Beginners Interactive NetLogo Dictionary (BIND)
Farsi / Persian
NetLogo User Community Models
## WHAT IS IT?
This is a set of simulations designed to show how two populations become different species, through a process called speciation. There are two types of speciation: allopatric, which relies of geographical isolation, and sympatric, which relies on behavioral isolation. This simulation uses three different modes to explore speciation: island, costum, and sympatric.
## HOW IT WORKS
The basic method this model uses for determining species is the amount of difference in a turtle's genome. Genomes are represented by lists of integers, and they are randomly "mutated" by having items replaced with new random integers. Turtles use sexual reproduction, and each turtle passes on genes to its offspring. In this way, mutations get passed on to future generations, and spread throughout populations. In the custom and island setups, turtles mate randomly with other turtles on the same patch as them. In sympatric, the method is slightly more complicated, and is explained further on.
## ISLAND MODE
This mode has two islands, each starting with identical populations of turtles. They carry out the same basic life cycles on each island, but through random mutation and geographical isolation they become increasingly genetically different. The plot to the left shows the average genetic similarity between the populations on the two islands. The internal similarity monitor shows an average genetic similarity within the turtles on the same island. The button island-speciation will run the go procedure until there is zero genetic similarity between the two islands.
## CUSTOM MODE
This mode starts with no turtles, and an all land setup. The buttons to the right are used to draw water or land, and place turtles. With this, the user can test different setups to see how speciation works with various setups. Additionally, a tracer can be placed, in order two illustrate how genes travel through populations. The tracer is colored red, and has a given mutation in its genome. The higher the number for the tracer-sequence, the more likely it is to be passed on to the next generation. All turtles with this sequence are then colored red, to show the spread.
n.b.: all the custom mode buttons can be used in the island mode as well.
## SYMPATRIC MODE
In this mode, not all turtles start identically. Half of the turtles mate only when on red flowers, the other half mate only on yellow flowers. The procedure sympatric-presentation uses color-coding and text output to explain the important concepts of the sympatric mode.
## HOW TO USE IT
First, use the chooser below the world to select a mode. Once a mode is selected, the Go and Setup buttons will run the spesific procedures for that mode. The spesifics of each mode are explained above.
The button "highlight-species" is used in all modes. It colors all of the turtles that a given turtle (slected by mouse click) can mate with.
The avg-generation monitor shows the average generation. Each turtle has a turtles-own variable called generation, and each new turtle has the generation of it's parent, plus one.
## THINGS TO NOTICE / THINGS TO TRY
In the island setup, the genetic similarity between the islands decreases at a punctuated rate, sometimes flatlining for many generations. Why does this effect occur? How might the size of a turtle's genome effect the rate of change in similarity, and this punctuation effect?
Using the custom drawing tools, notice how much geographical isolation is needed for speciation. By placing a tracer in one population, observe how the gene travels from one to another. In general, total isolation is needed for species to diverge entirely, and genes will eventually make their way from one population to another if they are at all connected. See if it is possible to connect the two islands at all and still have them diverge entirely.
In the custom mode, create isolated populations and watch how long it takes them to diverge (either by the highlight-species button or by inspecting turtles). Now, make new isolated populations, varying the starting size, or the area of land they have to move in. How does this affect the rate of speciation?
In the sympatric-presentation, a ring species is created. This is where there are some turtles too dissimilar to mate, but they can both mate with some shared set of other turtles. Because of this, their genetic material can mix in future generations, and there is no clearly defined boundery to the species. Is it possible to create such a species using geographical isolation? Why or why not?
Increase or decrease the amount of flowers in the speciation procedure. If there are too many or two few of either kind, the turtles that mate on those flowers may all die out. In this case, no speciation will ever be observed, since one type died out entirely.
## EXTENDING THE MODEL
In this model, the similarity between turtles does not factor into how they chose a mate (primerily for run time reasons). To the chose-mate procedures, try making a minimum similarity (using the can-mate? reporter) below which turtles will not mate. Does this affect the rate of speciation or how much isolation is required for species to diverge?
## NETLOGO FEATURES
This model stores genetic material as lists of integers. Offsprings' genomes are made by taking the larger of the two parents' genes for each possition in the list.
Similarity comparisons rely on 'foreach' and 'map' to compare the genomes of lists of turtles, and 'n-of' to take samples of populations, in order to reduce run time.
## CREDITS AND REFERENCES
Citation for NetLogo software:
Wilensky, U. (1999). NetLogo. http://ccl.northwestern.edu/netlogo/. Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL.
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