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

----- Original Message -----
From: <FlxLandry@aol.com>
Sent: Wednesday, August 24, 2005 3:26 PM

Well, carnosaurs have been held to be very active and unsprawling predators
before their actual systematic content was redesigned by cladistics (think
Bakker's works, or the first edition of The Dinosauria...).

(Actually, _this_ understanding is almost limited to D1. Novas moved the tyrannosaurs out just 2 years later.)

And as far as I know they still are all "big theropods", very
concordant with the picture we have when we think "carnosaur".

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.

The term  Dinosauria should not be wiped out
because for most lay people it means "any big  prehistoric beast".

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.

I tend to have a subjective preference for saving old names
even if their meaning has to change (isn't there a Brontosauria somewhere???),

I have always hated the name *Brontosaurus*. I mean, for comparison, elephants don't trample, and sauropods (yet another name I'm not quite happy with) weren't lizards, although closer to lizards than to elephants!

but there is also a practical reason for it: if we have to invent new names
every time cladistics show a new clade, we'll soon run out of names... 

Demonstrably untrue. :o)

Both approaches can generate a fair
amount of confusion, but I think it's better to see an already known name and
ask "what's it current definition(s)?" than to see a new name without a clue
of what it means. People not expert on a particular phylogenetic group should
still be able to read works about it.

When the concept -- which primarily means the contents -- changes too much, changing the meaning of the name along with it (as opposed to using a new name) will produce exactly this kind of confusion. When you've never seen the name before, you know you've never seen its meaning before.

There is another advantage of keeping using old names under cladistic
standards: it makes anybody see very clearly what the cladistic point of view makes
us discover. For example, it looks like most tetrapod phylogenies have wiped
the term Reptilia out, not to have it inlude birds or mammals, because it
wouldn't fit with the popular picture. But birds definitely are reptiles in
tree-thinking, and calling them sauropsids or anything else just won't change
anything about that. It will just prevent people from understanding that,
indeed, birds are derived reptiles.

I disagree on both counts: surprisingly many authors use Gauthier's definition of Reptilia ( = a crown-group: the most recent common ancestor of turtles, lizards and crocs), and this definition has changed the meaning of the name beyond recognition. On the one hand, not one "mammal-like reptile", however mammal-unlike (*Varanosaurus*...), is a reptile anymore; on the other hand, the birds have been added -- about twice as many species as the rest of Reptilia! The meaning of Reptilia has sort of rotated by 90°. Fortunately Sauropsida is currently a heterodefinitional synonym.

And then came Modesto and... and... someone (Systematic Biology, not long ago), found Gauthier's definition insufficient because the phylogenetic position of the turtles is so unclear, and redefined Reptilia, consciously and explicitly, as a homodefinitional synonym of Sauropsida. They thought Reptilia was more popular and should therefore be used instead of Sauropsida. I've written a reply, but it's lying in the computer in Vienna, where I don't have Acrobat; Systematic Biology (...a somewhat megalomaniac place to start publishing...) requires that papers be submitted as pdf, and over here I wouldn't have much time anyway.

Theropsida and Sauropsida were used in a remarkably modern sense by Goodrich (1916) (I've read the paper), have occasionally been used since then (for example on an old-fashioned family tree of mammals on a wall in the university here -- Paris VI), and are ideal choices for the two stem-based clades of which (plus their MRCA) Amniota consists. The main reason why they haven't been used more is the fact that they usually lacked ranks -- which they did because the Linnaean system doesn't have enough room for them.

A few days ago I was explaining to my best
friend that she was an amniote. As I had previously described what the "Bob the
basal amniote" looked like, she just couldn't see what the term meant. She
wouldn't catch why a very salamander-like creature AND her would be amniotes,
while salamanders and frogs wouldn't. That's because she was absolutely not
tree-thinking. I feel that using old names in trees just makes clearer what a
tree is.

Not sure what you mean. Amniota Haeckel, 1866, clearly is an old name, and one with which I'm quite happy... and I don't see why Old Bob would have looked that much more like a salamander than like a lizard. For example, he certainly had a seriously keratinized, rather dry skin.

After all, most of the  important dinosaur clades were
identified  well before  cladistics, on a morphological basis.

Their interrelationships, however, weren't. Remember when some people
thought Dinosauria was triphyletic simply because nobody had tried to show
otherwise?

Isn't that also because they were not really interested in finding that out?

I think it's rather the other way around. It took cladistics to show people that for a fully resolved phylogeny we don't need an unbroken chain of ancestors and descendants; it took cladistics to show them that lots of phylogenetically informative characters are everywhere in an organism, not just... like... five in the braincase, three in the ankle and one in the dorsal vertebrae.

What would that comparative study do in terms of phylogenetics? Would it be
computerless cladistics? Or would it produce a scenario-based phylogeny,
the scenario being based on "cladistics with 3 characters"?

