NetLogo Models Library:
## WHAT IS IT?
This model lets you conduct experiments in Mendelian genetics with cross fertilization in a population of flowering plants.
A population of plants is used to show two sets of patterns of gene expression. One of these set of patterns is between a dominant and recessive forms (alleles) of a gene. The other is between two co-dominant genes.
This population of plants can be fertilized in the wild using bees to transmit pollen from one plant to another, or the user can artificially cross fertilize some or all the plants by hand (using the mouse to transfer pollen from one plant to another). After fertilization, seeds immediately form. Once fertilized, the same plant can not be fertilized again in that same growing season.
Plants drop the seeds they create in the same location the parent plant was growing. The user can allow these seeds of the plants to grow in the same location or move, organize, and label the seeds to make better sense of the outcomes of various fertilization events, in the following season of plant growth.
Also the user can move plants to the greenhouse location to "over winter" the plants so that they do not die at the end of the growing season. Keeping a plant in the greenhouse, ensures that it can be used in future seasons for additional cross fertilization experiments. But plants in the greenhouse are only permitted to cross-fertilize their pollen to plants outside the greenhouse. Greenhouse plants can not be fertilized, unless they are moved outside the greenhouse.
## HOW IT WORKS
Plants have two possible genes that determine their expression of flower color: W or R. The genotype and phenotype each plant follows the following co-dominant gene expression patterns:
WW - white flower
WR or RW - pink flower
RR - red flower
Plants have two possible genes that determine their expression of plant height: T or t. The genotype and phenotype each plant follows the following dominant-recessive gene expression patterns:
TT or Tt or tT - tall
tt - small
Plants have two possible genes that determine their expression of leaf pattern: C or c. The genotype and phenotype each plant follows the following dominant-recessive gene expression patterns:
CC or Cc or cC - solid green leaf
cc - variegated green and yellow leaf
## HOW TO USE IT
SETUP - sets up the initial conditions set on the sliders.
GO - runs and stops the model.
NEXT SEASON advances the season. You must press this button to move the plants through their different stages of growth and reproduction.
CLEAR SELECTED - clears any plants or seeds from the currently selected field.
POLLINATE WITH BEES - randomly pollinates any plants that are not yet pollinated
INITIAL-SEEDS sets the number of initial seeds that appear randomly distributed in the world.
CHANCE-MUTATION sets the chance that a mutation is introduced when plants are fertilized from the known set of available genes W, R, T, t, C, and c. If a mutation is added, the result may be the genotype does not actually change, if the gene that was randomly replaced is replaced with the same gene as before or if the overall genotype has a different order for the genes, but not a different combination.
SHOW-FERTILIZATION-NETWORK shows lines between which plants have cross-fertilized. A circle represents self-fertilization
LABEL-SEEDS-AND-PLANTS? allows the user to assign a label to any seed or plant they move. The label will be inherited by the next generations of seeds the plant produces.
ADD-WILD-SEEDS? allows the user to add new random seeds during the fall or winter.
USE-GREENHOUSE? when on a section of the world will be designated as the greenhouse when SETUP is pressed.
Running through the seasons:
On SETUP, a number of seeds (set by INITIAL-SEEDS) are randomly distributed about a garden. These seeds carry three genes for each trait they express. One pair of genes is for the expression of plant height. The next pair of genes is for the expression of flower color. The last pair of genes is for leaf pattern.
When the user presses GO and then clicks on the NEXT SEASON button, the seeds begin to advance through different stages of plant growth. The five seasons used in the model are shown in the SEASON-NAME monitor: early spring, late spring, summer, fall, and winter.
In each season the user can do different things with the plants.
In early spring, the seeds germinate and begin the process of forming a new plant. In this season, the user can select any of the fields of plants and clear all the seeds out of that field.
In late spring, the plants grow large enough to see and the user can click and drag the plants to new locations (transplanting them).
In summer, the plants are fully grown and their expressed traits are now visible. Here again the user can select any of the fields of plants and clear all the seeds out of that field.
