Russian Journal of Genetics

, Volume 43, Issue 7, pp 757–768 | Cite as

Phylogeny of the order rodentia inferred from structural analysis of short retroposon B1

  • N. A. Veniaminova
  • N. S. Vassetzky
  • L. A. Lavrenchenko
  • S. V. Popov
  • D. A. Kramerov
General Genetics


A large-scale study of short retroposon (SINE) B1 has been conducted in the genome of rodents from most of the known families of this mammalian order. The B1 nucleotide sequences of rodents from different families exhibited a number of characteristic features including substitutions, deletions, and tandem duplications. Comparing the distribution of these features among the rodent families, the currently discussed phylogenetic relationships were tested. The results of analysis indicated (1) an early divergence of Sciuridae and related families (Aplodontidae and Gliridae) from the other rodents; (2) a possible subsequent divergence of beavers (Castoridae); (3) a monophyletic origin of the group Hystricognathi, which includes several families, such as porcupines (Hystricidae) and guinea pigs (Caviidae); (4) a possible monophyletic origin of the group formed by the remaining families, including six families of mouselike rodents (Myodonta). Various approaches to the use of short retroposons for phylogenetic studies are discussed.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Deininger, P.L. and Batzer, M.A., Mammalian Retroelements, Genome Res., 2002, vol. 12, no. 10, pp. 1455–1465.PubMedCrossRefGoogle Scholar
  2. 2.
    Kramerov, D. and Vassetzky, N., Short Retroposons in Eukaryotic Genomes, Int. Rev. Cytol., 2005, vol. 247, pp. 165–221.PubMedGoogle Scholar
  3. 3.
    Okada, N., SINEs, Curr. Opin. Genet. Dev., 1991, vol. 1, no. 4, pp. 498–504.PubMedCrossRefGoogle Scholar
  4. 4.
    Kapitonov, V.V. and Jurka, J., A Novel Class of SINE Elements Derived from 5S rRNA, Mol. Biol. Evol., 2003, vol. 20, no. 5, pp. 694–702.PubMedCrossRefGoogle Scholar
  5. 5.
    Nishihara, H., Smit, A.F., and Okada, N., Functional Noncoding Sequences Derived from SINEs in the Mammalian Genome, Genome Res., 2006, vol. 16, no. 7, pp. 864–874.PubMedCrossRefGoogle Scholar
  6. 6.
    Kramerov, D.A., Grigoryan, A.A., Ryskov, A.P., et al., Long Double-Stranded Sequences (dsRNA-B) of Nuclear Pre-mRNA Consist of a Few Highly Abundant Classes of Sequences: Evidence from DNA Cloning Experiments, Nucleic Acids Res, 1979, vol. 6, no. 2, pp. 697–713.PubMedCrossRefGoogle Scholar
  7. 7.
    Krayev, A.S., Kramerov, D.A., Skryabin, K.G., et al., The Nucleotide Sequence of the Ubiquitous Repetitive DNA Sequence B1 Complementary to the Most Abundant Class of Mouse Fold-Back RNA, Nucleic Acids Res., 1980, vol. 8, no. 6, pp. 1201–1215.PubMedCrossRefGoogle Scholar
  8. 8.
    Deininger, P.L., Jolly, D.J., Rubin, C.M., et al., Base Sequence Studies of 300 Nucleotide Renatured Repeated Human DNA Clones, J. Mol. Biol., 1981, vol. 151, no. 1, pp. 17–33.PubMedCrossRefGoogle Scholar
  9. 9.
