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Re: Bradytely (thanks Jaime) + Trees of Life





Thanks Jaime,
I completely agree with most everything you say below. As I have said before, cladistics is a wonderful and powerful tool when used appropriately, and I would certainly never use cyanobacteria (or choanoflagellates or even fish) as an outgroup in analyzing the relationships of bird groups. Bradytely in birds is indeed on a completely different scale from bradytely in bacteria, but I think the comparison was useful in challenging George's challenge to Charles (whose example I exaggerated in order to sort of throw George's challenge back at him).
And I also complete agree with you that dromaeosaurs were not bradytelic at all, and in my Interstate example, I said that evolutionary rates or speeds on the dromaeosaur "offramp" probably did not slow down. If the K-T extinction had killed off all of the birds (Aves) and some dromaeosaurs had survived and diversified instead during the Cenozoic, I'd be classifying birds as an extinct family (maybe two), and probably be defending a Class Dromaeosaurea (and trying to decide whether it is less arbitrary to put the bird family in Reptilea or Dromaeosaurea). I think we are agreeing far more than we are disagreeing, even though our taxonomic philosophies differ on some major points.
The only thing I would disagree with (below) is that I believe that is not nearly as difficult as you might think to determine what is plesiomorphic for "Archaea". Unlike Woese, I believe that they are a comparatively derived and later-evolving branch of thermophilic bacteria (and should be called Metabacteria, as Osawa and Hori named them way back in 1979, rather than the totally inappropriate name "Archaea" proposed in 1990).
The common ancestor of life on Earth (I use the term "Geobiota", rather than "Biota") was almost certainly eubacterial, arising about 3.9-4.0 billion years ago, but my present estimate is that Metabacteria ("Archaea") didn't evolve from a thermophilic eubacterium until about a billion years later (2.9-3.0 billion years ago). If so, the common practice of using "Archaea" as outgroup to Eubacteria is ludicrous, and is equivalent to using Aves as an outgroup to Reptilia (with the absurd result of dinosaurs coming out as the most primitive reptiles).
Since 1995, I have been warning that Woesian "Trees of Life" are almost certainly totally misrooted and badly skewed as a result. When such trees (actually just "Tree of Ribosomes") are finally discarded and real "Trees of Life" replace them, this will be a terrible black eye for cladistics, and for a while I suspect it will overshadow and throw a pall over the relative successes of cladistics in the study of dinosaurs. Therefore, as a believer in cladistic analysis, I cannot recommend that anyone embrace a Three Domain Classification of life. It's today's bandwagon, but in a few years it is likely to be a very "hot potato".
Some people think I sound too harsh or mean-spirited in my criticisms of strict cladism, but in a few years I may well be doing the same thing to strict eclecticists if the "Feducciary" camp uses a "hot potato" to unjustly "rev up" their attacks on cladistic analytical methodologies. I'm obviously not trying to win any popularity contests, and will continue unpopular challenges wherever I think they might do some good in the long run.
---We shall see, Ken
P.S. Will try to find those Darwin quotes and post them later today, but probably will not comment on them. The "tonight show" fallout has me worn out and I've obviously gotten somewhat grumpy as a result.
*********************************************************
From: "Jaime A. Headden" <qilongia@yahoo.com>
Reply-To: qilongia@yahoo.com
To: dinosaur@usc.edu
Subject: Bradytely and Evolutionary Distance: Plesiomorphy
Date: Thu, 11 Jan 2001 00:02:26 -0800 (PST)

Gotta say something that I have found difficult to put into my replies: Biologically speaking, any organism closer to its ancestors sets the benchmark for a descendant's comparison to other organisms one might want to include in an analysis [any, molecular or morphological]. This is the outgroup in a cladistic analysis, be it either of the above two fields, and even intuitive analyses. In unrooted groups for which one has difficulty selecting [or even it being problematic in selecting] an outgroup, as in Biota analyses like lots of the recent Archaea stuff coming out of specialist and generalist journals (Nature, PNAS, Systematic Biology, Molecular Biology, TREE, etc.) it is easier to think in terms of distance becuase then one cannot find a plesiomorphic condition ... as in what's plesiomorphic when one deals with Archaea? And can one say this simply?

