Quantitative Biology, Population Assessment.
Spring Term 2013.
Stochastic Population Models: Monte Carlo Simulation
This laboratory aims to:
 reinforce the concepts of stochastic models given in Population Biology lectures;
 extend your experience and expertise in MatLab programming;
 provide you with understanding of a simulation approach to understanding dynamic
systems.
Assessment problem
 The greater spotted macaw (GSM) is a flightless bird that lives in dense forest on
an island. The native forest has been reduced to 10 patches on 10 hill tops. The
macaw is unable to cross between forest patches. Each patch is able to support 10
breeding territories in which a pair is able to produce an average of 1.5 offspring
per year. Breeding is continuous throughout the year. The GSM has a maximal
life expectancy of 2 years, although this falls to 1 year at maximum density. A
hurricane last year removed all the GSM from 5 patches (and 10 remained in the
others).
 At the end of each hurricane season, and before the turtles start breeding, the
environmental manager has resources to catch and relocate 20 birds over a very
short time window. Unfortunately, GSM are nervous creatures, and there is a 20%
chance that they will die during the translocation.
 You may ask additional questions about the species and habitats.
 MatLab code for the basic situation will be provided and discussed during the
sessions.
 Using this information, design some numerical experiments to recommend a
movement strategy between habitats that maximises the chances of survival of the
metapopulation over the next 50 years.
Assessment
You should produce a report in the style of a scientific paper, with the following format.
1. Title.
2. Abstract: (not more than 100 words) describing what you did and what you found.
3. Introduction: (not more than 500 words) describing the scientific basis for the
investigation that you undertook.
4. Methods: (not more than 1000 words) a description of the way in which you
approached the problem, in sufficient detail that somebody else with the same level of
knowledge as yourself could undertake the same investigation (If it isn’t repeatable, it
isn’t science). You should include a list of the assumptions you are making.
5. Results: (no word limit; only 5 display items, i.e. figures and tables) the results of
your study, including graphical and tabular representation. You should also include
some information showing that you tested your program in a situation where you
knew what the answer would be. There is no word limit, but please restrain
yourselves. The limit is 5 figures and/or tables.
6. Conclusions: (not more than 500 words) a discussion of the results explaining what
the exercise has taught us in terms of population dynamics.
7. Bibliography: list of references.
8. Appendix: the complete annotated program code that you used to generate your
results.
1
Submission
Submit the paper by email to: graham.medley@warwick.ac.uk
Submit by noon 12pm on Wed 13th March (same as the qtl practical)
Programming Background
You are supplied with MatLab files: a script (dosims) and function (fsim, translocate,
plotSummary, plotRepetitions, calcExtinctions). These files run a simple simulation with a
variable number of populations, with birth and death being the only processes (events) that
can occur to each individual. Note that the code is not meant to be an example of “best
practice” – it does work, but it could be more efficient.
General Tasks:
1. Read the code and understand the logic. This will involve revision of the MatLab
language and programming environment. You are advised to go through the code line by
line, ensuring that you understand what each line does. Use the “help” files, including
typing “help xxx” at the command line. Start at the top of the script (dosims) and
concentrate on the function (fsim).
2. Think carefully about what you are going to have to do with the program before you start
meddling with it. Remember to thoroughly test the code you produce.
3. You will then have to conduct experiment(s) to address the ecological question above.
4. The discussion on programming and programming can be a group task.
Support:
Further guidance & clarification can be obtained from Graham Medley (Room B139; x24456;
graham.medley@warwick.ac.uk).
2