Free Access
Genet. Sel. Evol.
Volume 38, Number 6, November-December 2006
Page(s) 673 - 687
Published online 28 November 2006
References of  Genet. Sel. Evol. 38 (2006) 673-687
  1. Amores A., Force A., Yan Y.-L., Joly L., Amemiya C., Fritz A., Ho R.K., Langeland J., Prince V., Wang Y.-L., Westerfield M., Ekker M., Postlethwait J.H., Zebrafish hox clusters and vertebrate genome evolution, Science 282 (1998) 1711-1714 [CrossRef].
  2. Bowles J., Schepers G., Koopman P., Phylogeny of the SOX family of developmental transcription factors based on sequence and structural indicators, Dev. Biol. 227 (2000) 239-255 [CrossRef] [PubMed].
  3. Chiang E.F.-L., Pai C.-I., Wyatt M., Yan Y.-L., Postlethwait J., Chung B.-C., Two Sox9 genes on duplicated zebrafish chromosomes: expression of similar transcription activators in distinct sites, Dev. Biol. 231 (2001) 149-163 [CrossRef] [PubMed].
  4. Crémazy F., Soullier S., Berta P., Jay P., Further complexity of the human Sox gene family revealed by the combined use of highly degenerate primers and nested PCR, FEBS Lett. 438 (1998) 311-314 [CrossRef] [PubMed].
  5. Dayhoof M.O., Schiwartz R.M., Orcutt B.C., A model of evolutionary change in proteins, in: Dayhoof M.O. (Ed.), Atlas of protein sequence and structure, National Biomedical Research Foundation, Silver Spring, MD, 1978, pp. 345-352.
  6. De Martino S., Yan Y.-L., Jowett T., Postlethwait J.H., Varga Z.M., Ashworth A., Austin C.A., Expression of Sox11 gene duplicates in zebrafish suggests the reciprocal loss of ancestral gene expression patterns in development, Dev. Dynam. 217 (2000) 279-292.
  7. Denny P., Swift S., Brand N., Dabhade N., Barton P., Ashworth A., A conserved family of genes related to the testis determining gene, SRY, Nucleic Acids Res. 20 (1992) 2887 [PubMed].
  8. Devlin R.H., Nagahama Y., Sex determination and sex differentiation in fish: an overview of genetic, physiological and environmental influences, Aquaculture 208 (2002) 191-364 [CrossRef].
  9. Galay-Burgos M., Llewellyn L., Mylonas C.C., Canario A.V.M., Zanuy S., Sweeney G.E. Analysis of the Sox gene family in the European sea bass (Dicentrarchus labrax), Comp. Biochem. Phys. B 137 (2004) 279-284.
  10. Gubbay J., Collignon J., Koopman P., Capel B., Economou A., Münsterberg A., Vivian N., Goodfellow P., Lovell-Badge R., A gene mapping to the sex-determining region of the mouse Y chromosome is a member of a novel family of embryonically expressed genes, Nature 346 (1990) 245-250 [CrossRef] [PubMed].
  11. He S., Chen Y., Nakajima T., Sequences of cytochrome b gene for primitive cyprinid fishes in East Asia and their phylogenetic concerning, Chinese Sci. Bull. 46 (2001) 661-665.
  12. He S., Liu H., Chen Y., Kuwahara M., Nakajima T., Zhong Y., Molecular phylogenetic relationships of Eastern Asian Cyprinidae (Pisces: Cypriniformes) inferred from cytochrome b sequences, Sci. China Ser. C 47 (2004) 130-138 [CrossRef].
  13. Hoegg S., Brinkmann H., Taylor J.S., Meyer A., Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish, J. Mol. Evol. 59 (2004) 190-203 [CrossRef] [PubMed].
  14. Hughes A.L., Adaptive evolution of genes and genomes, Oxford University Press, New York, 1999.
  15. Kamachi Y., Cheah K.S.E., Kondoh H., Mechanism of regulatory target selection by the SOX high-mobility-group domain proteins as revealed by comparison of SOX1/2/3 and SOX9, Mol. Cell. Biol. 19 (1999) 107-120 [PubMed].
  16. Kamachi Y., Uchikawa M., Kondoh H., Pairing SOX off: with partners in the regulation of embryonic development, Trends Genet. 16 (2000) 182-187 [CrossRef] [PubMed].
  17. Koopman P., Schepers G., Brenner S., Venkatesh B., Origin and diversity of the Sox transcription factor gene family: genome-wide analysis in Fugu rubripes, Gene 328 (2004) 177-186 [CrossRef] [PubMed].
  18. Kumar S., Tamura K., Nei M., MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment, Brief. Bioinformatics 5 (2004) 150-163 [PubMed].
  19. Kumazawa Y., Yamaguchi M., Nishida M., Mitochondrial molecular clocks and the origin of euteleostean biodiversity: Familial radiation of perciforms may have predated the Cretaceous/Tertiary boundary, In: Kato M. (Ed.), The Biology of Biodiversity, Springer-Verlag, Hong Kong, 1999, pp. 35-52.
  20. Lecointre G., Philippe H., Vân Lê H.L., Le Guyader H., How many nucleotides are required to resolve a phylogenetic problem? The use of a new statistical method applicable to available sequences, Mol. Phylogenet. Evol. 3 (1994) 292-309 [PubMed].
