Re: Morpho v molecular (was Re: Tinamous: living dinosaurs)

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

Combined reply:

>  It has to be said that although the 'Polyphyletic Ratites'
>  hypothesis has support from molecular data, it isn't supported by
>  morphological data. As Jason mentioned, the phylogenetic analysis of
>  Dyke & Van Tuinen (2004), which was based on osteological characters,
>  recovered a monophyletic ratite clade that excluded tinamous
>  (Tinamidae). Instead, Tinamidae, _Lithornis_ and _Palaeotis_ came up
>  as successive outgroups to the ratite clade within Palaeognathae.
>  All too often we are quick to regard a molecular analysis as
>  inherently superior to a morphological one. Harshman &c invoke
>  convergence in postcranial characters (associated with secondary loss
>  of flight) as the explanation for why osteology-based analyses
>  produce a monophyletic ratite group. They might be right; but I
>  wouldn't assume that phylogenetic analyses are so easily fooled. So
>  I'm keeping an open mind on ratite/tinamou relationships.

Convergence due to flightlessness, plus convergence due to 
paedomorphosis (a common mechanism of evolving flightlessness which 
affects the entire body, so don't believe you can escape it by focusing 
on the braincase or something!), could easily do it. Happens all the 
time (Wiens et al. 2005, Syst. Biol.: "Ontogeny Discombobulates Phylogeny").

Of course, somebody sit down with the matrix by Dyke & van Tuinen and 
actually test this speculation. And they should add a lot more fossils.

The matrix by Livezey & Zusi has the same problems, especially a painful 
lack of fossils that cannot help but lead to long-branch attraction and 
other serious problems. It's just so big that fixing it would amount to 
_at least_ an entire American PhD thesis... and thesis committees, 
AFAIK, tend not to like monomaniac projects.

>  Mickey Mortimer <mickey_mortimer111@msn.com> wrote:
> > Has there ever been a case where a well established molecular-based
> > relationship was discarded due to morphology? There have been
> > molecular-based relationships that were later changed by better
> > molecular data which matched morphological ideas (e.g. guinea pigs
> > aren't rodents), but I don't know of any molecular-based
> > relationship which is consistantly found and which workers believe
> > is wrong.
>
>  I can think of two, off the top of my head.
>
>  1. Whippomorpha
>
>  Molecular-based phylogenetic analyses consistently recover a
>  Cetacea-Hippopotamidae clade (Whippomorpha or Cetancodonta) nested
>  inside Artiodactyla, as a derived artiodactyl clade. By contrast,
>  morphology-based phylogenetic analyses (which include fossil taxa)
>  fail to recover this "Whippomorpha" clade. Instead, purely
>  morphology-based analyses find a more basal position for whales
>  (Cetacea), as the sister taxon to Artiodactyla, with hippos closer
>  to pigs (Suiformes). (Uhen MD [2010; Annu. Rev. Earth Planet. Sci.
>  38:189–219] shows the two trees side by side, Figure 5).

This came after no less than three morphological analyses that did find 
Whippo^H^H^H^H^H Cetancodonta from 2003 onwards.

Did they, like, order any characters...?

>  By and large, paleo workers believe the molecular-based relationship
>  (Whippomorpha) is wrong.

Really?

>  2. Turtles (Testudines)
>
>  A recent morphology-based phylogenetic study of turtle origins
>  (Lyson et al. 2010; Biol. Lett. 2010 6: 830-833) found turtles to be
>  parareptilies, with Testudines as the sister taxon to the fossil
>  _Eunotosaurus_. This Testudines-_Eunotosaurus_ clade directly
>  contradicts molecular-based analyses, which found turtles to be
>  inside Diapsida, as the sister group to Archosauria.

There are three molecular hypotheses on where the turtles belong.

Some analyses have found them as the sister-group of the crocodiles 
alone. This is so obviously wrong that people don't talk about it much, 
but it's not much less well supported by molecular data alone than 
turtles as non-archosaurs.

The Amphibian Tree of Life (Frost & 18 others, 2006) found the turtles 
outside Diapsida!!! Of course, amniote relationships weren't the focus 
of this analysis of lissamphibian phylogeny, and the method that was 
used -- direct optimization implemented by POY: alignment and 
phylogenetics are done at the same time -- is not reliable, according to 
half of an entire issue of Systematic Biology.

One big problem with amniote phylogenetics using molecular data is that 
the squamates have zoomed off to do their own thing. It's not trivial to 
even just get them to cluster with *Sphenodon*. I think the lepidosaurs 
as a whole are regularly pulled out of Diapsida because of the poor 
taxon sample of amniotes, which cannot be increased because the 
unsampled amniote clades have all been extinct for a long time.

>  Convergence can occur at the molecular level too. As noted by Lyson
>  &c (and many others) molecular data is bedevilled by the same issus
>  as morphological data: taxon sampling, homplasy/convergence, rate
>  heterogeneity, missing data, etc.

And alignment is the *Deinotherium giganteum* in the room. It's being 
done by phenetic criteria...