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

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