ECOTROPH (ET): A TROPIC LEVEL BASED SOFTWARE FOR ASSESSING THE IMPACTS OF FISHING ON AQUATIC ECOSYSTEMS 

Fisheries Centre Research Reports 17(1) 2009

By Didier Gascuel, Laura Tremblay-Boyer and Daniel Pauly  

Download this report: Full Report 

DIRECTOR’S FOREWORD

Many researchers at the Fisheries Centre, from faculty to graduate students, are involved in ecosystem modelling, and not surprisingly this has resulted in the FC becoming well-known for expertise in this challenging field. 

This is obviously what motivated Prof. Gascuel to spend a sabbatical year at the Fisheries Centre, and this report, co-authored by one of our graduate students and one of our faculty, is the product of his visit. 

The ecosystem model and software presented in this report, called EcoTroph, represent both a stand-alone application and a module of the Ecopath with Ecosim (EwE) software, the flagship product of the FC. EcoTroph is thus not an alternative to Ecopath, but a useful complement, an alternative way of looking at ecosystems, and I hope to see more applications of this type – even from my own discipline, ecological/fisheries economics. This will enable us to get a full view of aquatic ecosystems and the services they provide. 

Finally, I wish to congratulate the institution that sponsored the study visits of Prof. Gascuel to Vancouver, in Canada, and of Ms. Tremblay-Boyer to Rennes, in France, for having enabled the exchanges, which led to this report. It is initiatives of this sort which are the lifeblood of successful research as documented in this report.

Rashid Sumaila, FC Director

CONTENTS

Director’s Foreword ............................................................................. 1

 1. Building the model: principles, assumptions and equations ................................................. 5

1.1. Origin of the model ........................................................................................................................ 5

1.2. EcoTroph: general principles ........................................................................................................ 6

1.3. EcoTroph: biomass and flow equations ...................................................................................... 10

1.4. EcoTroph and Ecopath: first comparison ................................................................................... 12

1.5. Flow kinetic equation ................................................................................................................... 14

1.6. Top-down control and biomass input control ............................................................................ 17

1.7. Catch equation and accessibility................................................................................................. 20

1.8. From steady-state to time- dynamic modelling .......................................................................... 22

2. Learning from the model: some generic rules of the ecosystem functioning ................... 24

2.1. Simulation of a virtual ecosystem: method ................................................................................. 24

2.2. Impact of transfer efficiency and flow kinetics on unexploited biomass ................................... 26

2.3. Impact of fishing on biomass ....................................................................................................... 27

2.4. Catch simulations ........................................................................................................................ 30

2.5. Dynamic model: impact of fishing on ecosystem stability ......................................................... 33

2.6. Concluding remarks on the theoretical approach ....................................................................... 35

3. The Catch Trophic Spectrum Analysis (CTSA) ................................................................... 37

3.1. From EcoTroph to the CTSA ....................................................................................................... 37

3.2. Testing the method on simulated data ....................................................................................... 38

3.3. Application to real case studies ................................................................................................... 41

4. Conclusion: the trophic level based approach ..................................................................... 42

PART II - ECOTROPH: A new tool in the EwE family ........................... 43

1. General information ............................................................................................................ 43

1.1. Structure of the EcoTroph routines: ........................................................................................... 43

1.2. Installation of the plug-in ............................................................................................................ 44

1.3. Additional information ................................................................................................................ 45

2. ET-Transpose: looking at an Ecopath model using EcoTroph ........................................... 45

2.1. What is it used for? ...................................................................................................................... 45

2.2. How it works................................................................................................................................ 45

2.3. How to use it ................................................................................................................................ 49

2.4. Example of application ................................................................................................................ 52

3. ET-CTSA: estimating input parameters of EcoTroph .......................................................... 53

3.1. What is it used for? ...................................................................................................................... 53

3.2. How it works ............................................................................................................................... 54

3.3. How to use ................................................................................................................................... 55

3.4. Example of application ............................................................................................................... 60

4. ET-Diagnosis: using EcoTroph for simulation and global diagnosis ................................. 60

4.1. What is it used for? ..................................................................................................................... 60

4.2. How it works ............................................................................................................................... 61

4.3. How to use it ................................................................................................................................ 61

4.4. Example of application: ............................................................................................................... 64

5. ET-Dynamic: using EcoTroph with time series .................................................................. 65

5.1. What is it used for? ...................................................................................................................... 65

5.2. How it works ............................................................................................................................... 66

5.3. How to use it ................................................................................................................................ 66

5.4. Example of application ................................................................................................................ 71

Acknowledgments ............................................................................... 73

References .......................................................................................... 73

Appendix I – A Non- continuous simulation of EcoTroph .................... 77

Appendix II – Estimating transfer efficiency from catch data .......... 80