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Higher-level systematics of rodents (Mammalia, Rodentia): Evidence from the mitochondrial 12S rRNA gene

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Abstract

Phylogenetic relationships among major rodent superfamilies traditionally have been difficult to establish because of the apparent high level of convergence and parallelism seen among morphological characters and/or rapid differentiation of rodent groups in the Paleocene/Eocene. Nucleotide sequence data from the mitochondrial 12S rRNA gene were used to clarify phylogenetic relationships among the major groups of rodents as defined by Brandt (1855) and Tullberg (1899). Based on the approximately 800 bp analyzed for the 12S rRNA gene in 59 mammalian species, including 25 of the 32 extant rodent families, the major rodent groups that could be defined as monophyletic clades were the Hystricognathi, the Muroidea, and the Geomyoidea. In addition, support for superfamilial sister-group relationships was found for Aplodontoidea with Sciuroidea and Dipodoidea with Muroidea.

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Literature Cited

  • Adachi, J., Cao, Y., and Hasegawa, M. (1993). Tempo and mode of mitochondrial DNA evolution in vertebrates at the amino acid level: Rapid evolution in warm-blooded vertebrates.J. Mol. Evol. 36: 270–281.

    PubMed  Google Scholar 

  • Adkins, R. M., and Honeycutt, R. L. (1994). Evolution of the primate cytochromec oxidase II gene.J. Mol. Evol. 38: 215–231.

    PubMed  Google Scholar 

  • Alland, M. W., and Honeycutt, R. L. (1992). Nucleotide sequence variation in the mitochondrial 12S rRNA gene and the phylogeny of African mole-rats (Rodentia: Bathyergidae).Mol. Biol. Evol. 9: 27–40.

    PubMed  Google Scholar 

  • Allard, M, W., Miyamoto, M. M., and Honcycutt, R. L. (1991). Tests for rodent polyphyly.Nature 353: 610–611.

    PubMed  Google Scholar 

  • Arnason, U., and Johnsson, E. (1992). The complete mitochondrial DNA sequence of the harbor seal,Phoca vitulina.J. Mol. Evol. 34: 493–505.

    PubMed  Google Scholar 

  • Arnason, U., Gullberg, A., and Widegren, B. (1991). The complete nucleotide sequence of the mitochondrial DNA of the fin whale,Balaenoptera physalus.J. Mol. Evol. 33: 556–568.

    Google Scholar 

  • Beintema, J. J., Rodewald, K., Braunitzer, G., Czelusniak, J., and Goodman, M. (1991). Studies on the phylogenetic position of the Ctenodactylidae (Rodentia).Mol. Biol. Evol. 8: 151–154.

    PubMed  Google Scholar 

  • Bibb, M. J., VanEtten, R. A., Wright, C. T., Walberg, M. W., and Clayton, D. A. (1981). Sequence and gene organization of mouse mitochondrial DNA.Cell 26: 167–180.

    PubMed  Google Scholar 

  • Black, C. C. (1965). Fossil mammals from Montana. 2. Rodents from the early Oligocene Pipestone Springs local fauna.Ann. Carnegie Mus. 38: 1–48.

    Google Scholar 

  • Brandt, J. F. (1855). Beitrage zur nahern Kenntniss der Saugethiere Russlands.Mem. Acad. Imp. St. Peterbourg Ser. 69: 1–375.

    Google Scholar 

  • Bremer, K. (1988). The limits of amino-acid sequence data in angiosperm phylogenetic reconstruction.Evolution 42: 795–803.

    Google Scholar 

  • Bremer, K. (1994). Branch support and tree stability.Cladistics 10: 295–304.

    Google Scholar 

  • Brown, W. M. (1980). Polymorphism in mitochondrial DNA of humans as revealed by restriction endonuclease analysis.Proc. Natl. Acad. USA 77: 3605–3609.

    Google Scholar 

  • Brown, W. M., Prager, E. M., Wang, A., and Wilson, A. C. (1982). Mitochondrial DNA sequences of primates: tempo and mode of evolution.J. Mol. Evol. 18: 225–239.

    PubMed  Google Scholar 

  • Bugge, J. (1971). The cephalic arterial system in New and Old World hystricomorphs, and in bathyergoids, with special reference to the systematic classification of rodents.Acta Anat. 80: 516–536.

    PubMed  Google Scholar 

  • Bugge, J. (1974). The cephalic arterial system in the insectivores, primates, rodents, and lagomorphs, with special reference to the systematic classification.Acta Anat. 87: 1–160.

    PubMed  Google Scholar 

  • Bugge, J. (1985). Systematic value of the carotid arterial pattern in rodents. In:Evolutionary Relationships among Rodents: A Multidisciplinary Analysis, W. P. Luckett and J.-L. Hartenberger, eds., pp. 355–379, Plenum Press, New York.

