Re: Hello (posted for C. Pretzman)

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Date: Tue, 31 Oct 1995 17:55:07 -0500
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To: paleonet-owner@nhm.ac.uk
From: cpretzma@postbox.acs.ohio-state.edu (Chip Pretzman)
Subject: Re: Hello (posted for J. Small)
Status: O

>Date: Mon, 30 Oct 1995 15:25:21 -0800
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>To: paleonet-owner@nhm.ac.uk
>From: bonebug@halcyon.com (Joe Small)
>Subject: Re: Hello
>Status: O
>
>Hello Chip Pretzman,
>     Is your offer to address question open to others too?  In the event you
>are entertaining questions regarding genetics as it relates to paleontology,
>I wonder if you can shed some light on an area where there seems to be some
>disagreement between biochemical studies and comparative anatomy:
>
>In the case of birds, there is an excellent discussion (we think?) of
>*Biochemical Classification of Birds* vs *Morphological Classification of
>Birds* in -Manual of Ornithology: Avian Structure & Function- by Proctor and
>Lynch (1993).  More recently we read of disagreements about the validity of
>genetic comparisons.
>
>Similarly, we remember reading of a revised classification of whales based
>on genetic comparisons.  The author(s) believe Sperm whales are more closely
>related to baleen whales than to any other toothed whales.  At least one
>paleo whale expert scoffs at the idea, but we observe some superficial
>similarities between Sperm whales and baleen whales while noting many
>differences between Sperm whales and other toothed whales. As we understand
>it, anatomists are loath to accept the idea that echolocation might have
>evolved 'twice', and teeth are here to stay.
>
>
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).

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.

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.

Cheers
CP