Supplementary material. Table 1: Summary of SIMA models, content, data sources and state of validation. References are in manuscript.
Model Type Content
Hydrodynamic Process based Equations for momentum, continuity and
Herzfeld (2018) conservation of heat and salt, employing the
hydrostatic and Boussinesq assumptions
applied on a curvilinear grid. Outputs from
the model include three-dimensional
distributions of velocity, temperature,
salinity, density, passive tracers, mixing
coefficients and sea-level. Inputs required by
the model include forcing due to wind,
atmospheric pressure gradients, surface
heat and water fluxes and open-boundary
conditions such as tides and low frequency
ocean currents.
Catchment Process based Flow model of the instantaneous flows of all
major freshwater systems discharging into
the area of interest.
Sediment Process based Multiple layers with a thin layer of easily
Wild-Allen et al (2018) resuspendable material overlying thicker
Margvelashvili (2009) layers of consolidated sediment. It deals
with viscosity, remineralization, and
resuspension.
Biogeochemical Process based Tracks the flux of N and P through three size
Wild-Allen et al (2018) structured phytoplankton and two
zooplankton groups, as well as
microphytobenthos, macroalgae, shellfish
Data sources
River inflow from gauged rivers.
Model-based boundary and initial
conditions taken from models
maintained by the Australian
Bureau of Meteorology.
Topography, precipitation, ET,
temperature and snow/ice cover
Parameter values have where
possible been sourced from
literature reporting local
observations in Chile or otherwise
found from model parameter data
libraries (Robson et al., 2018) or
modelling studies in Australian
temperate waters (Wild-Allen et
al., 2013; Wild-Allen &
Andrewartha 2016).
As for the sediment model.
Status
Hindcast for Dec 2014-Jan 2016.
Near real time mode post Jan
2016. Skill assessed versus
observed sea levels, sea surface
temperature and salinity.
Compared against gauged
rivers.
Predicted sediment
characteristics were found to
most closely match the
characteristics of locally
observed particles.
Validated (spatial and temporal)
against observations collected
in the region during 2015-16 by
IFOP and from 4 mooring
 beds, dissolved nutrient pools and 2 detritus
classes. It includes diffusion, gas exchange,
adsorption, nitrification/denitrification and
the main ecological processes associated
with primary production, consumption and
mortality. A full optical model is also
included.
Connectivity Statistical and Statistical particle tracking using flows from
Gorton and Condie Process based the hydrodynamic model. Current fields
(2018) from the near real time hydrodynamic
model were interpolated onto a regular
latitude-longitude grid (resolution ~ 0.005
degrees), along with wind fields. These
drivers were then used to drive the dispersal
model – seeded with a100 particles per grid
cell per day (in the user selected source/sink
location) over the user specified release
period. Final particle distributions are
presented in two ways: either as a
percentage (per grid cell) of all the particles
released ending up in that grid cell; or as a
cumulative exposure of cells to particles
over the dispersal time, again expressed as a
percentage of all the particles released.
These dispersal statistics were used to
calculate network connectivity metrics
between the aquaculture farms in the
region.
Farm scale Minimum realistic This farm-scale epidemiological model
Richards (2018) simulates fish growth, fish mortality, and
disease dynamics. The model considers
three fish species Atlantic salmon (Salmo
salar), Coho salmon (Oncorhyncus kisutch),
Parameters for particle behavior
taken from parameter repository
and the literature on the behavior
of Chilean pathogens (as
summarized in Table 2.1 of Gorton
and Condie 2018).
The model was parameterised
using data reported by industry to
SERNAPESCA as part of standard
production, mortality and disease
treatment reporting between
locations maintained by the
Chilean MUSEL project. Optical
model products are compared
against MODIS images.
No independent drifter data
was available for validation, but
the model utilises the validated
hydrodynamic model (see
above). Experts on the system
agree with the forecast
dispersal pathways, which also
concur with those from other
operational oceanography
products in the region (
https://www.ifop.cl/chonos/)
Model skill was high for Los
Lagos and Aysén regions, but
poorer for Magallanes due to
the sparse data for the region.
