Re: Phylogenies, science, tea-time and more...

[Michael Mortimer <mickey_mortimer111@msn.com>]

David Marjanovic wrote-

> I think when the contents of a clade change too much, the name should also 
> change. Carnosauria is not a good example, actually. Arguably Coelurosauria 
> is a better one.

I think Coelurosauria made it through rather nicely, actually.  
Coelophysoids are removed and tyrannosaurids were added, but it's rather 
similar otherwise.  And Huene even included tyrannosaurids.  Sure birds were 
"added", but most BAD advocates back in the day thought birds descended from 
compsognathid-like taxa anyway, so that was just a case of paraphyly.

> IMHO it should have been wiped out in 1975 when the birds were added, and 
> also because dinosaurs aren't lizards. (Owen did coin his Dinosauria as a 
> suborder of lizards.) But it's clearly too late for that.

What does the fact they aren't lizards matter?  Surely you wouldn't advocate 
changing all the taxa ending in -saurus that aren't squamates.

> Bootstrapping randomly eliminates a character from the matrix, randomly 
> duplicates another character, and then searches again for the most 
> parsimonious/likely tree. It does so the number of times the experimentator 
> chooses (500, 1000, 10000, so that each character has hopefully been 
> eliminated at least once). Then it counts the number of trees in which 
> every given clade occurs and outputs that number (usually as a percentage).

Close.  It doesn't actually eliminate one character and duplicate another.  
Rather, it creates each new matrix (pseudomatrix) by randomly choosing x 
characters from the original matrix of x characters.  So it's hypothetically 
possible for the same character to get chosen every time and the resulting 
pseudomatrix would consist of that character being weighted infinitely.

> Jackknifing does the same with taxa instead of characters. I don't know 
> why, but it's very rarely used.

So that's what jackknifing is...

> I do. However, often it doesn't make much difference. When a paper says 
> that the analysis was run with and without ordering multistate characters, 
> the results never differ by much, if at all. (I guess this means the 
> proportion of multistate characters in those matrices is so low that those 
> few characters don't matter...)

Just as a note of interest, running my analysis unordered REALLY changes the 
results.  Therizinosaurs become arctometatarsalians, troodontids become 
deinonychosaurs, oviraptorosaurs become avialans, Archaeopteryx becomes a 
troodontid, enantiornithines are monophyletic, etc.  Nearly all the small 
scale interrelationships change too.

Mickey Mortimer