This is a little far afield for anole aficionados, but recent years have seen a revolution in our picture of lizard (including snake) phylogeny. Traditionally, based on morphological analysis, lizards were thought to split into two groups, the iguanians (including anoles, other iguanids, agamids, and chameleons) and scleroglossans (everything else, including snakes). However, starting with a paper by Townsend et al. in 2004, a different picture emerged in which iguanians were nested high in lizard phylogeny, closely related to anguimorphs (such as alligator lizards, gila monsters, and monitors) and snakes. A series of subsequent studies came to essentially the same conclusion, most recently the output of the “Deep Scaly” NSF Tree of Life project which sequenced DNA from 44 genes.
I think that most of the field had come to accept that the molecular tree was correct. But along comes a paper by the morphology team of Deep Scaly, a remarkable analysis in which 194 species were all micro-CT scanned and examined in others ways, leading to a data set of more than 600 morphological characters, 247 never previously used in phylogenetic studies. Analyzed with state-of-the-art methods, the results resoundingly support the original morphological tree and give absolutely no morphological support for the new molecular tree. The authors do an excellent job in not being strident in insisting that the morphological tree is correct, but just highlighting how very unusual morphological evolution must have been if the molecular tree is correct. Moreover, the authors note that based on analyses including the molecular data, the “Archaeopteryx” of squamates, Huehuecuetzpalli mixtecus, is placed high in the phylogeny, rather than in the basal position where morphology has long placed it. If, indeed, the molecules are right, what does that say about our ability to ever reliably place fossil species in a phylogeny?
Either the morphological or the molecular tree is incorrect, and either molecular or morphological data have been evolving in a way for which there is no good explanation. This is truly a conundrum, which was the point of a perspective piece just published by David Hillis, Harry Greene, and me. We don’t have any answers, but thought it was an interesting enough question worthy of further attention.