Higher-level systematics of rodents and divergence time estimates based on two congruent nuclear genes

Molecular Phylogenetics and Evolution

Volumn 26, Issue 3, 2003, Pages 409-420

  Adkins, Ronald M ^a   Walton, Anne H ^b   Honeycutt, Rodney L ^c  

^a UNIVERSITY OF TENNESSEE COLLEGE OF MEDICINE   (United States)

^b AMHERST COLLEGE   (United States)

^c TEXAS A AND M UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANOMALUROMORPHA; APLODONTIDAE; CASTORIDAE; GERBILLINAE; GRAPHIURUS; HYSTRICOGNATHA; MURINAE; MYOXIDAE; PEDETES; PEDETIDAE; PRIMATES; RODENTIA; SCIURAVIDA; SCIURIDAE; SCIUROGNATHI; SIGMODONTINAE;

EID: 0037355121     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1055-7903(02)00304-4     Document Type: Article

References (51)

1. Adkins, R.M., Gelke, E.L., Rowe, D., Honeycutt, R.L., 2001. Molecular phylogeny and divergence time estimates for major rodent groups: evidence from multiple genes. Mol. Biol. Evol. 18, 777-791.
2. Anderson, S., Jones, J.K., 1984. Introduction. In: Anderson, S., Jones, J.K (Eds.), Orders and Families of Recent Mammals of the World. John Wiley and Sons, New York, pp. 1-10.
3. Beintema, J.J., Rodewald, K., Braunitzer, G., Czelusniak, J., Goodman, M., 1991. Studies on the phylogenetic position of the Ctenodactylidae (Rodentia). Mol. Biol. Evol. 8, 151-154.
4. Bugge, J., 1985. Systematic value of the carotid arterial pattern in rodents. In: Luckett, W.P., Hartenberger, J.-L. (Eds.), Evolutionary Relationships of Rodents: A Multidisciplinary Analysis. Plenum Press, New York, pp. 355-379.
5. Cao, Y., Fujiwara, M., Nikaido, M., Okada, N., Hasegawa, M., 2000. Interordinal relationships and timescale of eutherian evolution as inferred from mitochondrial genome data. Gene 259, 149-158.
6. Centers for Disease Control and Prevention (2000). Available from 〈http://www.cdc.gov/ncidod/diseases/hanta/hps〉.
7. DeBry, R.W., Sagel, R.M., 2001. Phylogeny of Rodentia (Mammalia) inferred from the nuclear-encoded gene IRBP. Mol. Phylogenet. Evol. 19, 290-301.
8. Eizirik, E., Murphy, W.J., O'Brien, S.J., 2001. Molecular dating and biogeography of early placental mammal radiation. J. Hered. 92, 212-219.
9. Farris, J.S., Kallersjo, M., Kluge, A.G., Bult, C., 1995. Testing significance of incongruence. Cladistics 10, 315-319.
10. Felsenstein, J., 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
11. Flynn, L.J., Jacobs, L.L., Cheema, I.U., 1986. Baluchimyinae, a new ctenodactyloid rodent subfamily from the Miocene of Baluchistan. Am. Mus. Novit. 2841, 1-58.
12. George, W., 1985. Reproductive and chromosomal characters of ctenodactylids as a key to their evolutionary relationships. In: Luckett, W.P., Hartenberger, J.-L. (Eds.), Evolutionary Relationships of Rodents: A Multidisciplinary Analysis. Plenum Press, New York, pp. 453-474.
13. Hartenberger, J.-L., 1998. Description de la radiation des Rodentia (Mammalia) du Paleocene superieur au Miocene: Incidences phylogenetiques. C. R. Acad. Sci. Paris 326, 439-444.
14. Hasegawa, M., Kishino, H., Yano, T., 1985. Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22, 160-174.
15. Hedges, S.B., Kumar, S., 1999. Technical comments: divergence times of eutherian mammals. Science. 285, 2031a.
16. Huchon, D.F., Catzeflis, M., Douzery, E.J.P., 1999. Molecular evolution of the nuclear von Willebrand factor gene in mammals and the phylogeny of rodents. Mol. Biol. Evol. 16, 577-589.
17. Huchon, D., Catzeflis, F.M., Douzery, E.J.P., 2000. Variance of molecular datings, evolution of rodents and the phylogenetic affinities between Ctenodactylidae and Hystricognathi. Proc. R. Soc. Lond. B 267, 393-402.
18. Huelsenbeck, J.P., Larget, B., Swofford, D., 2000. A compound poisson process for relaxing the molecular clock. Genetics 154, 1879-1892.
19. Jacobs, L.L., Downs, W.R., 1994. The evolution of murine rodents in Asia. In: Tomida, Y., Li, C., Setoguchi, T. (Eds.), Rodents and Lagomorph Families of Asian Origin and Diversification. National Science Museum Monograph, Tokyo, pp. 149-156.
20. Jaeger, J.J., 1988. Rodent phylogeny: new data and old problems. In: Benton, M.J. (Ed.), The Phylogeny and Classification of the Tetrapods, Vol. 2: Mammals. Clarendon Press, Oxford, pp. 177-199.
21. Ji, Q., Luo, Z.-X., Yuan, C.-X., Wible, J., Zhang, J.-P., Georgi, J.A., 2002. The earliest known eutherian mammal. Nature 416, 816-822.
22. Kumar, S., Hedges, S.B., 1998. A molecular timescale for vertebrate evolution. Nature 392, 917-920.
23. Lavocat, R., Parent, J.-R., 1985. Phylogenetic analysis of middle ear features in fossils and living rodents. In: Luckett, W.P., Hartenberger, J.-L. (Eds.), Evolutionary Relationships of Rodents: A Multidisciplinary Analysis. Plenum Press, New York, pp. 333-354.
24. Leakey, M.G., Ungar, P.s., Walker, A., 1995. A new genus of large primate from the late Oligocene of Lothidok, Turkana District, Kenya. J. Hum. Evol. 28, 519-531.