    Google Scholar 

  • Cao, Y., Adachi, J., Yano, T., and Hasegawa, M. (1994). Phylogenetic place of guinea pigs: No support of the rodent-polyphyly hypothesis from maximum-likelihood analyses of multiple protein sequences.Mol. Biol. Evol. 11: 593–604.

    PubMed  Google Scholar 

  • Catzeffis, F. M., Aguilar, J.-P., and Jaeger, J.-J. (1992). Muroid rodents: Phylogeny and evolution.Tree 7: 122–126.

    Google Scholar 

  • Chaline, J., and Mein, P. (1979).Les Rongeurs et L'evolution. Doin, Paris.

    Google Scholar 

  • Czelusniak, J., Goodman, M., Koop, B. F., Tagle, D. A., Shoshani, J., Braunitzer, G., Kleinschmidt, T. K., DeJong, W. W. and Matsuda, G. (1990). Perspectives from amino acid and nucleotide sequences on cladistic relationships among higher taxa of Eutheria.Curr. Mammal. 2: 545–572.

    Google Scholar 

  • Dawson, M. R., and Krishtalka, L. (1984). Fossil history of the families of recent mammals. In:Orders and Families of Recent Mammals of the World, S. Anderson and J. K. Jones, Jr., eds., pp. 11–57, John Wiley & Sons, New York.

    Google Scholar 

  • Dawson, M. R., Li, C. K., and Qi, T. (1984). Ecocene ctenodactyloid rodents (Mammalia) of eastern and central Asia. In:Papers in Vertebrate Paleontology Honoring Robert Warren Wilson, R. M. Mengel, ed., pp. 138–150, Carnegie Mus. Nat. Hist. Spec. Publ. 9.

  • D'Erchia, A. M., Gissi, C., Pesole, G., Saccone, C., and Arnason, U. (1996). The guinea-pig is not a rodent.Nature 381: 597–600.

    PubMed  Google Scholar 

  • DeWalt, T. S., Sudman, P. D., Hafner, M. S., and Davis, S. K. (1993). Phylogenetic relationships of pocket gophers (Cratogeomys and Pappogeomys) based on mitochondrial DNA cytochromeb sequences.Mol. Phyl. Evol. 2: 193–204.

    Google Scholar 

  • Dixon, M. T., and Hillis, D. M. (1993). Ribosomal RNA secondary structure: Compensatory mutations and implications for phylogenetic analysis.Mol. Biol. Evol. 10: 256–267.

    PubMed  Google Scholar 

  • Donoghue, M. T., Olmstead, R. G., Smith, J. F., and Palmer, J. D. (1992). Phylogenetic relationships of Dipscales based onrbcL sequences.Ann. Mo. Bot. Gard. 79: 333–345.

    Google Scholar 

  • Ellerman, J. R. (1940).The Families and Genera oof Living Rodents, Vols. I-II, British Museums (Natural History). London.

    Google Scholar 

  • Fahlbusch, V. (1979). Eomyidae-Geschichte einer Säugetierfamilie.Palaeotol. Z. 53: 88–97.

    Google Scholar 

  • Fahlbusch, V. (1985). Origin and evolutionary relationships among geomyoids. In:Evolutionary Relationships Among Rodents: A Multidisciplinary Analysis, W. P. Luckett and J.-L. Hartenberger, eds., pp. 617–630, Plenum Press, New York.

    Google Scholar 

  • Felsenstein, J. (1978). Cases in which parsimony or compatibility methods will be positively misleading.Syst. Zool. 27: 401–410.

    Google Scholar 

  • Felsenstein, J. (1985). Confidence limits on phylogenies: An approach using the bootstrap.Evolution 39: 783–791.

    Google Scholar 

  • Felsenstein, J. (1993).PHYLIP: Phylogeny Inference Package. Version 3.5c, University of Washington, Seattle.

    Google Scholar 

  • Fischer, T. V., and Mossman, H. W. (1969). The fetal membranes ofPedetes capensis, and their taxonomic significance.Am. J. Anat. 124: 89–116.

    PubMed  Google Scholar 

  • Flynn, L. J., Jacobs, L. L., and Lindsay, E. H. (1985). Problems in muroid phylogeny: Relationship to other rodents and origin of major groups. In:Evolutionary Relationships Among Rodents: A Multidisciplinary Analysis, W. P. Luckett and J.-L. Hartenberger, eds., pp. 589–616, Plenum Press, New York

    Google Scholar 

  • Flynn, L. J., Jacobs, L. L., and Cheema, I. U. (1986). Baluchimyinae, a new ctenodactyloid rodent subfamily from the Miocene of Baluchistan.Am. Mus. Novit. 2841: 1–58.

