NetLogo User Community Models
(back to the NetLogo User Community Models)
by Uwe Grueters
WHAT IS IT?
Neture is a NetLogo model that simulates how Nature works.
Neture simulates a terrestrial ecosystem at the interface of ecology and evolution.
The model embraces the three main ecosystem components: (1) the landscape environment, (2) the producers, and (3) the decomposers. It assembles processes that operate on a local spatial scale, endure decades, but progress with daily time steps.
HOW IT WORKS
Producer and decomposer species are both defined by a set of attributes. For an organism to belong to a certain species its attributes have to stay within the species-specific range. Exchange of genes leads to recombination of attributes. Mutation of attributes may take place - thereby giving rise to evolution and speciation.
As all living things in Neture producers and decomposers have energy supply either from sunlight or from organic matter and undergo metabolism for their maintenance, growth and reproduction. In Neture maintenance and growth metabolism is governed by "universal scaling laws" given by West, Brown & Enquist (2001) and Gilloly et al. (2001). Additional parameters with respect to plants and bacteria were obtained from Larcher (2003) and Elert, respectively.
(1) The landscape environment supplies energy to the biotic subsystem of producers. Allowance is made for spatial and/or temporal heterogeneity of the energy supplied across the landscape.
(2) The producers - or say - plants take up energy in the form of sunlight from the environment and use it for their metabolism.
A producer (species) is defined by its mass at birth, its maximum mass at maturity, the fraction of maximum mass at which generative reporduction starts, the seed dormancy and the germination probability.
Generative reproduction between a father and a mother plant takes place in the pollination range around the father plant. Supposing that lighter seeds are dispersed farther, the range of dispersal is made negatively dependent on the log mass at birth. Further assuming that heavier plants are taller and thus disperse their seeds farther, the dispersal range is made dependent on the log maximum mass. The effects considered to be additive are finally adjustable by you.
The dispersed seeds enter the soil seed bank, reside there at least for the species-specific seed dormancy and exhibit hardly any metabolism during that time (compare Solbrig 1980). After seed dormancy has passed by a seed germinates with a certain daily probability or it dies with the user-defined probability which summarizes effects of (biotic) soil mixing and predation on seed viability (Solbrig 1980).
An established producer either dies when its maintenance requirements are not fulfilled or when it has reached 99% of its maximum mass (determinate growth). Its residues enter the organic matter pool of the landscape patch, where it died.
(3) The decomposers are simulated as populations of bacteria that behave like single bacterium cells. This strategy for scaling down from the producer to the decomposer level shall cope with the consequences of the body sizes being distinct between the two groups.
A decomposer (species) is defined by its "spore" metabolic fraction, by the gene transfer probability and the movement to maintenance ratio.
When organic matter is scarce, bacteria tend to transform either into GASP phenotypes with reduced metabolism or into spores with negligible metabolism (Colwell & Huq 1994, Storz & Hengge-Aronis 2000). Their metabolism is fed by stored reserves and is used merely for maintenance. Under those threatening conditions bacteria are simulated to transfer genes and eventually develop mutations. When maintenance requirements cannot be satisfied any longer, the enduring form dies from starvation.
With plenty of organic matter bacteria are assumed to transfer genes with the probability set by the user.
Bacteria are at the bottom trophic level of the soil food web (Chapin (III.), Matson & Mooney 2002). Since true integration of higher trophic levels is beyond the scope of this model, their effect on bacteria populations is simulated as a decomposer mortality to be set by you.
Soil bacteria tend to form microfilms along soil macropores; they are considered to be translocated primarily by the activity of the soil meso- and macrofauna (Chapin (III.), Matson & Mooney 2002). You can choose the extent of this passive movement. Apart from that the movement to maintenance ratio allows to simulate effects of active movement.
The residues of dead bacteria or spores enter the organic matter pool of the landscape patch - thereby forming sort of a closed loop.
HOW TO USE IT
Before you start a model run please choose a SPECIES_RANGE, which defines the % deviation a species attribute is allowed to have before an organism is considered to belong to a different species. The default is 10%.
(1) Landscape environment: You may wish to manage settings of the landscape right before you start a model run, but it is also possible to change those settings later.