Nevertheless, the fits of the
 and rainbow trout (Oncorhyncus mykiss).
The growth and mortality models are
deterministic, while the disease model is
stochastic.
Bioeconomic Econometric Bioeconomic model of the production of
van Putten et al (2018) Atlantic salmon (Salmo salar), Coho salmon
(Oncorhyncus kisutch), and rainbow trout
(Oncorhyncus mykiss). The model marries a
simplified form of the farm-scale growth and
mortality models with an economic model
of production costs and revenue generation.
Benthic impacts Statistical An empirical biphasic impact-response curve
Bravo (2018) for benthos state in response to organic
loading. This was possible as both
abundance and diversity correlate with
organic matter, pH and redox in sediments.
The formulation of the curve was modified
from the standard Hill equation according
Veroli et al., (2015).
System The system model represents the entire
Fulton et al (2018) Input socioecological system of each of the
regions Los Lagos, Aysén and Magallanes. It
includes many individual components as
detailed below.
Environmental drivers The first components are the environmental
drivers (temperature, rainfall, irradiance and
current flows).
August 2010 and September 2017
The biological components of the
model are parameterized from
industry data held by SERNAPESCA
(spanning August 2010 to
September 2017). Economic data is
drawn from FAO (2018b),
production and treatment data
held by SERNAPESCA , SalmonChile
2017, and Chile Aduanas Customs
2018.
The curves were developed using
the database of the Informes
Sanitarios y Ambientales
Acuicultura (INFA) monitoring
program of SERNAPESCA (from
2012 to 2017).
The model draws on very many
data sources as detailed below
(with full parameterization given in
Fulton et al (2018)).
The physical drivers are taken from
the physical, biogeochemical and
connectivity models as well as
model predictions are quite
tight around the observations
(Richards 2018).
The results of the standard
parameterization of the model
have been verified by industry
experts in Chile.
While the relationships are
noisy (see data plots in Bravo
(2018)) the final curves are a
good representation of the
median and capture well the
nonlinear relationships between
benthic biomass, organic
enrichment and redox – the
relationships also capture the
thresholds in the response.
The overall model produces
plausible dynamics that
resonate with local residents (as
discussed in workshops held in
the region) and regional
statistics for production
recorded by government
agencies such as IFOP,
SERNAPESCA, SUBPESCA and

HABs Data-based A footprint of harmful algal blooms with all
components in this footprint suffering
mortality or modified rate parameters.
Benthos Statistical Seabed beta biodiversity characterization
map calculated from empirical observations
using the R package gradientForest (method
as of Ellis et al 2012; Pitcher et al 2012).
Sediment & water Statistical Scalars on input values are used to reflect
quality indices of the dynamic state of water
column and sediment conditions –
specifically nutrients, organic material and
oxygen levels.
Kelp beds Cellular automata A simple carrying capacity-based
formulation is used to represent the
biomass of kelp beds per cell.
Wild mussel banks Cellular automata Biomass model per area adapted from a
model for Mytilus galloprovincialis.
observational time series available
at
The footprints are represented by
stochastically drawing from the
historical locations of previous
blooms (using data supplied by
local oceanographers) and the
intensity of the bloom based on
historical observations or scenario
definition. Impact rates are taken
from literature and scaled based
on the intensity of the bloom (see
Fulton et al (2018) for more
details).
Biodiversity survey data was
accessed from the Fundacion
Huinay (Los Lagos), with data on
sediment and water quality
conditions from samples collected
by Instituto de Fomento Pesquero
(IFOP).
Scalars are derived from Soto and
Norambuena (2004) and Leipe et
al (2011).
The model is parameterized based
on Buschmann et al. (1994) and
Abreu et al (2009).
Wild mussel biomass was
initialised based on Flores et al
(2015), with growth model
Instituto Nacional de
Estasísticas
As the footprints are based on
observations, they match
historical patterns of
distribution.