    Haynes, S.R., Toomey, T.P., Leinwand, L., et al., The Chinese Hamster Alu-Equivalent Sequence: A Conserved Highly Repetitious, Interspersed Deoxyribonucleic Acid Sequence in Mammals Has a Structure Suggestive of a Transposable Element, Mol. Cell. Biol., 1981, vol. 1, no. 7, pp. 573–583.PubMedGoogle Scholar
  10. 10.
    Ullu, E. and Tschudi, C., Alu Sequences Are Processed 7SL RNA Genes, Nature, 1984, vol. 312, no. 5990, pp. 171–172.PubMedCrossRefGoogle Scholar
  11. 11.
    Daniels, G.R. and Deininger, P.L., A Second Major Class of Alu Family Repeated DNA Sequences in a Primate Genome, Nucleic Acids Res., 1983, vol. 11, no. 21, pp. 7595–7610.PubMedCrossRefGoogle Scholar
  12. 12.
    Zietkiewicz, E., Richer, C., Sinnett, D., et al., Monophyletic Origin of Alu Elements in Primates, J. Mol. Evol., 1998, vol. 47, no. 2, pp. 172–182.PubMedCrossRefGoogle Scholar
  13. 13.
    Roos, C., Schmitz, J., and Zischler, H., Primate Jumping Genes Elucidate Strepsirrhine Phylogeny, Proc. Natl. Acad. Sci. USA, 2004, vol. 101, no. 29, pp. 10 650–10 654.CrossRefGoogle Scholar
  14. 14.
    Labuda, D., Sinnett, D., Richer, C., et al., Evolution of Mouse B1 Repeats: 7SL RNA Folding Pattern Conserved, J. Mol. Evol., 1991, vol. 32, no. 5, pp. 405–414.PubMedCrossRefGoogle Scholar
  15. 15.
    Quentin, Y., A Master Sequence Related to a Free Left Alu Monomer (FLAM) at the Origin of the B1 Family in Rodent Genomes, Nucleic Acids Res., 1994, vol. 22, no. 12, pp. 2222–2227.PubMedCrossRefGoogle Scholar
  16. 16.
    Hartenberger, J.-L., The Order Rodentia: Major Questions on Their Evolutionary Origin, Relationships and Suprafamilial Systematics, in Evolutionary Relationship among Rodents, Luckett, W. and Hartenberger, J.-L., Eds., New York: Plenum, 1985, pp. 1–33.Google Scholar
  17. 17.
    Pavlinov, I., Sistematika sovremennykh mlekopitayushchikh (Systematics of Contemporary Mammals), Moscow: Mosk. Gos. Univ., 2003.Google Scholar
  18. 18.
    Krayev, A.S., Markusheva, T.V., Kramerov, D.A., et al., Ubiquitous Transposon-Like Repeats B1 and B2 of the Mouse Genome: B2 Sequencing, Nucleic Acids Res., 1982, vol. 10, no. 23, pp. 7461–7475.PubMedCrossRefGoogle Scholar
  19. 19.
    Den Dunnen, J.T. and Schoenmakers, J.G., Consensus Sequences of the Rattus norvegicus B1 and B2 Repeats, Nucleic Acids Res., 1987, vol. 15, no. 6, p. 2772.CrossRefGoogle Scholar
  20. 20.
    Bains, W. and Temple-Smith, K., Similarity and Divergence among Rodent Repetitive DNA Sequences, J. Mol. Evol., 1989, vol. 28, no. 3, pp. 191–199.PubMedCrossRefGoogle Scholar
  21. 21.
    Waterston, R.H., Lindblad-Toh, K., Birney, E., et al., Initial Sequencing and Comparative Analysis of the Mouse Genome, Nature, 2002, vol. 420, no. 6915, pp. 520–562.PubMedCrossRefGoogle Scholar
  22. 22.
    Gibbs, R.A., Weinstock, G.M., Metzker, M.L., et al., Genome Sequence of the Brown Norway Rat Yields Insights into Mammalian Evolution, Nature, 2004, vol. 428, no. 6982, pp. 493–521.PubMedCrossRefGoogle Scholar
  23. 23.
