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Re: Wukongopterus and Darwinopterus

> Let's see if all four possible combinations exist: - Long neck,
> long tail: diplodocids. - Short neck, short tail: ...are there any
> sauropods that count, actually...? - Short neck, long tail:
> dicraeosaurids. - Long neck, short tail: *Giraffatitan* sort of.
> I'd say they're not correlated. Of course, for an actual published
> study as opposed to a casual e-mail, it would be a good idea to
> actually measure that stuff and calculate the correlation
> coefficient.

 Interesting. I thought you'd go down the "how long is long? how short
 is short?" trail.

I did. That's what the "actually measure" stuff is about. First find what values exist, then divide the character into states accordingly. Wiens (2001) will tell you how. I'll see if I can find a pdf of that paper, though probably I can't.

 Arbitrary divisions work well in analysis. "> x" or "not" works good.

How do you know? Have you done any simulations?

Didn't think so. In fact, you haven't even read the copious literature on how to deal with potentially continuous characters.

>> 2) short manual toes vs. short pedal toes on stegosaurs;
> Certainly correlated -- a single adaptation for quadrupedal
> graviportal locomotion.

 Correlated? Perhaps. But now let's nest stegosaurs in Dinosauria. Are
 they still correlated? Doesn't this get to be a matter of opinion at
 one point or another?

Short answer: no.

Long answer: O'Keefe & Wagner 2001 (Syst. Biol. again). But that complicated method -- which tells you which characters in your matrix have too little phylogenetic signal and at the same time which ones are correlated -- is not implemented in any available software, you'd have to program it yourself...

 We might have nailed down the problem you're having with your trees.

I'm having a problem?

 The obvious in your estimation becomes "inapplicable".

The obvious is _by definition_ inapplicable.

When I can tell the state of one character by looking at _another_ character, the first one is correlated with the latter, and that means the two either must be merged, or the first one must be scored as unknown. If you don't do that, you're counting the same feature twice in the same matrix.

>> 4) number of caudal vertebrae versus loss of teeth in birds, etc.
>>  etc. etc. The list is endless.
> So what? That it's time-consuming and difficult does _not_ mean we
> shouldn't even try. To the contrary -- if it were completely
> impossible, _phylogenetics would be completely impossible!!!_
> Ignoring a problem never makes it go away.

 We're only trying to build a model here. So we don't wait until all
 the animals that ever lived are available for their analysis, we jump
 right in with a dozen to a dozen hundred taxa and build our model.

And? I don't see where the number of taxa comes into this.

 We're not trying to ignore a problem. As in calculus, we're trying to
 simplify it so it can be understood.

You're trying to simplify it way beyond that point.

 Let me ask you, once a fenestra appears, can it then disappear?

Yes, as explained yesterday at some length.

 If you ordered that character, you'd be making a mistake with all the
 best intentions.

It's a character with two states, so, as explained yesterday, ordering it or not doesn't change anything. As I asked yesterday: did you believe that "ordered" means "irreversible"?

> If you have 3 characters in your matrix that are correlated to each
> other, that's the same as having 1 character in it that shouts 3
> times as loud as the others. Because you gloss over this problem,
> the say-so you get is distorted.

 Not in my experience. My trees have included legless taxa, crestless
 taxa, toothless taxa and in all cases the overall suite of characters
 separates convergent appearances of all these traits.

That's assuming your topology is correct.

 So I don't buy your dutiful consideration.

I, too, am talking from experience.

 Simple "is-is not" dichotomy works very well. Avoids biases.

As I explained yesterday, it introduces biases by ignoring phylogenetic signal.

 By definition evolution is a slow process with minor changes
 between generations. I'm not making this up.

You are. The definition of evolution is "change with heritable modification". :-|

More importantly, we're talking about trees where each internode represents millions to tens of millions of years. The resolution of that isn't high enough to show what happens from one generation to another, or what happens within hundreds or thousands of generations.

>> Also, a good, healthy tree of sufficient size can sustain many
>> dozens of typos, if not all concentrated near a weak branch.
> This seems logical, but in fact it's backwards. The denser the
> taxon sampling, the shorter every internode will be -- and the
> fewer changes to the matrix will be required to overturn any of
> them.

 David, your scale is out of whack. We're talking about large clades,
 big branches. You're talking about uncles and cousins. The tens of
 million-years lineage that led to the redheads, blondes and brunettes
 will be unaffected.

No, what I'm saying is completely independent of scale. If you have a tree with plants and animals, and you add a fungus, the internode at the base of Animalia will be cut in two.

> I had this happen in my work. In this paper
> (scroll down to number 3) I added a taxon (*Brachydectes*) that
> broke up a long internode, and the bootstrap values in the clade
> that it held (Albanerpetontidae + Lissamphibia) _sank_ (fig. 6).
> That's perhaps counterintuitive, but it's logical: the added taxon
> is similar enough to that clade that, in some bootstrap replicates,
> it entered it.

 [...] When scoring for bone loss or bone fusion, as you do
 here, it gets very dicey, unless you handle it just so.

What do you mean?

 I also suggest no fewer than 50 taxa and no fewer than
 150 characters if you're dealing with serious unknowns.

Of course. We had to deal with that tiny matrix because we wanted to see if that matrix, with the original taxon and character sample* but with fewer mistakes in the matrix, still gives the same wacky result or a more orthodox one. (The latter happened.)

* As far as possible -- there were correlated characters, an all-zero ancestor, and other things in it that we couldn't let stand. There were even two characters that had to be split because they combined two independent characters each.

 I also suggest running through
 MacClade after you think you're done and review all the apomorphies.

In that case, the matrix was so small that I simply controlled every single cell against the literature, one by one.