Puget Sound recovery through the eyes of an Atlantis ecosystem model
1Raphael Girardin2Isaac Kaplan2Chris Harvey
1Long Live the Kings2NOAA Northwest Fisheries Science Center
Photo: IRMiller
Salmon recovery: survival of Salmon early stage in Puget Sound
Predation
?
Competition
Prey availability/ quality
time
biomass
time
biomass
Stormwater
Images: UMCES (IAN);
King County; NOAA; WDFW
Sutherland et al. (2011)
Atlantis dynamic structure
Hydrographicsubmodel
BiogeochemistryClimate,
oceanography
Fulton, E. A. 2004. Ecological Modelling, 173:371-406
Atlantis dynamic structure
Hydrographicsubmodel
Biogeochemistry
Habitat
Climate,oceanography
Food web
Ecologysubmodel
Human sectors
Human impactssubmodel
Fulton, E. A. 2004. Ecological Modelling, 173:371-406
Sutherland et al. (2011)
Atlantis dynamic structure
Hydrographicsubmodel
Biogeochemistry
Habitat
Climate,oceanography
Food web
Ecologysubmodel
Human sectors
Human impactssubmodel
3D dimensional structure of Atlantis
Daily/12h oceanographic fluxes
(water, heat, salinity)
into, out of each box are
controlled by a
circulation model
Fulton, E. A. 2004. Ecological Modelling, 173:371-406
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3D dimensional structure of Atlantis
Image: WDFW
South Georgia Straits
San Juan Islands Padilla
Bay
E Strait of Juan de Fuca Whidbey
Basin
Admiralty Inlet
Hood Canal
Central PugetSound
Carr-Nisqually
South Sound Inlets
Port Madison & Sinclair
Inlet
Gulf Island
Boundary boxes
Forage fish (here herring spawning ground)
4 primary producers, 5 zoo-
planktons, 12 invertebrates
33 fish composed of 19
salmon groups
3 birds, 4 selachians, 7
marine mammals
10 Benthic invertebrates
3 Birds
Shrimps
4 Rockfishes 19 Salmons
Puget Sound functional groups: California Current, EwE models, expert advice
Images: UMCES (IAN);
King County; NOAA; WDFW
Seastars
Kelp
Seagrass
Squids
Zooplankton and
phytoplankton
Bivalves
4 selachians
2 Herrings
3 Forage fishes
Small demersal
9 Primary producers and planktons
Urchins
Octopi
Benthic infauna
Crabs 4 Cetaceans,
3 Pinnipeds
2 Flatfishes
Large demersal
predators
Large gadoids
Salmon functional groups in Puget Sound Atlantis ModelImages: WDFW
Species Chinook
sub-stocks (wild
stocks/ Hatchery)
Skagit NisquallyHood Canal
Other Hatchery
Run type YearlingSub-
yearlingYearling
Sub-yearling
Sub-yearling
YearlingSub-
yearlingYearling
Sub-yearling
Species Coho Chum Pink Cutthroat trout
Canadian Salmonids
sub-stocks (wild
stocks/ Hatchery)
Skagit Deep South
Other Hatchery Other Hood Canal
Hatchery All All All
Run type YearlingFall Sub-yearling
Summer Sub-
yearling
Sub-yearling
Sub-yearling
All All
Salmon life cycle into Puget Sound Atlantis model
1) River 'larval' stage
• Recruitment in Atlantis
2) Juvenile stage
• ATLANTIS
3) Pacific ocean stage
• Simple Pop. model
4) Adult stage
• ATLANTIS
5) River 'reproduction'
stage
Few years
Image source: http://www.returntoelwha.com/
Predation/prey relationship in Atlantis
Copepods (mesozooplankton)
Microzooplankton(e.g ciliates)
Euphausiids(large zooplankton)
Diatoms (large phytoplankton)
Example: California Current sardine diets in an Atlantis simulation with increasing copepod abundance
Scenario with higher abundance of forage fish (Cherry Point herring and/or other forage fish) and availability of forage fish of the appropriate size Hypothesis: Decline in forage fish may limit early marine survival of Chinook and coho.
Scenario testing spawn timing of crabs: Hypothesis: match/mismatch of crab larvae and food needs of juv salmon is critical driver of salmon survival.
Scenario with effects of PDO and also climate change effects beginning in 1970’s.Hypothesis: this may have led to the change in salmon survival. Consider both climate “shift” and satellite data.
Scenario with increasing abundance of Noctiluca and gelatinous zooplankton. Hypothesis: shifts in energy flow toward Noctiluca and gelatinous zooplankton may decrease production of plankton species directly consumed by juvenile salmon.
Scenario artificially testing improved juvenile salmon growth: Hypothesis: if juvenile salmon grow faster, they may be able to grow enough to access a wider range of prey including herring; expect increased survival.
Prey availability/ quality
time
biomass
time
biomass
Salmon early marine survival hypotheses
Salmon early marine survival hypotheses
Competition
Scenario with higher abundance of forage fish (Herring
and/or other forage fish) and availability of forage fish of the appropriate size Hypothesis: adult forage fish might compete for food with wild juvenile salmon
Scenario reducing stocking of hatchery fish: Hypothesis: competition for food may limit wild juvenile salmon growth and survival.
Scenario without pink salmon or with a reduction of their biomass. Hypothesis: competition from pink salmon may contribute to decline in Chinook and coho, as well as interannual variability (‘zig zag’). Note also competition between pink and herring, with potential indirect effects on Chinook.
Salmon early marine survival hypotheses
Scenario with lower abundance of pinnipeds. Hypothesis: harbor seal consumption of smolts may be a major driver of early marine survival.
Scenario testing (artificially) higher abundances of gadoids/ forage fish. Hypothesis: Pinniped predation on smolts may have arisen due to lack of other prey resources.
Scenario artificially testing improved juvenile salmon growth: Hypothesis: if juvenile salmon grow faster, they may be able to grow beyond predator gape (e.g. birds) ; expect increased survival.
Scenario testing effect of stormwater. Hypothesis: juvenile development, survival, growth has declinedfor particular stocks due to toxins in stormwater at those locations.
Predation
Stormwater
Strength and limits of Atlantis: The Strategic Role of Atlantis
Atlantis is a “sandbox” for understanding: • Trophic interactions• Cumulative impacts (Climate change, nutrient loading,
fishing pressure…)• Trade-offs between management objectives• Socio-economics and human behaviour
NOT intended for tactical management decisions
NOT intended to replace fisheries stock assessments
NOT fast enough for intensive parameter estimation
Atlantis is resource intensive to develop
Scenarios run for several days
Not precise enough to study local small-scale scenarios