Yes and no... Take early dino evolution again: it looks quite likely that
changes in limb biomechanics were a very important aspect of dinosaur early
success. So it's not pointless to try to draw a scenario of how dino limbs
evolved from "thecodont" limbs (all those ankle reversals and
counter-reversals...). I don't say this should replace cladistics, but I think
it could have a bigger place along it.

I agree, though in this case I think a sufficiently robust phylogeny can disprove a scenario, while the opposite is almost impossible.

Or after you have done an analysis, even if it looks
quite well supported parsimony-wise, if it's in complete contradiction with what
the fossil record and paleogeography seem to indicate, then this should also
be taken into consideration.

OK, but in most cases, if a phylogeny doesn't fit the stratigraphy and the geography, I'll simply say the fossil record is too bad to fit better.

Of two _equally_ or almost equally parsimonious trees (whatever "almost" means...), however, I would prefer the one that fits the stratigraphy & geography better.

(There are extreme cases. Take the description of *Rapetosaurus*. It finds a clade (*Nemegtosaurus* + (*Rapetosaurus* + *Quaesitosaurus*)). I refuse to believe that, because *R.* is from Madagascar while *N.* and *Q.* are from the same formation in Mongolia. So, unsurprisingly, do the authors. In this case, however, the small taxon sampling and the incompleteness of most titanosaurs can very easily be blamed. *N.*, *R.* and *Q.* are the only titanosaurs with reasonably complete skulls, and of those, *N.* and *Q.* are _only_ known from those skulls.)

This is just extending parsimony, after all, though on a qualitative basis.

Yes -- taking into account that it's usually even more parsimonious to blame the incomplete fossil record.

It may not be reliable*, but it's scientific. I mean, the alternative would
in effect be to say that A is more closely related to C _because_ these
two only shares 3 apomorphies! See above.

Educated thinking and even intuition also are scientific, or else we would
still be living in prehistory.

Ermmm... no. Intuition is a perfectly valid method for _creating_ hypotheses. So is dreaming (Kekulé!). However, intuition is completely incapable of _testing_ hypotheses, and therefore it is _not_ scientific.

* This is something we can try to _quantify_. Some people prefer to draw
stippled lines -- I prefer to read "bootstrap value = 79 %". Yet another
big advantage of cladistics. (It is, however, possible to produce clades that
are both wrong and strongly supported...)

I do like stippled lines; they sometimes are scientifically very
parsimonious. :-) If our knowledge of some aspect of evolution is poorly known,
it's no dishonor to admit it while waiting for new papers and discoveries. 

It's even better to have a quantitative estimate of this uncertainty!

As I understand it, bootstrap value is something like an indicator of reliability
of a tree (which I admit is just as good or even better), but what is it exactly?

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). It can also construct a consensus tree of the individual bootstrap trees, which sometimes differs from the optimal tree, but such a consensus tree is very rarely published. (Certainly for space reasons. <g>)

Jackknifing does the same with taxa instead of characters. I don't know why, but it's very rarely used.

I think it just needs to be done carefully and explicitely. If time permits
(and as computers keep getting faster, it normally does), simply repeat the
analysis with different coding assumptions. Has been done in the literature.

This is fair science, but doesn't it show how thin the cladistic support for
a particular view of phylogeny is? I admit without any calculation it would
be worse. But the right way to code characters, if there is one, can only be
found with more and more thorough research, etc... You've already got my
point.

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...)

The thing  I can't grasp about parsimony is why one femur
character and another  cranial one should have more weight
than one single  vertebral  one, for example.

The reason is simple. There is no objective method of determining the true
weight of a character. So we must resort to parsimony.

It can be reasonably objective if it is discussed and everybody agrees (more
or less :-) in light of ontogeny, previous evolution, biomechanics, etc...

How so? How could this lead to a quantification (!) of the weight of a character?

Needless to say, to understand "previous evolution" you need a phylogeny. So it risks getting circular.

Model-based approaches that take branch length  into account, however, are
coming. There is one paper that uses Bayesian  methods for morphology
(...but doesn't explain how, at least not  yet).


Great. There certainly are methods to improve cladistics. However,  this
looks like more and more calculations and less and less calculation-free
thinking. I keep thinking it might be dangerous.

It is like substituting quantum mechanics for classical mechanics. The calculations do get a lot more difficult, and the results multiply, each coming with a probability attached. But the knowledge of these probabilities, as opposed to the illusion of certainty, is progress.

By the way, what are "Bayesian methods"?

[...] 

Looks very interesting, at it  seems to imply discussion both before and
after the actual calculation, which is  ideal.


Yes.

Anybody here has more precise info
(website, pdf, whatever) on how this  works?

No. But next time you come across a recent molecular phylogeny paper, look what it cites. Some years ago Systematic Biology had an article on Bayesian methods; I didn't understand it, though, because it was basically just math.

That said, Google has found this:
http://mrbayes.csit.fsu.edu/index.php