    Kim, J., Martignetti, J.A., Shen, M.R., et al., Rodent BC1 RNA Gene as a Master Gene for ID Element Amplification, Proc. Natl. Acad. Sci. USA, 1994, vol. 91, no. 9, pp. 3607–3611.PubMedCrossRefGoogle Scholar
  24. 24.
    Serdobova, I.M. and Kramerov, D.A., Short Retroposons of the B2 Superfamily: Evolution and Application for the Study of Rodent Phylogeny, J. Mol. Evol., 1998, vol. 46, pp. 202–214.PubMedCrossRefGoogle Scholar
  25. 25.
    Kramerov, D.A. and Vassetzky, N.S., Structure and Origin of a Novel Dimeric Retroposon B1-dID, J. Mol. Evol., 2001, vol. 52, no. 2, pp. 137–143.PubMedGoogle Scholar
  26. 26.
    Vassetzky, N.S., Ten, O.A., and Kramerov, D.A., B1 and Related SINEs in Mammalian Genomes, Gene, 2003, vol. 319, pp. 149–160.PubMedCrossRefGoogle Scholar
  27. 27.
    Nishihara, H., Terai, Y., and Okada, N., Characterization of Novel Alu-and tRNA-Related SINEs from the Tree Shrew and Evolutionary Implications of Their Origins, Mol. Biol. Evol., 2002, vol. 19, no. 11, pp. 1964–1972.PubMedGoogle Scholar
  28. 28.
    Serdobova, I.M. and Kramerov, D.A., Usage of Short Retroposons as Phylogenetic Markers, Dokl. Akad. Nauk SSSR, 1994, vol. 335, no. 5, pp. 664–667.Google Scholar
  29. 29.
    Kramerov, D., Vassetzky, N., and Serdobova, I., The Evolutionary Position of Dormice (Gliridae) in Rodentia Determined by a Novel Short Retroposon, Mol. Biol. Evol., 1999, pp. 715–716.Google Scholar
  30. 30.
    Felsenstein, J., Phylogenies from Gene Frequencies: A Statistical Problem, Systematic Zool., 1985, vol. 34, no. 3, pp. 300–311.CrossRefGoogle Scholar
  31. 31.
    Felsenstein, J., PHYLIP—Phylogeny Inference Package (Version 3.2), Cladistics, 1989, vol. 5, pp. 164–166.Google Scholar
  32. 32.
    Huchon, D. and Douzery, E.J., From the Old World to the New World: A Molecular Chronicle of the Phylogeny and Biogeography of Hystricognath Rodents, Mol. Phylogenet. Evol., 2001, vol. 20, no. 2, pp. 238–251.PubMedCrossRefGoogle Scholar
  33. 33.
    Huchon, D., Madsen, O., Sibbald, M.J., et al., Rodent Phylogeny and a Timescale for the Evolution of Glires: Evidence from an Extensive Taxon Sampling Using Three Nuclear Genes, Mol. Biol. Evol., 2002, vol. 19, no. 7, pp. 1053–1065.PubMedGoogle Scholar
  34. 34.
    Adkins, R.M., Gelke, E.L., Rowe, D., et al., Molecular Phylogeny and Divergence Time Estimates for Major Rodent Groups: Evidence from Multiple Genes, Mol. Biol. Evol., 2001, vol. 18, no. 5, pp. 777–791.PubMedGoogle Scholar
  35. 35.
    Adkins, R.M., Walton, A.H., and Honeycutt, R.L., Higher-Level Systematics of Rodents and Divergence Time Estimates Based on Two Congruent Nuclear Genes, Mol. Phylogenet. Evol., 2003, vol. 26, no. 3, pp. 409–420.PubMedCrossRefGoogle Scholar
  36. 36.
    Steppan, S., Adkins, R., and Anderson, J., Phylogeny and Divergence-Date Estimates of Rapid Radiations in Muroid Rodents Based on Multiple Nuclear Genes, Syst. Biol., 2004, vol. 53, no. 4, pp. 533–553.PubMedCrossRefGoogle Scholar
  37. 37.
    Opazo, J.C., A Molecular Timescale for Caviomorph Rodents (Mammalia, Hystricognathi), Mol. Phylogenet. Evol., 2005, vol. 37, no. 3, pp. 932–937.PubMedCrossRefGoogle Scholar