25. Luckett, W.P., 1985. Superordinal and intraordinal affinities of rodents: developmental evidence from the dentition and placentation. In: Luckett, W.P., Hartenberger, J.-L. (Eds.), Evolutionary Relationships of Rodents: A Multidisciplinary Analysis. Plenum Press, New York, pp. 227-276.
26. Luckett, W.P., Hartenberger, J.-L., 1985. Evolutionary relationships among rodents: comments and conclusions. In: Luckett, W.P., Hartenberger, J.-L. (Eds.), Evolutionary Relationships of Rodents: A Multidisciplinary Analysis. Plenum Press, New York, pp. 685-712.
27. Madsen, O., Scally, M., Douady, C.J., Kao, D.J., DeBry, R.W., Adkins, R., Amrine, H.M., Stanhope, M.J., de Jong, W.W., Springer, M.S., 2001. Parallel adaptive radiations in two major clades of placental mammals. Nature 409, 610-614.
28. Martin, T., 1993. Early rodent incisor enamel evolution: phylogenetic implications. J. Mamm. Evol. 1, 227-254.
29. McKenna, M.C., Bell, S.K., 1997. Classification of Mammals Above the Species Level. Columbia University Press, New York.
30. Miller, R.G., 1981. Simultaneous Statistical Inference, 2nd ed. Springer, New York.
31. Montgelard, C., Bentz, S., Tirard, C., Verneau, O., Catzeflis, F.M., 2002. Molecular systematics of Sciurognathi (Rodentia): The mitochondrial cytochrome b and 12s rRNA genes support the Anomaluroidea (Pedetidae and Anomaluridae). Mol. Phylogenet. Evol. 22, 220-233.
32. Murphy, W.J., Eizirik, E., Johnson, W.E., Zhang, Y.P., Ryder, O.A., O'Brien, S.J., 2001. Molecular phylogenetics and the origins of placental mammals. Nature 409, 614-618.
33. Nedbal, M.A., Honeycutt, R.L., Schlitter, D.A., 1996. Higher-level systematics of rodents (Mammalia, Rodentia): evidence from the mitochondrial 12S rRNA gene. J. Mamm. Evol. 3, 201-237.
34. Posada, D., Crandall, K.A., 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14, 817-818.
35. Sahni, A., 1985. Enamel structure of early mammals and its role in evaluating relationships among rodents. In: Luckett, W.P., Hartenberger, J.-L. (Eds.), Evolutionary Relationships of Rodents: A Multidisciplinary Analysis. Plenum Press, New York, pp. 133-150.
36. Sanderson, M.J., 1997. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol. 14, 1218-1231.
37. Sanderson, M.J., 2002. Estimating absolute rates of molecular evolution and divergence times in the absence of rate constancy. Mol. Biol. Evol. 19, 101-109.
38. Shimodaira, H., Hasegawa, M., 1999. Multiple comparisons of log-likelihoods with application to phylogenetic inference. Mol. Biol. Evol. 16, 1114-1116.
39. Sullivan, J., Swofford, D.L., 1997. Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics. J. Mamm. Evol. 4, 77-86.
40. Swofford, D.L., 1998. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods), ver. 4. Sinauer Associates, Sunderland, MA.
41. Tavare, S., Marshall, C.R., Will, O., Soligo, C., Martin, R.D., 2002. Using the fossil record to estimate the age of the last common ancestor of extant primates. Nature 416, 726-729.
42. Templeton, A.R., 1983. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the humans and apes. Evolution 37, 221-244.
43. Thorne, J.L., Kishino, H., Painter, I.S., 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15, 1647-1657.
44. Vianey-Liaud, M., 1985. Possible evolutionary relationships among eocene and lower Oligocene rodents of Asia, Europe and North America. In: Luckett, W.P., Hartenberger, J.-L. (Eds.), Evolutionary Relationships of Rodents: A Multidisciplinary Analysis. Plenum Press, New York, pp. 277-309.
45. Wahlert, J.H., 1985. Cranial foramina of rodents. In: Luckett, W.P., Hartenberger, J.-L. (Eds.), Evolutionary Relationships of Rodents: A Multidisciplinary Analysis. Plenum Press, New York, pp. 311-332.
46. Wood, A.E., 1985. The relationships, origin, and dispersal of the hystricognathous rodents. In: Luckett, W.P., Hartenberger, J.-L. (Eds.), Evolutionary Relationships of Rodents: A Multidisciplinary Analysis. Plenum Press, New York, pp. 475-513.
47. Wood, B.J., 1994. Rodents in agriculture and forestry. In: Buckle, A.P., Smith, R.H. (Eds.), Rodent Pests and Their Control. CAB International, Wallingford, UK, pp. 45-84.
48. Wu, C.-I., Li, W.-H., 1985. Evidence for higher rates of nucleotide substitution in rodents than in man. Proc. Natl. Acad. Sci. USA 82, 1741-1745.
49. Yang, Z., 2000. Phylogenetic Analysis by Maximum Likelihood (PAML), ver. 3.0. University College London, London, England.
50. Wyss, A.R., Flynn, J.J., Norell, M.A., Swisher III, C.C., Charrier, R., Novacek, M.J., McKenna, M.C., 1993. South America's earliest rodent and recognition of a new interval of mammalian evolution. Nature 365, 434-437.
51. Yoder, A.D., Yang, Z., 2000. Estimation of primate speciation dates using local molecular clocks. Mol. Biol. Evol. 17, 1081-1090.