I am one of "those molecular people" who finds these occasional flames
about molecular phylogenetics rather peculiar. I sometimes think that
the extreme points of view such as were espoused by Ludvig Mortberg
at the beginning of this thread, reflect the view that systematists
using molecular data are upstarts who never bothered to learn the true
and difficult methods of morphological systematics, and therefore don't
have any understanding of how organisms really function or evolved. In
fact, how organisms evolve is not the only interesting question to be
addressed with molecular data. Some of "those molecular people" are also
interested in how genes evolve. Ludvig Mortberg's statement illustrates
that this has not occurred to him - he assumes that all molecular
systematics is aimed at elucidating the relationships among organisms:
Mortberg wrote:
> I think that sequence information should only be used if nothing else
> works. If you can't identify any reliable morphological traits try
> sequencing a couple of genes with broad outgroups. What to sequence is
> hard to decide. Go for something linked to morphology or metabolism.
Currently, I am interested in the relationships among certain genes of
the immunoglobulin superfamily. How would finding something linked to
morphology or metabolism help me with this problem? Plainly it would
not. More importantly, how do I choose an appropriate outgroup for an
ancient family of vertebrate genes? I cannot simply take the sequence
for sharks or protochordates (if the sequences existed) as outgroups even
though that would be appropriate if I were trying to understand vertebrate
phylogeny. I have to settle for genes that appear to primordial based on
the structure of their protein products, and align them according to
similarity of both sequence and structure. While I would love to be sure
that I know which characters are homologous, similarity is the best I can
do at the moment. Perhaps die-hard anti-molecular types would suggest
that I should not even try such analyses, but that point of view that
would be completely antithetical to the spirit of scientific inquiry.
Just for the record, I am one of "those molecular people" who uses both
parsimony and outgroup analysis whenever possible, having been trained by
a tough morphological systematist who also uses molecular data. But not
being a religious person, I have occasionally also been known to do
neighbour-joining and maximum likelihood analyses.
Miriam Richards
Fred Hutchinson Cancer Research Center
Seattle, Washington
