How do phylogenetic experts evaluate results which use constraint trees? Are there examples in the literature where phylogenetic experts detail how they use constraint trees?
Here is my problem. I have 500 samples. These are five different "categories" of species A, B, C, D, E, 100 samples each.
Category A: A1, A2, A3, ..., A100 Category B: B1, B2, B3, ..., B100 Category C: C1, C2, C3, ..., C100 Category D: D1, D2, D3, ..., D100 Category E: E1, E2, E3, ..., E100
There are two classes of which these "categories" fit in: Class 1: A and B, Class 2: C, D, and E.
For the purpose of this discussion, let's say A=whale, B=dolphin, C=mouse, D=gerbil, E=hamster
When I do the analysis, there are some problems. The output tree resolves the samples into two classes which meet my expectations; it splits the samples into two groups: ( A & B) and ( C & D & E ). That's great. However, it doesn't resolve the species into separate categories, e.g. it mixes together "whale" samples with "dolphin" samples, and mixes together all the individual C, D, E . I see
(A1, B3, A27, B23, B2, A2, A3, A4, ....), (C3, C5, D72, D3, E1, E2...).
This would mean whale1 is more evolutionarily "related" to dolphin3 than whale 27.
I try to use a constrain tree instead to constrain each of these groups, using the form
((A1, A2, ..., A100), (B1, B2, ..., B100), (C1, C2, ..., C100), (D1, D2, ..., D100), (E1, E2, ..., E100))
Sure enough, my tree now resolves each "category" A, B, C, D, E into a distinct category.
Question 1: Isn't this cheating? I feel like I stipulated "resolve the tree in this manner I expected" and RAxML output that.
Question 2: How do I evaluate whether this is correct?
Question 3: For experts, could direct me to published literature which used this approach? Which papers used RAxML constraint trees?
Thanks for any help. I'm happy to clarify things.