How to do ancestor reconstruction given a tree and gene (name only) for every species?

Question

[yiuwingchung]

Hi, I am doing ancestor reconstruction

What I am having in hand is 2 things

1. a tree for 98 species

2. 98 lists of gene names (name only, without sequence, no information about gene family) for each of the 98 species

What I want to know is 2 things

1. gene gain and gene loss predicted in each branch
2. the genes that each node predicted to have

Can anyone suggest a software that can solve the problem? thank you very much

Answer 1

[Joseph Hughes]

You will want to do an ancestral state reconstruction. The are several packages in R which can do that such as APE and phytools and you can also do it in Mesquite and PAUP.

You will need to convert your gene list to a binary matrix of 0 for absence and 1 for presence for each of your genes. Then use this matrix of gene presence/absence to map against the species phylogeny using ancestral state reconstruction.