result interpretation for ancestral state construction

[nagar...@gmail.com]

Hi all,

I performed ancestral state reconstruction (ASR) for immune proteins that showed positive selection. I am interested in assessing the amino acid changes at the internal branches where the bifurcation/duplication happened before speciation. I need some help understanding the result file for the ASR analysis. Please clarify my doubts. Here are my queries:

1. In the rst.txt file, it was mentioned that branches 265-526 are ancestral; however, according to the results (below), branch 266 is defined by species YBM_7. Am I inferring this correctly?

2. what does "266..398" represent? Does it signify the total number of internal/terminal branches present after branch 266?

These are the following branches that I am interested in: 

"Branch 265:  266..398 (n=12.0 s= 3.0)

   4 GGA (G 0.988) -> GGG (G) 1.000
   5 ATT (I 0.999) -> ATC (I) 0.985
   9 GCC (A 0.621) -> TCC (S) 0.975
  14 AGA (R 0.552) -> GAA (E) 0.555
  15 TTC (F 1.000) -> GTC (V) 0.418
Branch 266:  398..263 (YBM_7)  (n=32.0 s= 8.0)
   6 AAT (N 0.999) -> AAC (N)
   7 ACC (T 0.894) -> ATC (I)
   8 CCA (P 0.996) -> --- (-)
  15 GTC (V 0.418) -> ACC (T)
  16 AAG (K 0.449) -> CGG (R)
  21 CCC (P 0.973) -> TCC (S)
For the sake of better understanding,  

•  Branch 265 is the root branch, and 
• branch 266 is an internal branch

It would be really helpful if someone could help me understand the ancestral state reconstruction analysis result.

Thank you.

Regards 

Nupur Nagar

[Sishuo Wang]

Dear  Nupur,

If i am not mistaken, 266..398 means node numbers 266 and 398 which together define a branch that are connected by the 2 nodes. In most phylo software the names of the tips are recoded from 1 to the number of the tips, followed by ancestral (internal) nodes.

At the same time, branches can also be named as Branch 1, Branch 2, etc.

Perhaps you could also attach your files so that others can better help you.

best,

sishuo