Phylogenetic Analysis In Eukaryotes

Question

[rajarapu.gangadher]

Hello,

How can we find the out group in phylogenetic analysis.

Thank you,

Gangadher Rajarapu

Answer 1

[klaugo]

I don't think that this question is at all trivial and I don't understand why it was down-voted. The choice of an outgroup is a crucial step in cladistic analysis because different outgroups can produce trees which are very different. As you know, an outgroup is the most closely related taxon to, but not the ancestor of, the set of taxa under study. Instead of settling for one outgroup it makes sense to experiment with a number of different ones. You might find this Introduction to Cladistic Analysis from Berkeley helpful.

[Leonor Palmeira]

Phylogenetic analysis is not necessarily used for cladistics, and the "Introduction to Cladistic Analysis" you recommend is rather confusing, as Gangadher Rajarapu is using 'phyml' for a maximum likelihood phylogenetic inference.

[klaugo]

What would you recommend?

[Leonor Palmeira]

Here is a very nice thread in biostars which gives a lot of information on this matter.

Answer 2

[Leonor Palmeira]

What do you mean exactly?

The outgroup is normally chosen before building the phylogeny. It is usually an organism (or sequence) expected to be more divergent from the rest of your sequences than all the other sequences.

Adding an outgroup allows you to then place a root on your tree (because you know the direction of evolution).