A molecular phylogeny of tortoises (Testudines: Testudinidae) based on mitochondrial and nuclear genes

Although tortoises of the family Testudinidae represent a familiar and widely distributed group of turtles, their phylogenetic relationships have remained contentious. In this study, we included 32 testudinid species (all genera and subgenera, and all species of Geochelone, representing 65% of the total familial species diversity), and both mitochondrial (12S rRNA, 16S rRNA, and cytb) and nuclear (Cmos and Rag2) DNA data with a total of 3387 aligned characters. Using diverse phylogenetic methods (Maximum Parsimony, Maximum Likelihood, and Bayesian Analysis) congruent support is found for a well-resolved phylogeny. The most basal testudinid lineage includes a novel sister relationship between Asian Manouria and North American Gopherus. In addition, this phylogeny supports two other major testudinid clades: Indotestudo + Malacochersus + Testudo; and a diverse clade including Pyxis, Aldabrachelys, Homopus, Chersina, Psammobates, Kinixys, and Geochelone. However, we find Geochelone rampantly polyphyletic, with species distributed in at least four independent clades. Biogeographic analysis based on this phylogeny is consistent with an Asian origin for the family (as supported by the fossil record), but rejects the long-standing hypothesis of South American tortoises originating in North America. By contrast, and of special significance, our results support Africa as the ancestral continental area for all testudinids except Manouria and Gopherus. Based on our systematic findings, we also propose modifications concerning Testudinidae taxonomy.