More taxo-computational distractions

[James Francis Lyons-Weiler]

On Mon, 1 Dec 1997, Magnus Liden wrote:

>
> The term "basal" appplied to a cladogram/phylogenetic tree only designates
> a clade (or OTU) that is sistergropup to a large and speciose (or better:
> OTU-ose) clade in an assymetric tree. It bears no connotation what-so-ever
> to degree of "primitiveness". Only CHARACTERS can be labelled plesio- or
> apomorphic, not TAXA! An isolated "basal" branch should be expected to be
> on average just as "advanced" as any other OTU. There is no logical or
> biological reason to expect a priori that some OTUs are more "archaic" or
> "generalized" than others.

        Quite right, all around.  I use the term "plesiomorphy content"
        to refer to the amount of plesiomorphy (for a specified group)
        any taxon has retained for a set of characters.
.
> This common misconception is, I believe, partly coupled to the
> (non-supported and rather mystical) idea that the rate of anagenesis is
> directly coupled to the "rate of cladogenesis" (which in turn is believed
> to be, on average, correlated to the number of extant recognized OTUs in a
> sub-tree).
>
>
> >SO: Are there any good windows to the past?
> >Are there phylogenies where it really functions somewhat like this:
> >Many groups which have a lot of apomorphic characters, but some extremely
> >basal, more plesiomorphic groups which may serve as "windows to the past".
> >I want to get examples from the whole bandwidth of biological systematics
> >of
> >               "WINDOWS TO THE PAST"
>
> I advice you to be extremely suspicious about all such claims (especially,
> but not only, if tree topology is used as an argument), as they are usually
> based on circular reasoning, and a preconviction that such "windows" are to
> be expected.
>
        I agree entirely.  These preconvictions and expectations
        amount to _positivism_ .  Care must be taken with this
        term, though - it's not "optimism".  Second, people in
        the past have labeled all sorts of modes of inference
        as "positivistic".  As I have come to use it, a positivistic
'       phylogenetic inference is one that is based on the expectation
        that evolution has been benevolent enough to leave behind
        phylogenetic signal.

James Lyons-Weiler