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Re- Evolutionary tree of *all* proteins

Ulrich Melcher biocukm at OKWAY.OKSTATE.EDU
Fri Oct 14 11:09:17 EST 1994

In response to Ed Rybicki (whose comments are appended below):

Convergent sequence evolution is, as R. Doolittle pointed out in TIBS earlier 
this year (TIBS 19: 15-18, 1994), very difficult to prove.  Yet, that it is 
difficult to prove does not mean that it has not occurred.

I think we (Lartey, Voss and myself, ms in preparation) may have come across a 
case where convergent sequence evolution has occurred during the evolution of 
the ribgrass mosaic virus subgroup of tobamoviruses.  In their RNA genomes the 
movement and coat protein cistrons overlap for 25 codons.  In other 
tobamoviruses there is no overlap or a shorter overlap.  The ancestral cistron 
in the overlap region can be deduced to be the coat protein one.  So, the C-
termini of the movement proteins of the RMV subgroup and those of the other 
subgroups are encoded by non-homologous nucleotides (i.e., not having a common 
ancestor).  There is a low level of sequence similarity of the C-terminal 
sequences of RMV subgroup movement proteins with the similarly placed sequences 
of subgroup 2 tobamoviruses.  Thus, we have similar amino acid sequences encoded 
by non-homologous nucleotides.  I think that is what is meant by convergent 
sequence evolution.  The situation will certainly complicate phylogenies based 
on movement protein amino acid sequences since all alignment algorithms will put 
the C-termini together in some fashion, even though they are encoded by non-
homologous nucleotides.

In article <MAILQUEUE-101.941014094806.416 at molbiol.uct.ac.za> 
ED at molbiol.uct.ac.za ("RYBICKI, ED") writes:
>> From:          mcdonald at wsuhub.uc.twsu.edu
>> Subject:       Re: Evolutionary tree of *all* proteins
>> evolution by sequence convergence.  It is quite possible
>> that, for some important cellular functions, there are
>> a few protein motifs that outperform all others.  Therefore,
>> there may be strong selection among some proteins to
>> develop such a motif.  The point is that, in this scenario,
>> we have proteins becoming more similar in sequence due to
>> selection over time (i.e., convergent evolution).
>> comparative genetic maps, etc.).  Otherwise, I think sequence
>> difference gives a good estimate of evolutionary distance
>> but does not necessarily reveal the direction of evolution
>> (i.e., are the proteins headed their seperate ways or are
>> they on a collision course?).
>Ah, but DO protein sequences ever converge?  I know a lot of people 
>have said they do, but at least one rather authoratative figure has 
>recently said that they do NOT - at least, not in such a way as to 
>obscure their phylogenies (Doolittle RF, (1994).  Convergent 
>evolution: the need to be explicit.  Trends in Biochemical Sciences 
>19: 15-18).
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