How To Tell If The Third Codon Position Is Saturated?

Question

[Paul]

If you are looking at a few sequences by eye, how do you tell if the third codon position is saturated?

[Casey Bergman]

Saturation roughly means the point at which multiple substitutions have occurred at the same degenerate (mainly 3rd but but sometimes 1st) codon position, such that it is not possible to accurately estimate sequence divergence. Unfortunately, saturation is not a precisely defined term, which is why it may not be possible to find a clear reference for this on the web.

[Neilfws]

I think you mean the third codon position.

[Pierre Lindenbaum]

what means "saturation" for a codon ?

[Casey Bergman]

@neilfws - edited as suggested

[Pierre Lindenbaum]

Thank you Casey.

Answer 1

[Casey Bergman]

@david w is correct that this should be done more quantitatvely, but one quick eyeball method you can use if you know the phylogenetic relationship of your sequences is to look for rampant parallel changes at 3rd positions, e.g.

human         CTTGGA
dog           CTAGGG
fugu          CTTGGG
zebrafish     CTAGGA

Answer 2

[David W]

I don't see how you could do it by eye, but it's easy enough to do saturation plots.

DAMBE has an option to do it automatically, otherwise just calculate the uncorrected distance (P) among the 3rd codon positions of your sequences then do the same using corrected (e.g. HKY) distances. If the data is not saturated you'd expect a straight line whereas an alignment with saturation will give you a curve since P will be underestimating the number of changes (people often plot transitions and transversions separately)