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Fwd: Cope's Rule in Dinos



Forwarded comments from David Hone on Hone et al. 2005 (Macroevolutionary
trends in the Dinosauria: Cope's rule).

---------- Forwarded message ----------
From: David Hone <d.hone@lrz.uni-muenchen.de>
Date: Jan 27, 2006 10:07 AM
Subject: Re: Dinosauricon: Cope's Rule in Dinos
To: "T. Michael Keesey" <keesey@gmail.com>

I would appreciate it if you could forward this to the DML for me:

....................................

Just a few short (ish) rejoinders to some of David's comments. These
have been truncated (partly for space) so I would advise would be
readers to read all his comments in full first:

[Keesey - here is the original post: http://dml.cmnh.org/2006Jan/msg00317.html ]

David Marjanovic wrote:
> IMHO (i) would not be the operation of any "rule" but the inevitable
> result of body size diversification restricted by a minimum
> size near which the ancestor is. So Cope's rule seems to be
> defined as "everything that, however superficially, looks
> like Cope's rule".

Yep! This one was overstated a little. In fact it should be termed
Cope's Rule sensu lato (a soft interpretation). This will be corrected
in a paper I and colleagues have in review on a similar study on
Mesozoic birds. Therefore, dinosaurs as a whole, can be seen to be
diverging rather than just increasing. As stated, some lineages DO show
Cope's Rule sensu stricto, notably the tyrannosaurs, (although the
discovery of new, small tyrannosaurs may have 'broken' that one too).

> p. 588:
> "We used total adult body length in metres [...] to indicate >body size 
> [...]."
> Many of these lengths are potentially quite shaky estimates.

Agreed. However, to be honest there was little we could do. Within the
scope of the project (this was based on my MSc thesis) we simply could
not get every data point we needed or check them all. Many had to be
referred from publications other than the original descriptions.
However, given the (mostly) huge difference in sizes I'm not sure this
make any real difference to the outcome. After all, for the purposes of
our comparisons, its really irrelevant if a sauropod is estimated at 15
or 30m in length if we are comparing it to one that is only 10m. You
will still get a very positive result and a correct interpretation of
how those organisms are evolving. The whole thing was a bit of a quick
and dirty method, but I do not believe it suffers for that, and had
shown great promise (Alroy 2000).

> I use several osteological measurements instead -- but I can't
> guarantee that these will be better correlated to mass! Most
> or all of them can vary independently of the size of the rest
> of the body, and the program can't combine them.

Almost certainly an improvement, although David and I have discussed
some potential problems off-list. Length does confer some advantages
and again was the most easily available proxy for mass for this study.

> While laudably taking phylogeny into account, it does not
> include any attempt to infer the body size of any ancestor.
> Instead it is forced to assume that the old taxa are direct
> ancestors of their closest known young relatives.

Again, I'm not sure this is a problem. One cannot identify ancestors,
so a proxy is required. However, the above is slightly
misrepresentative: the older taxa are assumed to be sister-taxa to the
ancestors of the recent taxa. This is still a large assumption, but it
is fair to allow that sister-taxa are usually very similar. Also, by
definition, that is how we are inferring the body size of the unknown
'ancestor'.

> The program I'm using gets around this constraint
> and even takes branch length into account (after all a lot of
> evolution can happen in tens of millions of years).

True, but also very little can happen at times. Either way, significant
changes in size should still be observed and detected.

> "using a recent supertree of 272 genera (Pisani et al., 2002),
> the most inclusive dinosaur phylogeny available."
> A supertree is a time-averaged consensus of opinions about
> phylogeny, no matter (in this case) how well supported those
> opinions were when they were produced, let alone how well
> supported they are now after the discovery of new data.

I'm not sure if this is a comment on my paper or not, however, I will
say that we can only use the best data at the time, however bad we
think it is now. At the time, I was using the supertree before it had
even been published (very new!) and the new analyses in the dinosauria
II were still a few years away. Redoing the analysis now might yield
very different results (though I would not expect it to do so). Matt
Carrano's much more detailed Cope's Rule in dinos analysis (2005)
produced very similar results to mine suggesting reliability of our
methods.

> "A comparison in which the later taxon is larger than the
> earlier taxon supports Cope's rule. Under the null hypothesis
> of no body size trend, around half of such comparisons should
> show a size increase and the remainder a size decrease, with
> the mean change across all comparisons not differing
> significantly from zero."
> This null hypothesis works only if there's no minimal body
> size. IMHO there are several different such minima. For
> examples theropods may have
> been limited by competition with mammals, lizards and so on.

