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Individual based modeling of growth and survival of Atlantic Cod ( Gadus morhua ) and Lesser Sandeel ( Ammodytes marinus ) larval stages. Zeren Gürkan, Asbjørn Christensen, Henrik Mosegaard DTU Aqua, Charlottenlund Castle, Denmark. My background. BSc in Biology, METU, Turkey

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zeren g rkan asbj rn christensen henrik mosegaard dtu aqua charlottenlund castle denmark

Individual based modeling of growth and survival of Atlantic Cod (Gadusmorhua) and Lesser Sandeel (Ammodytesmarinus) larval stages

Zeren Gürkan, Asbjørn Christensen, Henrik Mosegaard

DTU Aqua, Charlottenlund Castle, Denmark

Summer course 2009

my background
My background
  • BSc in Biology, METU, Turkey
  • MScE in Env. Engr., DTU, Denmark
  • Grad. study in Env. Engr., METU & PhD for 1 year in Bio.&Agr. Engr., UGA, USA

Summer course 2009

contents of presentation
Contents of presentation
  • SUNFISH project summary
  • PhD research contents
    • Results from literature review
        • Prey field for fish models – Feeding conditions
        • Existing bioenergetic models
  • Initial bioenergetic Individual-Based Model (IBM) formulations

Summer course 2009

my phd research objectives
My PhD research objectives
  • They are embedded in and address several tasks in SUNFISH
  • Main objectives are identifying and modeling key biological processes that affect growth and survival of larval and juvenile cod and sandeel by giving emphasis to responses to local physical and feeding conditions
  • Existing bioenergetic individual-based models (IBMs) will be developed and coupled to biogeochemical models of the North Sea together with other SUNFISH partners
  • The coupled models will be used to simulate responses of biological processes of drift, growth and survival to climate change effects as conditions of physical and biogeochemical spatio-temporal fields, and formulate future sustainable ecosystem management strategies

Summer course 2009

sunfish sustainable fisheries climate change and the north sea ecosystem
SUNFISH - “Sustainable fisheries, climate change and the North Sea ecosystem”
  • Global climate change will challenge fisheries and ecosystem management in the seas
  • Primary and secondary production and distribution, feeding, growth, and survival of fish will be affected by changes in temperature, wind conditions, river runoff, currents
  • It will be more difficult to separate effects of fishing from those of environmental changes, to identify biological reference points, and to develop management strategies for sustainable fisheries
  • Well-founded assessment of the population dynamics of the North Sea fish stocks is necessary

Summer course 2009


SUNFISH is a collaborative project of several Danish and international institutes

  • It aims to improve the scientific basis and predictions of effects of climate change on the North Sea ecosystem and the sustainable fisheries management in the North Sea
  • It will provide an integrated modeling framework for developing optimal and sustainable fisheries management strategies, based on description of mechanisms of processes instead of extrapolations of observed trends, to predict the outcomes of climate change on the North Sea ecosystem
  • It focuses on cod and sandeel, which are key species in the North Sea ecosystem and economically important to the Danish fishery

Summer course 2009


SUNFISH tasks from work packages I contribute to :

  • Formulation of a model describing food intake of larvae based on literature & growth of cod larvae
  • IBM model of larval cod growth based on biological process models of growth
  • IBM model of larval cod survival
  • Predictions of the spatio-temporal distribution of larvae based on IBM models
  • Comparison of predicted larval distribution and size with survey observations
  • Identification of processes limiting survival of early life stages
  • Comparison of predicted distribution of settled cod with distribution observed in surveys
  • Spatio-temporal analysis of the predicted probability of survival to settling of eggs spawned in different areas
  • Estimation of sandeel growth in relation to biophysical conditions

Summer course 2009


Methods include the use of predictions of conditions in the North Sea in past and future accounting for climate change scenarios by BSHcmod and HYCOM hydrodynamic models, which are coupled to 3-D biogeochemical model, ERGOM, as basis of analyses of spatio-temporal variation in growth and survival of the fish early life stages

  • Survival will be modeled using Letcher type IBM and hydrographic approach. Estimates of energy intake and expenditure will produce model of growth. Effects of local physical conditions and behavioral aspects will be included

Summer course 2009

initial bioenergetic ibm formulations
Initial bioenergetic IBM formulations
  • Sandeel Population Analysis Model (SPAM) assumes von Bertalanffy temperature modulated growth model (Christensen)
  • I develop this to a detailed model based on Letcher et al. (1996) formulation
  • Energy intake and expenditure are combined
  • Function of temperature, food abundance and quality
  • Includes explicit descriptions of physiological processes and behavioral aspects

