Using SINEs to probe ancient explosive speciation: "Hidden" radiation of African cichlids?

Molecular Biology and Evolution

Volumn 20, Issue 6, 2003, Pages 924-930

  Terai, Yohey ^a   Takahashi, Kazuhiko ^a   Nishida, Mutsumi ^b   Sato, Tetsu ^c   Okada, Norihiro ^a  

^a Tokyo Institute of Technology ^*  (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c Nature Conservation Division   (Japan)

Author keywords

AFC family; African Great Lakes; Cichlid; Exclusive speciation; Incomplete lineage sorting; Retroposon; SINE

Indexed keywords

ADAPTATION; ARTICLE; CICHLID; GENE INSERTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POINT MUTATION; RADIATION; SEQUENCE ANALYSIS; SPECIES DIFFERENTIATION;

BASE SEQUENCE; CICHLIDS; DNA PRIMERS; PHYLOGENY; POINT MUTATION; SHORT INTERSPERSED NUCLEOTIDE ELEMENTS; SPECIES SPECIFICITY;

CICHLIDAE; INSERTION SEQUENCES; PISCES; STEATOCRANUS; TILAPIA;

EID: 0037910330     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msg104     Document Type: Article

References (37)

1. Avise, J. C. 2000. Phylogeography: the history and formation of species. Harvard University Press, Cambridge.
2. Cohen, A. S., M. G. Soreghan, and C. A. Scholz. 1993. Estimating the age of formation of lakes: an example from Lake Tanganyika, east African rift system. Geology 21:511-514.
3. Cook, J. M., and M. Tristem. 1997. 'SINEs of the times' - transposable elements as clade markers for their hosts. Trends Ecol. Evol. 12:295-297.
4. Coulter, G. W. 1991. The benthic fish community. Pp. 151-199 in G. W. Coulter, ed. Lake Tanganyika and its life. Oxford University Press, New York.
5. Farias, I. P., G. Orti, and A. Meyer. 2000. Total evidence: molecules, morphology, and the phylogenetics of cichlid fishes. J. Exp. Zool. 288:76-92.
6. Farias, I. P., G. Orti, I. Sampaio, H. Schneider, and A. Meyer. 2001. The cytochrome b gene as a phylogenetic marker: the limits of resolution for analyzing relationships among cichlid fishes. J. Mol. Evol. 53:89-103.
7. Fryer, G., and T. D. Iles. 1972. The cichlid fishes of the Great Lakes of Africa: their biology and evolution. Oliver & Boyd, Edinburgh.
8. Greenwood, P. H. 1984. African cichlids and evolutionary theories. Pp. 141-154 in A. A. Echelle and I. Kornfield, eds. Evolution of fish species flocks. University of Maine at Orono Press, Orono.
9. Greenwood, P. H. 1991. Speciation. Pp. 86-102 in M. H. A. Keenleyside, ed. Cichlid fishes: behaviour, ecology and evolution. Chapman & Hall, London.
10. Hamada, M., N. Takasaki, J. D. Reist, A. L. DeCicco, A. Goto, and N. Okada. 1998. Detection of the ongoing sorting of ancestrally polymorphic SINEs toward fixation or loss in populations of two species of char during speciation. Genetics 150:301-311.
11. Mayer, W., H. Tichy, and J. Klein. 1998. Phylogeny of African cichlid fishes as revealed by molecular markers. Heredity 80:702-714.
12. Meyer, A. 1993. Phylogenetic relationships and evolutionary processes in east African cichlid fishes. Trends Ecol. Evol. 8: 279-284.
13. Miyamoto, M. M. 1999. Perfect SINEs of evolutionary history? Curr. Biol. 9:R816-R819.
14. Moran, P., and I. Kornfield. 1993. Retention of an ancestral polymorphism in the Mbuna species flock (Teleostei: Cichlidae) of Lake Malawi. Mol. Biol. Evol. 10:1015-1029.
15. Moran, P., and I. Kornfield. 1995. Were population bottlenecks associated with the radiation of the Mbuna species flock (Teleostei: Cichlidae) of Lake Malawi? Mol. Biol. Evol. 12: 1085-1093.
16. Nagl, S., H. Tichy, W. E. Mayer, N. Takahata, and J. Klein. 1998. Persistence of neutral polymorphisms in Lake Victoria cichlid fish. Proc. Natl. Acad. Sci. USA 95:14238-14243.
17. Nagl, S., H. Tichy, W. E. Mayer, I. E. Samonte, B. J. McAndrew, and J. Klein. 2001. Classification and phylogenetic relationships of African Tilapiine fishes inferred from mitochondrial DNA sequences. Mol. Phylogenet. Evol. 20:361-374.
