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Re: Princeton Field Guide



----- Original Message ----

From: David Marjanovic <david.marjanovic@gmx.at>
>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.)

No. How you define species is relatively meaningless. Frankly, what you call 
any 
given taxon is meaningless too: it's just for convenience. This list goes round 
and round discussing the nuances of definitions and  clades, but is only ever 
vaguely concerned (at best) with  paleobiological questions, and the accuracy 
of 
data presented in papers: do people here ever critically consider aspects of 
papers other than the taxonomy and cladistic analyses? 


The point of having a robust taxonomy is to recognise diversity accurately: ie. 
how many independent lineages are present at any given point in time. Whether 
you split a lineage into multiple genera (Centrosaurines), species 
(Chasmosaurus), or just have taxon A, B etc (e.g. Horner et al, 1992), doesn't 
really matter, so long as you understand the diversity correctly. Naming 
everything as monospecific genera facilitates communication, and dealing with 
cladograms, but too often it also leads to false impressions of diversity that 
doesn't really exist.


>> 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) contin
 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).

The problem with using ordered multistates, is that it will bias your result 
towards your preconceived idea, however correct your preconceived idea may be. 
This runs against the philosophy that your phylogenetic analysis should avoid 
subjectivity, even if that subjectivity seems well-founded. I agree that 
multistates are a possible answer, but they do not help much in deciphering the 
effects of ontogeny, nor how to code for this. Shifts in timing of development 
of features (heterochrony) is discernible with good ontogenies and strat data, 
but unless your taxa are either fully mature, or are of comparable immaturity, 
then you get a hellish mess when coding, and ordered multistates won't help. At 
the moment, we are probably stuck with a "best method is still very flawed" 
approach.