Ancient SINEs from African endemic mammals

Molecular Biology and Evolution

Volumn 20, Issue 4, 2003, Pages 522-527

  Nikaido, Masato ^a   Nishihara, Hidenori ^a   Hukumoto, Yukio ^b   Okada, Norihiro ^a  

^a TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^b Hiroshima City Asa Zoological Park   (Japan)

Author keywords

Afrotheria; Genome; Monophyletic; Phylogenetic; SINE; Taxon

Indexed keywords

AFRICA; ARTICLE; DUGONG; ELEPHANT; GENOME; INSECTIVORE; MAMMALIAN GENETICS; MONOPHYLY; NONHUMAN; PHYLOGENY; SHORT INTERSPERSED REPEAT; TAXON;

AFRICA; ANIMALS; BASE SEQUENCE; EVOLUTION, MOLECULAR; HYRAXES; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; SEQUENCE HOMOLOGY, NUCLEIC ACID; SHORT INTERSPERSED NUCLEOTIDE ELEMENTS;

CHRYSOCHLORIDAE; ELEPHANT; ELEPHANTIDAE; MAMMALIA; PROCAVIIDAE; SORICIDAE; TENRECIDAE; TUBULIDENTATA;

EID: 0037387452     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msg052     Document Type: Article

References (51)

