Well you seem to have really answered nothing. I already know about the mutations in DNA, but it doesn't "JUST" happen. Something has to tell that tree it needs a defensive system. Something has to tell the DNA string to change. And instinct has absolutely nothing to do with a persons tatse prefrences or individuality.
Matt, let me give you a very analogous situation that happens over a much shorter duration of time. I raise goats. Goats get parasites ("worms.") I monitor each goat quite frequently and look for signs that the goat needs medicine to eliminate these parasites. Unfortunately, the medicine does not kill 100% of the parasites. Some of them are weakened, but do not die. If I administer this medicine too frequently, what I would end up with are parasites that are resistant to the medications.
What you seem to be asking is how do these parasites "know" to evolve. They don't. There is natural variation provided by occasional genetic mutations. Not all mutations are beneficial. Some mutations cause organisms to die much more quickly. Some mutations do absolutely nothing. But, some mutations give organisms a slight advantage whatever is selecting organisms to die in their environment. In my case, occasionally, there is a parasite that's just slightly less affected by the medication, and more likely to be weakened, but... survive. If that parasite reproduces, then unless there is another genetic mutation, that gene that benefits the organism is passed on and on and on. And, over generations of parasites, some will have mutations that cause them to die more quickly or not survive at all; some will have mutations that provide a slight beneficial advantage over others. Unless I succeed in killing 100% of the parasites - something difficult to do - then over the course of years, I am slowly selecting for the parasites that are most resistant to that medication. (We of course, take steps to reduce this effect.)
This is seen in medicine every day. Look at how many bacteria have developed over the past several decades to be resistant to many of the antibiotics that are on the market. Do you understand how that happens? God just doesn't say "hey, I'm not done creating here. I think I'll create a new variety of bacteria." There is no shortage of examples like this where we see evolutionary changes in organisms.
Now, since you brought up the case of trees, all you have to do is realize that these very slight changes are going to occur over a much longer span of time. And, you also need to realize that the changes occurred in both species simultaneously. A great example of this is elm trees. In the Himalayan area, where Dutch elm disease apparently spread from, the fungus and the trees evolved side by side. Over 100's of generations of trees (that's a long time), and many many more generations of fungus later, the trees survive attacks of the fungus, and the fungus has become more potent against elm trees. Once that fungus made its way into Europe and North America, via imports, it's wreaked havoc on the trees that did not evolve side by side with it, wiping out virtually all of the trees that it's encountered. And now, hybrids are being selected (by humans) which carry the genes from those resistant strains in the Himalayas or wherever they are, so that trees can be replanted in the US and Europe that are resistant. If humans suddenly weren't around to modify the environment & plant these trees, then what we would possibly see is the very slow spread of the surviving trees from portions of Asia where they exist into the rest of Asia and Europe, over 10's of thousands of years. Unless, of course, the trees were geographically isolated.
And, speaking of geographically isolated populations, we're just getting into some more of the basic nuts and bolts of understanding evolution.
In short, though, your objections to evolutions seem to stem from (pun intended) ignorance. "Wow, it's so complicated that I think I'd be too dumb to understand. Therefore... it was magic."