The resulting biodiversity maps
match regional water column
and bathymetry patterns as well
as major geographic breaks. The
patterns concur with expert
knowledge of distributions in
the region.
As the relationships are based
on observations, they match
historical patterns.
The patterns concur with expert
knowledge of distributions in
the region and their evolution
through time.
The patterns concur with expert
knowledge of distributions in
the region and their evolution

Sealions and whales Agent based Agent based model of key marine mammals
in the region. These animals move toward
the highest prey biomasses in their
immediate vicinity (which can include
salmon pens for the sealions). Food
demand is based on what is needed given an
age dependent growth rate (which in turn is
set as the increment needed to meet
observed size at age). Mortality is applied
stochastically, with the probability of death
conditioned on: (i) a background level of
0.004 per month; (ii) the level of shipping
traffic; and (iii) condition.
Wild fish and Age structured Biomass based metapopulation model of
invertebrates cellular automata key target species in the region - hake,
sardine, urchin, crab.
Terrestrial vegetation Cellular automata Metapopulation model of land cover types,
including agriculture, plantations and
grassland-forest succession and disturbance.
Salmon farms Agent based The growth, production and mortality (due
minimum realistic to pathogens and background mortality)
were based on the simplified for the of the
farm-scale model used in the bioeconomic
model. Schools of wild/escaped salmonids
are also tracked (including breeding and
parameterized based on
Bustamante and Branch (1996).
Rates were taken from
observations shared by
researchers working in the region,
SeaLifeBase
( https://www.sealifebase.org/)
and Rosas et al (1993), SUBPESCA
(1999), Venegas et al (2002), Vilata
et al (2010) and Reyes et al (2013).
Parameterised based on stock
assessments supplied by IFOP and
Punt et al (2016)
Initialised using data from
www.ide.cl and
en.datachile.io/explore/geo.
Parameterisation based on Gray
et al (2006) and Heckbert (2013).
In addition to parameters taken
from the bioeconomic and farm-
scale models. Caligus (parasite)
levels were estimated using
SERNAPESCA held data from
August 2010 and December 2017.
through time.
The numbers and distribution
concur with observations taken
in the region and census counts
over the past 15 years.
The biomass (and catch levels
supported) concur with the
IFOP assessments. The spatial
distributions and depletion
patterns through time concur
with local expert knowledge.
The evolution of land use
through time matches the
general patterns observed for
the regions (as stored in
historical maps and GIS layers
held by www.ide.cl).
The validated state is as of the
farm-scale and bioeconomic
models, with projected
numbers per week of parasites
a close fit to 2017 observations.
 naturalization if they survive to appropriate
ages).
Mussel farms Agent based The mussel farm model tracks growth and
production per farm (via tracking size and
numbers per string on the farm) using the
formulations of Marambio et al (2012). Spat
is collected from wild banks – via a
‘harvesting’ rate.
Algal farms Agent based Biomass production per algal farm – using
the same equations as for wild kelp beds but
with seeding and harvesting.
Fishing Agent based Commercial, artisanal and indigenous fishing
are represented by a simple catch-per-unit-
effort and economics-based effort allocation
model. Effort is applied based on distance
from port and CPUE. Effort levels are re-
scaled if quota levels are modified by the
management model and zoning can stop
access to specific locations.
Processing plants Cellular automata A modified form of the manufacturing
model (see below) is fed by fishing and
aquaculture products landed in the local
port.
Mussel farms were initialized Production levels agree with
based on lease data from those recorded by IFOP for
SUBPESCA. Mussel production was 2012-2017.
parameterized using Toro et al
(2004) and Marambio et al (2012).
Spat collection were tuned to
reproduce the volume of
production observed (reported by
IFOP) in 2012-2017.
Algal farms were initialized based Production levels agree with
on lease data from SUBPESCA. those recorded by IFOP for
Algal production on farms was 2012-2017.
parameterized based on literature
values (spanning numerous
Chilean and international studies)
as detailed in Fulton et al (2018).
