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Re: Tree of Life webpage

 As a follow up to the questions I had on the TOL webpage, I must ask
 about the phylogeny they present for the stem tetrapods...


Incidentally, be aware that although it says "Michel Laurin" on the label, the position of *Whatcheeria* is based on another (and, frankly, way outdated) phylogenetic hypothesis. Maybe Jennifer Clack inserted it. For crying out loud, all three sufficiently well preserved whatcheeriids are known to retain the preopercular bone!

 The TOL presents Temnospondyls as diverging before the
 Amniote-Amphibian split, which would seem to suggest they weren't
 amphibians at all, but rather some sister taxa to Amphibians&[Amniotes]

Yes. This is the "lepospondyl hypothesis" on the origin of Lissamphibia*, found by Michel in a series of papers ending in Vallin & Laurin (2004) starting with his PhD thesis in 1994 (on seymouriamorphs); also found by the PhD thesis of Kat Pawley (2006 -- you can download all the interesting chapters here http://www.lib.latrobe.edu.au/thesis/public/adt-LTU20061124.124055/index.html), by the PhD thesis of Damien Germain (2008 -- supervised by Michel, but done very independently), and by... Marjanovic & Laurin (2008, 2009).

* That's the crown-group: frogs, salamanders, caecilians, and maybe albanerpetontids.

 Whereas wikipedia's Temnospondyl page seems to firmly place them
 within Amphibia (ie after the amniotes split from the linage that
 gave rise to modern amphibians), and suggests lissamphibians may even
 be a branch of the temnospondyl tree (rather than a side-branch like
 the lepospondyls).

Yes. This is the "temnospondyl hypothesis" on the origin of Lissamphibia. The latest paper that found it is Ruta & Coates (2007). Because that analysis is based on a big matrix, and for historical reasons, this hypothesis is currently the most widespread one among people who work on Paleozoic limbed vertebrates.

 Meanwhile the Labyrinthodontia page presents a phylogeny

Why does it present a phylogeny? With one exception in 1985, nobody ever seems to have believed it ( = big non-amniote limbed vertebrates) was a clade, and the term has hardly been used for the last 20 years.

 that seems to confirm the TOL phylogeny (as far as the Temnospondyls go,
 but not as far as Westlothiana and Seymouriamorphs) despite naming stem
 tetrapods as amphibians.

Westlothiana is pretty clearly the basalmost known amphibian, or anyway lepospondyl.

 Wikipedia also presents seymouria and westlothania as closer to
 amniotes than amphibians, whereas TOL presents them as basal to both.

 So what are the views of people on this list. Did the following
 emerge before or after the modern amphibians and modern amniote
 linages split?
> Temnospondyls
> Seymouriamorphs


And I haven't even mentioned the "polyphyly hypothesis" yet.

Its normal version (Anderson et al. 2008; also supported by Carroll up to 2007 [and I think his new book], even though the results of his phylogenetic analysis in 2007 say something different) has the frogs and salamanders sitting in the temnospondyls, just like in the temnospondyl hypothesis (except for the version where the frogs are amphibamids and the salamanders are branchiosaurids, but this has _never_ been found by a phylogenetic analysis), but the caecilians among the "microsaurian" lepospondyls. Then there's a weirdo version (McGowan 2002; results of Carroll 2007), where again the caecilians are "microsaurs"... and the "microsaurs" and all other lepospondyls sit _inside the temnospondyls_.

We (2008) showed that the results McGowan (2002) found were due to the mistakes in his data matrix. We (2009: supp. inf.) further showed that the results Anderson et al. (2008) found were due to the mistakes in their data matrix. Both matrices actually support the lepospondyl hypothesis.

Damien Germain (thesis 2008) showed that correcting hundreds of mistakes in the matrix by Ruta & Coates (2007) leads to the lepospondyl hypothesis being found as one step more parsimonious than the temnospondyl hypothesis. Because he didn't have time to go on (French theses are time-limited, and Damien had no financing...), I am continuing this work right now. As of today, Mesquite claimed the lepospondyl hypothesis to be seven steps more parsimonious; PAUP* is now running overnight.

See you in Bristol next week!

PS: It goes without saying that I don't imagine the current broadside to be the last word. Seven steps out of 1808 is not a lot. The matrix by Ruta & Coates (2007), the largest properly published one (Pawley made several larger ones), has 102 taxa and 339 characters, of which 335 are parsimony-informative; I merged lots of correlated characters, so only 300 characters are left, which is less than three times the number of taxa. Indeed, I can easily think of several characters that are potentially interesting to not just limbed-vertebrate phylogeny in general, but the question of lissamphibian origins in particular, and that are missing from that matrix. Furthermore, the matrices of Vallin & Laurin (2004), Anderson et al. (2008)/Marjanovic & Laurin (2009), and Ruta & Coates (2007)/Marjanovic, Germain & Laurin (in prep.) each contain both taxa and characters that are missing from both others... and there's no chroniosuchian in any of them... We are living in interesting times.

Too bad my abstract was only accepted as a poster presentation. Saturday, September 26th.

PPS: The bootstrap tree of Laurin & Reisz (1999) is right: the temnospondyls are more closely related to us than the anthracosaurs/embolomeres are, not vice versa.