From daemon Wed Sep 25 09:00:16 1996
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Date: Wed, 25 Sep 96 10:50 CDT
From: THEODORE GARLAND JR <TGARLAND@macc.wisc.edu>
Subject: readings
To: JOE@GENETICS.WASHINGTON.EDU
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Status: RO

25 Sept. 96
 
Hi Joe,
 
     Here are some suggestions for the comparative method seminar.
 
(1) Papers about what the problem is.
 
Ridley's (1983) book might be useful, maybe the first couple of chapters?
I haven't looked at it for a while.
 
Harvey and Mace (1982) might be OK too, although a bit dated.  It is all
about "taxonomy" as opposed to phylogeny.  And, it spends a lot of time on
RMA versus least-squares regression issues (an earlier one of Paul's phases
... he does sometimes go off the deep end ...).
 
Before that, an earlier Harvey and Clutton-Brock paper could be useful,
probably one of these:
 
Clutton-Brock, T. H., and P. H. Harvey. 1977. Primate ecology and social
     organization. J. Zool., Lond. 183:1-39.
Clutton-Brock, T. H., and P. H. Harvey. 1979. Comparison and adaptation.
     Proc. R. Soc. Lond. B 205:547-565.
Clutton-Brock, T. H., and P. H. Harvey. 1984. Comparative approaches to
     investigating adaptation. Pages 7-29 in J. R. Krebs and N. B. Davies,
     eds. Behavioral ecology: An evolutionary approach. 2nd ed. Blackwell,
     Oxford. 493 pp.
 
I haven't looked at this for a while either, but it might be a good
introduction.  Be careful, though, because it really does present some of
the methods confusingly and even incorrectly (this was still from that
awkward time when Paul hadn't completely converted to phylogenetic as
opposed to taxonomic thinking).  Maybe just use their introductory things.
Pagel, M. D., and P. H. Harvey. 1988. Recent developments in the analysis
     of comparative data. Q. Rev. Biol. 63:413-440.
 
Then how about chapter 2 in Harvey and Pagel (1991)?
 
One thing to watch out for in most of the foregoing is that they emphasize
comparative approaches FOR STUDYING ADAPTATION.  That usually involves
correlating phenotypic variation with environmental variation (sensu lato).
Of course, comparative approaches are more generally useful for studying
"correlated evolution," e.g., of different aspects of the phenotype.  And
aspects of the phenotype can show correlated evolution for reasons that
have nothing to do with adaptation per se, such as genetic correlation
(maybe caused by characters being functionally related, which causes
pleiotropic effects) and genetic drift.  Sorry, Joe, I don't mean to bring
coal to Newcastle, but students often get the wrong (or at least an
incomplete) impression from reading the Harvey et al. papers that seem to
be hung up on studying adaptation, mainly, I guess, because that's what
behavioral ecologists usually want to do!
 
And finally I would use Garland and Adolph (1994).  Note, however, that
this does not agonize about the problem; rather, it suggests solutions,
emphasizing independent contrasts.
 
 
(2) Papers opposing the contrasts literature.
 
Probably not so much papers by Coddington.  But, you might check the
following:
Coddington, J. A. 1990. Bridges between evolutionary pattern and process.
     Cladistics 6:379-386.
Coddington, J. A. 1992. Avoiding phylogenetic bias. (review of Harvey and
     Pagel) TREE 7:68-69.
Coddington, J. A. 1994. The roles of homology and convergence in studies of
     adaptation. Pages 53-78 in P. Eggleton and R. I. Vane-Wright, eds.
     Phylogenetics and ecology. Linnean Society Symposium Series Number 17.
     Academic Press, London.
Craig, C. L., G. D. Bernard, and J. A. Coddington. 1994. Evolutionary
     shifts in the spectral properties of spider silks. Evolution 48:287-
     296.
 
Carpenter, on the other hand, seems more overtly hostile, the most recent
expression of which can be found in:
Wenzel, J. W., and J. M. Carpenter. 1994. Comparing methods: adaptive
     traits and tests of adaptation. Pages 79-101 in P. Eggleton and R. I.
     Vane-Wright, eds. Phylogenetics and ecology. Linnean Society Symposium
     Series Number 17. Academic Press, London.
 
And the following seems like a fairly direct response to that chapter:
Pagel, M. D. 1994. The adaptationist wager. Pages 29-51 in P. Eggleton and
     R. I. Vane-Wright, eds. Phylogenetics and ecology. Academic Press,
     London.
 
This paper is kind of interesting, though perhaps a little technical:
Bjorklund, M. 1994. The independent contrast method in comparative biology.
     Cladistics 10:425-433.
 
Finally, note that Garland and Adolph (1994, pp. 817-821) includes a
section on "Alternative Views on Hypothesis Testing and Inference:
Cladistics contra Statistics."  You can imagine where WE stand, of course,
but this section tries to explain some of the differences in world views
(as charitably as possible ...).
 
     Hope that helps.  Let me know if you want any clarifications or
further suggestions.  And, when you finish the semester, I wouldn't mind
having a copy of your syllabus or readings list.  I am currently using
Emilia's book in a graduate seminar.  I have only read a few chapters so
far, and nothing seems to jump out at me for the needs you described.
 
Cheers,
Ted