Phylogeny of iguanian lizards inferred from 29 nuclear loci, and a comparison of concatenated and species-tree approaches for an ancient, rapid radiation

• Published in: Molecular phylogenetics and evolution 2011-11, Vol.61 (2), p.363-380
• Main Authors: Townsend, Ted M., Mulcahy, Daniel G., Noonan, Brice P., Sites, Jack W., Kuczynski, Caitlin A., Wiens, John J., Reeder, Tod W.
• Format: Article
• Language: English
• Subjects: Acrodonta; Agamidae; Animals; Anolis; Bayes Theorem; Bayesian analysis; Cell Nucleus - genetics; Chamaeleonidae; Cladding; Coalescing; Concatenation; data collection; DNA; ecology; Evolution; Evolution, Molecular; Genes; Iguania; Likelihood Functions; lizards; Lizards - classification; Lizards - genetics; Loci; Models, Genetic; monophyly; Nuclear DNA; nucleotide sequences; paraphyly; Phylogenomics; Phylogeny; Phylogeography; Pleurodonta; rapid methods; Recognition; Sequence Analysis, DNA; Species tree; Squamata; Trees
• ISSN: 1055-7903; 1095-9513
• DOI: 10.1016/j.ympev.2011.07.008

[Display omitted] ► We perform a phylogenetic analysis of iguanian lizards using 29 nuclear loci. ► Most acrodont iguanian relationships are resolved with high support. ► Pleurodont relationships recovered with high Bayesian and variable likelihood support. ► Pleurodonts are inferred to have originated in North America and dispersed southward. ► Anolis removed from Polychrotidae and placed in Dactyloidae. Iguanian lizards form a diverse clade whose members have been the focus of many comparative studies of ecology, behavior, and evolution. Despite the importance of phylogeny to such studies, interrelationships among many iguanian clades remain uncertain. Within the Old World clade Acrodonta, Agamidae is sometimes found to be paraphyletic with respect to Chamaeleonidae, and recent molecular studies have produced conflicting results for many major clades. Within the largely New World clade Pleurodonta, relationships among the 12 currently recognized major subclades (mostly ranked as families) have been largely unresolved or poorly supported in previous studies. To clarify iguanian evolutionary history, we first infer phylogenies using concatenated maximum-likelihood (ML) and Bayesian analyses of DNA sequence data from 29 nuclear protein-coding genes for 47 iguanian and 29 outgroup taxa. We then estimate a relaxed-clock Bayesian chronogram for iguanians using BEAST. All three methods produce identical topologies. Within Acrodonta, we find strong support for monophyly of Agamidae with respect to Chamaeleonidae, and for almost all relationships within agamids. Within Pleurodonta, we find strong Bayesian support for almost all relationships, and strong ML support for some interfamilial relationships and for monophyly of almost all families (excepting Polychrotidae). Our phylogenetic results suggest a non-traditional biogeographic scenario in which pleurodonts originated in the Northern Hemisphere and subsequently spread southward into South America. The pleurodont portion of the tree is characterized by several very short, deep branches, raising the possibility of deep coalescences that may confound concatenated analyses. We therefore also use 27 of these genes to implement a coalescent-based species-tree approach for pleurodonts. Although this analysis strongly supports monophyly of the pleurodont families, interfamilial relationships are generally different from those in the concatenated tree, and support is uniformly poor. However, a species-tree analysis usi