    Google Scholar 

  • Frye, M. S., and Hedges, S. B. (1995). Monophyly of the order Rodentia inferred from mitochondrial DNA sequences of the genes for 12S rRNA, 16S rRNA, and tRNA-Valine.Mol. Biol. Evol. 12: 168–176.

    PubMed  Google Scholar 

  • Gatsey, J., Hayashi, C., DeSalle, R., and Vrba, E. (1994). Rate limits for mispairing and compensatory change: The mitochondrial ribosomal DNA of antelopes.Evolution 48: 188–196.

    Google Scholar 

  • Gaudin, T. J., Wible, J. R., Hopson, J. A., and Turnbull, W. D. (1996). Reexamination of the morphological evidence for the cohort Epitheria (Mammalia, Eutheria).J. Mammal. Evol. 3: 31–79.

    Google Scholar 

  • George, W. (1985). Reproductive and chromosomal characters of ctenodactylids as a key to their evolutionary relationships. In:Evolutionary Relationships Among Rodents: A Multidisciplinary Analysis, W. P. Luckett and J.-L. Hartenberger, eds., pp. 453–474, Plenum Press, New York.

    Google Scholar 

  • George, W. (1993). The strange rodents of Africa and South America. In:The Africa-South America Connection, W. George and R. Lavocat, eds., pp. 119–141. Clarendon Press, Oxford.

    Google Scholar 

  • Gilbert, D. G. (1994). SeqPup, a biological sequence editor and analysis program for multiple computer systems. Published electronically on the Internet at ≪ftp://iubio.bio.indiana.edu/molbio/seqpup/≫.

  • Gingerich, P. D., Smith, D. H., and Simons, E. L. (1990). Hind limbs of EoceneBasilosaurus: Evidence of feet in whales.Science 249: 154–157.

    Google Scholar 

  • Graur, D., and Higgins, D. G. (1994). Molecular evidence for the inclusion of cetaceanswithin the order Artiodactyla.Mol. Biol. Evol. 11: 357–364.

    PubMed  Google Scholar 

  • Graur, D., Hide, W. A., and Li, W.-H. (1991). Is the guinea-pig a rodent?Nature 351: 649–652.

    PubMed  Google Scholar 

  • Graur, D., Duret, L., and Gouy, M. (1996). Phylogenetic position of the order Lagomorpha (rabbits, hares and allies).Nature 379: 333–335.

    PubMed  Google Scholar 

  • Gutell, R. R., Weiser, B., Woese, C. R.,and Noller, H. F. (1985). Comparative anatomy of 16-S-like ribosomal RNA.Prog. Nucleic Acid Res. Mol. 32: 155–216.

    Google Scholar 

  • Hartenberger, J.-L. (1971). Contribution à l'étude des genersGliravus etMicroparamys (Rodentia) de l'Eocéne d'Europe.Palaeovertebrata 4: 97–135.

    Google Scholar 

  • Hartenberger, J.-L. (1980). Données et hypothèses sur la radiation initiale des Rongeurs.Palaeovert. Mém. Jub. R. Lavocat, pp. 285–301.

  • Hartenberger, J.-L. (1985). The order Rodentia: Major questions on their evolutionary origin, relationships, and suprafamilial systematics. In:Evolutionary Relationships Among Rodents: A Multidisciplinary Analysis, W. P. Luckett and J.-L. Hartenberger, eds., pp. 1–33, Plenum Press, New York.

    Google Scholar 

  • Hendy, M. D., and Penny, D. (1989). A framework for the quantitative study of evolutionary trees.Syst. Zool. 38: 297–309.

    Google Scholar 

  • Higgins, D. G., Bleasby, A. J., and Fuchs, R. (1992). Clustal V: Improved software for multiple sequence alignment.CABIOS 8: 189–191.

    PubMed  Google Scholar 

  • Hillis, D. M., and Bull, J. J. (1993). An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis.Syst. Biol. 42: 182–192.

    Google Scholar 

  • Holm, S. (1979). A simple sequentially rejective multiple test procedure.Scand. J. Stat. 6: 65–70.

    Google Scholar 

  • Honeycutt, R. L., and Adkins, R. M. (1993). Higher level systematics of eutherian mammals: An assessment of molecular characters and phylogenetic hypotheses.Annu. Rev. Ecol. Syst. 24: 297–305.

    Google Scholar 

  • Honeycutt, R. L., Nedbal, M. A., Adkins, R. M., and Janecek, L. L. (1995). Mammalian mitochondrial DNA evolution: A comparison of the cytochromeb and cytochromec oxidase II genes.J. Mol. Evol. 40: 260–272.

    PubMed  Google Scholar 

  • Huelsenbeck, J. P. (1995). Performance of phylogenetic methods in simulation.Syst. Biol. 44: 17–48.

