Phylogeny of lizards from Pyron et al.
In a monumental undertaking, Alexander Pyron and colleagues have just produced a molecular phylogeny for 4,161 species of lizards (including snakes), more than 40% of the 9400+ species described to date. The paper, now available online at BMC Evolutionary Biology, is a blockbuster, containing 28 figures, one an overview of the entire phylogeny and the remainder walking through lizard-life one clade at a time.
The analysis is based on sequence data from 12 commonly used and phylogenetically informative molecular markers (seven nuclear genes, five mitochondrial). On average, 12,896 base pairs of sequence data are available per species and, as is necessary in an endeavor such as this, the data set is incomplete, with an average of only 19% of base pair data being available for any given species.
The results are generally very concordant with recent molecular phylogenies, perhaps not surprising given that these data have been used in the most recent studies. The overall picture of lizard phylogeny is little-changed from what we’ve seen in recent molecular phylogenetic publications, but there are a few surprises at lower levels. You’ll have to peruse the paper yourself to check out your favorite group, as there’s way too much in it to go through here.
Of course, what readers of AA really want to know is: what does the phylogeny say about anole relationships? And, in fact, the results are for the most part concordant with previous studies. Perhaps surprising to many readers, the analysis supports the monophyly of the eight clades recognized by Nicholson et al. as separate genera. Well, almost. In contradiction to the paper’s statement, Nicholson et al.’s Anolis is not monophyletic because A. argenteolus is placed as the sister-taxon to the Xiphosurus clade (which contains Chamaeleolis and the ricordii group), rather than occurring with other species placed into the restricted Anolis. This is an odd finding, contradicting both Nicholson et al. and the Alfoldi et al. genome paper analysis, with the implication that the transparent lower eyelids of A. argenteolus and its putative sister taxon A. lucius are not homologous, but I don’t buy it. Other than that, I didn’t find anything too exciting in this phylogeny, though further scrutiny (it’s enormous) may turn up interesting relationships I didn’t notice.
Other than this one exception, however, the Nicholson et al. eight fare well. Nonetheless, the authors of this paper do not follow the Nicholson et al. taxonomic suggestion of subdivision, stating: “since Anolis is monophyletic as previously defined, we retain that definition here…for continuity with the recent literature.”
Probably the most interesting finding concerns the closest relative to anoles, a topic of great uncertainty. This analysis strongly confirms that Polychrus is not the sister group to Anolis; rather, Polychrus appears related to the hoplocercids, which means that it’s dewlap must be convergent with the anole flasher. To whom, then, are anoles related? The answer appears to be the basiliscines (Corytophanidae in more modern parlance), the morphologically diverse and fascinating neotropical group containing not only basilisks, but also Corytophanes and the little-known Laemanctus.
Two last points: first, as noted above, there’s lots of missing data. Clearly, this is not the last word and, in particular, the question of the sister taxon to Anolis cries out for further study. Second, as the authors note, this paper will be of inestimable value in conducting comparative studies spanning the entire lizard radiation. To facilitate such, the authors have made available a Newick file containing the phylogeny (if you don’t know what this means, suffice to say that it’s a very helpful move that will make it easy to use this phylogeny in comparative studies).
Now, let’s get out and sequence the other 5000 species and finish the job!
[Editor’s Update, March 18, 2014]: I was mistaken in saying that the Pyron et al. tree found only one inconsistency with the Nicholson et al. genera. In addition to the exception noted above, Nicholson et al. place christophei in their Chamaelinorops clade, but Pyron et al. find it allying with species that Nicholson et al. put in Xiphosurus.
A new journal focused on the natural history of Caribbean fauna and flora has just been announced. As the sample cover to the left illustrates, it might be a great place to publish observations on our favorite critters. The journal has a distinguished board of editors and the webpage states:
Manuel Leal recently observed this A. stratulus in Puerto Rico licking a leaf high in the forest at El Verde. He 
