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From your source it looks as if they compared three closely related forms of the ADH3 protein-- "We have characterized three prevertebrate forms of the parent enzyme of this family, including one from an urochordate (Ciona intestinalis) and two from cephalochordates (Branchiostoma floridae and Branchiostoma lanceolatum)".

I used Blast to search out, using Ciona intestinalis, similar sequences. You can see from my listing that fish ADH3 is closer than the other 2 species used in your citation. Why is that, in light of your assertion?

You have to be careful comparing sequences, particularly fairly distantly related ones. BLAST is generally used for searching for related sequences; other methods are generally used for doing quantitative comparisons.

I pulled up three sequences; Ciona ADH3, Branchistoma floridae (a cephalohordate) ADH3, and Danio (zebrafish) ADH (number not specified) Here is the N terminus amino acid sequence:


C -GKVINCSAAVAWG...P...KKP.....-..-LS.IE....K..I..QVA.....PP.....K.....A.....HEV...RIK..VMAT.GVC.HTDAFTLSGEDP.....EAAFP.....VILGHEG.
B AGKPISCRAAVAWE...A...KKP.....-..-LV.IE....T..I..EVA.....PP.....K.....A.....HEV...RIK..VLAT.GVC.HTDAYTLSGADS.....EGKFP.....VVLGHEG.
D AGKVIKCRAAVAWE...P...KAP.....-..-LM.ME....E..I..EVA.....PP.....Q.....E.....GEI...RIK..VIAT.GLC.HTDLYHLVDGDK.....-RGFP.....VVLGHES.

Without weighting particular kinds of substitutions, I get 16 mismatches between Ciona and Branchiostoma, 23 mismatches between Ciona and Danio, and 27 mismatches between Branchiostoma and Danio. Of course, you'd really want to do this over the whole genome, not one end of one protein; I think the pros weight some mismatches more heavily than others; and this is a really tough example, because probably all three lines diverged at nearly the same time a long time ago.

I am impressed, though. There are damn few non-specialists who would go look at the raw data as you have.