Re: something's wrong here: Qianosuchus phylogeny

[David Marjanovic <david.marjanovic@gmx.at>]

----- Original Message ----- 
From: "Jaime A. Headden" <qilongia@yahoo.com>

> <There is nothing magical with the (morpho-)species level here. Couple of 
> years
> ago, SciAm printed a cladogram with _H. erectus_ and _H. sapiens_ as 
> sister
> species: very fine, except putting them in as unitary taxa assumes a 
> priori
> that the former isn't paraphyletic with regard to the later.>

That's a genuine problem, but it hardly ever, if at all, occurs with 
Mesozoic terrestrial vertebrates.

>  While it is likely *H. erectus* (as likely with *H. ergaster*) is
> paraphyletic with regards to *H. sapiens*, this doesn't affect what David 
> M.
> was talking about, in response to what Dave P. was talking about, which 
> was
> individual/specimen verus collective OTU capsulization (i.e., putting a
> [hopefully] monophyletic group of taxa into a single operating taxonomic 
> unit).

I was actually trying to make Mike Keesey's point, which is that using 
populations would be ideal. The closest thing we have to populations of 
Mesozoic terrestrial vertebrates is most likely something like the currently 
recognized so-called species.

> In these, the chosen OTUs are not tending to be inclusive, but subsidiary.

The subsidiarity principle of the EU is that every decision should be made 
at the appropriate geographic level, so I think you are saying the chosen 
OTUs are nested within each other. But what do you mean by "inclusive" then?

>  Closest sister taxa in cladistics are in fact given as the closest known 
> form
> to the basal taxa that _could_ have given rise to the more derived sister
> taxon, so that, say, *Scleromochlus* represents a descendant of the
> paraphyletic group from which also sprang Pterosauria, based on Benton's
> phylogeny.

(Which, importantly, is the same as saying that Pterosauria represents ( = 
is) a descendant of the paraphyletic group from which *Scleromochlus* is 
descended.)

> David M. mentions in the post that he is testing on this method

Not rigorously. I only mentioned one case where I've seen that it doesn't 
matter much. In general, I do recommend against using large taxa as OTUs, 
especially if their internal phylogeny is unknown or poorly supported.

>  I would argue it should be done case by case, but for the most part, 
> exclude
> all juveniles and suspect juveniles, and run trees with them with 
> constricted
> outgroups to test for variability in the tree.

Or exclude all ontogeny-related characters, but that requires identifying 
all of them, which is difficult.

> They also tend to cause
> long-branch attraction, something tested for in living species recently, 
> though
> I should not be mentioning this without providing a cite (I am not on my 
> own
> computer where I keep my reference works, and I am very tired at the 
> moment).

You are probably thinking of the Systematic Biology paper by Wiens et al. 
(2005) the title of which begins with "Ontogeny Discombobulates Phylogeny". 
It shows that the neotenic salamanders tend to form a spurious clade in 
morphological but not molecular analyses, and that this artifact disappears 
if they are coded as unknown for ontogeny-related characters.