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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.  Arbitrary divisions work well in analysis. "> x" or "not" works 
>> 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? Isn't opinion something to be avoided?
>> 3) wide skull vs. orbits on skull roof on batrachomorphs;
> That term has fallen out of fashion. Do you mean temnospondyls and 
> lissamphibians? When the skull is so flat that it has no lateral side, the 
> orbits will be on the dorsal side, obviously; this means that, when the skull 
> is flat (in which cases it will also be wide), the character that describes 
> the position of the orbits must be scored as _inapplicable_. Taller skulls 
> like a hippo's can have the orbits in several positions.

We might have nailed down the problem you're having with your trees. The 
obvious in your estimation becomes "inapplicable".
>> 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. We're not trying to ignore a 
problem. As in calculus, we're trying to simplify it so it can be understood.
>> ordered vs. unordered: so difficult to determine with convergence and
>> parallelism.
> That doesn't even enter the question. Ordering is something that's determined 
> before the analysis. The states of a potentially continuous or meristic 
> character must be ordered (Wiens 2001, Syst. Biol.) because you already used 
> that assumption for partitioning the character into states in the first place 
> -- the assumption that it's easier to go from a state to a similar state than 
> to a morphologically distant one.

Let me ask you, once a fenestra appears, can it then disappear? If you ordered 
that character, you'd be making a mistake with all the best intentions.
> Yes, there are cases where it's tricky, and there are cases where both 
> ordering and not ordering are too simple and stepmatrices are needed. Cry me 
> a river. Phylogenetics is hard work.
>> Best to just let the suite have its say-so if there's any question.
> 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. So I don't buy your dutiful 
consideration. Simple "is-is not" dichotomy works very well. Avoids biases.
>> Evolution abhors apomorphies, preferring parsimony.
> You're making this up.
> You are making this up.
> "...and stop anthropomorphizing her, she hates that." There is no mechanism 
> that informs a mutation that it has already happened elsewhere and therefore 
> must not happen again. What did you think?!?

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

> I had this happen in my work. In this paper 
> http://dpc.uba.uva.nl/cgi/t/text/text-idx?c=ctz;sid=d42a482bca8fcb6eec9a4635192c370d;tpl=browse-toc-77.tpl
>  (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.

I think I mentioned this earlier, but bears repeating. (If not, apologies.) 
When scoring for bone loss or bone fusion, as you do here, it gets very dicey, 
unless you handle it just so. I also suggest no fewer than 50 taxa and no fewer 
than 150 characters if you're dealing with serious unknowns. I also suggest 
running through MacClade after you think you're done and review all the 
apomorphies. Some will be genuine. Others not. I'm sure you're already doing 
all this already. I don't envy you having chosen the most difficult clade in 
all Vertebrata to work with. 
>> "Weasel" words (i.e. could, can, might, may, would, should, possibly,
>> recheck the quality, correlated, heterodox, believe, etc. ) are signs
>> that specific data are being side-stepped. "An apple a day keeps the
>> doctor away" is a falsifiable statement. An apple a day (can, may, is
>> believed to) keep the doctor away" is not. I trust no referee who
>> relies on weasel words when falsifiable data is on the table.
> That's short-sighted of you. I used "can" because it happens in some cases 
> (pers. obs.) but not in others (pers. obs.). It's not predictable.

Then use "in THESE cases yes, and in THESE cases no." You actually answered 
better than I could.

Best ,

David Peters

> Also, I'm allergic to apples.