NetLogo User Community Models
by Thomas C. Jones (Submitted: 02/12/2008)
WHAT IS IT?
PopGen Fishbowl is an agent-based population genetics simulation. The program contains the tools to conduct virtual experiments violating all the assumptions of Hardy-Weinberg theory. You can explore the effects of:
HOW IT WORKS
The agents are fish in a small pond. Tracked is a single incomplete-dominant gene that affects color (RR = red; Rr = pink; rr = white). When fish come together (and are of opposite sex) they may breed, producing offspring following mendelian inheritance patterns. The model simulates overlapping generations, with reproduction occurring whenever fish may meet.
Monitored data include:
Graphed data include:
HOW TO USE IT
To start, set sliders:
Press the ‘Set up’ button and fish will appear in the pond. Press ‘Go’ and the fish will swim around and breed new fish. The population should grow and hover around 100 fish. All three colors should persist, though the frequency of the R allele may drift over time (and given enough time may become fixed at 100% or extinct). Note: it is possible that the fish may not breed fast enough and the population go extinct (Skull ‘n Bones), in which case ‘Set up’ and ‘Go’ again.
Below is a list of the model parameters and their functions
THINGS TO NOTICE
This model illustrates microevolution of allele/genotype frequencies by simulating interactions among individuals and mendelian inheritance. If you slow things down you can see little ‘explosions’ of fish fry from breeding events. Because of this, there are several things which might prevent the population from behaving as expected. For example:
If Init-N is low, the fish may not find a suitable partner and breed fast enough and the population may die out (Allee effect).
If the population is all of one sex, they will not breed
If mortality = 0 (no random mortality), the population will stop breeding/evolving at its carrying capacity.
THINGS TO TRY
This model is designed as a teaching tool. It is ideal for inquiry-based learning, as students can design ‘virtual experiments’ and collect/analyze data in a spread sheet. Pedagogically, this may be preferable to the model exporting data.
One approach would be to lead students through an experiment (e.g. effect of carrying capacity on average (and variance in) time to fixation, and then ask them a question and have them design and conduct experiments to answer it.
EXTENDING THE MODEL
With just the controls to tweak the five conditions for Hardy-Weinberg equilibrium it is hard to fit this model on a small screen.
It might be helpful to be able to divide the world into separate ponds an monitor them, particularly if you could see migration from one to the othe
The great of this model over many (non-Netlogo) others is the ability to see what’s going on in the population. For example, allele fixation is not just a value or plot going to 0 or 1.0, all the fish are then the same color. The fact that it is an actual simulation means that there is variation in results, which is biologically realistic.
The most similar model I know of is the commercially available Evobeaker ®.
CREDITS AND REFERENCES
PopGen Fishbowl 1.0 (2008)
Thanks to U. Wilensky and all who created Netlogo, for creating an environment in which a code-phobic professor can work.
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