Re: Thoughts on the biggest morphological bird analysis

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

> If we hold Livezey and Zusi's analysis to the same standards as huge
> molecular analyses in regards to support (say 95% bootstrap liklihood)

That's too strict. Bootstrap is well known to produce too low support 
values, just like how Bayesian posterior probabilities are generally too 
high (they always tend to be 100 % even for rather obvious cases of 
long-branch attraction -- Zhang et al. 2005 Systematic Biology).

> --Struthioniformes
>   |--Struthionidae
>   `--Rheidae

That's another case of convergence, I bet. Adding *Palaeotis* and 
*Diogenornis* should be interesting.

> `--Anseres
>    |--Anseranatidae
>    `--Anatidae

Isn't that Anatoidea?

>      |--Pygopodo-tubinares

It goes without saying that the ICZN mandates the deletion of the hyphen. 
Not that I care... well, instead of "avoiding the controversy", Livezey and 
Zusi set themselves at odds with both the ICZN and the PhyloCode...

> What this says to me is that the relationships of major neoavian taxa may 
> be
> forever beyond morphological resolution if only recent taxa are included.

You could well be right.

> In Asher et al. (2003), two of the best supported clades are bats plus
> flying lemurs, and pangolins plus anteaters.

I hope that's pangolins plus Xenarthra as a whole!

> (e.g. Paton and Baker, 2006; 12902 characters)

Is that the mitochondrial genome?

> I have to agree with David regarding Livezey and Zusi's fear of missing
> data.  There's no reason Dinornithiformes and Aepyornthiformes should be
> excluded when we have complete skeletons.

Actually... as described on pages 9 and 10...

"Two subfossil taxa -- Aepyornithiformes and Dinornithiformes -- for which 
character states were only marginally recovered, were excluded for the 
primary global search, and provisionally placed by means of two different 
protocols. This measure was taken because simple analysis of these 
imperfectly known, broadly similar, large ratites led to an apparently 
artefactual couplet -- 'long-branch' distortions exacerbated by missing data 
(Wiens, 2005) -- as sister-group of other ratites exclusive of Apterygidae. 
First, each was analysed in the absence of the other in a global, 
unconstrained analysis. Second, each was separately placed by means of 
heuristic searches in which the primary tree was used as a backbone 
constraint. The Dinornithiformes were scored as two families (Dinornithidae 
and Emeidae) as approximated by Cracraft (1976a, b) and Worthy and Holdaway 
(2002) during character analyses, but analysed as a single, merged taxon in 
light of their virtually identical scores. Accordingly, the 'trimmed-merged' 
data matrix provided in digital form by Livezey & Zusi (2006) comprised 150 
ingroup taxa and 35 outgroups."

But they kept *Rahonavis* in? And accepted at face value the sister-group 
relationship of ostrich and rhea, two other "broadly similar, large 
ratites"? Please.

> Fossils are the morphologist's only hope
> at combating such detailed convergence.

We know how Mayr will spend the rest of this year... :-)