Re: Ancestors [was: Re: And while on the theory of phylogenetic reconstruction...]

["Jonathan R. Wagner" <jonathan.r.wagner@mail.utexas.edu>]

David Marjanovic wrote (quoting me):

> >     Ok, since no-one seems to want to go near this, I'll give it a
try...
> I wanted to, but I didn't have time until now, and

Took me all week to get a reply together...


> > ([...] see the popularity of the term "basal,"
> > a politically correct form of "primitive").
> That's indeed how it's used a lot. _Properly_, though, "basal" means "as
far
> away as possible from the clade I'm interested in at the moment". For

    Yeah... which demonstrates that it is a relative term, and has no
objective meaning (as an adjective). "Basal amniote" requires a very clear
statement of, as you put it, the clade within Amniota in which the author
*is* interested. Why go to this trouble, rather than just saying what you
mean (e.g., non-sauropsid amniotes, non-saurian reptiles)? The only
objectively "basal" part of a tree is the lowest NODE (and then, only if it
is rooted); "basal" cannot be applied objectively to a TAXON. "Basal to
(clade name or ostensive definition here)" is more acceptable, as in
"turtles are basal to Sauria," with basal used as an adverb in a strictly
relative manner. This use is objective when there are no intervening ("less
basal") taxa in the analysis. But why not just say "turtles represent the
extant sister-group to Sauria" and say EXACTLY what you mean? Note that you
*could* properly say "Sauria is basal to turtles" as well, something most
people don't seem to appreciate. I find statements containing "outside of
______" to be just as clear as saying "basal" or "basal to", arguably
moreso, and this terminology avoids an adverb that is commonly misused.

    The real upshot is that the term basal ("at the base") implies some form
of unequivocal directionality in a tree. While a rooted tree does have an
unequivocal "up" direction, i.e., time, this directionality is relative
among branches. There is no unequicoval "highest point" and therefore no
unquivocal basis for comparing "how high" something is because there is no
one standard of reference. To compare, in stratigraphy, you might have a
"basal member" and an "upper member" of a formation, because there is
unequivocally one top and one bottom to the formation at any particular
locality. Trees have n "tops" for n taxa, and there is no objectivity in
preferring one top over the other (although you still hear people use the
adjectives "derived," "more derived," or "well-nested" to describe taxa).

    Further, in most cases, people consider several successive serial
outgroups to all be "basal," often this is a stem-group, although sometimes
(e.g., Archaeobatrachian frogs) it is the comb-like part of a tree of extant
animals. This can suggest, consciously or unconsciously, that a paraphyletic
group might have some objective commonality. Generally, paraphyletic groups
considered "basal" are labelled so by local convention, e.g., hadrosaur
workers consider hadrosaurs outside of _Hadrosaurus_+_Lambeosaurus_ to be
"basal." How is a non-specialist supposed to interpret a report of "a new
basal hadrosaur?" Where do they look for this information? Is the use of the
term "basal" informative in this context? Further, I'm quite sure that many
folks would balk at certain hadrosaurs being "basal" by that definition,
because they contain what are considered to be "key" apomorphies of the
group. This, then, is simply "primitive" and "advanced" recast as "basal"
and "derived." As the old Virginia Slims ads used to say, you've come a long
way, baby!


> example, there is a paper on the phylogenetic position of turtles, [...]
> and then says that mammals are the basalmost amniotes [...]

    I NEED THIS REFERENCE NOW! I have a moldy, half-finished manuscript
titled "Mammals are basal amniotes," and I need this reference!


> > The approach taken by many
> > phylogenetic systematists (including people who would call themselves
> > "cladists")
> Is there a difference? AFAIK not.

    Some people use "cladist" to signify those phylogenetic systematists of
the mindset that parsimony is the only appropriate optimality criterion for
phylogenetic inference. This group is exemplified by the AMNH systematics
community, and many of the members of the Willi Hennig Society. There seems
to be a connotation that many "cladists" in this sense means pattern
cladist, although this is certainly not true (e.g., Arnold Kluge). I tend to
call such folks Kladists (with a K), a practice I got from George Olshevsky.
I hesitate to identify myself in biological circles as a "cladist," because
of the connotations noted above... I usually say I'm a phylogenetic
systematist, which handily covers Kladists and non-Kladists. Of course, in
biological circles, there are few people who really do not fall under that
definition anymore (HINT HINT).


> >  Would you consider Pleistocene _Homotherium_ (the "sabertoothed tiger")
> > to be a reasonable descendant of Holocene _Felis concolor_
> > (the mountain lion), simply because both are found in California?
> (Did you mean "ancestor"?)

D'oh!


> There is a probable example of a real polytomy. Every Mediterranean island

    This certainly wouldn't be the only possible example...


> of sufficient size has its own lizard species (*Podarcis*), [...]
> when the sea came back, the populations on the islands all
> became isolated at the same time, representing a speciation that isn't a
> dichotomy but a polytomy with some 8 branches.

    For the record, what David describes here is a SPECIES polytomy. It is
possible that, when sufficiently sensitive molecular markers are recovered,
it will be found that organisms within each species share more recent common
ancestors with members of some of the other species than with members of
others. This situation could be made even more complex by lineage sorting
within each species. That would be a case of conflict between organism trees
and species trees, and is another case in which one has to take even a
well-supported tree with a grain of salt.


> > Similarly, at least in theory, the treatment of
> > all taxa as terminals is a technical necessity.
> If only because the currently available programs can't do otherwise.

    Not just the programs... we would need to have algorithms in place to
reasonably deal with the problem.


> > speciation, ancestry and descent, hybridization, and other phenomena
that
> > are considered very likely to actually occur in nature cannot be
represented
> > directly through an analysis (yet).
> Don't hold your breath,

I'm not, but I'm banking my dissertation on it, which is arguably worse.


> but there is an approach similar to cladistics that
> has been used in linguistics and seems to do just this. I'll send the
> citation tomorrow...

Please do... I've been trying to sell the reticulation working group here at
UT on applications to linguistics, but they are very set on parametric
approaches using only biologically relevant models. I'm certainly not going
to hold my breath on this, though... until recently, work on reticulation
has proceeded at a glacial pace.

Later,

Wagner