1. Amrine, H. M., and M. S. Springer. 1999. Maximum-likelihood analysis of the Tethythere hypothesis based on a multigene data set and a comparison of different models of sequence evolution. J. Mammal. Evol. 6:161-176.
2. Batzer, M. A., and P. L. Deininger. 2002. Alu repeats and human genomic diversity. Nat. Rev. Genet. 3:370-379.
3. Blin, N., and D. W. Stafford. 1976. A general method for isolation of high molecular weight DNA from eukaryotes. Nucleic Acids Res. 3:2303-2308.
4. 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.
5. de Jong W. W., J. A. M. Leunissen, and G. J. Wistow. 1993. Eye lens crystallins and the phylogeny of placental orders: evidence for a macroscelid-paenungulate clade? Pp. 5-12 in F. S. Szalay, M. J. Novacek, and M. C. McKenna, eds. Mammal phylogeny: placentals. Springer Verlag, New York.
6. de Jong, W. W., A. Zweers, and M. Goodman. 1981. Relationship of aardvark to elephants, hyraxes and sea cows from alpha-crystallin sequences. Nature 292:538-540.
7. Endoh, H., and N. Okada. 1986. Total DNA transcription in vitro: a procedure to detect highly repetitive and transcribable sequences with tRNA-like structures. Proc. Natl. Acad. Sci. USA 83:251-255.
8. Fischer, M. S. 1989. Hyracoids, the sister-group of perissodactyls. Pp. 37-56 in D. R. Prothero, and R. M. Schoch, eds. The evolution of perissodactyls. Oxford University Press, New York.
9. Fischer, M. S., and P. Tassy. 1993. The interrelation between Proboscidea, Sirenia, Hyracoidea, and Mesaxonia. The morphological evidence. Pp. 217-234 in F. S. Szalay, M. J. Novacek, and M. C. McKenna, eds. Mammal phylogeny: placentals. Springer Verlag, New York.
10. Hamada, M., Y. Kido, M. Himberg, J. D. Reist, C. Ying, M. Hasegawa, and N. Okada. 1997. A newly isolated family of short interspersed repetitive elements (SINEs) in coregonid fishes (whitefish) with sequences that are almost identical to those of the SmaI family of repeats: possible evidence for the horizontal transfer of SINEs. Genetics 146: 355-67.
11. Hattori, M., A. Fujiyama, T. D. Taylor et al. (60 co-authors). 2000. The DNA sequence of human chromosome 21. Nature 405:311-320.
12. Hedges, S. B. 2001. Afrotheria: plate tectonics meets genomics. Proc. Natl. Acad. Sci. USA 98:1-2.
13. International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
14. Kajikawa, M., and N. Okada. 2002. LINEs mobilizes SINEs in the eel through a shared 3′ sequence. Cell 111:433-444.
15. Kazazian, H. H. Jr. 2000. L1 retrotransposons shape the mammalian genome. Science 289:1152-1153.
16. Kido, Y., M. Aono, T. Yamaki, K. Matsumoto, S. Murata, M. Saneyoshi, and N. Okada. 1991. Shaping and reshaping of salmonid genomes by amplification of tRNA-derived retroposons during evolution. Proc. Natl. Acad. Sci. USA 88: 2326-2330.
17. Kordis, D., and F. Gubensek. 1998. Unusual horizontal transfer of a long interspersed nuclear element between distant vertebrate classes. Proc. Natl. Acad. Sci. USA 95:10704-10709.
18. Lavergne, A., E. Douzery, T. Stichler, F. M. Catzeflis, and M. S. Springer. 1996. Interordinal mammalian relationships: evidence for paenungulate monophyly is provided by complete mitochondrial 12S rRNA sequences. Mol. Phylogenet. Evol. 6:245-258.
19. Madsen, O., P. M. Deen, G. Pesole, C. Saccone, and W. W. de Jong. 1997. Molecular evolution of mammalian aquaporin-2: further evidence that elephant shrew and aardvark join the paenungulate clade. Mol. Biol. Evol. 14:363-371.
20. Madsen, O., M. Scally, C. J. Douady, D. J. Kao, R. W. DeBry, R. Adkins, H. M. Amrine, M. J. Stanhope, W. W. de Jong, and M. S. Springer. 2001. Parallel adaptive radiations in two major clades of placental mammals. Nature. 409:610-614.
21. Murphy, W. J., E. Eizirik, W. E. Johnson, Y. P. Zhang, O. A. Ryder, and S. J. O'Brien. 2001a. Molecular phylogenetics and the origins of placental mammals. Nature 409:614-618.
22. Murphy, W. J., E. Eizirik, S. J. O'Brien et al. (11 co-authors). 2001b. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294:2348-2351.
23. Nikaido, M., F. Matsuno, H. Abe, M. Shimamura, H. Hamilton, H. Matsubayasi, and N. Okada. 2001. Evolution of CHR-2 SINEs in cetartiodactyl genomes: possible evidence for the monophyletic origin of toothed whales. Mammal. Genome 12:909-915.
24. Novacek, M. J. 1992. Mammalian phylogeny: shaking the tree. Nature 356:121-125.
25. Okada, N. 1991a. SINEs. Curr. Opin. Genet. Dev. 1:498-504.
