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

Shani Blanga-Kanfi 2 Hector Miranda 1 3 Osnat Penn 0 Tal Pupko 0 Ronald W DeBry 1 Dorothe Huchon 2 0 Department of Cell Research and Immunology, George S Wise Faculty of Life Sciences, Tel-Aviv University , Tel-Aviv 69978 , Israel 1 Department of Biological Sciences, University of Cincinnati , Box 210006, Cincinnati, Ohio, 45221-0006 , USA 2 Department of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University , Tel-Aviv 69978 , Israel 3 Department of Biology, Texas Southern University , 3100 Cleburne Street, Houston, TX 77004 , USA Background: Rodentia is the most diverse order of placental mammals, with extant rodent species representing about half of all placental diversity. In spite of many morphological and molecular studies, the family-level relationships among rodents and the location of the rodent root are still debated. Although various datasets have already been analyzed to solve rodent phylogeny at the family level, these are difficult to combine because they involve different taxa and genes. Results: 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. Conclusion: 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. - Background 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 classification does not reflect evolutionary relationships [7,8]. The second system, proposed by Tullberg, divides rodents into two suborders, Sciurognathi and Hystricognathi, based on the position of the incisors and the angle of the jaw [9]. The monophyly of Hystricognathi has been accepted, based on the identification of additional morphological synapomorphies, but the Sciurognathi are usually considered to be paraphyletic [10]. Debates on the relationships within Sciurognathi and their relationships with Hystricognathi are the subject of numerous morphological papers [reviewed in [11]]. Molecular studies were expected to clarify the relationships among rodents. However, early studies based on molecular data complicated the understanding of rodent evolution by suggesting that rodents are paraphyletic [12-14]. These results initiated lively debates concerning evolutionary relationships among rodents and their place among placental mammals [15-17]. Phylogenetic conclusions supporting rodent paraphyly have been criticized, because they were based on a very limited taxonomic sampling. It has been suggested that increasing the sampling of rodent diversity [2] and/or mammalian diversity [18] would have supported rodent monophyly. Additionally, over-simplified models have been shown to erroneously support rodent paraphyly [19]. Recent analyses based on a representative sampling of rodent taxonomic diversity and using modelbased methods of sequence analysis have strongly supported the monophyly of rodents [20-24]. Within Rodentia, molecular analyses suggest that rodents are divided into seven well-supported clades: 1-Anomaluromorpha (scaly-tailed flying squirrels, springhares), 2Castoridae (beavers), 3-Ctenohystrica (gundi, porcupines, guinea-pigs), 4-Geomyoidea (pocket gophers, pocket mice), 5-Gliridae (dormice), 6-Myodonta (rats, mice, jerboas), and 7-Sciuroidea (mountain beavers, squirrels, woodchucks) [25-28]. However, several evolutionary relationships within Rodentia are still debated. Recent studies have suggested that these seven clades are clustered into three main lineages: 1 Anomaluromorpha, Castoridae, Geomyoidea, and Myodonta together form the "mouse-related clade"; 2 Sciuriodea and Gliridae form the "squirrel-related clade"; and 3 Ctenohystrica forms the third lineage [29-32]. However, most studies have not been able to solve the relationships among these three clades. Recently, Montgelard et al. [32] analyzed mitochondrial genes as well as nuclear exonic and intronic sequences, and found significant support in favor of a basal position of the "mouse-related clade". This result was dependent on the removal of the fastest evolving characters from the dataset, suggesting that mutational saturation might explain the inconclusive placement of the rodent root. More generally, Rodriguez-Ezpeleta et al. [33] have shown that weakly supported nodes can sometimes be explained by the presence of conflicting phylogenetic and non-phylogenetic signal in a dataset. Three methods to reduce the non-phylogenetic information have been suggested: identification and removal of fast-evolving positions, character-recoding (e.g., RY coding), and the use of a siteheterogenous mixture model (e.g., CAT) [34]. Here, we aimed to resolve rodent relationships at the family level and above. We established a comprehensive dataset including six nuclear gene fragments from 41 rodent species together with eight outgroup species. We were able to solve most evolutionary relationships among rodent families. In order to minimize conflicting signals and thus solve the debated basal rodent relationships, we applied the three methods suggested by Rodriguez-Ezpeleta et al. [33]. We show that none of these methods, nor the use of more complex evolutionary models, can significantly solve basal rodent relationships. Additionally, some of our analyses, surprisingly, suggest a basal positio (...truncated)