The SMOOTHNESS and RANGE sliders allow for spatial heterogeeneity.
The SMOOTHNESS slider alters the patch-to-patch change in the energy supply.
When the RANGE slider is set to zero you are dealing with a homogeneous landscape, when RANGE is set to the maximum 100 the energy supply is made heterogeneous and varies between 0 and 100.
Turning on the CHANGING-LANDSCAPE? switch leads to temporal heterogeneity.
The LANDSCAPE-CHANGE-RATE slider alters the speed with which the energy supply changes.
The PENERGY_MULTIPLICATOR slider allows to adjust the energy input to realistic units.
With the PATCH_COLOR chooser you can color the landscape by the energy, the usable energy or by the organic matter.
As usual pressing the SETUP button prepares for a model run.
(2) Producers: Afterwards you may populate the landscape with producers by pressing the
INSERT PRODUCERS button. Before doing so you can set the NUMBER_PRODUCERS and the location of producers (XCOR_PRODUCERS, YCOR_PRODUCERS) to be inserted. Below are sliders for setting the attributes of the producers within the min-/max-limits given by the inputs. External effects on the behavior of producers are on sliders located on the left hand side (POLLINATION_RANGE, DISPERSAL_RANGE, SEED_MORTALITY). Seeds are being displayed on the landscape as empty squares, whereas established producers are shown as empty triangles. Producers belonging to different species are depicted in different colors.
(3) Decomposers: Subsequently, it is required to insert decomposers. You can do so by pressing the INSERT_DECOMPOSERS button. The landscape is then homogeneously populated with NUMBER_DECOMPOSERS representing the number of decomposers to be inserted per patch. Once again you can choose decomposer attributes within limits using the sliders at the bottom. Sliders for introducing external effects, such as PASSIVE_MOVEMENT and DECOMPOSER_MORTALITY, are located on the left hand side.
Spores are being displayed as filled squares, while fully active decomposers are displayed using a bacterium-like shape. As with producers the color of a decomposer depends on the species which it belongs to.
After you have made those arrangements start the model run by pressing the GO button.
Have fun to watch the unfolding mass and enery dynamics on top-level monitors and plots.
At any time you can initiate evolutionary processes and speciation by setting the MUTATION_PROBABILITY to a non-zero value. Enjoy watching the attributes of new species and their population dynamics on species-specific plots located at the very right.
THINGS TO TRY AND NOTICE
I am still at the beginning of model exploration. Initially, my principal interest was to find regions of species coexistence in the vast multi-dimensional parameter space.
This is what I would recommend you to try first as well. Developing hypotheses about species coexistence and testing them with Behavior Space experiments will give you many opporutinities to learn how Neture works.
Here are some basic results and ideas that emerged from them:
I was unsuccessful to detect regions of producer species coexistence by varying the energy supply in planned two-species experiments on a homogeneous landscape (-> Is spatial or temporal heterogeneity a sine qua non for coexistence and diversity?). Almost always the species with higher maximum mass won. There was one exception from that: At very low energy supplies even the first generation of heavier plants was not able to reproduce and died already.
Next I tried to compensate the consequences of higher maximum mass in terms of dispersal by reducing the mass at birth for the heavier species in experiments. I thought that might change the outcome of the competition. But unfortunately, this did not change anything. The heavier species remained the winner.
My next attempt was to study the effects of the external factor "dispersal range" on the experimental results. Although reduced dispersal range was likely to increase intra-species competition, it did not alter the outcome of the competition.
Returning to the above mentioned exception I conducted an experiment with extreme landscape heterogeneity (RANGE = 100). The idea here was that the competition by the heavier species would be excluded on very low energy patches. It did not work out that way - since even dispersal of seeds by the heavier species drove the lighter species to extinction. I thought further that some extra space would be necessary to prevent seed dispersal from reaching those patches and achieving protection. Whatsoever, I have not tried it yet.
Nonetheless, I was finally successful and found a region of species coexistence, but the result was surprising and unexpected in many respects: The region was located at a high energy supply. Lighter plants resided on patches with high energy supply, while low energy patches were populated by heavier plants. I can send you the experimental settings. So do not hesitate to ask me at firstname.lastname@example.org .
