Deriving The Sequence Of The Recent Ancestor

Question

[ngsgene]

Am working with genome sequences of A. thaliana species - and trying to derive the sequence of the recent ancestor of A.thaliana.

Looking at the consensus of multiple Thaliana strains at a given position and comparing it to that of Lyrata I can think of some possibilities to determine the base of the recent ancestor of A.thaliana.

I am looking for some feedback from the community, leads to literature that use algorithms to identify not the most recent common ancestor but the just the recent ancestor of the species.

[ngsgene]

What I have been thinking is A.thaliana & A.lyrata would have a recent common ancestor while I am more inclined to know the ancestor of A.thaliana - so it shouldn't be 'common' - perhaps there's another apt word for it.

[Bert Overduin]

It's not clear to me what you mean by recent ancestor as opposed to recent common ancestor. Isn't an ancestor of a particular species not always common to this species and another species?

[ngsgene]

It should be recent common ancestor - for the multiple strains of Thaliana it is a 'recent common ancestor'

Answer 1

[Michael Barton]

I think you can use codeml to generate the ancestor sequence from your group of thaliana sequences. You'll need the phylogeny of sequences in newick format though.

[ngsgene]

Thanks Michael - codeml is useful!

[Michael Barton]

You're welcome. I hope you enjoy the biostar community and continue to participate here.

Answer 2

[Niek De Klein]

I don't know how far you want to go into the subject, but I would suggest Ancestral Sequence Reconstruction by David Liberles (http://www.oxfordscholarship.com/oso/public/content/biology/9780199299188/toc.html). Chapter 4 onwards goes into computational methods. If this goes in to deep there are lots of papers, just google ancestral sequence reconstruction.

[ngsgene]

I'll look into the book certainly. thanks!