School of Computer Science and Software Engineering
Monash University
Computer Science Honours (1608), Clayton Campus
Research Proposal - Semester 1, 2004
Modelling Fish Populations for Sustainability
By: James Bernard, ID: 18166075
Supervisors: Charles Twardy, David Green, and Charles Todd
List of Contents
1. Introduction
2. Research Context
3. Research Plan and Methods
a) Methodologies
b) Proposed thesis chapter headings
c) Timetable
d) Potential difficulties
e) Special facilities required
4. Deliverables
5. Bibliography
1. Introduction
This project aims to examine the Murray Cod (Maccullochella peeli) the largest freshwater fish in
Australia. Recreational fishing has severely diminished the number of Murray Cod in the Murray
River. With the help of the Department of Sustainability and Environment (DSE) we plan to
model the fish population for sustainability assuming current practices persist.
Our project investigates three major principles:
I) Age-Length Growth Models
II) Stock recruitment
III) Population models
Murray River Rules & Regulations stipulate all Murray Cod between 500mm and 1100mm are
eligible for fishing. Age-length growth models can therefore be used to determine at what age the
majority of fish leave the population. A potential problem is that the Murray Cod may not reach
maturity before 500mm and so could not reproduce.
Recruitment models can determine population increases in the Murray Cod. Recruitment models
determine how many offspring female fish will produce. Usually larger fish will produce more
eggs.
Given the above information we can generate population models to determine the sustainability
of the Murray Cod population for various scenarios. Then we can see whether there needs to be a
change in regulation to maintain their existence.
2. Research Context
Previous studies have produced established age-length growth models for the Murray Cod.
However we are not aware of any full population models for the Murray Cod. There are
population models for the closely related Trout Cod (Maccullochella macquariensis).
I) Age-Growth Models
In 1992 the Department of Conservation and Natural Resources performed a comprehensive
study to determine the age and growth of the Murray Cod using thin-sectioned otoliths
(Anderson, 1992). Otoliths are minute calcareous particles found in the inner ear of vertebrates.
They can be used to determine the age of the specimen. The study produced a von Bertalanffy
age-growth model that provided a means to determine a fish’s age given its length or weight.
Figure 1: von Bertalanffy growth-in-length curve for male and female Murray cod (Anderson,
1992)
Figure 2: von Bertalanffy length-weight curve for male and female Murray cod (Anderson,
1992)
The von Bertalanffy age-growth model may however produce ‘serious overestimates of the
reconstructed mean length at age’ (Sainsbury, 1980) when using growth increment data to create
the model. Anderson’s von Bertalanffy curve does not suffer from this problem, however our data
set does consist of lengths and growth increment data so other curves should be investigated.
The Gompertz age-growth model is recommended for fish when ‘growth is notoriously variable,
changing dramatically between seasons and sites (Troynikov, 1998).’ Studies suggest the Murray
Cod behave similarly, yet the Gompertz age-growth model has not been used to model the growth
of the Murray Cod. Troynikov uses the Gompertz model on recapture data indicating it does not
suffer from the same drawbacks as the von Bertalanffy model.
[Side Note: Sainsbury uses the argument that since this is the case for the von Bertalanffy curve
the same can be argued for all age-growth models based on recapture data.
We can do either of the following:
 Remove the two paragraphs (since we didn’t use recapture data to produce our models)
 Test Sainsbury’s argument and state that the reason we didn’t use recapture to model
our curve was because of Sainsbury’s reasoning. We can then argue that Troynikov’s
curves suffer from this weakness!]
The Murray Cod’s length and weight can vary depending on the nutrient environment.
II) Stock Recruitment
The Department of Sustainability and Environment have calculated various recruitment models
using Trout Cod (Maccullochella Macquariensis) data (Todd, 2003). The Trout Cod dwells
closely to the Murray Cod. The tested models were:
 Beverton-Holt
 Ricker
 Biomass
The Beverton-Holt model suggests that recruitment approaches an asymptote at high stock
densities, while the Ricker model describes the situation where recruitment reaches a maximum
at some intermediate level of stock size. The Ricker model is likely to apply when the adult fish
compete with, or prey on, the pre-recruits (Allison, 1999).
Figure 3: Hypothetical patterns of recruitment models (Allison, 1999)
Allison suggests the Shepherd model is a more versatile combination of the Ricker and BevertonHolt models.
III) Population Models
The most well known population models build on the recruitment models. The Ricker and
Beverton-Holt methods are the most commonly used. Once you know the size of the current
population and have determined the recruitment of the population, you need to estimate the
survival rate of the fish at a given age. This information can then be used to forecast the fish
population at any given time.