26. -. 1991b. SINEs: short interspersed repeated elements of the eukaryotic genome. Trends Ecol. Evol. 6:358-361.
27. Okada, N., and K. Ohshima. 1995. Evolution of tRNA-derived SINEs. Pp. 61-79 in R. J. Maraia, ed. The impact of short interspersed repetitive elements (SINEs) on the host genome. R. G. Landes Company, Austin, Tex.
28. Okada, N., A. M. Shedlock, and M. Nikaido. 2002. TE mapping in molecular systematics. in P. Capy, ed. Mobile genetic elements and their application in genomics. Humana Press, USA (in press).
29. Ozawa, T., S. Hayashi, and V. M. Mikhelson. 1997. Phylogenetic position of mammoth and Steller's sea cow within Tethytheria demonstrated by mitochondrial DNA sequences. J. Mol. Evol. 44:406-413.
30. Porter, C. A., M. Goodman, and M. J. Stanhope. 1996. Evidence on mammalian phylogeny from sequences of exon 28 of the von Willebrand factor gene. Mol. Phylogenet. Evol. 5:89-101.
31. Rogers, J. 1985. Origins of repeated DNA. Nature 317:765-766.
32. Scally, M., O. Madsen, C. J. Douady, W. W. de Jong, M. J. Stanhope, and M. S. Springer. 2001. Molecular evidence for the major clade of placental mammals. J. Mammal. Evol. 8:239-277.
33. Schmid, C. W. 1996. Alu: structure, origin, evolution, significance and function of one-tenth of human DNA. Prog. Nucleic. Acid. Res. Mol. Biol. 53:283-319.
34. Schmid, C., and R. Maraia. 1992. Transcriptional regulation and transpositional selection of active SINE sequences. Curr. Opin. Genet. Develop. 2:874-882.
35. Serdobova, I. M., and D. A. Kramerov. 1998. Short retroposons of the B2 superfamily: evolution and application for the study of rodent phylogeny. J. Mol. Evol. 46:202-214.
36. Shedlock, A. M., and N. Okada. 2000. SINE insertions: powerful tools for molecular systematics. BioEssays 22:148-160.
37. Glu-derived families of SINEs. Mol. Biol. Evol. 16:1046-1060.
38. Shimamura, M., H. Yasue, K. Ohshima, H. Abe, H. Kato, T. Kishiro, M. Goto, I. Munechika, and N. Okada. 1997. Molecular evidence from retroposons that whales form a clade within even-toed ungulates. Nature 388:666-670.
39. Shoshani, J. 1993. Hyracoidea-Tethytheria affinity based on myological data. Pp. 235-256 in F. S. Szalay, M. J. Novacek, and M. C. MacKenna, eds. Mammal phylogeny: placentals. Springer Verlag, New York.
40. -. 1998. Understanding proboscidean evolution: a formidable task. TREE 13:480-487.
41. Shoshani, J., and M. C. McKenna. 1998. Higher taxonomic relationships among extant mammals based on morphology, with selected comparisons of results from molecular data. Mol. Phylogenet. Evol. 9:572-584.
42. Springer, M. S., G. C. Cleven, O. Madsen, W. W. de Jong, V. G. Waddell, H. M. Amrine, and M. J. Stanhope. 1997. Endemic African mammals shake the phylogenetic tree. Nature. 388:61-64.
43. Stanhope, M. J., O. Madsen, V. G. Waddell, G. C. Cleven, W. W. de Jong, and M. S. Springer. 1998a. Highly congruent molecular support for a diverse superordinal clade of endemic African mammals. Mol. Phylogenet. Evol. 9:501-508.
44. Stanhope, M. J., V. G. Waddell, O. Madsen, W. W. de Jong, S. B. Hedges, G. C. Cleven, D. Kao, and M. S. Springer. 1998b. Molecular evidence for multiple origins of Insectivora and for a new order of endemic African insectivore mammals. Proc. Natl. Acad. Sci. USA 95:9967-9972.
45. Takasaki, N., S. Murata, M. Saitoh, T. Kobayashi, L. Park, and N. Okada. 1994. Species-specific amplification of tRNA-derived short interspersed repetitive elements (SINEs) by retroposition: a process of parasitization of entire genomes during the evolution of salmonids. Proc. Natl. Acad. Sci. USA 91:10153-10157.
46. Ullu, E., and C. Tschudi. 1984. Alu sequences are processed 7SL RNA genes. Nature 312:171-172.
47. van Dijk, M. A. M., O. Madsen, F. Catzeflis, M. J. Stanhope, W. W. de Jong, and M. Pagel. 2001. Protein sequence signatures support the African clade of mammals. Proc. Natl. Acad. Sci. USA 98:188-193.
48. Waddell, P., N. Okada, and M. Hasegawa. 1999. Towards resolving the interordinal relationships of placental mammals. Syst. Biol. 48:1-5.
49. Weiner, A. M. 1980. An abundant cytoplasmic 7SRNA is complementary to the dominant interspersed middle repetitive DNA sequence family in the human genome. Cell 22:209-218.
50. Weiner, A. M., P. L. Deininger, and A. Efstratiadis. 1986. Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu. Rev. Biochem. 55:631-661.
51. Whidden, H. P. 2002. Extrinsic snout musculature in Afrotheria and Lipotyphla. J. Mammal. Evol. 9:165-187.