    Google Scholar 

  • Irwin, D. M., Kocher, T. D., and Wilson, A. C. (1991). Evolution of the cytochromeb gene of mammals.J. Mol. Evol. 32: 128–144.

    PubMed  Google Scholar 

  • Jacger, J. J. (1988). Rodent phylogeny: New data and old problems. In:The Phylogeny and Classification of the Tetrapods, Vol. 2, Mammals, M. J. Benton, ed., pp. 177–199, Clarendon Press, New York.

    Google Scholar 

  • Janke, A., Feldmaier-Fuchs, S., Thomas, W. K., Von Haeseler A., and Pääbo, S. (1994). The marsupial mitochondrial genome and the evolution of placental mammals.Genetics 137: 243–256.

    PubMed  Google Scholar 

  • Jukes, T. H., and Cantor, C. R. (1969). Evolution of protein molecules. In:Mammalian Protein Metabolism, H. N. Munro, ed., pp. 21–132, Academic Press, New York.

    Google Scholar 

  • Kallersjo, M., Farris, J. S., Kluge, A. G., and Bult, C. (1992). Skewness and permutation.Cladistics 8: 275–287.

    Google Scholar 

  • Keohavong, P., and Thilly, W. G. (1989). Fidelity of DNA polymerase in DNA amplification.Proc. Natl. Acad. Sci. 86: 9253–9257.

    PubMed  Google Scholar 

  • Kimura, M. (1980). A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences.J.Mol. Evol. 16: 111–120.

    PubMed  Google Scholar 

  • Klingener, D. (1964). The comparative myology of four dipodoid rodents (generazapus, Napaeozapus, Sicista, andJaculus).Misc. Publ. Mus. Zool. Univ. Mich. 124: 1–100.

    Google Scholar 

  • Korth, W. W. (1994).The Tertiary Record of Rodents in North America, Plenum Press, New York.

    Google Scholar 

  • Kraus, F., Jarecki, L., Miyamoto, M. M., Tanhauser, S. M., and Laipis, P. J. (1992). Mispairing and compensational changes during the evolution of mitochondrial ribosomal RNA.Mol. Biol. Evol. 9: 770–774.

    PubMed  Google Scholar 

  • Kumar, S., Tamura, K., and Nei, M. (1993).MEGA: Molecular Evolutionary Genetics Analysis, Version 1.01, Pennsylvania State University, University Park.

    Google Scholar 

  • Landry, S. O. (1957). The interrelationships of the New and Old World hystricomorph rodents.Univ. Calif. Publ. Zool. 56: 1–118.

    Google Scholar 

  • Lavocat, R. (1951).Révision de la Faune des Mammiféres Oligocénes d'Auvergne et du Valay, Editions “Science et Avenir,” Paris.

    Google Scholar 

  • Lavocat, R. (1973). Les Rongeurs du Miocène d'Afrique orientale. I. Miocène inférieur.Mém. Trav. EPHE Inst. Montpellier 1: 1–284.

    Google Scholar 

  • Lavocat, R. (1988). Un rogeur Bathyergidé nouveau remarquable du Miocène de Fort Ternan (Kenya).C.R. Acad. Sci. Paris Ser. II 306: 1301–1304.

    Google Scholar 

  • Lavocat, R., and Parent, J.-P. (1985). Phylogenetic analysis of middle ear features in fossils and living rodents. In:Evolutionary Relationships Among Rodents: A Multidisciplinary Analysis, W. P. Luckett and J.-L. Hartenberger, eds., pp. 333–354, Plenum Press, New York.

    Google Scholar 

  • Li, C. K., and Ting, S.-Y. (1985). Possible phylogenetic relationship of Asiatic eurymylids and rodents, with comments on mimotonids. In:Evolutionary Relationships Among Rodents: A Multidisciplinary Analysis, W. P. Luckett and J.-L. Hartenberger, eds., pp.35–58, Plenum Press, New York.

    Google Scholar 

  • Li, C. K., Zheng, J.-J., and Ting, S.-Y. (1989). The skull ofCocomys lingchaensis, and early Eocene ctenodactyloid rodent of Asia. In:Papers on Fossil Rodents, in Honor of Albert Elmer Wood, C. C. Black and M. R. Dawson, eds, pp. 179–192, Nat. Hist. Mus. Los Angeles Co., Sci. Ser.,30.

  • Li, W.-H., Guoy, M., Sharp, P. M., O'Huigin, C., and Yang, Y. W. (1990). Molecular phylogeny of Rodentia, Lagomorpha, Primates, Artiodactyla, and Carnivora and molecular clocks.Proc. Natl. Acad. Sci. USA 87: 6703–6707.

    PubMed  Google Scholar 

  • Li, W.-H., Hide, W. A., Zharkikh, A., Ma, D.-P., and Graur, D. (1992). The molecular taxonomy and evolution of the guinea pig.J. Hered. 83: 174–181.

