Re: Huge morphological analysis reconfirms deep branch relationships among Squamates

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

John Scanlon wrote, truncatedly:

>  The Gauthier et al. paper is a massive milestone, but it's hard to
>  believe anybody thinks a morphology-only analysis is worth presenting
>  when there is so much molecular evidence out already.

There are several obvious reasons.

1) Do molecular and morphological evidence eventually converge on a 
common solution? Only morphological evidence can answer that!
2) Molecular datasets cannot place fossils, a question that is 
interesting in its own right. Not everything is about extant species.
3) Molecular data have their own problems; they're not automatically 
more flawless than morphological data. One of these is that fossils can 
break up long branches -- but only in datasets that contain 
morphological data.

>  In my PhD (finished in 1996) I got scolecophidians nested within
>  anilioids on morphology, and thought the following procedure was
>  fairly obvious:
>
>  "The effect of convergence associated with fossorial habits must
>  therefore be taken into account in subsequent research cycles,
>  preferably by some method less ad hoc than arbitrarily deleting or
>  weighting characters. Reanalysis with removal of taxa (in one case
>  the three scolecophidian families, in the other the four anilioid
>  taxa) converts apparent synapomorphies of both groups into
>  autapomorphies of one or the other, and should allow the systematic
>  position of each to be determined free of the effects of convergence
>  between them."
>
>  As this was a pretty late thought (2nd last paragraph in the thesis)
>  I didn't check if it had been done before, but the answer is:
>  apparently not. The same method was subsequently published by
>  Siddall and Whiting (1999) as a way of dealing with long-branch
>  attraction in molecular analyses, but I've never actually used it in
>  a published analysis (e.g. anilioids and scolecophidians got
>  separated by additional data, so it wasn't necessary) and I don't
>  know if anyone else has either.

It has been done fairly often, just not -- apparently -- in analyses of 
squamate phylogeny.

>  Conrad (2008) didn't do it, and it looks like Gauthier et al (2012)
>  don't do it either. I haven't re-run their analyses with the
>  relevant deletions (e.g. including only one of Dibamidae,
>  Amphisbaenia, Serpentes in Conrad) but I expect they would end up in
>  different places across the tree when not pulled together by
>  convergence. Anyone want to try it?
>
>  Another interesting thing in Gauthier et al. is the fact they cite
>  M=FCller et al (2011) on the stem-amphisbaenian _Cryptolacerta_ but
>  don't include this fossil in their analysis. (Facepalm)

*headdesk*
*headdesk*
*headdesk*

Failure of peer review.