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Re: origin of bats/suspect trees? (combined answer)

----- Original Message ----- From: "David Peters" <davidpeters@att.net>
Sent: Sunday, June 22, 2008 3:19 PM

Need to DNA test Ptilocercus and Nandinia alongside bats and
dermoptera among other outgroups.

*Nandinia* hasn't been, but the three others have been in the same molecular analysis with each other and with carnivorans plenty of times.

2. The authors state: "Because morphology based phylogenies of
extant bats conflict with those based on gene sequences..."
So...until DNA tests support morphology and vice versa (we can see
the same problems within the Reptilia where even DNA testing does
not agree with other DNA testing), DNA tests among varying genera
will always be suspect. Within genera, the evidence is stronger as
any CSI TV show will testify. And occasionally DNA gets lucky.

It is _painfully_ obvious that you don't have the slightest idea what you're talking about. You have even stooped to the genericometer fallacy! Argh.

Insults noted.

Show me I'm wrong, and I'll apologize immediately.

Name two reptile DNA tests that agree with one another
and reflect morphology.

(For example, your use of "DNA test" shows you don't know what you're talking about.)

The last three or four molecular lepidosaur analyses agree with each other except in the precise resolution of the Toxicofera trichotomy. They disagree with all morphological analyses so far (most drastically in the position of Iguania, which the morphological analyses put as the sister-group of the rest of Squamata rather than next to anguimorphs and snakes), but all of those are rather small, and the molecular topology does explain some morphology like the venom glands which have, unexpectedly, been recently found in lots of anguimorphs and iguanians. The latest morphological analysis (description of *Saichangurvel*, in an AMNH publication from this or last year) finds the traditional morphological topology again, but expresses doubts about it.

Hey, the genes were right about the whales and the hippos, even though nobody believed it for years.

Or do you mean amniote phylogeny? On that topic, all analyses of the last 10 or so years agree, except on the position of the turtles. And turtles are a problem morphologically as well as molecularly -- long-branch attraction evidently rules in both cases.

Either data matrices of tetrapod phylogeny are utterly abnormal (delete postcranials and get phylogenetic grass!), or what you say is utterly unrealistic.

I like that euphemism. "phylogenetic grass" .

That's a dysphemism. :-)

Doesn’t matter which characters. Delete cranials. Delete post- cranials. Delete axials. Delete every other character, or every tenth. If you test like this, you’ll see what I mean.

Sure, David, trees get damaged the more you take away. You guys are always so polarized. Take away less, less damage.

I don't see what your point is. Check out your own quote above: I interpreted it as saying that when you delete large chunks of your matrix nothing changes in the topology, which is hard to imagine.

Getting back to bats: At least we should be looking for non-volant mammals with SOME bat characters, like broad flat ribs, reduced distal ulna, pedal proportions, wrist fusions, tooth counts, tooth shapes, etc. Funny thing is, there are such creatures, and they are arboreal, they’re just not cats, pigs and hedgehogs.

This is not at all surprising.

A reduced distal ulna comes with elongate forelimbs. Almost inevitably.

not birds, not pterosaurs, not primates.

Because they do things with their forelimbs that other animals with elongate forelimbs either don't do or do with the radius. I can't think of anything off the top of my head, but that doesn't mean there isn't anything...

Pedal proportions -- climbing.

sloths are different than lemurs. Do we count bats among the climbers?

Sloths don't climb, they hang, with the notable exception of the Pleistocene megalonychid *Diabolotherium* (Pujos, de Iuliis, Argot & Werdelin 2007, Zool. Syst. Linn. Soc. 149:179--235).

Wrist fusions -- all over the place. Isn't there individual variations in humans in whether the centrale fuses to the 3rd distal carpal or not?
Tooth counts -- diet and head size & shape.
Tooth shapes -- diet.

: ) Nice to see Drs. Martin and Feduccia again. It's all about the suite of characters, David. Evidence accumulates until there's more here than there.

That's what I'm talking about: tooth counts and shapes are correlated with each other, so that they are in reality -- for phylogenetic purposes -- fewer characters than you think. Some wrist fusions (not others) carry no or almost no phylogenetic signal because they change so often -- remember, there are tests that show how much phylogenetic signal a character contains.

And the whole list makes up less than 10 characters anyway.

This is coffee talk, cocktail chatter. You're not getting the main course. Just open your mind to possibilities unexplored until now.

Why don't you wait till you have served the main course? Why don't you wait till you have published? Then we'll be able to discuss your analysis in a meaningful way. Until then it's something we can choose to believe or not -- that's not science.

And "you should have an open mind -- but not so far open that your brains fall out."

So Nandinia isn't the African Palm Civet?

"African", yes. "Palm", yes. "Civet", no -- not for over 10 years now. _Never_ be content with reading Google snippet previews. Actually click the links to the results and read them! And never trust websites that don't look scientific on the phylogeny of anything. Even large parts of Wikipedia are way out of date.

David, the literature is not all-inclusive, nor is it gospel. If it were, we could all go home right now.

So your analysis has found that, contrary to all studies of the last 10 years, *Nandinia* is in fact a viverrid? That's great. It's just that, based on your question, I thought you simply didn't know about any of these studies and believed everyone still considered it a viverrid.

So why step on someone else's toes when all they are doing is
raising their hand with a question and a possible solution for a
problem that __no one__  else has ventured a guess on?

You come in, claim you have solved all those problems, and don't let us see your data or your analysis because you haven't published.

And which problem is it that "no one else has ventured a guess on"? It's not the phylogenetic position of Chiroptera.

Again, these are only part of the formula. Do you walk around angry and sarcastic all the time? Or only when you respond to new hypotheses?

No, when I respond to hypotheses that are presented as gospel long before they have reached the publication stage. Publication first, discussion second. Otherwise we literally cannot tell what you are talking about.

But more importantly, your presentation gives the impression that you are not well acquainted with either the data or the methods of analysis -- especially that you have no idea whatsoever about molecular phylogenetics. In other words, you don't seem to understand what you are talking about, and you don't seem to understand _that_ you don't seem to understand what you are talking about. Jaime and TMK have done it in more polite ways than I, but it's all the same: you look as if we need to teach you some science, and that's what we are trying to do.