    PubMed  Google Scholar 

  • Lindsay, E. H. (1977).Simimys and origin of the Cricetidae (Rodentia: Muroidea).Geobios 10: 597–623.

    Google Scholar 

  • Lockhart, P. J., Steel, M. A., Hendy, M. D., and Penny, D. (1994). Recovering evolutionary trees under a more realistic model of sequence evolution.Mol. Biol. Evol. 11: 605–612.

    Google Scholar 

  • Luckett, W. P. (1980). Monophyletic or diphyletic origin of Anthropoidea and Hystricognathi: Evidence of the fetal membranes: in:Evolutionary Biology of the New World Monkeys and Continental Drift, R. L. Ciochon and A. B. Chiarelli, eds., pp. 347–368, Plenum Press, New York.

    Google Scholar 

  • Luckett, W. P. (1985). Superordinal and intraordinal affinities of rodents: Developmental evidence from the dentition and placentation. In:Evolutionary Relationships Among Rodents: A Multidisciplinary Analysis, W. P. Luckett and J.-L. Hartenberger, eds., pp. 227–276, Plenum Press, New York.

    Google Scholar 

  • Luckett, W. P., and Hartenberger, J.-L. (1985). Evolutionary relationships among rodents: Comments and conclusions. In:Evolutionary Relationships Among Rodents: A Multidisciplinary Analysis, W. P. Luckett and J.-L. Hartenberger, eds., pp. 685–712, Plenum Press, New York.

    Google Scholar 

  • Luckett, W. P., and Hartenberger, J.-L. (1993). Monophyly or polyphyly of the order Rodentia: Possible conflict between morphological and molecular interpretations.J. Mammal. Evol. 1: 127–147.

    Google Scholar 

  • Lundberg, J. G. (1972). Wagner networks and ancestors.Syst. Zool. 21, 398–413.

    Google Scholar 

  • Ma, D.-P., Zharkikh, A., Graur, D., VandeBerg, J. L., and Li, W.-H. (1993). Structure and evolution of opossum, guinea pig, and porcupine cytochromeb genes.J. Mol. Evol. 36: 327–334.

    PubMed  Google Scholar 

  • Maddison, W. P., and Maddison, D. R. (1992).MacClade: Analysis of Phylogeny and Character Evolution, Version 3.0, Sinauer Associates, Sunderland, MA.

    Google Scholar 

  • Maddison, W. P., Donoghue, M. J., and Maddison, D. R. (1984). Outgroup analysis and parsimony.Syst. Zool. 33: 83–103.

    Google Scholar 

  • Maier, W., and Schrenk, F. (1987). The hystricomorphy of the Bathyergidae, as determined from ontogenetic evidence.Z. Saugetierk. 52: 156–165.

    Google Scholar 

  • Martin, T. (1992). Schmelzstruktur in den Inzisiven alt- und neuweltlicher hystricognather Nagetiere.Palaeovertebrate Mèm. Extra. 1–168.

  • Martin, T. (1993). Early rodent incisor enamel evolution: phylogenetic implications.J. Mammal. Evol. 1: 227–254.

    Google Scholar 

  • Matthew, W. D. (1910). On the osteology and relationships ofParamys, and the affinities of the Ischyromyidae.Bull. Am. Mus. Nat. Hist. 28: 43–72.

    Google Scholar 

  • McKenna, M. C. (1975). Toward a phylogenetic classification of the Mammalia. In:Phylogeny of the Primates, W. P. Luckett and F. S. Szalay, eds., pp. 21–46, Plenum Press, New York.

    Google Scholar 

  • McLaughlin, C. A. (1984). Protrogomorph, sciuromorph, castorimorph, myomorph (geomyoid, anomaluroid, pedetoid and ctenodactyloid) rodents. In:Orders and Families of Recent Mammals of the World, A. Anderson, and J. K. Jones, Jr. eds., pp. 267–288, Wiley, New York.

    Google Scholar 

  • Meng, J. (1990). The auditory region ofReithroparamys delicatissimus (Mammalia, Rodentia) and its systematic implications.Am. Mus. Novit. 2972: 1–35.

    Google Scholar 

  • Milinkovitch, M. C., Orti, G., and Meyer, A. (1993). Revised phylogeny of whales suggested by mitochondrial ribosomal DNA sequences.Nature 361: 346–348.

    PubMed  Google Scholar 

  • Miller, G. S., and Gidley, J. W. (1918). Synopsis of the supergeneric groups of rodents.J. Wash. Acad. Sci. 8: 431–448.

    Google Scholar 

  • Mindell, D. P., and Honeycutt, R. L. (1990). Ribosomal RNA in vertebrates: Evolution and phylogenetic applications.Annu Rev. Ecol. Syst. 21: 541–566.

