiotic habitats: bedrock, sand, mud, and a fourth abiotic habitat which corresponds to man-made structures such as wind-mill parks, pipelines etc.
Table J. Total Stock Biomass, TSB (tonnes), and natural mortalities (M), target fishing mortalities (F) and TACs (tonnes) in 2012, for the seven species groups included in the FISHRENT model and TSB and F from the Atlantis model, also input for the FISHRENT model.
Table K. Danish fleet segments operating either in the Kattegat (KA), the Western Baltic (WB) or in both areas (KAWB) in 2012.
Table L. Catch value and catch value distribution for the 9 Danish fleet segments operating in the Kattegat and/or the Western Baltic in 2012.The table shows that Netters and liners less than 12 meters, and Trawlers 12–15 meters, 15–18 meters and 18–24 meters cover more than 85% of the total catch value. It has therefore been decided to focus on these four fleet segments in the model evaluations.
Table M. Economic input data for the 4 fleet segments included in the FISHRENT model, based on 2012 data.
Table N. Species prices (1000 €/tonnes) based on 2012 landings data.
Table O. Revenue and effort Fractions in Kattegat and Western Baltic of total Revenue obtained and effort exerted in 2012 in all waters by the four fleet segments included in the FISHRENT model.
Table P. Catch value fraction (%) of species included in the FISHRENT model of total catch value in 2012 for the four fleet segments included in the model.
Table Q. TAC shares for the four fleet segments included in the FISHRENT model for each of the 7 species groups.
Table R. Cobb-Douglas intercept parameters (tonnes) used in the FISHRENT model
Table S. Annual average total Baltic Sea biomass [metric tons] of all active biological groups in the Baltic Atlantis model averaged over the last five years (from a total of year 60). For vertebrates, for which good constraints on abundance/biomass distributions were available, “x initial” factor difference as relative to initial/expected conditions is given as well.
Table T. Total revenue (mill EUR) over the period 2012–2037 for the four fleet segments in each of the four scenarios. Revenue is shown over all waters shown, together with revenue in Kattegat and in the Western Baltic
Table U. Total fuel costs (mill EUR) over the period 2012–2037 for the four fleet segments in each of the four scenarios. Fuel costs are shown over all waters shown, together with fuel costs in Kattegat and in the Western Baltic
Table V. Total crew costs (mill EUR) over the period 2012–2037 for the four fleet segments in each of the four scenarios. Crew costs are shown over all waters shown, together with crew costs in Kattegat and in the Western Baltic
Table W. Total variable costs (mill EUR) over the period 2012–2037 for the four fleet segments in each of the four scenarios. Variable costs are shown over all waters shown, together with variable costs in Kattegat and in the Western Baltic
Table X. Total capital costs (mill EUR) over the period 2012–2037 for the four fleet segments in each of the four scenarios. Capital costs are shown over all waters shown, together with capital costs in Kattegat and in the Western Baltic
Table Y. Total fixed costs (mill EUR) over the period 2012–2037 for the four fleet segments in each of the four scenarios. Fixed costs are shown over all waters shown, together with fixed costs in Kattegat and in the Western Baltic
Table Z. Total profits (1000 EUR) (mill EUR) over the period 2012–2037 for the four fleet segments in each of the four scenarios. 'Profits are shown over all waters shown, together with profit in Kattegat and in the Western Baltic
(ZIP)