Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades

We present here the largest protein-coding dataset used to study rodent relationships. It comprises six nuclear genes, 41 rodent species, and eight outgroups. Our phylogenetic reconstructions strongly support the division of Rodentia into three clades: (1) a "squirrel-related clade", (2) a "mouse-related clade", and (3) Ctenohystrica. Almost all evolutionary relationships within these clades are also highly supported. The primary remaining uncertainty is the position of the root. The application of various models and techniques aimed to remove non-phylogenetic signal was unable to solve the basal rodent trifurcation.Sequencing and analyzing a large sequence dataset enabled us to resolve most of the evolutionary relationships among Rodentia. Our findings suggest that the uncertainty regarding the position of the rodent root reflects the rapid rodent radiation that occurred in the Paleocene rather than the presence of conflicting phylogenetic and non-phylogenetic signals in the dataset.The order Rodentia is the most diverse among placental mammals: extant rodent species represent half of the placental diversity (2,277 species divided into 33 families) [1]. Morphological phylogenetic approaches have identified characters supporting a common origin (monophyly) of rodents, and clustered rodents and lagomorphs (rabbits, pikas) in a clade called Glires [2]. Morphological studies also generally agree on the number and content of rodent families [1,3,4]. However, the description of the relationships among rodent families has been confounded by rampant convergent evolution of morphological characters [5]. Based on morphological characters, rodents have been divided into either two or three suborders. The first system, suggested by Brandt, divides rodents into three suborders, Myomorpha, Sciuromorpha, and Hystricomorpha, based on the position of masticatory muscles (the masseters) [6]. However, it has since been proven that this character is homoplasic and that this classifica