    Google Scholar 

  • Miyamoto, M. M., and Goodman, M. (1986). Biomolecular systematics of eutherian mammals: Phylogenetic patterns and classification.Syst. Zool. 35: 230–240.

    Google Scholar 

  • Naylor, G., and Kraus, F. (1995). The relationship betweens andm and the retention index.Syst. Biol. 44: 559–562.

    Google Scholar 

  • Nedbal, M. A., Allard, M. W., and Honeycutt, R. L. (1994). Molecular systematics of hystricognath rodents: Evidence from the mitochondrial 12S rRNA gene.Mol. Phylo. Evol. 3: 206–220.

    Google Scholar 

  • Nixon, K. C., and Carpenter, J. M. (1993). On outgroups.Cladistics 9: 413–426.

    Google Scholar 

  • Noller, H. F. (1984). Structure of ribosomal RNA.Annu. Rev. Biochem. 53: 119–116.

    PubMed  Google Scholar 

  • Novacek, M. (1985). Cranial evidence for rodent affinities. In:Evolutionary Relationships Among Rodents: A Multidisciplinary Analysis, W. P. Luckett and J.-L. Hartenberger, eds., pp. 59–81, Plenum Press, New York.

    Google Scholar 

  • Novacek, M. (1990). Morphology, paleontology, and the higher clades of mammals. In:Current Mammalogy, Vol. 2, H. H. Genoways, ed., pp. 507–543, Plenum Press, New York.

    Google Scholar 

  • Novacek, M. (1992). Mammalian phylogeny.: Shaking the tree.Nature 356: 121–125.

    PubMed  Google Scholar 

  • Novacek, M. J., Wyss, A. R., and McKenna, M. C. (1988). The major groups of eutherian mammals. In:The Phylogeny and Classification of the Tetrapods, Vol. 2. Mammals, M. J. Benton, ed., pp. 31–71, Clarendon Press, New York.

    Google Scholar 

  • Otiang'a-Owiti, G. E., Oduor-Okelo, D., and Gombe, S. G. (1992). Foetal membranes and placenta of the springhare (Pedetes capensis larvalis Hollister).Afr. J. Ecol. 30: 74–86.

    Google Scholar 

  • Patterson, B., and Wood, A. E. (1982). Rodents from the Deseadan Oligocene of Bolivia and the relationships of the Caviomorpha.Bull. Mus. Comp. Zool. 149: 371–543.

    Google Scholar 

  • Perna, N. T., and Kocher, T. D. (1995). Unequal base frequencies and the estimation of substitution rates.Mol. Biol. Evol. 12: 359–361.

    Google Scholar 

  • Phillippe, H., and Douzery, E. (1994). The pitfalls of molecular phylogeny based on four species, as illustrated by the Cetacea/Artiodactyla relationships.J. Mammal. Evol. 2: 133–152.

    Google Scholar 

  • Porter, C. A., Goodman, M., and Stanhope, M. J. (1996). Evidence on mammalian phylogeny from sequences of exon 28 of the von Willebrand factor gene.Mol. Phylogenet. Evol. 5: 89–101.

    PubMed  Google Scholar 

  • Rice, W. R. (1989). Analyzing tables of statistical tests.Evolution 43: 223–225.

    Google Scholar 

  • Sahni, A. (1985). Enamel structure of early mammals and its role in evaluating relationships among rodents. In:Evolutionary Relationships Among Rodents: A Multidisciplinary Analysis, W. P. Luckett and J.-L. Hartenberger, eds., pp. 133–150, Plenum Press, New York.

    Google Scholar 

  • Saiki, R. K., Gelfand, D. H., Stoeffel, S., Scharf, S. J., Higuchi, R., Horn, G. T., Mullis, K. B., and Erlich, H. A. (1988). Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase.Science 239: 487–491.

    PubMed  Google Scholar 

  • Saitou, N., and Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees.Mol. Biol. Evol. 4: 406–425.

    PubMed  Google Scholar 

  • Sankoff, N. (1975). Minimal mutation of trees of sequences.SIAM J. Appl. Math. 28: 35–42.

    Google Scholar 

  • Sarich, V. M. (1985). Rodent macromolecular systematics. In:Evolutionary Relationships Among Rodents: A Multidisciplinary Analysis, W. P. Luckett and J.-L. Hartenberger, eds., pp. 423–452, Plenum Press, New York.

    Google Scholar 

  • Sarich, V. M., and Cronin, J. E. (1980). South American mammal molecular systematics, evolutionary clocks, and continental drift. In:Evolutionary Biology of the New World Monkeys and Continental Drift, R. L. Ciochon and A. B. Chiarelli, eds., pp. 399–421, Plenum Press, New York.

