Biochemical Systematics (posted for J. Small)

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Date: Wed, 1 Nov 1995 19:30:54 -0800
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To: paleonet-owner@nhm.ac.uk
From: bonebug@halcyon.com (Joe Small)
Subject: Biochemical Systematics (Was:Hello)
Status: O


>Reply
>
>Yes, my offer is open to anyone, but I may not have the time to answer
>completely or quickly due to research time constraints.
>
>I need to read the Proctor and Lynch manuscript first.  Validity of genetic
>comparisons is troubled by the myriad of ways of analysing sequence data,
>and many researchers appear to be trying different methods, and algorithms,
>until they reach an endproduct of analysis that they like(uuugggggghhhh! Bad
>Science).
>
Okay, I had to do some work.  Procter and Lynch, in turn, Credit * Sibley,
Ahlquist and Monroe 1988; Sibley and Ahlquist 1990; and [especially] Sibley
and Monroe 1990, Distribution and taxonomy of birds of the world, New Haven;
Yale University Press *  for the 'Biochemical Classifican of Birds' in their
(P & L's ) book.
In addition they offer (in part) the following, "... our increasing
knowledge of biochemistry and the properties of protein molecules has opend
up exciting new possibilities for taxonomists.  By systematically comparing
the DNA of one bird species against other birds.... taxonomists have an
additional alternative for clarifying the relations among bird groups.  ..."
There is a passing reference to critical review by Houde 1987; Raikow 1985;
Shields and Helm-Bychowski 1988).

>This, I feel, makes genetic and morphological comparisons difficult.  Not
>all is lost, since there are ways out.  I think that classifications based
>on genetic sequence data largely reflect physiological changes that cannot
>be compared to morphological changes, because morphological changes occur at
>different rates, and may be disconnected from genomic changes, the vast
>majority of which are hidden. Morphological genes, or 'pattern genes' as I
>like to call them, represent a very small fraction of the genome.  However,
>one must choose with care the genes that one uses to generate gene trees,
>which do not always correspond with morphological species trees.
>

>Biochemical classification can involve protein comparisons and basal genetic
>comparisons. Which are you alluding to?  I tend to work with non-coding
>genes, ie. ribosomal RNA genes which can serve as molecular clocks and allow
>the determination of times of ancestral splits.

Is this based on the assumption that genomic changes occur at a constant
rate?  Is that a valid assumption?  If so, are the degrees-of-relatedness
based on proabability statistics? Some recent article I read (Discover
magazine, I think) discredits avian genetic classification as having been
based on a 400 base sequence; too short to have any credibility.  !!??
>
>Genetic comparisons transcend morphological problems like convergence if you
>pick the right gene.  In the case of birds, I really believe that the
>Epidomax flycatchers(hope I spelt that right?  People on this server take
>great pleasure in pointing out your every mistake, and drool over it) are a
>group of very closely related species, or even subspecies that differ only
>in their vocal abilities. Heck, my wife is a coloratura soprano and I am a
>bass!  These are phenotypic differences which perhaps should be discounted.
>The phenotypes of these birds are identical, and only genetic analysis of a
>few well chosen genes will answer this species question.  I suspect that the
>same holds true for a variety of species.  Let's take another view. Frogs
>are frogs. The South American tree frog is very distinct genetically from
>the Xenopus(S. AFrican tree frog), yet I would challenge anyone to
>distinguish the two skeletons after they have been fossilized over millions
>of years and largely disarticulated.
>
>I get stoned, I might get shot, but morphology, in my opinion, is a tenous
>science, and that is why I urge people to get on the genetic bandwagon
>because that is where things are headed. It is too bad that a small band of
>rebels make things difficult, but I expect that, and I will endeavor to lead
>them in the right direction as best I know how.
>
>Thanks for your response and interest.  I will follow up on your queries by
>reading about the studies you alluded to and get back with you.
>

Thank you again for your response.  It seems a bit risky for paleontologists
to make classification assertions based on morphological
comparisons....especially in the case of whales, where living specimens are
available.
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Joe Small                              Editor of 'Fossil News -
                                       Journal of Amateur Paleontology'
                                       Monthly journal for the enthusiastic
bonebug@halcyon.com                    amateur
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