Relative spacial analyses, distance logarhythms, evolutionary rates patterns, these have an effect further down the tree, since there, that's all that separates "you" from "them." In higher organisms -- generally those that may no longer be capable of LTG and unmitigated transposon activity [maybe just occasional] -- organisms become more selectively enhanced and one can start picking out how the genes effect biology in a much
more dynamic fashion than weeding out the bacteria from the eukaryans, and "them" from the archaeans. Evolution speeds up... there are many more things for cyanobacteria and plantaeans to do on land than on the water, new realms to explore; liquid media are restrictive enough. Compared to chickens, cyanobacteria are more bradytelic.


"You've conquered the land, now what are you going to do?" The velociraptor answers, "Fly!"

  An organism diversifies, and its descedants vary more from the
basal stock than the stock itself varies within itself. A new
organism emerges, and morphologically and possibly ecologically,
it is distinct (systematists like calling these things "taxa,"
which at its root, is a "group" of organisms whose shared
relationship is greater than their's ancestor's is to any of
them -- they are a whole in every sense of the word, possibly a
smaller collective than the original stock). But one does not
leave the dinosaurs alone now that the pretty little birds have
sprouted all over the place and are taking over from the
pterosaurs -- no, there's still things little dromaeosaurs can
do that haven't left us in a sweat trying to catch those
starlings and comparing them to orioles to see _how_ much
difference there is. They can split off a new "taxon" for one
thing. They're not cyanobacteria, for crying out loud.

  Let me try to use an example, with some difficulty phrasing
what I'm trying to say:

  *Gallus* and *Phasianus* share more base pairs then either
does with *Grus*, so this is rendered:

--+-----Grus
  `--+--Gallus
     `--Phasianus

  So chickens are closer to pheasants than are cranes. Add
something like *Chauna*, and we get tinamous falling roughly
outside this tree:

--+--------Chauna
  `--+-----Grus
     `--+--Gallus
        `--Phasianus

  The add *Hesperornis* and *Ichthyornis* which, by all recent
accounts and contra the phylogeny of Cracraft, fall about this
way:

--+--------------Hesperornis
  `--+-----------Ichthyornis
     `--+--------Chauna
        `--+-----Grus
           `--+--Gallus
              `--Phasianus

  Now, before this gets pedantic [too much :)] we can note that
some birds represent the plesiomorphic condition by the lack of
certain features, primarily of the skull. Chauna is
plesiomorphic then to the chicken+crane group, and as such lack
these ascending features than makes neognaths so cool and fun to
look at. It can then be termed the outgroup to the chicken+crane
group, for which the name Neognathae has been applied.
Furthermore, one can posit the following scenario: in their
evolution, neognaths looked something like tinamous [for this
exercise, taxon "A"], had a lot of the same features, with one
or two additions. This small basalmost neognath [taxon "B"]
would produce offspring that may have developed a new feature or
two, and compared to the tinamou, it would look a little
different [taxon "C"], perhaps, but evolution just sped up, and
taxon C would differ by far more than taxon B does from A. You
can use successive groups of exclusive populations, label them
taxa, and count the differences. The further from the tinamou
you get, the more distinct the end of the chain becomes. But not
from its immediate ancestors, and herein lies the key to
cladistics: immediate ancestors will vary less than distant one,
and plotting them helps resolve how much; plesiomorphy is a
strong factor in systematics. Distance is relative, and
comparing chickens to cyanobacteria is ridiculous unless you
include a good long series of ancestors of the chicken. At some
point it becomes feasible to establish the length of a taxon [by
the above definition] and the variance within it, but it seems
flawed to refer to the distances of other groups to calibrate a
separate taxon without looking at each intermediate population
along described pathways -- interstates.

  A last example, close to home: Ceratopsidae have numerous
autapomorphies that perhaps rival any other dinosaur group. So
do Ankylosauria. Slowly, we find basal forms along these
highways that reduce the distance each organism differs from a
set group as one takes into account the truly gradistic
relationship of _all_ taxa. I'm assuming of course taxa just
don't pop out of thin air.

=====
Jaime A. Headden

  Aaaaaaaaaaaaaaaaaaaahhhhhhhhhhhhhhhhhhr-gen-ti-na
  Where the Wind Comes Sweeping Down the Pampas!!!!

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