Oligochaeta molecular phylogeny

Kirk Fitzhugh fitzhugh at rcf-fs.usc.edu
Thu Jun 15 17:49:44 EST 2000


At 10:17 AM 6/15/2000 +0100, Fredrik Pleijel wrote:
>Not sure I disagree, but on the other hand, when looking at the results I 
>wouldn't have too many problems assuming the plane did have a fair 
>amount of speed when hitting the ground.  
>
>Maybe planes are easier?

Exactly my point! To say some group of worms have a "high rate" of sequence
evolution is meaningless unless one can assign some temporal framework.
Let's say one claims species A and B diverged 50 million years ago. How is
one to say what "rate" of evolution has occurred within each lineage? What
if all pertinent changes occurred during the first one million years, and
for the subsequent 40 million years nothing happened? Within the span of 50
million years all one could say is that the rate of change is low! It is
only in the context of time that rate has any meaning. If, as generally is
the case, one ignores time, then any statement of sequence rate is vacuous.

There is, however, a more disturbing aspect to the moleculoid bandwagon,
which goes to the comments by Bruce Stockley, forwarded by Torin Morgan:

>In molecular terms we know average mutation rates, and may have more 
>accurate mutation rates based on empirical data.  We know the type of 
>mutations that occur most frequently, and we have the fossil record to 
>calibrate certain events.

Let's say one has a set of specimens, from which they "observe" that
position 556 of each specimen has an A. Our perceptions tell us we "see"
the same nucleotide among these individuals. Most systematists then go so
far as to say, "this A at position 556 indicates homology." If one asks the
definition of homology, they might respond, "shared similarity due to
common ancestry." Historically, this is an accurate definition; one has
causally accounted for the perception of similarity by way of "historical
continuity." The problem is that historical continuity is denied at the
point mutation rates are invoked. To say there is a mutation rate is to
automatically claim that some of the observed A's are not due to common
ancestry, which is in violation of any homology hypothesis, much less any
statement that one observes the same type of property among a group of
individuals. There is a logical flaw in the use of homology, then the use
of rates. To use rates, one must do so at the point of inferring homology
hypotheses, then rename all those observations that are then known to be
spurious. One certainly would not group flies with birds because each have
"wings." If, as Bruce Stockley states, the empirical evidence is so
overwhelming for mutation rates, then there must be provided a
straightforward method for answering the question, "why do I observe A's at
position 556 among these individuals?" The answer is that these A's are not
the same historical properties, just like fly wings are not the same
historical properties as bird wings. To invoke rates requires an answer
that is to determine which of these A's really are not the same thing,
rename them, then proceed with trying to causally account for shared
similarities by way of cladograms. I would also ask how it is then that one
is to perform cladistic analyses that satisfy the "requirement of total
evidence" when some characters are not amenable to rate assumptions whereas
others are. Consensus techniques will not work here for philosophical
reasons that most have overlooked. These are problems that can only be
dealt with at the level of inferring homology hypotheses, not cladograms.

Bruce Stockley also suggests,

>On a less glib note, it does all come down to the fossil record to provide 
>a second opinion as to the actual cladogram/phylogram accuracy, not only in 
>terms of pattern but also in terms of branch lengths.

Actually, fossils provide little sense of "accuracy," and definitely no way
of determining "branch lengths." Accuracy from the fossil record carries
with it the substantial assumption that the record is so remarkably
complete as to be infallible. The sequence of nodes on cladograms only
provide hypotheses that one character was temporally derived subsequent to
some other character. Fossils can do no better than give minimum ages of
divergence between nodes and/or terminal taxa. It would be impossible to
assign branch lengths from such data, unless one is claiming they can
identify fossil ancestors. If one claims that cladogram branches should
denote character changes between a node and a terminal, then once again
they will have to deal with the empirical problem of denying their own
perceptions of shared similarity.

Thanks for "listening."

Kirk

"A man must be downright crazy to deny that science has made many true
discoveries. But every single item of scientific theory which stands
established today has been due to Abduction."

C.S. Peirce
------------------------------------------  
Kirk Fitzhugh, Ph.D.
Associate Curator of Polychaetes
Research & Collections Branch
Los Angeles County Museum of Natural History
900 Exposition Blvd
Los Angeles CA 90007
Phone:   213-763-3233
FAX:     213-746-2999
e-mail:  fitzhugh at bcf.usc.edu
------------------------------------------


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