Phylogeny and divergence-date estimates of rapid radiations in muroid rodents based on multiple nuclear genes

Systematic Biology

Volumn 53, Issue 4, 2004, Pages 533-553

  Steppan, Scott J ^a   Adkins, Ronald M ^b   Anderson, Joel ^c  

^a FLORIDA STATE UNIVERSITY   (United States)

^b Univ of TN Health Sciences Center   (United States)

^c SOUTHWEST FOUNDATION FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

Adaptive radiation; Calibration; Classification; Molecular clock; Murinae; Sigmodontinae

Indexed keywords

CALOMYSCUS; CRICETINAE; GERBILLINAE; MAMMALIA; MURINAE; NESOMYINAE; RHIZOMYINAE; RODENTIA; SIGMODONTINAE; SPALACINAE;

EID: 4344665270     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150490468701     Document Type: Article

References (87)

1. Adkins, R. M., E. L. Gelke, D. Rowe, and R. L. Honeycutt. 2001. Molecular phylogeny and divergence time estimates for major rodent groups: Evidence from multiple genes. Mol. Biol. Evol. 18:777-791.
2. Adkins, R. M., A. H. Walton, and R. L. Honeycutt. 2003. Higher-level systematics of rodents and divergence time estimates based on two congruent nuclear genes. Mol. Phylogenet. Evol. 26:409-420.
3. Barome, P. O., M. Monnerot, and J. C. Gautun. 2000. Phylogeny of the genus Acomys (Rodentia, Muridae) based on the cytochrome b mitochondrial gene: Implications on taxonomy and phylogeography. Mammalia 64:423-438.
4. Baskin, J. A. 1978. Bensonomys, Calomys, and the origin of the phyllotine group of neotropical cricetines (Rodentia: Cricetidae). J. Mammal. 59:125-135.
5. Baskin, J. A. 1986. The late Miocene radiation of Neotropical sigmodontine rodents in North America. Contributions to Geology, University of Wyoming, Special Paper 3:287-303.
6. Cao, Y., M. Fujiwara, M. Nikaido, N. Okada, and M. Hasegawa. 2000. Interordinal relationships and timescale of eutherian evolution as inferred from mitochondrial genome data. Gene 259:149-158.
7. Carleton, M. D. 1980. Phylogenetic relationships in neotomine-peromyscine rodents (Muroidea) and a reappraisal of the dichotomy within New World Cricetinae. Misc. Publ. Mus. Zool., Univ. Mich. 157:1-146.
8. Carleton, M. D., and G. G. Musser. 1984. Muroid rodents. Pages 289-379 in Orders and families of recent mammals of the world (S. Anderson and J. K. Jones, Jr., eds.). John Wiley and Sons, New York.
9. Catzeflis, F. M., A. W. Dickerman, J. Michaux, and J. A. W. Kirsch. 1993. DNA hybridization and rodent phylogeny. Pages 159-172 in Mammalian phylogeny: Placentals (F. S. Szalay, M. J. Novacek, and M. C. McKenna, eds.). Springer-Verlag, New York.
10. Chaline, J., and J. D. Graf. 1988. Phylogeny of the Arvicolidae (Rodentia): Biochemical and paleontological evidence. J. Mammal. 69:22-33.
11. Chaline, J., P. Mein, and F. Petter. 1977. Les grandes lignes d'une classification évolutive des Muroidea. Mammalia 41:245-252.
12. Chevret, P., C. Denys, J.-J. Jaeger, J. Michaux, and F. M. Catzeflis. 1993a. Molecular evidence that the spiny mouse (Acomys) is more closely related to gerbils (Gerbillinae) than to true mice (Murinae). Proc. Natl. Acad. Sci. U.S.A. 90:3433-3436.
13. Chevret, P., C. Denys, J. J. Jaeger, J. Michaux, and F. Catzeflis. 1993b. Molecular and paleontological aspects of the tempo and mode of evolution in Otomys (Otomyinae, Muridae, Mammalia). Biochem. Syst. Ecol. 21:123-131.
14. Conroy, C. J., and J. A. Cook. 1999. mtDNA evidence for repeated pulses of speciation within arvicoline and murid rodents. J. Mammal. Evol. 6:221-245.
15. Conroy, C. J., and J. A. Cook. 2000. Molecular systematics of a holarctic rodent (Microtus: Muridae). J. Mammal. 81:344-359.
16. Czaplewski, N. J. 1987. Sigmodont rodents (Mammalia; Muroidea; Sigmodontinae) from the Pliocene (early Blancan) Verde Formation, Arizona. J. Vertebr. Paleontol. 7:183-199.
17. D'Elía, G. 2000. Comments on recent advances in understanding sigmodontine phylogeny and evolution. Mastozoolog. Neotrop. 7:47-54.
