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

David wrote:

>I object to the use of  "Carnosauria" because that name comes with a concept 
>(big theropod...  pictures like Burian's semi-sprawling *Tarbosaurus*). At 
>least it's  anchored to *Allosaurus* :-)

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...). And as far as I 
know they still are all "big theropods", very  concordant with the picture we 
have when we think "carnosaur". The term  Dinosauria should not be wiped out 
because for most lay people it means "any big  prehistoric beast". I tend to 
a subjective preference for saving old names  even if their meaning has to 
change (isn't there a Brontosauria somewhere???),  but there is also a 
reason for it: if we have to invent new names  every time cladistics show a 
new clade, we'll soon run out of names... 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.
There is  another advantage of keeping using old names under cladistic 
standards: it makes  anybody see very clearly what the cladistic point of view 
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.  A few days ago I was explaining to my best 
friend that she was an amniote. As I  had previously described what the "Bob 
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.

>> Ja! But the problem is  that in a large part of current dino research 
>> anatomy
>>  is no more than a tool for building some matrix, that, stuffed into  some
>> computer program, will release the new version of a phylogeny,  just to be
>> destroyed two months later. I'm not saying cladistics are  coming from 
>> nowhere  and
>> pointless, just that they  seem to be a little bit too overriding these 
>> days.

>There  are two reasons. Firstly, the number of characters used per study  
>currently grows faster than linearly. Some people add tens of characters  to 
>their matrices and publish the updates on average once per year. The  other 
>is the addition of taxa -- by discovery. *Eotyrannus*, *Dilong*  and perhaps 
>*Tanycolagreus* and the redescribed *Coelurus* can tell us  more about the 
>phylogenetic position of Tyrannosauroidea than we could  have found out 

That's why we need more detailed  anatomical (re)descriptions and less 
hastily done computer analyses. Huge  amounts of horizontal study are necessary 
produce a little amount of vertical  one, if you see what I mean. And it looks 
like many people want to go straight  to the vertical knowledge 
(reconstructing evolutionary patterns) before the  hard, dry and boring 
horizontal (mostly 
anatomical) work is done.

>A  deep knowledge of anatomy can contribute a lot to finding previously  
>overlooked characters and to coding them correctly (like, coding  
>non-independent characters as one character rather than 2 or 10,  
>them as size- and/or ontogeny-related...). And it should.  :-)

Yes, and explicitely.

>> 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  

Isn't that also because they were not really  interested in finding that out? 
With the fossils we now have at our disposal, if  we try to draw a picture of 
how the early evolution of dinosaurs, their  monophyly can be very strongly 
supported (by diagnosis, and by building an  anatomically compelling 
evolutionary scenario) without using cladistics. If they  confirm that, all the 
If they don't, we have to take another look, but  not necessarily to find them 
to be right.

>What would that comparative  study do in terms of phylogenetics? Would it be 
>computerless cladistics?  Or would it produce a scenario-based phylogeny, 
>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. Or after you have  done an analysis, even if it looks 
quite well supported parsimony-wise, if it's  in complete contradiction with 
the fossil record and paleogeography seem to  indicate, then this should also 
be taken into consideration. This is just  extending parsimony, after all, 
though on a qualitative basis. If the  phylogenetic picture that comes from a 
tree is not that neat, that is if you  can't easily transform it into a 
story of how evolution happened, then  alternative scenarios could be at 
least mentioned, even if they're a little less  parsimonious from a strictly 
quantitative and anatomical point of view. Some  works include this, but most 

>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. They should not replace  quantitative methods, 
just highlight both their strenghts and  weaknesses.

>I like reweighting, though. But then, it is _dishonest_  to _only_ publish 
>reweighted trees, as the "Basal Ornithopoda" chapter  of D2 does.
>* This is something we can try to _quantify_. Some  people prefer to draw 
>stippled lines -- I prefer to read "bootstrap  value = 79 %". Yet another 
>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. 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?

>Every once in a while a very strongly supported  clade emerges, and people 
>think "why didn't I think of that earlier".  Take the molecular analyses 
>again and again and again make whales  and hippos sistergroups. 
>used to think it must be wrong.  But early this year and late last year 
>morphological analyses found the  same. The mystery of artiodactyl phylogeny 
>is no longer the position of  the whales but that of the ruminants!

Well, as there was very little  tree-thinking before cladistics, people 
probably were not looking for the right  things. I just say that tree-thinking 
should not stop to be thinking because  it's got a very handy calculation tool.

>> [...] if some new  species is described from just one incomplete
>> specimen, then a  discussion on its phylogenetic position, based
>> on careful   examination of what is known
>> (I mean, an actual TEXT about that),  should work  just as well,
>> or better, than a computer  calculation.

>I think this depends on how detailed the computerized  analysis is. If it's 
>as detailed as the text, it should be at least as  reliable.

But you need a lot of text to show that said analysis is really  good. That 
was just the text I was actually talking about. It keeps being  absolutely 
necessary to make good science, even if you get a lot of help from  computer 

>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 

>> 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...

>Model-based approaches that take branch length  into account, however, are 
>coming. There is one paper that uses Bayesian  methods for morphology 
>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.

>> I feel  cladistics are sometimes a bit like asking  "are American
>>  democrats or republicans?", and answering that according to the   last
>> elections it's most parsimonious to conclude they're  republicans. I know
>> that this is a very rough caricature, but  anybody working in cladistics is
>> confronted to just that kind of  problem.
>> By the way, what are "Bayesian   methods"?

>They try to resolve precisely this problem! :-) It would  help if I had 
>actually understood them... anyway... this approach has  been used in many 
>recent molecular analyses. You start with... I don't  know how you start. I 
>only remember the two most important features: The  results come with 
>"posterior probabilities", a support value similar to  bootstrap & 
>except more reliable, because it's based on a  kind of statistics called 
>(Markov chain Monte Carlo); and you can  apply complex weighting schemes 
>(GTR...) by not giving everything the  same "prior probability". The main 
>advantage is that it produces  probabilites rather than yes-or-no answers.

Looks very interesting, at it  seems to imply discussion both before and 
after the actual calculation, which is  ideal. Anybody here has more precise 
(website, pdf, whatever) on how this  works?

>>As far as I know,  knowing  that
>>tyrannosaurs are closer to birds than to allosaurs did not  improve  in any 
>>our understanding of how  tyrannosaurs lived.

>It has. To start with, phylogenetic bracketing  teaches us that the default 
>assumption should be that *Tyrannosaurus  rex* had feathers, while the 
>evidence is at best equivocal for  *Allosaurus*. Then we can go on about... 
>perhaps its respiratory system,  which may well have been more birdlike than 
>that of *Allosaurus*, which  in turn could imply different metabolic rates, 
>different running speeds,  whatever. Even how we interpret the biomechanics 
>of its legs, hips and  tail is influenced by our knowledge on its 
>phylogenetic position. And so  on. Hey, its brain!

Point taken.

>Really. "Nothing makes sense  in evolution, except in the light of a good 
>phylogeny". I'll try to look  up the exact wording and the authors. :-)

Right. And, may I add, nothing  makes sense in phylogeny except in the light 
of, well, a good many things many  analyses unfortunately don't have. :-)

Best regards,

Félix  Landry