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Re: Princeton Field Guide



 Denver Fowler wrote:

 Without wanting to get too drawn into species vs genus etc, one of
 the key points I presented at SVP, and that Greg has touched on in
 his post, is that by using analysis of stratigraphy and ontogeny
 (amongst other factors), species become testable hypotheses. Defining
 taxa is NOT just opinion: this is the old paradigm, little changed
 form the days of Marsh and Cope, where every slight variation in
 morphology was defined as a new taxon. Coding "taxa" for cladistic
 analyses cannot test the validity of species in the same way ...
 although we can use this approach to show that juvenile specimens not
 only tend to plot more basally than the adult forms, but also that
 they are often the very reason for polytomy disasters, erosion of
 node strength and CI/RI.

Having watched your talk (and John Scannella's) with great interest, I think the taxa you talk about (anagenetic lineages bounded by cladogenesis and extinction) are LITUs. They are species under some concepts but not, or not necessarily, under others; you should not call them "species" unless you make this explicit.

(Obviously, calling them "species" is probably the best way to deal with them under rank-based nomenclature which requires that you call _something_ "species" anyway. Still, whether two organisms belong to the same species only becomes a testable hypothesis once you've picked a species concept.)

 Defining all variation as 1's and 0's makes morphology black and
 white, but with a good fossil record (and the Late Cretaceous of
 North America is exceptional) you get so many shades of grey that
 this approach is becoming less useful.

This is simply an argument for treating (potentially) continuous characters as such in phylogenetic analyses. The best way I know is stepmatrix gap-weighting (Wiens 2001, Syst. Biol.): each measurement is treated as a separate state of an ordered character (which usually means that every taxon gets its own state), and the costs of transition between the states are made proportional to the actual morphological distances between them (rather than being set to 1 or to 1 / [number of states in the character] or suchlike).

(Complications can arise because PAUP* only allows 32 states per character. Wiens [2001] suggested averaging in such cases.)

I have used this approach for two characters in the paper accessible from here http://dpc.uba.uva.nl/cgi/t/text/text-idx?c=ctz;sid=d42a482bca8fcb6eec9a4635192c370d;tpl=browse-toc-77.tpl if you scroll down to issue 3. Was very time-consuming, but worked nicely.