Otherwise try to find this region yourself. Can you explain why this happens at all?
Since it is well known that high species richness is frequently associated with infertile conditions, try also to find regions of coexistence in the domain of overall low energy supply.
However, this all involves filling spatial niches with species. But is there a way to fill temporal niches with species as well? Recall that seed dormancy may open up such possibilities. Play around with that parameter and try to address the above question.
Extend the search for species coexistence also to the realms of temporal landscape heterogeneity (by turning on the changing-landscape? switch). The potentials of filling temporal niches seem promising, since the energy used often falls remarkably behind the available energy when temporal fluctuation is allowed for.
Try to do similar planned experiments with inserted decomposer species. An option might be to let "non-sporulating" species of higher active motility compete with spore-forming species that are merely moved passively.
When you think you have learned enough about how Neture works, give up the initial constraints and allow evolution and speciation to enter the scene. I would recommend to insert a number of diverging producer and decomposer species, let a dynamic equilibrium develop and then - by setting the MUTATION_PROBABILITY non-zero - let the "evolutionary damn burst". This setting will alter your search fundamentally: Try now to find regions of maximum species packaging or - in other words - regions of maximum species richness and diversity.
Please send me your insights of how Neture works together with the experimental settings from which you gained your insights. My e-mail address is: email@example.com
EXTENDING THE MODEL
Here are just few hints:
- Based on your insights make Neture as diverse as Nature.
- Integrate an above-ground consumer food web.
- Integrate a sol food web consisting of nematodes, micro-arthropods, enchythraeids and earthworms. West, Brown & Enquist (2001) and Gilloly et al. (2001), respectively, have parameters for other groups of organisms as well. Let actions of these animals afffect the bacterial populations directly (by predation) and indirectly (by soil mixing).
- Think about alternatives for scaling down from producers to decomposers - alternatives, that take into account spatial heterogeneity in the decomposers' world.
Code for the implementation of the landscape was taken from the NetLogo User Community model "Fitness_Landscape". http://ccl.northwestern.edu/netlogo/models/community/Fitness_Landsacape
The species counts and species attributes plots followed the example given in the "Echo" model contained in the NetLogo Models Librariy.
UIBM - the Universal Individual-Based Model.
Project website: http://uibm-de.sourceforge.net
Project administrator: Dr. Uwe Grueters, firstname.lastname@example.org
- West G.B., Brwon J.M. & Enquist B.J.(2001): A genereral model for ontogenetic growth. Nature 413, pp. 628-631
- Gilloly J.F. et al. (2001): Effects of size and temerperature on metabolic rate.
Science 293, pp. 2248-2251
- Larcher W. (2003): Physiological plant ecology. Springer
- Elert G.: The Physics Factbook: Mass of a bacterium. http://hypertextbook.com/facts/2003/LouisSiu.shtm
- Solbrig O.T. (1980): Demography and evolution in plant populations. University of California Press
- Colwell R.R. & Huq A. (1994: Chapter 9: Vibrios in the environment: Viable but non-culturalble Vibrio cholerae. pp. 117-135
In: Wachsmuth K., Blake P.A. & Olsvik Ø. (1994): Vibrio cholerae and cholera: molecular to global perspectives. ASM Press
- Storz G. & Hengge-Aronis R. (2000): Bacterial stress responses. ASM Press
- Chapin (III.) F.S. , Matson P.A., Mooney H.A. (2002): Principles of terrestrial ecosystem ecology. Birkhäuser
In academic publications any references to this model should refer to:
- Grueters U. (2011): Neture - a NetLogo model that simulates how Nature works. http://ccl.northwestern.edu/netlogo/models/community/Neture
In all other publications please use:
Copyright 2011 Dr. Uwe Grueters. All rights reserved.
Permission to use, modify or redistribute this model is hereby granted, provided that both of the following requirements are followed:
a) this copyright notice is included.
b) this model will not be redistributed for profit without permission from Uwe Grueters. Contact Uwe Grueters at email@example.com for appropriate licenses related to redistribution for profit.