18. D'Elía, G. 2003. Phylogenetics of sigmodontinae (Rodentia, Muroidea, Cricetidae), with special reference to the akodont group, and with additional comments on historical biogeography. Cladistics 19:307-323.
19. Denys, C., and J. Michaux. 1992. La troisième molaire supérieure chez les Muridae d'Afrique tropicale et le cas des genres Acomys, Uranomys et Lophuromys. Bonn. Zool. Beitr. 43:367-382.
20. Denys, C., J. Michaux, F. Catzeflis, S. Ducrocq, and P. Chevret. 1995. Morphological and molecular data against the monophyly of Dendromurinae (Muridae: Rodentia). Bonn. Zool. Beitr. 45:173-190.
21. Dickerman, A. W. 1992. Molecular systematics of some New World muroid rodents. Ph.D. dissertation, University of Wisconsin-Madison.
22. Dubois, J. Y. F., F. M. Catzeflis, and J. J. Beintema. 1999. The phylogenetic position of "Acomyinae" (Rodentia, Mammalia) as sister group of a Murinae plus Gerbillinae clade: Evidence from the nuclear ribonuclease gene. Mol. Phylogenet. Evol. 13:181-192.
23. Ducroz, J. F., V. Volobouev, and L. Granjon. 1998. A molecular perspective on the systematics and evolution of the genus Arvicanthis (Rodentia, Muridae): Inferences from complete cytochrome b gene sequences. Mol. Phylogenet. Evol. 10:104-117.
24. Ducroz, J. F., V. Volobouev, and L. Granjon. 2001. An assessment of the systematics of arvicanthine rodents using mitochondrial DNA sequences: Evolutionary and biogeographic implications. J. Mamm. Evol. 8:173-206.
25. Elton, C. 1942. Voles, mice and lemmings. Clarendon Press, Oxford.
26. Engel, S. R., K. M. Hogan, J. F. Taylor, and S. K. Davis. 1998. Molecular systematics and paleobiogeography of the South American sigmodontine rodents. Mol. Biol. Evol. 15:35-49.
27. Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
28. Flynn, L. J., L. L. Jacobs, and E. H. Lindsay. 1985. Problems in muroid phylogeny: Relationships to other rodents and origin of major groups. Pages 589-616 in Evolutionary relationships among rodents (W. P. Luckett and J.-L. Hartenberger, eds.). Plenum Press, New York.
29. Fratti, F., C. Simon, J. Sullivan, and D. L. Swofford. 1997. Evolution of the mitochondrial cytochrome oxidase II gene in Collembola. J. Mol. Evol. 44:145-158.
30. Hänni, C., V. Laudet, V. Barriel, and F. M. Catzeflis. 1995. Evolutionary relationships of Acomys and other murids (Rodentia, Mammalia) based on complete 12S ribosomal-RNA mitochondrial gene-sequences. Isr. J. Zool. 41:131-146.
31. Hartenberger, J. L. 1998. Description of the radiation of the Rodentia (Mammalia) from the Late Paleocene to the Miocene; phylogenetic consequences. C. R. Acad. Sci. Ser. II-A 326:439-444.
32. Hendriks, W., J. Leunissen, E. Nevo, H. Bloemendal, and W. W. de Jong. 1987. The lens protein alpha A-crystallin of the blind mole rat, Spalax ehrenbergi: Evolutionary change and functional constraints. Proc. Natl. Acad. Sci. U.S.A. 84:5320-5324.
33. Hershkovitz, P. 1972. The Recent mammals of the Neotropical region: A zoogeographic and ecologic review. Pages 311-431 in Evolution, mammals, and southern continents (A. Keast, F. C. Erk, and B. Glass, eds.). State University of New York, Albany.
34. Hillis, D. M., D. D. Pollock, J. A. McGuire, and D. J. Zwickl. 2003. Is sparse taxon sampling a problem for phylogenetic inference? Syst. Biol. 52:124-126.
35. Hooper, E. T., and G. G. Musser. 1964. The glans penis in neotropical cricetines (Muridae) with comments on classification of muroid rodents. Misc. Publ. Mus. Zool., Univ. Mich. 123:1-57.
36. Huchon, D., F. M. Catzeflis, and E. J. P. Douzery. 2000. Variance of molecular datings, evolution of rodents and the phylogenetic affinities between Ctenodactylidae and Hystricognathi. Proc. R. Soc. Lond. Ser. B-Biol. Sci. 267:393-402.
37. Huchon, D., O. Madsen, M. Sibbald, K. Ament, M. J. Stanhope, F. Catzeflis, W. W. de Jong, and E. J. P. Douzery. 2002. Rodent phylogeny and a timescale for the evolution of glires: Evidence from an extensive taxon sampling using three nuclear genes. Mol. Biol. Evol. 19:1053-1065.
38. Huelsenbeck, J. P., and B. Rannala. 1997. Phylogenetic methods come of age: Testing hypotheses in an evolutionary context. Science 276:227-232.
