Re: New paper on Neoaves

[Michael Mortimer <mickey_mortimer111@msn.com>]

David Marjanovic wrote-

> > Here's one case that highlights the problem.  Naylor and Brown (1998) used
> > over 12,000 bases (from 19 mitochondrial genes) and recovered 100% 
> > bootstrap
> > support for a clade that comprised vertebrates and echinoderms to the
> > exclusion of amphioxus (lancelet).  This topology was recovered regardless
> > of the method of analysis.
>
> Since this was 1998 (you know, when some people honestly believed Rodentia 
> was paraphyletic to the rest of Placentalia, and Passeriformes the 
> sister-group to all other extant birds), I'll simply blame the model, and 
> perhaps the fact that Bayesian analysis was not yet available.

Or maybe Amphioxus isn't a chordate.  There have been a ton of new basal 
deuterostome discoveries lately, and the molecular analysis of Delsuc et al. 
(2006) seemed fine with that arrangement.

> The reason is obvious: molecular characters all look the same and are thus 
> very boring, with the few exceptions of those that can be treated like 
> morphological ones (e. g. the unique 9-bp deletion in BRCA1 that is an 
> autapomorphy of Afrotheria).

Also the phenotypic results of the nucleotide changes are often difficult to 
determine.  It will be great once we can do this regularily, but considering 
how much work we have still to do on the human genome, functionally figuring 
out the genomes of all the other random organisms won't happen for quite 
some time.

> BTW, the "Ontogeny Discombobulates Phylogeny" paper (Wiens et al., Syst. 
> Biol, February 2005) has a couple of clades that have high Bayesian 
> posterior probabilities and are nevertheless clearly spurious. However, 
> these based on are morphological data of paedomorphic salamanders (miscoded 
> as if they were metamorphosed adults).

Well, high morphological support is easy to get wrong.

Mickey Mortimer