As you can see, this folder contains, in addition to the file you're reading, (1) a copy of GenScope version 1.1 (2) the Dragon species file, and (3) an organism file called "Evolution."
The file opens at the population level. There are two environments, water (the blue stuff) and land (the yellow stuff). The water contains a herd of zero-legged dragons, the land is empty. One of the environment rules (take a look under "Options: Environment options...") states that zero-legged dragons can only live in water. Another says that four-legged dragons can only live on land. Two-legged guys, ignored in the rules, can live anywhere. Additional rules (denoted "Barrier rules" -- check 'em out) don't let the zero- and four-legged varieties cross the water-land barrier. This keeps them from wandering into hostile territory and dying. (You may occasionally find a dragon in the wrong environment. This sometimes happens when two dragons mate very close to the boundary and their offspring are actually born on the other side of the boundary from their parents. The unfortunate babies to whom this happens die in the next cycle.)
Click on "Start." The zero-legged dragons start milling about, mating with each other and having zero-legged babies (remember: zero legs breed true in dragons). They bump up against the barrier but are unable to escape from the water. However, every once in a while a spontaneous mutation (check out the mutation rate under "Options: Population options") occurs, which makes a two-legged baby. These little guys don't start off knowing that they can live on land, but sooner or later they blunder out of the water anyway. Although they are perfectly capable of wandering back, they tend not to do this because the food supply is more plentiful on land (check "Show food consumption" under "Population" to see the grass being eaten) and dragons, though not very smart, know enough not to go from a patch with lots of food to one that has little.
The inevitable happens. As time goes by, the two-legged dragons find each other, fall in love, mate, and have, on average, one in four offspring with four legs. These poor creatures thrive on land but can never go back in the water whence they emerged many generations ago.
Voilà -- speciation!
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