MEGA: Infer ancestral states

Question

[cv.napping]

Need some help.

I'm working with a phylogenetic tree of a protein in mega and when i click on show all ancestral states it shows letters like M, D, L I in front of nodes. (I read somewhere they are posterior probabilities but not much info there n dont understand what that meant too) I'm using this option for the first time so dont understand how to interpret this and use it in my understanding of the evolution of the said protein. Any help would be greatly appreciated.

[Whetting]

I assume that these letters are the reconstructed state at each node.

[cv.napping]

Okay, mbut how to interpret these states of yours?

[Whetting]

OK, let me answer your question with a question. What is the goal of ancestral state reconstruction? What question are you asking?

[cv.napping]

The goal of an ancestral state reconstruction is to get the sequence of the ancestral gene. I'm not sure how to interpret these states 'M' , 'L' etc.

Answer 1

[Joseph Hughes]

When conduction the ancestral state for a protein in MEGA, you will need to reconstruct the stat for each site in turn. The letters that you see at the nodes correspond to the ancestral state for one site only. Depending on which node you are interested in, you will get the ancestral sequence by determining the amino acid at that node for each of your sites.