In article <schwarze-220594183224 at fennel.bio.caltech.edu> schwarze at starbase1.caltech.edu (Erich Schwarz) writes:
>Which brings me to my question for the "group mind" out there: is there
>any reasonable algorithm by which one might distinguish motifs that had
>arisen from convergent rather than divergent evolution? Intuitively it
>seems that, by the time a "motif" becomes 60 or so amino acids long (e.g.,
>the homeo box), it is probably impossible for it to have arisen
>convergently. Meanwhile, one instance of three residues (the catalytic
>triad in trypin et al. versus subtilisin et al.) is probably a rock-solid
>case of convergent evolution. How does one draw a line through the middle
>ground between these extremes?
I'd say that we can't. We don't know and probably can't guess the
relevant probabilities. The probability that two similar sequences
were convergently evolved depends on how new sequences are generated.
What's the probability of arriving at the same protein fold
independently, how many new sequences were generated (and how? by exon
shuffling of previous domains?), and what selective pressures would
refine two unrelated but structurally similar proteins towards the
same consensus sequence?
Even identical sequences could have been convergently evolved, if
nature generates new sequence fast enough and there's strong selection
pressure towards a particular sequence. Not very likely, mind you,
but I wouldn't try to draw any lines in the sand.
For instance, in vitro RNA evolution experiments are now possible in
the laboratory. You start with a mix of 10^14 or so different RNAs and
select out the ones that are fit for some function, like binding a
target protein. It's possible to re-run the same selection experiment
and get exactly or nearly the same sequences out at the end. There's
no possibility that they're related "evolutionarily" (barring PCR
contamination), so this is "convergent" evolution, but the sequences
can be identical.
--
- Sean Eddy
- MRC Laboratory of Molecular Biology, Cambridge, England
- sre at mrc-lmb.cam.ac.uk