    Google Scholar 

  • Schlosser, M. (1884). Die nager des europäischen Tertiärs nebst betrachtungen über die organisation und die geschichtliche entwicklung der nager überhaupt.Palaeontographica 31: 1–184.

    Google Scholar 

  • Shoshani, J., Goodman, M., Czelusnaik, J., and Braunitzer, G. (1985). A phytogeny of Rodentia and other eutherian orders: parsimony analysis utilizing amino acid sequences of alpha and beta hemoglobin chains. In:SIAM J. Appl. Math. 28: 35–42.

  • Simpson, G. G. (1945). The principles of classfication and a classification of mammals.Bull. Am. Mus. Nat. Hist. 85: 1–350.

    Google Scholar 

  • Springer, M. S., Hollar, L. J., and Burk, A. (1995). Contemporary substitutions and the evolution of the mitochondrial 12S rRNA gene in mammals.Mol. Biol. Evol. 12: 1138–1150.

    PubMed  Google Scholar 

  • Stehlin, H. G., and Schaub, S. (1951). Die Trigonodontie der simplicidentatenNager.Schweiz. Palaeontol. Abh. 67: 1–385.

    Google Scholar 

  • Stirton, R. A. (1935). A review of Tertiary beavers.Univ. Calif. Publ. Geol. Sci. 23: 391–458.

    Google Scholar 

  • Sullivan, J., Holsinger, K. E., and Simon, C. (1995). Among-site rate variation and phylogenetic analysis of 12S rRNA in sigmodontine rodents.Mol. Biol. Evol. 12: 988–1001.

    PubMed  Google Scholar 

  • Swofford, D. L. (1993).PAUP: Phylogenetic Analysis Using Parsimony, Version 3. 1, Illinois Natural History Survey, Champaign.

    Google Scholar 

  • Swofford, D. L., and Olsen, G. J. (1990). Phylogeny reconstruction. In:Molecular Systematics, D. M. Hillis and C. Moritz, eds., pp. 411–501, Sinauer, Sunderland, MA.

    Google Scholar 

  • Swofford, D. L., Olsen, G. J., Waddell, P. J. and Hillis, D. M. (1996). Phylogenetic inference. In:Molecular Systematics, 2nd ed., D. M. Hillis C. Moritz, and B. K. Mable, eds., pp. 407–514, Sinauer, Sunderland, MA.

    Google Scholar 

  • Tajima, F. (1993). Simple methods for testing the molecular evolutionary clock hypothesis.Genetics 135: 599–607.

    PubMed  Google Scholar 

  • Tajima, F., and Nei, M. (1984). Estimation of evolutionary distance between nucleotide sequencesMol. Biol. Evol. 1: 269–285.

    PubMed  Google Scholar 

  • Tamura, K., and Nei, M. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.Mol. Biol. Evol. 10: 512–526.

    PubMed  Google Scholar 

  • Tanaka, M., and Ozawa, T. (1994). Strand asymmetry in human mitochondrial DNA mutations.Genomics 22: 327–335.

    PubMed  Google Scholar 

  • Tindall, K. R., and Kunkel, T. A. (1988). Fidelity of DNA synthesis by theThermus aquaticus DNA polymerase.Biochemistry 27: 6008–6013.

    PubMed  Google Scholar 

  • Tullberg, T. (1899). Ueber das system der Nagetiere: Eine phylogenetische Studie.Nova Acta Reg. Soc. Sci. Upsala Ser. 3 18: 1–514.

    Google Scholar 

  • Vianey-Liaud, M. (1985). Possible evolutionary relationships among Eocene and Lower Oligocene rodents of Asia, Europe and North America. In:Evolutionary Relationships Among Rodents: A Multidisciplinary Analysis, W. P. Luckett and J.-L. Hartenberger, eds., pp. 277–309, Plenum Press, New York.

    Google Scholar 

  • Wahlert, J. H. (1972).The Cranial Foramina of Protrogomorphous and Sciuromorphous Rodents: An Anatomical and Phylogenetic Study. Ph.D. thesis. Harvard University, Cambridge, MA.

    Google Scholar 

  • Wahlert, J. H. (1977). Cranial foramina and relationships of theEutypomys (Rodentia, Eutypomyidae).Am. Mus. Novit. 2626: 1–8.

    Google Scholar 

  • Wahlert, J. H. (1978). Cranial foramina and relationships of the Eomyoidea (Rodentia, Geomorpha). Skull and upper teeth ofKansasimys.Am,. Mus. Novit. 2645: 1–16.

    Google Scholar 

  • Wahlert, J. H. (1983). Relationships of the Florentiamyidae (Rodentia, Geomyoidea) based on cranial and dental morphology.Am. Mus. Novit. 2769: 1–23.

    Google Scholar 

  • Wahlert, J. H. (1985). Cranial foramina of rodents. In:Evolutionary Relationships Among Rodents: A Multidisciplinary Analysis, W. P. Luckett and J.-L. Hartenberger, eds., pp. 311–332, Plenum Press, New York.

