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With 61 species occurring mostly in the Andes and adjacent lowland areas, Stenocercus lizards represent one of the most widespread and well-represented Andean vertebrate groups. Phylogenetic relationships among species of Stenocercus are inferred using different datasets based on mitochondrial DNA sequence data of 35 species and morphological data of 59 species. Among morphological data, polymorphic and meristic/morphometric characters are coded under the frequency parsimony and gap-weighting methods, respectively, and the accuracy of these methods is tested. When both types of characters are included, the resulting tree topology is more similar to the topologies obtained from analyses of DNA sequence data than those topologies obtained after exclusion of one or both types of characters. The phylogenetic hypotheses inferred including 59 species of Stenocercus (dataset 1) and excluding those species for which DNA data were not available (dataset 2) are generally congruent with each other, as well as with previously published hypotheses. The most parsimonious tree obtained from analysis of dataset 2 is used in a dispersal-vicariance analysis to infer ancestral areas and major biogeographical events. Species of Stenocercus are divided into two major clades. Clade A has diversified mostly in the central Andes, with a few species in the northern Andes and one species in the southern Andes. Clade B is more widespread, with species in the northern, central, and southern Andes, as well as in the Atlantic lowlands and Amazon basin. The most recent common ancestor of Stenocercus is inferred to have occurred in the eastern cordillera of the central Andes. Given morphological similarity and altitudinal distribution of some species nested in a northern-Andes clade, as well as the relatively recent uplift of this Andean region, it is possible that species in this clade have diverged as recently as the mid-Pliocene.