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Oh! And this part: I found this article which explains a lot of what I was curious about, although it does not address (at least not completely) why we do not see species undergoing major transformations between species today.

No one is going to address why we do not see snakes turn into birds and fly away today. You know how you ~~creationists~~ people who aren't creationists but don't accept evolution actually do accept "microevolution?" We see microevolution. That's all we think we should see. There is in fact only one evolution.

You see, most of us don't think evolution has some kind of limit that says, "You can't adapt any further away from the rest of your created kind." That's a creationist distinction. There's just this point called "speciation," before which you can remeld two populations which had been drifting apart but beyond which they really don't re-meld.

Actually, it's not even a precise point. Cross-fertility declines slowly over the generations until it's below replacement levels for attempted crosses. Lions and tigers are still cross-fertile but at low rates. Their hybrids are even less fertile. Horses and donkeys are cross-fertile but their offspring are almost never fertile. (But once in a blue moon, it happens.)