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Open Access Highly Accessed Research article

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

Shani Blanga-Kanfi1, Hector Miranda24, Osnat Penn3, Tal Pupko3, Ronald W DeBry2 and Dorothée Huchon1*

Author Affiliations

1 Department of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel

2 Department of Biological Sciences, University of Cincinnati, Box 210006, Cincinnati, Ohio, 45221-0006, USA

3 Department of Cell Research and Immunology, George S Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel

4 Department of Biology, Texas Southern University, 3100 Cleburne Street, Houston, TX 77004, USA

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BMC Evolutionary Biology 2009, 9:71  doi:10.1186/1471-2148-9-71

Published: 2 April 2009

Abstract

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.