Snake origin paper fails due to genomics and fakes an ancestral snake skull

Watanabe et al. 2019
“demonstrate that highly diverse phenotypes, exemplified by lizards and snakes, can and do arise from differential selection acting on conserved patterns of phenotypic integration.”

To build their phylogenetic tree, Watanabe 2019 report,
“To conduct comparative phylogenetic methods, we constructed a time-calibrated phylogenetic tree by using a published time calibrated molecular phylogeny of extant squamates (Zheng and Weins 2016) and incorporating extinct taxa based on previous systematic work and fossil occurrence data from the Paleobiology Database (paleobiodb.org). We grafted extinct taxa onto the extant tree by applying the equal-branching method based on the mean of first occurrence age range. Although the phylogenetic placement of Mosasauria within squamates remains ambiguous, Plotosaurus was placed within the molecular phylogeny as a sister taxon to Serpentes (“Pythonomorpha hypothesis”) and Polyglyphanodon as sister to iguanians in accordance with the phylogeny based on combined molecular and morphological data.”

Taxon exclusion is once again the problem here.
Too few fossil taxa appea in the Watanabe et al. cladogram. The keyword ‘outgroup’ is not found in the text or SuppData. Watanabe et al. report, “Sphenodon was not included in analyses with the exception of morphospaces.” As a result the highly derived legless amphisbaenid, Dibamus, was chosen as the outgroup. That is wrong, according to the large reptile tree (LRT, 1524 taxa) in which iguanids are plesiomorphic basalmost squamates. Sphenodontids and tritosaurs are outgroups in the LRT, are not represented.

Mosasaurs, like Plotosaurus, arise from varanids in the LRT. The clade Pythonomorpha is not recovered by the LRT.

Snake ancestors (none of which appear in Watanabe et al.) arise from Jurassic gekko-like ancestors, like Tchingisaurus and ending with tiny Tetraphodophis (Fig. 1). The list of snake ancestors includes terrestrial taxa, like Ardeosaurus, and aquatic taxa, like Pontosaurus. Fossorial (burrowing) snakes arise as derived taxa, not primitive forms. 

Quoting the NHM.AC.UK press release,
“Prof Goswami says, ‘There is a lot of debate about how snakes evolved, but we think we have traced the ancestral skull shape. Lots of scientists have speculated that maybe snake ancestors lived in water, which made them lose their legs. So it’s surprising that the patterns we saw led us to a semi-fossorial animal.’” 

There is no debate
when you use the last common ancestor approach based on phenomic (trait-based) phylogenetic analyses. Following in the footsteps of those who imagined pterosaur ancestors, the Watanabe team imagined a snake ancestor for no reason, because the LRT provides a long list of snake ancestors going back to Silurian jawless fish.

Gene studies
work well in criminal identification closely related taxa within a genus. Genomics fail for various reasons in deep time studies. This is something paleontologists and biologists need to realize. If you want results in which all derived taxa demonstrate gradually accumulating traits, you have to use trait-based studies and fossil taxa. Why turn your back on proven results in favor of a method you hope works, but never does?

References
Watanabe A, Fabre A-C, Felice RN, Maisano JA, Müller J, Herrel A and Goswami A 2019. Ecomorphological diversification in squamates from conserved pattern of cranial integration. www.pnas.org/cgi/doi/10.1073/pnas.1820967116
Zheng Y and Wiens JJ and 2016. Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species. Mol. Phylogenet. Evol. 94, 537–547.

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