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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.