In the fall the plants are ready to cross-fertilize or self-fertilize. Plants have both female and male plant structures. When you enter fall you will be asked if you want to pollinate with bees (randomly). You can answer YES and all the plants will be cross-pollinate. If you answer NO you can cross-pollinate using the mouse and you can later have the remaining plants cross-pollinate by pressing the POLLINATE WITH BEES button. To pollinate using the mouse click on a plant, hold the mouse button down and drag to another plant. Once a plant is fertilized, its flower closes up and a seed appears. It may no longer be fertilized by pollen, but it may continue to offer its pollen for the fertilization of other plants. Plants in the greenhouse (the upper right green quadrant of the world) are only permitted to cross-fertilize their pollen to plants outside the greenhouse. Greenhouse plants can not be fertilized, unless they are moved outside the greenhouse.
In the winter, the user can move the seeds that resulted from pollination to new locations by clicking and holding the mouse button down when the mouse cursor is positioned over a seed. The seed may be dragged to an open patch, but may not be placed on a patch where a seed already is located. Once the mouse button is released, the seed is dropped in the open patch under it. If the user turns the ADD-WILD-SEEDS? switch on, then the user may also click on open patches to add new wild seeds to the garden plot. These have a white box around them to help distinguish them from seeds that were created through a previous fertilization event on in the world.
In the early spring, the cycle of plant growth starts all over again from the seeds remaining in the garden
## THINGS TO NOTICE
What happens when you cross pollinate two pink plants? Are the results always the same?
What must be true about the two parents for the offspring of them to always end up with a white flowered plant?
When you cross pollinate a tall plant with a tall plant, are all the offspring tall? Are most? What percentage or fraction of the offspring is tall?
Is there any fertilization plan you can find that will guarantee that you end up with all tall plants?
In the wild, what percentage or fraction of the plants are short and white?
## THINGS TO TRY
Try to self-pollinate many of the plants to see what outcome those give. Continue self pollinating the plants until they breed true - which is to say, they consistently give the same characteristics in the next generation.
Move the plants and seeds into different areas of the screen to conduct different experiments in those areas. Label your plants to describe the parent's characteristics.
## EXTENDING THE MODEL
Plants could drop multiple seeds (e.g. four or five) like in a pea pod of a pea plant.
Mendel used pea plants to conduct similar experiments. In his peas, flower color was not co-dominant, it was dominant vs. recessive for white vs. violet.
Mendel also discovered other traits that follow these types of relationships:
The inflated vs. wrinkled seeds.
The color of the seed (green vs. yellow).
Inflated vs. wrinkled seed pod.
The color of the seed pod (green vs. yellow)
The distribution of the flowers along the stem.
## NETLOGO FEATURES
An output area is used to give instructions to the user.
The model makes heavy use of the MOUSE-* and USER-* primitives to allow the user to interact with the model.
## CREDITS AND REFERENCES
This model is a part of the BEAGLE curriculum (http://ccl.northwestern.edu/simevolution/beagle.shtml)
Other references to Gregor Mendel's 1865 paper "Versuche ueber Pflanzen-Hybriden" and a revised version of the English translation by C.T. Druery and William Bateson, "Experiments in Plant Hybridization", can be found at http://www.mendelweb.org/Mendel.html
## HOW TO CITE
If you mention this model in a publication, we ask that you include these citations for the model itself and for the NetLogo software:
* Novak, M. and Wilensky, U. (2007). NetLogo Plant Hybridization model. http://ccl.northwestern.edu/netlogo/models/PlantHybridization. Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL.
* Wilensky, U. (1999). NetLogo. http://ccl.northwestern.edu/netlogo/. Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL.
## COPYRIGHT AND LICENSE
Copyright 2007 Uri Wilensky.
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This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ or send a letter to Creative Commons, 559 Nathan Abbott Way, Stanford, California 94305, USA.
Commercial licenses are also available. To inquire about commercial licenses, please contact Uri Wilensky at firstname.lastname@example.org.