TY - JOUR
T1 - Rodent phylogeny revised
T2 - Analysis of six nuclear genes from all major rodent clades
AU - Blanga-Kanfi, Shani
AU - Miranda, Hector
AU - Penn, Osnat
AU - Pupko, Tal
AU - Debry, Ronald W.
AU - Huchon, Dorothée
N1 - Funding Information:
We thank F. Catzeflis (curator of the tissue collection of the Institut des Sciences de l'Evolution de Montpellier), the University of Alaska Museum, the Cleveland Metroparks, the Louisiana State University Museum of Natural Science, the Texas Cooperative Wildlife Collection, the Museum of Southwestern Biology, the Rotterdam Zoo and the Zoological Society of Philadelphia, as well as all donors and collectors of tissue: T. Arrizabalaga, M. R. Banta, M. Bebehani, C.J. Bonar, J. Cook, M. Corti, D. L. Dittmann, D. Eilam, C. G. Faulkes, P. Gouat, L. Granjon, J. Hayes, R.L. Honeycutt, R. Hoyt, J. Jarvis, N. Kronfeld-Schor, M. Mensink, P. Perret, D. Schlitter, D.S. Semple, M.S. Springer, R. Stuebing, J. Terkel, J. Trupkiewicz, E. Pelé, J.-C. Vié, and V. Volo-bouev. We would also like to thank Frida Belinky for running the CAT model analysis, Lily Kredy-Farhan for designing primers, and Naomi Paz for revising the English text. OP is a fellow of the Converging Technologies scholarship program. This work was supported by the United States-Israel Binational Science Foundation (BSF; 2004-407 to DH and RWD) the National Science Foundation (NSF; DEB-0075306 to RWD) and the High Council for Scientific and Technological Cooperation between France-Israel (to DH and TP).
PY - 2009
Y1 - 2009
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=65349177696&partnerID=8YFLogxK
U2 - 10.1186/1471-2148-9-71
DO - 10.1186/1471-2148-9-71
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AN - SCOPUS:65349177696
SN - 1471-2148
VL - 9
JO - BMC Evolutionary Biology
JF - BMC Evolutionary Biology
IS - 1
M1 - 71
ER -