Gene trees, species and species trees in the Ctenosaura palearis clade

The growing use of molecular systematics in conservation has increased the importance of accurate resolution of taxonomic units and relationships. DNA data relate most directly to genealogies, which need not have perfect relationships with species limits and phylogenies. We used a multilocus gene tree approach to elucidate the relationships between four endangered Central American iguanas. We found support for the proposition that the described species taxa correspond to distinct evolutionary lineages warranting individual protection. We combined gene trees to estimate a phylogeny using Bayesian Estimation of Species Trees (BEST), minimizing deep coalescence, Species Trees from Average Ranks (STAR), and traditional concatenation. The estimate from concatenation conflicted with the other methods, likely owing to the disproportionate effect of mtDNA on concatenated analyses. This illustrates the importance of appropriate treatment of multilocus sequence data in phylogenetics. Our results indicate that these species have gone through recent and rapid speciation, resulting in four closely related narrow-range endemics.