    Google Scholar 

  • Wahlert, J. H. (1993). The fossil record. In:Biology of the Heteromyidae, H. H. Genoways and J. H. Brown, eds., pp. 1–37, Am. Soc. Mammal. Spec. Publ. 10.

  • Wahlert, J. H., Sawitzke, S. L., and Holden, M. E. (1993). Cranial anatomy and relationships of dormice (Rodentia, Myoxidae).Am. Mus. Novit. 3061 1–32.

    Google Scholar 

  • Wang, B. (1994): The Ctenodactyloidea of Asia. In:Rodent and Lagomorph Families of Asian origins and Diversification, Y. Tomida, C. Li, and T. Setoguchi, eds., pp. 35–47, National Science Museum Monographs No. 8, Tokyo.

  • Wheeler, W. C. (1990) Nucleic acid sequence phylogeny and random outgroups.Cladistics 6: 363–367.

    Google Scholar 

  • Wheeler, W. C. (1992). Extinction, sampling and molecular phylogenetics. In:Extinction and Phylogeny, M. Novacek and Q. Wheeler, eds., pp. 205–215, Columbia University Press, New York.

    Google Scholar 

  • Wheeler, W. C., and Honeycutt, R. L. (1988). Paired sequences difference, in ribosomal RNAs: Evolutionary and phylogenetic implications.Mol. Biol. Evol. 5: 90–96.

    PubMed  Google Scholar 

  • Wilson, R. W. (1949). Early Tertiary rodents of North America.Carnegie Inst. Washington Publ. 584: 67–164.

    Google Scholar 

  • Winge, H. (1924).Pattedyr-slaegter: Vol. 2, Hagerups, H. Forlag, Copenhagen.

    Google Scholar 

  • Wood, A. E. (1937). The mammalian fauna of the White River Oligocene. II. Rodentia.Trans. Am. Philos. Soc. 28: 155–169.

    Google Scholar 

  • Wood, A. E. (1955). A revised classification of the rodents.J. Mammal. 36: 165–187.

    Google Scholar 

  • Wood, A. E. (1957). What, if anything, is a rabbit?Evolution 11: 417–425.

    Google Scholar 

  • Wood, A. E. (1959). Eocene radiation and phylogeny of the rodents.Evolution 13: 354–361.

    Google Scholar 

  • Wood, A. E. (1965). Grades and clades among rodents.Evolution 19: 115–130.

    Google Scholar 

  • Wood, A. E. (1980). The Oligocene rodents of North America.Trans. Am. Philos. Soc. 70: 1–68.

    Google Scholar 

  • Wood, A. E. (1985). The relationships, origin, and dispersal of the hystricognathous rodents. In:Evolutionary Relationships Among Rodents: A Multidisciplinary Analysis, W. P. Luckett and J.-L. Hartenberger, eds., pp. 475–513, Plenum Press, New York.

    Google Scholar 

  • Woods, C. A. (1972). Comparative myology of jaw, hyoid, and pectoral appendicular regions of New and Old World hystricomorph, rodents.Bull. Am. Mus. Nat. Hist. 147 117–198.

    Google Scholar 

  • Woods, C. A., and Hermanson, J. W. (1985). Myology of hystricognath rodents: an, analysis of form, function, and phylogeny. In:Evolutionary Relationships Among Rodents: A Multidisciplinary Analysis, W. P. Luckett and J.-L. Hartenberger, eds., pp. 515–548, Plenum Press, New York.

    Google Scholar 

  • Wyss, A. R., Flynn, J. J., Norell, M. A., Swisher, C. C., III, Charrier, R., Novacek, M. J., and McKenna, M. C. (1993). South America's earliest rodent and recognition of a new interval of mammalian evolution.Nature 365: 434–437.

    Google Scholar 

  • Yang, Z. (1993). Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites.Mol. Biol. Evol 10: 1396–1401.

    PubMed  Google Scholar 

  • Yang, Z. (1994). Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods.J. Mol. Evol. 39: 306–314.

    PubMed  Google Scholar 

  • Zharkikh, A., and Li, W.-H. (1992). Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. I. Four taxa with a molecular clock.Mol. Biol. Evol. 9: 1119–1147.

    PubMed  Google Scholar 

  • Zuker, M. (1989). On finding all suboptimal foldings of an RNA molecule.Science 244: 48–52.

    PubMed  Google Scholar 

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Nedbal, M.A., Honeycutt, R.L. & Schilitter, D.A. Higher-level systematics of rodents (Mammalia, Rodentia): Evidence from the mitochondrial 12S rRNA gene. J Mammal Evol 3, 201–237 (1996). https://doi.org/10.1007/BF01458181

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