  21. Li W.-H., Rate of gene silencing at duplicate loci: A theoretical study and interpretation of data from tetraploid fishes, Genetics 95 (1980) 237-258 [PubMed].
  22. Lynch M., Gene duplication and evolution, Science 297 (2002) 945-947 [CrossRef].
  23. Lynch M., Conery J.S., The evolutionary fate and consequences of duplicate genes, Science 290 (2000) 1151-1155 [CrossRef].
  24. Lynch M., Conery J.S., The evolutionary demography of duplicate genes, J. Struct. Funct. Genomics 3 (2003) 35-44 [CrossRef] [PubMed].
  25. Maere S., De Bodt S., Raes J., Casneuf T., Van Montagu M., Kuiper M., Van de Peer Y., Modeling gene and genome duplications in eukaryotes, Proc. Natl. Acad. Sci. USA 102 (2005) 5454-5459 [CrossRef] [PubMed].
  26. Mavropoulos A., Devos N., Biemar F., Zecchin E., Argenton F., Edlund H., Motte P., Martial J.A., Peers B., Sox4b is a key player of pancreatic alpha cell differentiation in zebrafish, Dev. Biol. 285 (2005) 211-223 [CrossRef] [PubMed].
  27. Nadeau J.H., Sankoff D., Comparable rates of gene loss and functional divergence after genome duplications early in vertebrate evolution, Genetics 147 (1997) 1259-1266 [PubMed].
  28. Nei M., Kumar S., Molecular evolution and phylogenetics, Oxford University Press, New York, 2000.
  29. Nei M., Rogozin I.B., Piontkivska H., Purifying selection and birth-and-death evolution in the ubiquitin gene family, Proc. Natl. Acad. Sci. USA 97 (2000) 10866-10871 [CrossRef] [PubMed].
  30. Otto S.P., Whitton J., Polyploid incidence and evolution, Ann. Rev. Genet. 34 (2000) 401-437.
  31. Postlethwait J., Amores A., Cresko W., Singer A., Yan Y.-L., Subfunction partitioning, the teleost radiation and the annotation of the human genome, Trends Genet. 20 (2004) 481-490 [CrossRef] [PubMed].
  32. Prince V.E., Pickett F.B., Splitting pairs: the diverging fates of duplicated genes, Nat. Rev. Genet. 3 (2002) 827-837 [CrossRef] [PubMed].
  33. Romer A.S., Vertebrate Paleontology, 3rd edn., The University of Chicago Press, Chicago & London, 1966, pp. 356-357.
  34. Rzhetesky A., Nei M., Theoretical foundation of the minimum-evolution method of phylogenetic inference, Mol. Biol. Evol. 10 (1993) 1073-1095 [PubMed].
  35. Schepers G.E., Teasdale R.D., Koopman P., Twenty pairs of Sox: extent, homology, and nomenclature of the mouse and human Sox transcription factor gene families, Dev. Cell 3 (2002) 167-170 [CrossRef] [PubMed].
  36. Sneath P.H.A., Socal R.R., Numerical taxonomy, Freeman, San Francisco, CA, 1973.
  37. Van de Peer Y., Taylor J.S., Braasch I., Meyer A., The ghost of selection past: Rates of evolution and functional divergence of anciently duplicated genes, J. Mol. Evol. 53 (2001) 436-446 [CrossRef] [PubMed].
  38. Vandepoele K., De Vos W., Taylor J.S., Meyer A., Van de Peer Y., Major events in the genome evolution of vertebrates: Paranome age and size differ considerably between ray-finned fishes and land vertebrates, Proc. Natl Acad. Sci. USA 101 (2004) 1638-1643 [CrossRef] [PubMed].
  39. Wegner M., From head to toes: the multiple facets of Sox proteins, Nucleic Acids Res. 27 (1999) 1409-1420 [CrossRef] [PubMed].
  40. Wilson M., Koopman P., Matching SOX: partner proteins and co-factors of the SOX family of transcriptional regulators, Curr. Opin. Genet. Dev. 12 (2002) 441-446 [CrossRef] [PubMed].
  41. Wittbrodt J., Meyer A., Schartl M., More genes in fish?, Bioessays 20 (1998) 511-515 [CrossRef].
  42. Wright E.M., Snopek B., Koopman P., Seven new members of the Sox gene family expressed during mouse development, Nucleic Acids Res. 21 (1993) 744 [PubMed].
  43. Yan Y.-L., Willoughby J., Liu D., Crump J.G., Wilson C., Miller C.T., Singer A., Kimmel C., Westerfield M., Postlethwait J.H., A pair of Sox: distinct and overlapping functions of zebrafish Sox9 co-orthologs in craniofacial and pectoral fin development, Development 132 (2005) 1069-1083 [CrossRef] [PubMed].
  44. Zhou R., Cheng H., Zhang Q., Guo Y., Cooper R.K., Tiersch T.R., SRY-related genes in the genome of the rice field eel (Monopterus albus), Genet. Sel. Evol. 34 (2002) 129-137 [EDP Sciences] [CrossRef] [PubMed].