Question

In comparing species using a protein cladogram and a DNA cladogram, how do you know which cladogram is correct or the most accurate? Do you think one of the cladograms is better or more reliable than the other? Why?

Answer 1

In comparing species using a protein cladogram and DNA cladogram, DNA cladogram is correct and DNA is more informative - atleast in the case of analysing a protein superfamily and its fold. The proteins you are looking at in a superfamily are very widely diverged,  and over that span of evolutionary time there is far too much likelihood of multiple substitution at the single DNA base (and thus more unobservable intermediate mutations, causing the divergence time to be underestimated); thus using the DNA data to generate the alignment is very likely to lead to alignment that do not reflect the actual mutational history and thus incorrect phylogenetic tree . The protein sequence is under selective constraint for protein function and protein structure , and these are conserved over much longer period than the individual codon choices.This is precisely the reason that BLAST searches for distant protein homologs, which are likely the evidence on which your superfamily of proteins was defined in the first place, use protein sequence comparisions instead of DNA sequence comparisions. even when comparing aligned DNA sequence, unless the organism are closely related the alignment should be constructed at the protein level and then the amino acid should be replaced by their codon sequences to generate the DNA sequence alignment.

To put a finger on that , the primary reason to align the DNA sequence instead of the protein sequence is that there may have been insertion and deletion at the DNA level that could shift the reading frame of the c-terminal segment of the protein , or an insertion deletion pair that shifts a reading frame to a (short) segment of the protein sequence. in these cases a single event (or a pair of events) can chane a (short) segment of amino acid sequence, leading the protein sequence alignment to overestimate the divergence time between the two proteins . However (a) this is the very rare event because (b) the protein sequence is generally intolerant of that much change . If that much change can be accepted at that position in the protein , then the part of protein must not be under very strong selection , and will not be terribly relevant to the structure of protein.

In general i think it will be very difficult to estimate divergence times for organisms that diverged as long ago as, say , a bacterium and a mammal, both of which contribute a member of same protein superfamily . The rate of evolution of two organism that are that different is very likely to be quite different, and thus the "molecular clock" . This is why the DNA cladogram is is more reliable then protein cladogram