Summer course 2009


SPAM (SLAM - Christensen et al., 2008)


Spatial SD (bank variability)

Suitable sandeel banks


Interbank exchanges of sandeel larvae


Summer course 2009

generic larval ibm letcher et al 1996
Generic larval IBM - Letcher et al. (1996)

Flow diagram - All functions are dependent

on larval size. 5 submodels determine prey

encounter, foraging, bioenergetics-growth,

starvation, and predation rates. Major

processes affecting each submodel are in the

pointed boxes. Characteristics of the larvae’s

environment (food and predators) are in the

boxes with horizontal arrows. The model

calculates growth rates for each larva every

time step. Each simulation may start with a

certain number of larvae all with a specified


Summer course 2009

growth submodel
Growth submodel

Ingestion, I

(Assimilation efficiency)

(Total costs) Specific dynamic action, SDA & egestion, E

(Routine metabolism) Weight, W

Summer course 2009

foraging submodel applies optimal foraging model charnov 1976
Foraging submodel : Applies optimal foraging model (Charnov, 1976)

Maximum consumption, total mass eaten, and masses of four prey types eaten under nominal conditions and optimal foraging model

Summer course 2009

foraging submodel varying ingestion
Foraging submodel varying ingestion

2 preys

Summer course 2009


Hypothesis - Bottom-up cascade.

Recent statement by Beaugrand et al.

(2003) says recruitment failure of many

species in the North Sea is linked to the

change in distribution and composition

of warm (Calanus helgolandicus) and

cold (C. finmarchicus) water

zooplankton, which is potentially

driven by regional warming. It will be

analyzed further with the bioenergetic

IBMs developed using zooplankton

model outputs from SUNFISH partners

and ‘Continuous Plankton Recorder’

(CPR) time series data.

Summer course 2009


Sir Alister Hardy Foundation for Ocean Science (SAHFOS) provided the CPR data for NS area of several taxa of plankton included in diets of cod and sandeel

  • One use of this database will be to realize the prey conditions as input to the model
  • Calibration & validation of model results

Summer course 2009

phd project contents hypotheses
PhD project contents - Hypotheses
  • Climate change effects. Recent progress by SUNFISH partners allows improved description of water turbidity, turbulence, and light penetration in relation to meteorological forcing factors. These three factors strongly affect feeding success and efficiency as well as predation risk. Future climate scenarios anticipate stronger winds on average and therefore, it is highly relevant to explore the biological impacts on early life stages using the developed bioenergetic IBMs.

PhD Seminar 2009

phd project contents hypotheses23
PhD project contents - Hypotheses
  • Optimal life history analysis. The ecological fitness of a species depends on the traits characterizing its entire life history. Traits in early life stages and of individuals including behavioral aspects may matter in determining the ecological fitness of a species. Evolutionary mechanisms have optimized these traits for each species in its ecosystem niche. The fitness of alternative life histories may shift relative to each other due to direct and indirect climate change effects, which may mean a regime shift in the ecosystem. The project can explore these aspects for cod and sandeel early life stages. Optimal life history analysis also constitutes a useful consistency check of the developed bioenergetic IBMs.

PhD Seminar 2009

phd project contents hypotheses24
PhD project contents - Hypotheses
  • The physical and biogeochemical fields with sufficient spatial resolution will be available within the SUNFISH project to explore biological consequences. The processes on which climatic effects are quantified include drift, growth and survival of zooplankton and fish. The bioenergetic IBMs developed will be coupled to operational biogeochemical models for North Sea with other members of the SUNFISH project simulating climatic effects on total biomass and on spatio-temporal distribution, composition and nutritional value of zooplankton.

PhD Seminar 2009

phd project contents hypotheses25
PhD project contents - Hypotheses
  • The distribution and composition of warm (C. helgolandicus) and cold (C. finmarchicus) water zooplankton has a distinct spatial and seasonal pattern. How the spatial and temporal heterogeneity and composition of the zooplankton community, which may include species with different nutritional values, affect recruitment predictions of cod and sandeel will be examined.
  • Operational biogeochemical models most often assume a constant or otherwise simplified grazing rate from planktivorous biomass while elementary estimates suggest the grazing rate is highly variable over the seasonal cycle. Possibility of improving the performance of current operational biogeochemical models by implementing a feedback loop of fish grazing on zooplankton to demonstrate the importance of grazing dominated either by cod or sandeel larvae at a locality will be examined.

PhD Seminar 2009