Squamate tree of life: Gearty and Gauthier 2014 JVP abstracts

Resolving the relationships of the Squamate tree of life.
An assessment of new approaches and problems.

In their JVP 2014 abstract Gearty and Gauthier (2014) mix morphological and molecule data on Squamates and this becomes ‘detrimental’ (their words, not mine) to results. So actually they do not resolve relationships. It’s just a topic header. And there’s no mention of the third squamate clade, the Tritosauria, which probably messes up their results, as earlier reported by Conrad (2008, see below) .

From the abstract:
“Since the division of The Deep Scaly Project into separate morphological and molecular teams, a truly integrated project of wide scope has not been attempted. Much more can be done to understand how the members of Squamata are related to one another through an approach that combines the importance of both morphological and molecular evolution. Here we have developed a novel three-step methodological approach to squamate phylogenetics that incorporates the newest phylogeny-creating techniques and data from previous morphological and genetic analyses. First, we analyze a large squamate morphological dataset using Lewis’s Mkv model under both a Bayesian and maximum likelihood framework. Second, we incorporate a previously constructed squamate DNA dataset and analyze the combined data within a ‘total evidence’ framework. Finally, we adopt a methodology that treats genes, rather than nucleotides, as the character of interest. We find that the separate analyses of the morphological and molecular datasets, even under Bayesian and maximum likelihood frameworks, still result in drastically different relationships between higher-order clades within Squamata.

Additionally, we find that the combination of these two datasets results in a phylogeny with limited support for either topology, although it definitively leans in the direction of the molecular results.

Finally, by reducing the molecular dataset to gene characters, we find significantly lower support for the higher-order relationships that are strongly supported in previous analyses. By combining these data with our morphological dataset, we discover that we have inversed the effect of the power in numbers problem.

We conclude that combining datasets, although possibly detrimental to results, should be treated as a source of understanding how the datasets may differ and how they may reflect different evolutionary histories.”

So, ladies and gentlemen… 
Take a lesson from Gearty and Gauthier and don’t mix genetics with morphology. I would trust genetics to find my long lost brother, or a criminal, but not to find any long lost clades. As we learned earlier here, not only can genes be homoplastic, but wrong interpretations can skew results.

From Conrad 2008
Most known squamates fit within one of the seven major radiations (Iguania, Gekkota, Lacertoidea, Scincoidea, Anguimorpha, Amphisbaenia, and Serpentes), but some fossil taxa defy placement within any of these groups. Recent descriptive and phylogenetic work suggests that some fossil taxa fall outside of the crown-group represented by this framework. Among these are Huehuecuetzpalli mixtecus (Reynoso, 1998), Hoyalacerta sanzi (Evans and Barbadillo, 1999; Evans et al., 2004), Scandensia ciervensis, ‘bavarisaurids’, and ‘ardeosaurids‘.

All of the misfits listed above, but the ardeosaurids, are tritosaurs. The ardeosaurids are proto-snakes. So this clade has been long recognized, just not identified in the literature. Yet.

Recent work
I’ve done some recent work with basal squamates from the Early Cretaceaous lithographic limestones and I’ll present a few of them here soon. For now, the tree topology here remains pretty darn close (but new taxa are being added, now up to 425).

References
Gearty W and Gauthier J 2014. Resolving the relationships of the squamate tree of life. An assessment of new approaches and problems. JVP abstracts 2014.

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