A heuristic approach of maximum likelihood method for inferring phylogenetic tree and an application to the mammalian SOX-3 origin of the testis-determining gene SRY

FEBS Letters

Volumn 463, Issue 1-2, 1999, Pages 129-132

  Katoh, Kazutaka ^a   Miyata, Takashi ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

Evolution; Heuristic approach; Maximum likelihood method; Molecular phylogeny; SOX family; SRY

Indexed keywords

ARTICLE; CONTROLLED STUDY; GENE CLUSTER; GENETIC ANALYSIS; MAMMAL; MAXIMUM LIKELIHOOD METHOD; MOLECULAR EVOLUTION; PHYLOGENY; PRIORITY JOURNAL; TESTIS; X CHROMOSOME;

ALGORITHMS; ANIMALS; DATABASES, FACTUAL; DNA-BINDING PROTEINS; HIGH MOBILITY GROUP PROTEINS; HUMANS; LIKELIHOOD FUNCTIONS; NUCLEAR PROTEINS; PHYLOGENY; SEX-DETERMINING REGION Y PROTEIN; TRANSCRIPTION FACTORS;

EUTHERIA; MAMMALIA; METATHERIA; STAPHYLOCOCCUS PHAGE 3A;

EID: 0033452908     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0014-5793(99)01621-X     Document Type: Article

References (36)

1. Felsenstein J. J. Mol. Evol. 17:1981;368-376.
2. Kishino H., Miyata T., Hasegawa M. J. Mol. Evol. 30:1990;151-160.
3. Felsenstein, J. (1993) PHYLIP: phylogenetic inference package, Version 3.5c, Department of Genetics, University of Washington, Seattle, WA.
4. Olsen G.J., Matsuda H., Hagstrom R., Overbeek R. CABIOS. 10:1994;41-48.
5. Yang, Z. (1995) Phylogenetic analysis by maximum likelihood (PAML), Version 1.1, Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA.
6. Adachi, J. and Hasegawa, M. (1996) Computer science monographs, No. 28, MOLPHY version 2.3: Programs for molecular phylogenetics based on maximum likelihood, The Institute of Statistical Mathematics, Tokyo.
7. Strimmer K., von Haeseler A. Mol. Biol. Evol. 13:1996;964-969.
8. Suga, H., Hoshiyama, D., Kuraku, S., Katoh, K., Kubokawa, K. and Miyata, T. (1999) J. Mol. Evol. (in press).
9. Swofford, D.L., Olsen, G.J., Waddell, P.J. and Hillis, D.M. (1996) Phylogenetic inference, in: Molecular Systematics (Hillis, D.M., Moritz, C. and Mable, B.K., Eds.), 2nd edn., pp. 407-514, Sinauer Associates, Sunderland, MA.
10. Sinclair A.H., Berta P., Palmer M.S., Hawkins J.R., Griffiths B.L., Smith M.J., Foster J.W., Frischauf A.M., Lovell-Badge R., Goodfellow P.N. Nature. 346:1990;240-244.
11. Berta P., Hawkins J.R., Sinclair A.H., Taylor A., Griffiths B.L., Goodfellow P.N., Fellous M. Nature. 348:1990;448-450.
12. Jager R.J., Anvret M., Hall K., Scherer G. Nature. 348:1990;452-454.
13. Harley V.R., Jackson D.I., Hextall P.J., Hawkins J.R., Berkovitz G.D., Sockanathan S., Lovell-Badge R., Goodfellow P.N. Science. 255:1992;453-456.
14. Ferrari S., Harley V.R., Pontiggia A., Goodfellow P.N., Lovell-Badge R., Bianchi M.E. EMBO J. 11:1992;4497-4506.
15. Capel, B. and Lovell-Badge, R. (1993) The Sry gene and sex determination in mammals, in: Advances in Developmental Biology (Wassarmen, P., Ed.), Vol. 2, pp. 1-35, JAI Press.
16. Koopman P., Gubbay J., Vivian N., Goodfellow P., Lovell-Badge R. Nature. 351:1991;117-121.
17. Hacker A., Capel B., Goodfellow P., Lovell-Badge R. Development. 121:1995;1603-1614.
18. Foster J.W., Graves J.A. Proc. Natl. Acad. Sci. USA. 91:1994;1927-1931.
19. Stevanovic M., Lovell-Badge R., Collignon J., Goodfellow P.N. Hum. Mol. Genet. 2:1993;2013-2018.
20. Collignon J., Sockanathan S., Hacker A., Cohen-Tannoudji M., Norris D., Rastan S., Stevanovic M., Goodfellow P.N., Lovell-Badge R. Development. 122:1996;509-520.
21. Soullier S., Jay P., Poulat F., Vanacker J.M., Berta P., Laudet V. J. Mol. Evol. 48:1999;517-527.
22. Saitou N., Nei M. Mol. Biol. Evol. 4:1987;406-425.
23. Whitfield L.S., Lovell-Badge R., Goodfellow P.N. Nature. 364:1993;713-715.
24. Tucker P.K., Lundrigan B.L. Nature. 364:1993;715-717.
25. Pamilo P., O'Neill R.J. Mol. Biol. Evol. 14:1997;49-55.
26. Feng D.F., Doolittle R.F. J. Mol. Evol. 25:1987;351-360.
27. Needleman S.B., Wunsch C.D. J. Mol. Biol. 48:1970;443-453.
28. Thompson J.D., Higgins D.G., Gibson T.J. Nucleic Acids Res. 22:1994;4673-4680.
29. Felsenstein J. Evolution. 39:1985;783-791.
30. O'Neill R.J., Brennan F.E., Delbridge M.L., Crozier R.H., Graves J.A. Proc. Natl. Acad. Sci. USA. 95:1998;1653-1657.
31. Felsenstein, J. (1993) PHYLIP (Phylogeny Inference Package), version 3.5c, Department of Genetics, University of Washington, Seattle, WA.
32. Graves J.A. Bioessays. 17:1995;311-320.
33. Lahn B.T., Page D.C. Science. 278:1997;675-680.
34. Ohno, S. (1967) Sex Chromosomes and Sex-linked Genes, Springer-Verlag, New York.
35. Charlesworth B. Science. 251:1991;1030-1033.
36. Hodgkin J. Bioessays. 14:1992;253-261.