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Molecular constraints with Conrad (2008)

In preparation for something else, I was interested to see the effects of constraining for the molecular topology produced by Pyron et al. (2013) in a large squamate morphological data set (Conrad, 2008).

Instead of using TNT, I employed Wilson's treespace search in PAUP (which is similar to the settings used in TNT by Conrad). Since I was only interested in some quick and dirty results, I limited the iterations to 100. The constraint I used was limited: (Rhynchocephalia(Dibamus((Gekko,Pygopus)((Scincinae(Cordyloidea(Xantusia,Lepidophyma)))((Tupinambinae(Lacertidae(Rhineuridae(Bipes(Trogonophidae,Amphisbaenidae)))))(((Liotyphlops_albirostris,Typhlops_lineolatus)(Leptotyphlops_goudottii(Anilioidea,Xenopeltis,othermacrostomata)))((Leiocephalus,Iguanidae)((Lanthanotus_borneensis,Shinisaurus,Vniloticus)(Anniella,HelodermaSUSP,Xenosaurus,Anguis)
)))))))) and based off of the one given to me by Mickey Mortimer for an earlier similar test (though he was using the molecular tree from the Toxicofera paper), though I added some taxa he did not have put to consideration. I also played with different versions of the constraint to force some relationships or allow certain taxa to float within the tree.

The results-

Unconstrained tree 3795 steps
Topology above enforced 3942 steps
Topology above enforced (except for snakes, so that snakes could float in the tree) 3905 steps, but it collapsed all squamate relationships aside from the broad groups. In these trees, snakes were the sisters to amphisbaenians within the Amphisbaenia+Lacertidae clade.
Topology above enforced, except for snakes, the burrowing scolecophidians deleted 3849 steps, snakes were still sisters to amphisbaenians
Topology above enforced, including snakes, the burrowing scolecophidians deleted less than 3900 steps (forgot to write it down), in this tree, mosasaurs are the sisters to snakes instead of being varanoids

I noticed at this point that Acontiinae (a clade of legless skinks) was falling with the dibamids and I wondered how this might be affecting the tree, I deleted Acontiinae and re-ran with the same restrictions (topology enforced, no scolecophidians) - 3823 steps, mosasaurs and snakes were still sister taxa.
I then restored scolecophidians to this, it resulted in a collapsed squamates as above aside from the broad groups (though curiously anguimorpha collapsed)

I don't think there's anything too shocking here, this is similar to what many others have found, though Müller et al. (2011) managed to find non-varanoid pythonomorphs (snakes and mosasaurs) together while including scolecophidians in their matrix (though they excluded many fossil and living taxa in the process and ran an actual combined analysis of molecular and morphological characters rather than using constraints as I did).

I'd like to repeat this later with a large constraint that uses all of the living taxa employed by Conrad to see if that has any impact. It would also be interesting to see where the numerous putative stem-scincogekkonomorphs that have been described since Conrad (2008) and where they would fall in a molecular scaffold where Scleroglossa is not monophyletic. Many of the stem-scincogekkonomorphs in Conrad's tree became stem-squamates instead, and many stem-autarchoglossans and stem-anguimorphs fell elsewhere in tree. Updating the codings for Dinilysia based on recent papers would probably also be good, as well as adding other basal (maybe) snakes like Coniophis, Najash, and more madtsoiids (such as Sanajeh and Yurlunggur). Obviously one would wonder too if Cryptolacerta may have any impact as it might alter some of the states as interpreted for basal amphisbaenians and make it less parsimonious for snakes to group within that clade.

Conrad, 2008 Phylogeny and systematics of squamata (Reptilia) based on morphology http://digitallibrary.amnh.org/dspace/handle/2246/5915
Pyron et al., 2013 A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes http://www.biomedcentral.com/content/pdf/1471-2148-13-93.pdf

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