If we assume a theoretical minimal size of say, 50cm then this is not a
problem. If we use 'reality' then this is actually still not much of a problem.
For any given clade there was only 1 smallest known taxon. All others
were, by definition, larger. Thus only one comparison for a given clade
will potentially suffer from the problem described above. All other
taxa ('large' or 'small') can potentially shrink to the size of the
smallest taxa. So if they could shrink, grow or stay the same and they
grew then this is positive evidence for a trend towards large size.


> p. 589:
> "In comparisons where the bauplan is varied (e.g. within the Stegosauria)"
>Stegosauria???
>  ?fig. 1: *Patagonykus* is shown as Kimmeridgian or earlier.
> IIRC it's as young as *Alvarezsaurus*. *Avimimus* is shown as
> the sister-group of Alvarezsauridae because not enough studies
> where it's an oviraptorosaur were included in the supertree.

Yes, but we are talking about length as a mass proxy. The bodies of the
stegosaurids became increasingly robust for a given length (i.e.
scaling factors would have to be drastically altered) and this had to
be allowed for in our comparisons. Again, this needs to be put into
context: if you are dealing with drastically different lengths, (e.g. 1m
vs 5m) then even significant changes in bauplan really will not stop
you getting a realistic result of the longer animal weighing
significanly more than the smaller animal.
This is actually supposed to be a correcting factor. Cope, nor anyone
else, has said *how* things were supposed to be measured as being
'bigger'. We picked length as a proxy for mass, but where it was
probably insufficent (as with all the examples above) we were fortunate
that the differences were so great it would probably not affect the
true outcome of any of the individual comparisons.

....huge chunk of discussion omitted which does not need comment....

 >Take-home message: "Nothing makes sense in evolution, except
> in the light of a good phylogeny!"

True! But how do you know the phylogeny IS good? I'll leave that one
for the philosophers. And, yes, I am a cladist, but there are lots of
problems with just about every published tree somewhere. When working
from an evolutionary perspective, you have to use what is the best data
available to you at the time (see comments above, and more below).

> p. 590: "Phylogenetic analyses of the fossil data require that
> both the phylogeny and the fossil record are adequate for the
> purpose. We used the method of Benton (1995) to test the
> goodness of fit between the phylogeny and the stratigraphy."

This is a really good and simple method. Plus you can (as we did) test
it at multiple levels. It really doesn't get enough attention and I
think would greatly add to an awful lot of "evolution based on
phylogeny" studies. Off topic but worth mentioning.

> "[...] we tested both orders and each family and superfamily
> independently." A bit too much reliance for my taste, but it can't matter much
>-- all those taxa are monophyletic after all.

Again, see Alroy for testing at different phylogentic levels, and
contrast with Jablonski 1997. If you are feeling really dramatic, look
at Kingsolver & Pfennig, 2005.

> "Notably, the size increases occur at various starting sizes
> and so the size change is not just a result of beginning with
> small genera."
>This would be true if there were either no minimum size for
> dinosaurs or if the minimum size were the same for all
> dinosaur clades. I can't imagine that either of these
> possibilities is the case, see above.

I would argue differently! See above. You must not fall into the trap
of thinking this is just one analysis. There were multiple analyses at
different levels and for different clades. Not all were discussed in
any great detail (limitations of space) but numerous analyses did not
include the smallest taxa, and they still got larger.

> Minor nitpicking: *Archaeopteryx* is Late Jurassic as shown in
> fig. 1, not "mid" as mentioned on p. 590, and "Late
> Cretaceous" starts with a capital letter.

This and a couple (oh, alright LOADS) of other points. Of course I
accept any errors as my own (damn those co-authors and referees for not
checking! ;-).

[Keesey: I thought I did, but I don't really recall ... maybe an earlier draft?]

However, a) a few or even a lot of spelling errors are not the end of
the world, b) as stated above, we were perhaps overly reliant on
non-primary data sources.

> - As mentioned above many of these taxa are so incomplete that
> I wouldn't dare estimate a total length. *Unenlagia*,
> *Therizinosaurus* and *Antarctosaurus* for instance.

