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

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.


 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...