18. Nei, M. 1987. Molecular evolutionary genetics. Columbia University Press, New York.
19. Nishida, M. 1997. Phylogenetic relationships and evolution of Tanganyikan cichlids: a molecular perspective. Pp. 1-24 in H. Kawanabe, M. Hori, and M. Nagoshi, eds. Fish communities in Lake Tanganyika. Kyoto University Press, Kyoto, Japan.
20. Okada, N. 1991. SINEs: short interspersed repeated elements of the eukaryotic genome. Trends Ecol. Evol. 6:358-361.
21. Pamilo, P., and M. Nei. 1988. Relationships between gene trees and species trees. Mol. Biol. Evol. 5:568-583.
22. Parker, A., and I. Kornfield. 1997. Evolution of the mitochondrial DNA control region in the Mbuna (Cichlidae) species flock of Lake Malawi, east Africa. J. Mol. Evol. 45:70-83.
23. Poll, M. 1986. Classification des Cichlidae du lac Tanganyika: tribus, genres et espèces. Mém. Acad. Roy. Belg. Cl. Sci. 45:5-163.
24. Salzburger, W., A. Meyer, S. Baric, E. Verheyen, and C. Sturmbauer. 2002. Phylogeny of the Lake Tanganyika cichlid species flock and its relationship to the central and east African haplochromine cichlid fish faunas. Syst. Biol. 51:113-135.
25. Shedlock, A. M., M. C. Milinkovitch, and N. Okada. 2000. SINE evolution, missing data, and the origin of whales. Syst. Biol. 49:808-817.
26. Shedlock, A. M., and N. Okada. 2000. SINE insertions: powerful tools for molecular systematics. BioEssays 22:148-160.
27. Streelman, J. T., and S. A. Karl. 1997. Reconstructing labroid evolution with single-copy nuclear DNA. Proc. R. Soc. Lond. Ser. B 264:1011-1020.
28. Streelman, J. T., R. Zardoya, A. Meyer, and S. A. Karl. 1998. Multilocus phylogeny of cichlid fishes (Pisces: Perciformes): evolutionary comparison of microsatellite and single-copy nuclear loci. Mol. Biol. Evol. 15:798-808.
29. Sültmann, H., W. E. Mayer, F. Figueroa, H. Tichy, and J. Klein. 1995. Phylogenetic analysis of cichlid fishes using nuclear DNA markers. Mol. Biol. Evol. 12:1033-1047.
30. Takahashi, K., Y. Terai, M. Nishida, and N. Okada. 1998. A novel family of short interspersed repetitive elements (SINEs) from cichlids: the patterns of insertion of SINEs at orthologous loci support the proposed monophyly of four major groups of cichlid fishes in Lake Tanganyika. Mol. Biol. Evol. 15:391-407.
31. Takahashi, K., M. Nishida, M. Yuma, and N. Okada. 2001a. Retroposition of the AFC family of SINEs (short interspersed repetitive elements) before and during the adaptive radiation of cichlid fishes in Lake Malawi and related inferences about phylogeny. J. Mol. Evol. 53:496-507.
32. Takahashi, K., Y. Terai, M. Nishida, and N. Okada. 2001b. Phylogenetic relationships and ancient incomplete lineage sorting among cichlid fishes in Lake Tanganyika as revealed by analysis of the insertion of retroposons. Mol. Biol. Evol. 18:2057-2066.
33. Takahata, N. 1989. Gene genealogy in three related populations: consistency probability between gene and population trees. Genetics 122:957-966.
34. Terai, Y., K. Takahashi, and N. Okada. 1998. SINE cousins: The 3′-end tails of the two oldest and distantly related families of SINEs are descended from the 3′ ends of LINEs with the same genealogical origin. Mol. Biol. Evol. 15:1460-1471.
35. Van Oppen, M. J. H., C. Rico, G. F. Turner, and G. M. Hewitt. 2000. Extensive homoplasy, nonstepwise mutations, and shared ancestral polymorphism at a complex microsatellite locus in Lake Malawi cichlids. Mol. Biol. Evol. 17:489-498.
36. 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.
37. Zardoya, R., D. M. Vollmer, C. Craddock, J. T. Streelman, S. Karl, and A. Meyer. 1996. Evolutionary conservation of microsatellite flanking regions and their use in resolving the phylogeny of cichlid fishes (Pisces: Perciformes). Proc. R. Soc. Lond. Ser. B 263:1589-1598.