Chapter 2 is all about basic phylogenetic techniques.
Some notes:
-Hennig's Auxiliary Principle=always assume homology in the absence of contrary evidence.
-convergence and parallelism are both homoplasies
-it is not always true that the outgroup has plesiomorphic characters
-isomorphic=topologically identical -I've never heard this term used for this before
-"there is only 1 true phylogeny" -is there? what about cases with reticulating speciation or horizontal gene transfer? what evidence do we have to make this assumption? are there any other scenarios where this might not be the case?
-I think it is odd that the entire internode is supposed to be the ancestor, but then we plot character states/transformations on the internode. Isn't this a bit misleading?
-I found the exercises in chapt. 2 to be too time consuming! They should have put just 1 or 2 simple examples in to get their point across. Then, in the answers, they don't even give you a diagram of the tree. If we are going to put all that work in to do the exercises, the least they could do is make the answers as clear as possible. Jeesh.
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I think everyone found the Chapter 2 exercises time consuming. But I think that was kind of the point. As in, "this is why a computer does this".
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