Through their taxonomic and phenotypic diversity, rodents constitute a very distinctive placental order. Indeed, with over 2277 described species (Wilson and Reeder, 2005; Fabre et al., 2012), they represent more than 40% of mammalian biodiversity.
In nearly every continent, rodents have colonised all terrestrial ecosystems from tropical deserts to arctic tundra, and from tropical and temperate to boreal forests. They display an astonishing diversity in that they have repeatedly colonised these ecological niches on most continents (Upham and Patterson, 2012; Schenk et al., 2013) and even on isolated archipelagos via the crossing of the Wallace and Lydekker lines to Australia (e.g. Indo-Pacific rats; Rowe et al., 2008; Fabre et al., 2013a). Following these continental dispersals, rodent adaptations converged on a wide array of locomotor repertoires (Samuels and Valkenburgh, 2008) and diets (e.g. vermivory: Musser, 1982; Balete et al., 2007; Samuels, 2009; Charles et al., 2013). Their success has often been connected to their wide-ranging diets, their cranio-dental specialisations (Hunter and Jernvall, 1995; Jernvall, 1995), their small-to-medium size, and their short generation time (Spradling et al., 2001). These recurrent adaptations and striking diversity have created difficulties for inferring their phylogenetic relationships (Luckett and Hartenberger, 1985). Despite some early methodological controversies (Graur et al., 1991), the use of molecular systematics has enabled the rodent tree of life to be deciphered and revealed a broad array of previously unexpected relationships and convergences. Mirroring research progress on Placentalia, the first rodent nuclear gene phylogenies (Huchon et al., 1999; Madsen et al., 2001; DeBry, 2003) have paved the way for understanding the higher-level relationships among rodents and revealed a strong biogeographical footprint (Huchon and Douzery, 2001; Mercer and Roth, 2003; Steppan et al., 2004a; Schenk et al., 2013). Since then, phylogenetic studies on Rodentia (Huchon et al., 1999; DeBry and Sagel, 2001; Montgelard et al., 2008; Blanga-Kanfi et al., 2009) as well as on Placentalia (Meredith et al., 2011) have benefited from the sequencing of mitochondrial DNA, nuclear markers and SINE/retroposons, and provided a large body of multi-locus molecular characters.