Appropriate Outgroups For Paralog Families

Question

[vilsnk]

Hi All

I am very new to phylogenetic tree construction and am looking for advice on my method for choosing appropriate outgroups. I'm looking at constructing phylogenetic trees for Mycobacterium Tuberculosis paralog families. I have been using a low stringency nucleotide blast to find orthologs to the genes in my gene families and using these as the outgroups. A guiding principle, as I understand it, for outgroup choice is that the outgroup sequence should be related to the members of the gene family but not more so than any of the family members are to each other. My problem is that I am unsure how to judge this criterion and always seem to obtain trees that contain the outgroup in a cluster with one of the members of the family when rooting on the midpoint. Should I simply ignore this and root on the branch with the outgroup I have chosen or is this an indication that the outgroup and the family sequence are too closely related?

Thank you for your patience.

EDIT: I'm using the ML construction method with protein coding nucleotide sequences using a multiple codon alignment (MUSCLE) in MEGA6.

Answer 1

[biostar]

You can select any gene from Human or mammals that belongs to the same gene family. You cannot ignore outgroup for phylogenetic analysis unless you only want to do neighbor joining tree (which is not used to/preferred to examine evolutionary changes across the lineages) BTW, we need to know what kind of gene/protein you are analyzing? If it is conserved gene family you can simply use the outgroup as I mentioned above. If you want to see evolutionary changes across the taxa then I would suggest you to perform the evolutionary model test and contruct maxmium likelihood tree with BS of 100 replicates. The easiest way to do all these is by using MEGA software.. But to be specific, we need to know what you are working on...

[vilsnk]

Thanks for replying.

I'm using the ML construction method with protein coding nucleotide sequences using a multiple codon alignment (MUSCLE) in MEGA6.

[vilsnk]

I'm not actually sure how deeply conserved the families are since there is not that much published but initial blast searches seem to suggest homologs do exist across multiple taxa.