39. Huelsenbeck, J. P., and F. Ronquist. 2003. MrBayes: A program for the Bayesian inference of phylogeny, 3.0. Rochester, New York.
40. Hughes, A. L., and R. Friedman. 2000. Evolutionary diversification of protein-coding genes of hantaviruses. Mol. Biol. Evol. 17:1558-1568.
41. ICZN. 1999. International code of zoological nomenclature, 4th edition. The International Trust for Zoological Nomenclature, London.
42. Iturralde-Vinent, M., and R. MacPhee. 1999. Paleogeography of the Caribbean region: Implications for Cenozoic biogeography. Bull. Am. Mus. Nat. Hist. 238:1-95.
43. Jacobs, L. L., and W. R. Downs. 1994. The evolution of murine rodents in Asia. Pages 149-156 in Rodent and lagomorph families of Asian origins and diversification (Y. Tomida, C. K. Li and T. Setoguchi, eds.). National Science Museum Monographs, Tokyo.
44. Jacobs, L. L., and E. H. Lindsay. 1984. Holarctic radiation of Neogene muroid rodents and the origin of South American cricetids. J. Vertebr. Paleontol. 4:265-272.
45. Jansa, S. A., S. M. Goodman, and P. K. Tucker. 1999. Molecular phylogeny and biogeography of the native rodents of Madagascar (Muridae: Nesomyinae): A test of the single-origin hypothesis. Cladistics 15:253-270.
46. Kishino, H., and M. Hasegawa. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA data, and the branching order in Hominoidea. J. Mol. Evol. 29:170-179.
47. Kumar, S., and S. B. Hedges. 1998. A molecular timescale for vertebrate evolution. Nature 392:917-920.
48. Lavocat, R. 1973. Les Rongeurs du Miocene d'Afrique oriental 1. Miocene inférieur. Mém. Trav. Inst. Montpellier E.P.H.E. 1:1-284.
49. Lavocat, R. 1978. Rodentia and Lagomorpha. Pages 69-89 in Evolution of African mammals (V. J. Maglio and H. B. S. Cooke, eds.). Harvard University Press, Cambridge, Massachusetts.
50. Marshall, L. G. 1979. A model for paleobiogeography of South American cricetine rodents. Paleobiology 5:126-132.
51. Michaux, J., and F. Catzeflis. 2000. The bushlike radiation of muroid rodents is exemplified by the molecular phylogeny of the LCAT nuclear gene. Mol. Phylogenet. Evol. 17:280-293.
52. Michaux, J., A. Reyes, and F. Catzeflis. 2001. Evolutionary history of the most speciose mammals: Molecular phylogeny of muroid rodents. Mol. Biol. Evol. 18:2017-2031.
53. Mills, J. N., M. D. Bowen, and S. T. Nichol. 1997. African arenaviruses: Coevolution between virus and murid host? Belg. J. Zool. 127:19-28.
54. Musser, G. M., and M. D. Carleton. 1993. Family Muridae. Pages 501-756 in Mammal species of the world: A taxonomic and geographic reference, 2nd ed. (D. E. Wilson and D. M. Reeder, eds.). Smithsonian Institution, Washington, DC.
55. Musser, G. M., and M. D. Carleton, in press. Superfamily Muridae. in Mammal species of the world: A taxonomic and geographic reference, 3rd ed. (D. E. Wilson and D. M. Reeder, eds.). Smithsonian Institution, Washington, DC.
56. Pardiñas, U. F. J., G. D. D'Elia, and P. E. Ortiz. 2002. Sigmodontinos fósiles (Rodentia, Muroidea, Sigmodontinae) de América del Sur: Estadoactual de su conocimiento y prospectiva. J. Neotrop. Mammal. 9:209-252.
57. Patterson, B., and R. Pasqual. 1972. The fossil mammal fauna of South America. Pages 247-309 in Evolution, mammals, and southern continents (A. Keast, F. C. Erk, and B. Glass, eds.). SUNY Press, Albany, New York.
58. Posada, D., and K. A. Crandall. 1998. Modeltest: Testing the model of DNA substitution. Bioinformatics 14:817-818.
59. Reig, O. A. 1980. A new fossil genus of South American cricetid rodents allied to Wiedomys, with an assessment of the Sigmodontinae. J. Zool. (Lond.) 192:257-281.
60. Reig, O. A. 1984. Distribuição geográfica e história evolutiva dos roedores muroides sulamericanos (Cricetidae: Sigmodontinae). Rev. Bras. Genét. 7:333-365.
61. Robinson, M., F. Catzeflis, J. Briolay, and D. Mouchiroud. 1997. Molecular phylogeny of rodents, with special emphasis on murids: Evidence from nuclear gene LCAT. Mol. Phylogenet. Evol. 8:423-434.
