NS  Vol.5 No.2 , February 2013
Natural selection in vertebrate evolution under genomic and biosphere biases based on amino acid content: Primitive vertebrate hagfish (Eptatretus burgeri)
Abstract: Cluster analyses using the amino acid content predicted from the coding regions (13 genes) of complete vertebrate mitochondrial genomes as traits grouped selected vertebrates into two clusters, terrestrial and aquatic vertebrates. Exceptions were the hagfish (Eptatretus burgeri), thought to be an early ancestor of vertebrates, and the black spotted frog (Rana nigromaculata), which is terrestrial as an adult and aquatic as a larva. These two species fall into the terrestrial and aquatic clusters, respectively. Using the nucleotide (G, C, T and A) content in the coding and non-coding regions, and in the complete genome as traits, similar results were obtained but with some additional exceptions. In addition, phylogenetic analyses of 16S rRNA sequences produced a consistent result. The results of this study indicated that vertebrate evolution is controlled by natural selection under both an internal bias as a result of nucleotide replacement genomic rules, and an external bias caused by environmental biospheric conditions.
Cite this paper: Sorimachi, K. , Okayasu, T. , Ohhira, S. , Masawa, N. and Fukasawa, I. (2013) Natural selection in vertebrate evolution under genomic and biosphere biases based on amino acid content: Primitive vertebrate hagfish (Eptatretus burgeri). Natural Science, 5, 221-227. doi: 10.4236/ns.2013.52033.

[1]   Cobbett, A., Wilkinson, M. and Wills, M. (2007) Fossils impact as hard as living taxa in parsimony analyses of morphology. Systems Biology, 17, 753-766. doi:10.1080/10635150701627296

[2]   Zuckerkandl, E. and Pauling, L.B. (1962) Molecular disease, evolution, and genetic heterogeneity. In: Kasha, M. and Pullman, B., Eds., Horizons in Biochemistry, Academic Press, New York, 189-225.

[3]   Sorimachi, K. (1999) Evolutionary changes reflected by the cellular amino acid composition. Amino Acids, 17, 207-226. doi:10.1007/BF01361883

[4]   Fleischman, R.D., Adams, M.D., White, O., Clayton, R.A., Kirkness, E.F., Kerlavage, A.R., Bult, C.J., Tomb, J.F., Dougherty, B.A., Merrick, J.M., et al. (1995) Wholegenome random sequencing and assembly of Haemophilus influenzae Rd. Science, 269, 496-512. doi:10.1126/science.7542800

[5]   Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921. doi:10.1038/35057062

[6]   Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G., Sutton, G.G., Smith, H.O., Yandell, M., Evans, C.A., et al. (2001) The sequence of the human genome. Science, 291, 1304-1351. doi:10.1126/science.1058040

[7]   Sorimachi, K. and Okayasu, T. (2003) Gene assembly consisting of small units with similar amino acid composition in the Saccharomyces cerevisiae genome. Mycoscience, 44, 415-417. doi:10.1007/s10267-003-0131-2

[8]   Sorimachi, K., Itoh, T., Kawarabayasi, Y., Okayasu, T., Akimoto, K. and Niwa, A. (2001) Conservation of the basic pattern of cellular amino acid composition of archaeobacteria during biological evolution and the putative amino acid composition of primitive life forms. Amino Acids, 21, 393-399. doi:10.1007/s007260170004

[9]   Sorimachi, K. and Okayasu, T. (2008) Codon evolution is governed by linear formulas. Amino Acids, 34, 661-668. doi:10.1007/s00726-007-0024-3

[10]   Rudner, R., Karkas, J.D. and Chargaff, E. (1968) Separation of B. subtilis DNA into complementary strands. 3. Direct analysis. Proceedings of the National Academy of Sciences, 60, 921-922. doi:10.1073/pnas.60.3.921

[11]   Mitchell, D. and Bridge, R. (2006) A test of Chargaff’s second rule. Biochemical and Biophysical Research Communications, 340, 90-94. doi:10.1016/j.bbrc.2005.11.160

[12]   Okayasu, T. and Sorimachi, K. (2009) Organisms can essentially be classified according to two codon patterns. Amino Acids, 36, 261-271. doi:10.1007/s00726-008-0059-0

[13]   Sorimachi, K. and Okayasu, T. (2008) Universal rules governing genome evolution expressed by linear formulas. The Open Genomics Journal, 1, 33-43.

[14]   Saitou, N. and Nei, M. (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4, 406-425.

[15]   Woese, C.R. and Fox, G.E. (1977) Phylogenetic structure of the prokaryotic domain: The primary kingdoms 2. Proceedings of the National Academy of Sciences of the United States of America, 74, 5088-5090. doi:10.1073/pnas.74.11.5088

[16]   Weisburg, W.G., Barns, S.M., Pelletier, D.A. and Lane, D.J. (1991) 16S ribosomal DNA amplification for phylogenetic study. Journal of Bacteriology, 173, 697-703.

[17]   Janvier, P. (2010) Micro RNAS revive old views about jawless vertebrate divergence and evolution. Proceedings of the National Academy of Sciences of the United States of America, 107, 19137-19138. doi:10.1073/pnas.1014583107

[18]   Sorimachi, K. and Okayasu, T. (2004) Classification of eubacteria based on their complete genome: Where does Mycoplasmataseae belong? Proceedings of the Royal Society B, 271, s127-s130. doi:10.1098/rsbl.2003.0141

[19]   Qi, Z.H. and Wei, R.Y. (2011) A combination dimensionality reduction approach to codon position patterns of eubacteria based on their complete genomes. Journal of Theoretical Biology, 272, 26-34. doi:10.1016/j.jtbi.2010.12.014

[20]   Sorimachi, K., Okayasu, T., Ohhira, S., Fukasawa, I. and Masawa, N. (2012) Evidence for the independent divergence of vertebrate and high C/G ratio invertebrate mitochondria from the same origin. The Natural Science, 4, 479-483. doi:10.4236/ns.2012.47064