Someone did, thats where we got our data (I'm not going through my
records for just this post). As I have said above (and will reiterate
here, lucky you) time forced our hand on some issues. Not a great
excuse, but honest. I simply could not cross reference every single
point from multiple data sources. Alternatively, you can certainly
argue that conservatism of bauplan of closely related species allows
for accurate (or sufficiently accurate) estimates (see Seebacher's
papers). And again, it is really irrelevant if Antarctosaurus is 30, 40
or 50m long when comparing it to a 20m taxon. What we were primarily
looking for was a significant increase in size over a significant
period of time. Picking minor inconsistencies or dodgy estimates does
not undermine the methods as a whole or the results they produce,
especially given they huge positive figures we found. You would have to
down-scale an awful lot of our estimates by a significant margin to
even dent the overall outcome.

> - The size of *Dilophosaurus* is not known. The only known
> specimen is subadult. Thus *D.* was most probably not slightly
> smaller but quite a bit bigger than *Liliensternus*.

See above.

>  - Comparing *Alvarezsaurus* with *Avimimus* relies on a
>  probably wrong phylogeny (see above).

See above above: you can only use what is available. This and a few
other comments of a similar nature should really be directed at the
supertree itself, rather than our use of it. However, i would say that
all tests (see Wilkinson et al 2005) suggest that this is one of very
few accurate supertrees. My stratigraphic analysis (Benton 1995)
suggests that it is very conservative at all levels, and it was
composed of a total of 126 published phylogenies. This is a huge number
and covered some groups (obviously especially theropods and 'birds') in
particular depth. Again, we carried out a number of analyses which were
not dependent on the phylogeny and returned similarly positive results.
This could end up as a circular argument, but does suggest that: the
methods, the stratigraphy, the phylogeny and the results were all
pretty conservative and thus, self-supporting.

> - The age difference of *Carnotaurus* and *Majungatholus* is
> given as 28.2 Ma. Off the top of my head this assumes that *Carnotaurus* is
> Early Cretaceous. Indeed this was the age published in the
> description, but, as has been known for many years, *C.* comes
> from a different formation that is much younger, IIRC
> Campanian, so the difference to the Maastrichtian
> *Majungatholus* shrinks to some 10 Ma or less.

As above, I may well have picked up only the original date. Although I
am defending an individual point (here and elsewhere) it holds true for
the whole analysis: we picked comparisons that were separated by a
considerable period of time not only to 'allow' sufficient evolution to
occur (as implied by Alroy) but also to allow for such issues.

> - *Alamosaurus* as currently understood ( = any sauropod from
> the Campanian or Maastrichtian of North America) could contain
> any number of "genera" of different sizes.

Again, we were using taxa from the supertree. 'as currently
understood': the bulk of this analysis was undertaken in 2000/2001.
This must be accepted as my failing for not checking the validity of
individual taxa that were included, but as the supertree was based on
recent, published phylogenies, and Adam Yates, Max Langer and Mike
Benton covered the original, I assumed (bad word) that all invalid taxa
had been purged (as indeed many were).

......big sections on sauropod phylogenies.....
See above!

 >The silhouette of *Argentinosaurus* is a fantasy portrait,
> except for a few things like the length of the lower legs. I think it was
> made for *Apatosaurus* and scaled up. See above for *Alamosaurus*

Yep! But it looks pretty, which is why the editors asked me to add
them. Obviously we picked the big dramatic ones to make it look nice.
The observant will have noticed that they were redrawn (pinched) from
the Pisani supertree or the dinosauricon.com (both with permission).

> The study of the evolution of body size is in its infancy.
> Every paper in this field is much better than all its
> predecessors, and this state of
> affairs is likely to continue for several more years.

Certainly! As we have shown you can end up reliant one 1 or 2 factors.
However, as a final defence of my work, I would point to the fact that
essentially this paper includes a number of very different analyses
(phylogeny, stratigraphy, oldest vs youngest, biggest vs smallest,
Jablonski polygons, basic scatter graph) and all of them point to the
same answer. For all the criticisms (whether you the reader, think i
have defended them successfully or not) I think it fair to say that the
variety and strength of all these analyses suggest that the results are
very real (if overstated a little) and that dinosaurs showed repeated
growth towards large size, down numerous lineages. This is nicely
illustrated by the drops in size after extinctions which fits 'classic'
theory of large size being a negative adaptation for surviving
extinction events (see Hone & Benton 2005).

Well, I hope some of you survived to the end of this. More importantly
I hope you have a better understanding of some of the complexities.
Obviously editorial reasons meant that some of this stuff was written
and did not make it into the final version or perhaps this would have
been a little clearer to begin with. Well, until the next CR
discussion.

If anyone wishes to contact me on this or other issues, please do so
at: d.hone AT lrz.uni-muenchen.de  (spam avoidance).