  38. 38.
    Quentin, Y., Emergence of Master Sequences in Families of Retroposons Derived from 7sl RNA, Genetics, 1994, vol. 93, nos. 1–3, pp. 203–215.Google Scholar
  39. 39.
    Carrol, R., Vertebrate Paleontology and Evolution, New York: Freeman, 1988.Google Scholar
  40. 40.
    Reyes, A., Pesole, G., and Saccone, C., Long-Branch Attraction Phenomenon and the Impact of Among-Site Variation on Rodent Phylogeny, Gene, 2000, vol. 259, nos. 1–2, pp. 177–187.PubMedCrossRefGoogle Scholar
  41. 41.
    D’erchia, A.M., Gissi, C., Pesole, G., et al., The Guinea-Pig Is Not a Rodent, Nature, 1996, vol. 381, no. 6583, pp. 597–600.PubMedCrossRefGoogle Scholar
  42. 42.
    Murphy, W.J., Eizirik, E., O’Brien, S.J., et al., Resolution of the Early Placental Mammal Radiation Using Bayesian Phylogenetics, Science, 2001, vol. 294, no. 5550, pp. 2348–2351.PubMedCrossRefGoogle Scholar
  43. 43.
    Shimamura, M., Yasue, H., Ohshima, K., et al., Molecular Evidence from Retroposons that Whales Form a Clade within Even-Toed Ungulates, Nature, 1997, vol. 388, no. 6643, pp. 666–670.PubMedCrossRefGoogle Scholar
  44. 44.
    Stoneking, M., Fontius, J.J., Clifford, S.L., et al., Alu Insertion Polymorphisms and Human Evolution: Evidence for a Larger Population Size in Africa, Genome Res., 1997, vol. 7, no. 11, pp. 1061–1071.PubMedGoogle Scholar
  45. 45.
    Watkins, W.S., Rogers, A.R., Ostler, C.T., et al., Genetic Variation Among World Populations: Inferences from 100 Alu Insertion Polymorphisms, Genome Res., 2003, vol. 13, no. 7, pp. 1607–1618.PubMedCrossRefGoogle Scholar
  46. 46.
    Nikaido, M., Nishihara, H., Hukumoto, Y., et al., Ancient SINEs from African Endemic Mammals, Mol. Biol. Evol., 2003, vol. 20, no. 4, pp. 522–527.PubMedCrossRefGoogle Scholar
  47. 47.
    Rothenburg, S., Eiben, M., Koch-Nolte, E., et al., Independent Integration of Rodent Identifier (ID) Elements into Orthologous Sites of Some RT6 Alleles of Rattus norvegicus and Rattus rattus, J. Mol. Evol., 2002, vol. 55, no. 3, pp. 251–259.PubMedCrossRefGoogle Scholar
  48. 48.
    Van De Lagemaat, L.N., Gagnier, L., Medstrand, P., et al., Genomic Deletions and Precise Removal of Transposable Elements Mediated by Short Identical DNA Segments in Primates, Genome Res., 2005, vol. 15, no. 9, pp. 1243–1249.PubMedCrossRefGoogle Scholar
  49. 49.
    Terai, Y., Takahashi, K., Nishida, M., et al., Using SINEs to Probe Ancient Explosive Speciation: “Hidden” Radiation of African Cichlids?, Mol. Biol. Evol., 2003, vol. 20, no. 6, pp. 924–930.PubMedCrossRefGoogle Scholar

Copyright information

© Pleiades Publishing, Inc. 2007

Authors and Affiliations

  • N. A. Veniaminova
    • 1
  • N. S. Vassetzky
    • 1
  • L. A. Lavrenchenko
    • 2
  • S. V. Popov
    • 3
  • D. A. Kramerov
    • 1
  1. 1.Engelhardt Institute of Molecular BiologyRussian Academy of SciencesMoscowRussia
  2. 2.Severtsov Institute of Ecology and EvolutionRussian Academy of SciencesMoscowRussia
  3. 3.Moscow ZooMoscowRussia

Personalised recommendations