Parameterised based on IFOP Production (catch and effort)
fishing data for the regions and levels agree with those
numbers of vessel transits as recorded by IFOP for 2012-
recorded on 2017.
https://www.marinetraffic.com
Initialised using data from Production levels agree with
www.ide.cl and those recorded by IFOP and
en.datachile.io/explore/geo. Rates industry bodies for 2012-2017.
of employments, costs and
processing rates are from
information from plants in the
region.
Economics Econometric Simple economic input-output flow of costs
and revenue. With the volume of production
dictated by the individual industry models
(see below) and time series of interest rates,
cost of living, and economic demand per
industry sector.
Tourism Agent based This model tracks the usage of the area by
different kinds of tourists – ecotourists,
comfortable budget travelers and mass
tourism. It is based on the formulations of
Casagrandi and Rinaldi (2002) as updated by
Fulton et al (2017).
Shipping Agent-based Traffic flow model following the movements
of 4 classes of vessel in the region (along
navigational routes):
I. Large (> 150000 DWT)
II. Medium (10,000 – 150,000 DWT)
III. Small (< 10,000 DWT; including well
boats)
IV. Local (outboards, smaller motor cruisers
etc)
Numbers are scaled based on local
demographics and number of instances of
the other industries modelled in the region.
Terrestrial industries Cellular automata Farming, plantations, logging, mining,
energy generation, manufacturing and
urban retail and services were modelled
using the equations of Fulton et al (2017)
modified to reflect local decision-making
Initial conditions and relevant rates
for demand taken from Chilean
census and the annual and
quarterly reports of the Instituto
Nacional de Estasísticas
Initialised using data from
www.ide.cl and
en.datachile.io/explore/geo
The transport routes and
frequency of operation of well
boats was taken from data
accessed from
https://www.marinetraffic.com.
The spatial location was digitised
into a GIS shapefile manually using
QGIS 2.14.
Initialised using data from
www.ide.cl and
en.datachile.io/explore/geo
Gross economic imports,
revenues, production and
employment match the
magnitude and seasonal
patterns across industries and
regions recorded in the
quarterly reports of Instituto
Nacional de Estasísticas
Number of visits and changing
tourism mix through time
follows the general patterns and
volume recorded by
government departmental
statistics (e.g. as available from
Instituto Nacional de
Estasísticas)
Volume of vessels using the
navigation channels and ports
per size class concurs with the
records available from the port
authorities and
https://www.marinetraffic.com.
Gross level of production per
industry per region concurs with
the volumes recorded in the
quarterly reports of Instituto
Nacional de Estasísticas.
 and operational practices in each of the
three regions.
Human demography Agent based Simple age structured population model of
indigenous and other communities in the
region. Equations modified from Meadows
et al (1972). Tracks permanent residents,
temporary residents and Fly-in Fly-out (FIFO)
worker population.
Social influence and Network Networks of information flow and sharing
information flow between actors within the individual
community (demographic) and sector
models
Social perception Minimum realistic Empirical relationship between activity
levels and environmental state and the
‘happiness and satisfaction’ of the different
community components.
Government rules Input Government regulations and decision rules.
Initialised using data from Chilean
census, www.ide.cl and
en.datachile.io/explore/geo and
parameterized using values from
Engelen et al (1997) and Fulton et
al (2017).
These networks elicited in direct
consultation with local
communities.
Empirical relationships taken from
qualitative (signed diagraph)
models of connections elicited
from the local population during
workshops in the regions.
Details of the individual rules were
taken from the relevant Chilean
government departments. Spatial
zoning was sourced from
www.ide.cl and
en.datachile.io/explore/geo
Numbers per major settlement
and total numbers per region
are within 10-20% of those
recorded by the Chilean census
time series.
Applied as is without further
validation – the results of the
models have been found to be
plausible by local workshop
participants with provides
confidence in the fidelity of the
approach.
Outcomes per modelled social
group under scenario
perturbations agree with
expectations from local focus
groups.
Input rather than model output.
However, the resulting model
dynamics have been found to
be plausible by workshop
participants in the regions.