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Re: Cladistics (was Sci. Am. - present)



>Where the number of specimens is large compared to the number of changes,
>and where the number of ?changes back? is small, the most parsimonious
>solution is likely to be fairly correct.

True - but as the number of changes relative to number of taxa drops, the
amount of possible resolution also drops.  It's actually possible to have a
too-low rate of evolution.


 Such a situation might correspond
>to a dozen closely-related vertebrates taken over a five million year
>stretch, or gently mutating viruses being relatively frequently examined.
>
>However, as we depart form scenarios such these, the truth becomes
>increasingly complex.  Characteristics have time to revert, and we sometimes
>have just a few fossils interspersed by many millions of years.  Sometimes
>an event (such as loss of flight) has actually occured on a separate
>occasion for the majority of the flightless fossils in our group.  In cases
>such as these the simplest solution is not what actually happened.


You're referring, tangentially, to the long-branch attraction problem.  For
molecular data, there are actually ways of suspecting this as a possible
concern - relative rate tests, for example.  Moreover, if we follow a total
evidence approach, I don't see that this is necessarily a problem.

You keep referring to flightlessness, so let's use a proper dinosaurian
example.  Consider an analysis of Avialae in which Mononykus, hesperornis,
ostritches, kiwis, elephant birds, moas, flightless geese, Galapagos
flightless cormorants, giant auks, and dodos are considered among many
other taxa.  I have never seen anyone simply score "Does it fly?  Y/N" as a
character.  Instead, specific morphological features - presence of a keeled
sternum, features of the musculature of the shoulder (where preserved), and
so on would be included.  If we code morphology from all over the skeleton,
are we likely to see all of these flightless things fall out together?  I
submit that the answer is "no."  In fact, analyses including some of these
taxa have been conducted, and we've never seen, for example, ratites and
flightless cormorants falling out as sister taxa.  The information from the
entire skeleton - not to mention the molecular data - strongly outweigh any
confusion that might have arisen from the fact that ratites and flightless
cormorants do not fly.

If flightlessness arose multiple times, it should leave slightly different
morphological signatures each time - and these signatures need not be
reflected in the whole skeleton.  I understand your concern, but for the
flightlessness example to fly (pardon the pun), I'd like to see some
evidence that it has actually caused problems in real analyses.  Other
cases like this - snout shape in crocs, limblessness in squamates, shell
shape in gastropods - indicate that convergence is not necessarily a huge
problem.




>
>In those circmstances, the best we could do would be to guess an expected
>number of reversions/changes etc over the time (v.diff) and select from that
>solution space.

You're referring to maximum likelihood, which is a standard procedure for
molecular data.  But it's model driven, and appropriate models for
morphology are lacking.


This would be more accurate than simply *minimising* the
>assumed number of changes, but of course the possible solutions will grow
>exponentially with the number of changes, and each will have similar and
>vanishingly small probabilities.  Sometimes our data will be so sparse that
>the number of changes that actually occurred exceeds the number of fossils.
>There will come a time where there just isn?t enough information available
>for the algorithm to have any chance of finding the correct solution.  Under
>these conditions it will soflty and silently drift away from reality,
>leaving behind only an impressive set of maximums, likelihoods etc for our
>delectation - and confusion.
>
>Where the simplest solution (consistent with the data as it appears) is the
>right one, cladistics will find it.  However this is rather like the stopped
>clock being right twice a day.


Do you have some stats to back you up on this?  (Hint - there are lots of
stats out there arguing quite the opposite, that parsimony is much more
accurate most of the time.)



[shortened]



>We?re trying to find something that works.  Cladistics works a bit (although
>I?m rather surprised someone hasn?t knocked it on the head as an infallible
>tool once and for all by now)


Not sure what you mean, but are you aware of any paper touting it as
infallible?



.  By using characters we have some reason
>to believe will render valid the assumptions it has to make,


And you would measure the validity of these characters by............?



chris


-=--=--=--=--=--=--=--=--=--=
Christopher Brochu, Ph.D.

Postdoctoral Research Scientist
Department of Geology
Field Museum of Natural History
Lake Shore Drive at Roosevelt Road
Chicago, IL  60605  USA

phone:  312-922-9410, ext. 469
fax:  312-922-9566

cbrochu@fmppr.fmnh.org