62. Rosenberg, M. S., and S. Kumar. 2003. Taxon sampling, bioinformatics, and phylogenomics. Syst. Biol. 52:119-124.
63. Ruedas, L. A., and J. A. Kirsch. 1997. Systematics of Maxomys Sody, 1936 (Rodentia: Muridae: Murinae): DNA/DNA hybridization studies of some Borneo-Javan species and allied Sundaic and Australo-Papuan genera. Biol. J. Linn. Soc. 61:385-408.
64. Salazar-Bravo, J., J. W. Dragoo, D. S. Tinnin, and T. L. Yates. 2001. Phylogeny and evolution of the neotropical rodent genus Calomys: Inferences from mitochondrial DNA sequence data. Mol. Phylogenet. Evol. 20:173-184.
65. Sambrook, E., F. Fritsch, and T. Maniatis. 1989. Molecular cloning. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
66. Sanderson, M. J. 2002. Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach. Mol. Biol. Evol. 19:101-109.
67. Sarich, V. 1985. Rodent macromolecular systematics. Pages 423-452 in Evolutionary relationships among rodents: A multidisciplinary analysis (W. P. Luckett and J.-L. Hartenberger, eds.). Springer-Verlag, Berlin.
68. Savage, J. M. 1974. The isthmian link and the evolution of neotropical mammals. Natural History Museum, Los Angeles County, Contributions in Science 260:1-51.
69. Shimodaira, H., and M. Hasegawa. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16:1114-1116.
70. Simpson, G. G. 1945. The principles of classification and a new classification of mammals. Bull. Am. Mus. Nat. Hist. 85:1-350.
71. Simpson, G. G. 1950. History of the fauna of Latin America. Am. Sci. 38:361-389.
72. Simpson, G. G. 1980. Splendid isolation. The curious history of South American mammals. Yale University Press, New Haven.
73. Slaughter, B. H., and J. E. Ubelaker. 1984. Relationships of South American cricetines to rodents of North America and the Old World. J. Vertebr. Paleontol. 42:255-264.
74. Smith, M. F., and J. L. Patton. 1999. Phylogenetic relationships and the radiation of sigmodontine rodents in South America: Evidence from cytochrome b. J. Mamm. Evol. 6:89-128.
75. Steppan, S. J. 1995. Revision of the leaf-eared mice Phyllotini (Rodentia: Sigmodontinae) with a phylogenetic hypothesis for the Sigmodontinae. Fieldiana: Zool. 80:1-112.
76. Steppan, S. J. 1996. A new species of Holochilus (Rodentia: Sigmodontinae) from the middle Pleistocene of Bolivia and its phylogenetic significance. J. Vertebr. Paleontol. 16:522-530.
77. Steppan, S. J., B. L. Storz, and R. S. Hoffmann. 2004. Nuclear DNA phylogeny of the squirrels (Mammalia: Rodentia) and the evolution of arboreality from c-myc and RAG1. Mol. Phylogenet. Evol. 30:703-719.
78. Steppan, S. J., and J. Sullivan. 2000. The emerging statistical perspective in systematics: A comment on Mares and Braun. J. Mammal. 81:260-270.
79. Swofford, D. L. 2002. PAUP*. Phylogenetic analysis using parsimony (*and other methods), 4. Sinauer Associates, Sunderland, Massachusetts.
80. Swofford, D. L., G. J. Olsen, P. J. Waddell, and D. M. Hillis. 1996. Phylogenetic inference. Pages 407-514 in Molecular systematics (D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer Associates, Sunderland, Massachusetts.
81. Templeton, A. 1987. Nonparametric inference from restriction cleavage sites. Mol. Biol. Evol. 4:315-319.
82. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
83. Verneau, O., F. Catzeflis, and A. V. Furano. 1998. Determining and dating recent rodent speciation events by using L1 (LINE-1) retrotransposons. Proc. Natl. Acad. Sci. U.S.A. 95:11284-11289.
84. Weksler, M. 2003. Phylogeny of Neotropical oryzomyine rodents (Muridae: Sigmodontinae) based on the nuclear IRBP exon. Mol. Phylogenet. Eval. 29:331-349.
85. Wu, C.-I., and W.-H. Li. 1985. Evidence for higher rates of nucleotide substitution in rodents than in man. Proc. Natl. Acad. Sci. U.S.A. 82:1741-1745.
86. Yang, Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J. Mol. Evol. 39:306-314.
87. Yang, Z., N. Goldman, and A. Friday. 1995. Maximum likelihood trees from DNA sequences: A peculiar statistical problem. Syst. Biol. 44:384-399.