3. Research Plans and Methods
a. Methodologies
i. Applications
b. Proposed thesis chapter headings
Abstract
1. Introduction
2. Literature Review
3. Methods
a. Growth Models
b. Recruitment
c. Population Modelling
4. Results
5. Conclusion
6. Appendices
7. References
c. Timetable
Date
Activity
Thursday, 22 April 2004
Monday, 26 April 2004
Wednesday, 28 April 2004
Monday, 3 May 2004
Monday, 10 May 2004
First Draft Research Proposal to Supervisor
Research Proposal Finalised
Research Proposal Due
Commence Literature Review (on Growth Models)
Prepare Interim Presentation
Thursday, 20 May 2004
Interim Presentation Rehearsal
Thursday, 27 May 2004
First Draft Literature Review to Supervisor
Monday, 31 May 2004
Thursday, 3 June 2004
Conclude Best Growth Model for Murray Cod
Interim Presentation
Monday, 7 June 2004
Literature Review Draft Finalised
Friday, 11 June 2004
Literature Review Draft Due
Monday, 14 June 2004
Friday, 16 July 2004
Monday, 26 July 2004
Wednesday, 28 July 2004
Monday, 2 August 2004
Thursday, 26 August 2004
Wednesday, 8 September 2004
Thursday, 9 September 2004
Thursday, 23 September 2004
Monday, 27 September 2004
Thursday, 14 October 2004
Monday, 25 October 2004
Commence Research on Population Modelling
Literature Review to Supervisor
Literature Review Finalised
Literature Review Due
Commence summarising conclusion for Thesis
First Thesis Draft to Supervisor
First Thesis Draft Due
Prepare presentation for ASFB Conference
Presentation at ASFB Conference (Adelaide)
Prepare Final Presentation
Final Presentation Rehearsal
Final Presentation
Tuesday, 2 November 2004
Thesis Final Report Due
Tuesday, 2 November 2004
Research Log Book Due
Thursday, 11 November 2004
Web Site Due
To be added:
May – sometime
Expedition to collect re-capture data with DSE
June – sometime
Collect new re-capture data to validate Growth Model
d. Potential difficulties
We may not have enough biological data to predict the Murray Cod age-growth model and
consequently the population model. The main questions we need answered are:
 At what age does the Murray Cod start reproducing?
o Does it depend on the fish’s age or length?
 Does the size of the fish vary depending on the environment (area of water) they reside?
Since we do not know how old the Murray Cod are when they start reproducing (in the wild) we
can only use information gathered from aquaculture data (considered to be an ideal
environment). However the Murray River is nowhere near an ideal breeding ground. Therefore
we cannot confidently determine the exact age or length the fish start reproducing in the wild.
Tag and re-capture data is very limited and more data will be required to validate our models.
We also need to take into account that there is 10-20% sampling error as larger fish are generally
hard to measure.
e. Special facilities required
There are no special facilities required for the purpose of completing this research project
however certain facilities have been visited to aid the understanding of the project.
These facilities are:
 The Arthur Rylah Institute for Environmental Research located in Heidelberg,
Melbourne.
 A fishing expedition on the Murray River to conduct further data sampling (tag and recapture).
4. Deliverables
a) In the thesis: a methodology for solving the problem as completely as possible, identifying
ways to test and supplement assumptions.
b) In the thesis: a first-pass estimate and analysis of performance and limits of our estimate.
c) Working code for (b) in WinBUGS or another agreed-upon system.
5. Bibliography
Allison, E.H., Contributions to ecology from the study of recruitment in fish populations.
Hydrobiologia The International Journal of Aquatic Sciences December 1999, Volume 416, p 1-11
Anderson, J.R., Morison, A.K., and Ray, D.J. 1992. Age and growth of Murray cod Maccullochella
peelii (Perciformes : Percichthyidae), in the lower Murray-Darling basin, Australia, from thinsectioned otoliths. Australian Journal of Marine and Freshwater Research, 43: 983-1013.
Sainsbury, K.J. 1980. Effect of individual variability on the von Bertalanffy growth equation.
Canadian Journal of Fisheries and Aquatic Sciences, 37: 241-247.
Todd, C.R., Nicol, S.J., and Koehn, J.D. Density-dependence uncertainty in population models for
the conservation management of trout cod, Maccullochella macquariensis Ecological Modelling,
Volume 171, Issue 4, 1 February 2004, Pages 359-380
Troynikov, V.S., and Gorfine, H.K. Alternative approach for establishing legal minimum lengths
for abalone based on stochastic growth models for length increment data. Journal of Shellfish
Research, Volume 17, Number 3, Pages 827-831, 1998.
Troynikov, V.S., Day, R.W., and Leorke, A.M. Estimation of seasonal growth parameters using a
stochastic Gompertz model for tagging data. Journal of Shellfish Research, Volume 17, Number 3,
Pages 833-838, 1998.
“WinBugs Contents” (1996-2003) The Bugs Project Overview [online], Available:
http://www.mrc-bsu.cam.ac.uk/bugs/overview/contents.shtml [Accessed: 27th April 2004]