chloroplast and other genes (was Lucy in Newsweek)

Ken Kinman kinman2 at YAHOO.COM
Mon Apr 5 23:14:57 CDT 2004

Hi Don,
     I am more optimistic (although some barking up wrong trees will no doubt still occur a decade hence).  Whole genomes will allow us to move beyond the current dependence on relatively unreliable sequence similarities (based on individual bases).  Larger indels (within genes) will tell us a whole lot more, and unusual combinations of gene order will tell us even more.  Such information (preferably substantiated with congruent morphological data) will answer many phylogenetical issues with very little doubt remaining.  The interrelationships of apes will no doubt be solved once the orangutan genome is sequenced.  I'm sure the chimpanzee genome will come first with a lot of fanfare, but doubts will remain until orangutan whole genomes are available.

      Beyond great apes, a lot of other phylogenies will be resolved as well in a ten-year time frame, although in some cases misrooting could remain a problem for some groups (I am trying to prepare malacologists to avoid such misrooting in molluscs, but whether they will heed such advice remains to be seen).  The information coming out of whole genomes will be enormous, solving many problems relatively quickly, but in other places there will be premature pronouncements, continued misrooting, and continued debate.  It will really vary a lot from taxon to taxon.  We will never have ALL the answers (fossil groups in particular will continue to remain the most problematic), but the number of phylogenetic problems we can resolve with confidence should increase dramatically with time.  It will be fossil taxa in particular that will keep paraphyletic taxa useful well beyond our lifetimes.  By then, the naturalness of paraphyly will have been rediscovered even by those who are now diehard strict cladists.  In the meantime, a lot of unpleasantness will divide the systematics community even as we continue to move forward.
            ----- Cheers,
                        Ken Kinman
From:  Don.Colless at CSIRO.AU
Subject:  Re: chloroplast and other genes (was Lucy in Newsweek)
Comments: To: deepreef at BISHOPMUSEUM.ORG

 My impression is that some 10 years ago we were given the impression that once complete genomes were available we would have all the answers.
The interesting feature of all this is, that if and when we arrive at a nice final picture of the genome, we will be committed to the results of something like a parsimony analysis for a final, definitive phylogeny. Yet, we'll still know - or SHOULD know - that undetected homoplasy may have us barking up the wrong tree!

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