1. Foreword

   • Motoo Kimura
   • Takashi Gojobori
   • Tomoko Ohta

   EditorialNotes Pages: S1 - S1

2. Neutral and Nonneutral Mutations: The creative mix—evolution of complexity in gene interaction systems

   • Emile ZuckerkandI

   OriginalPaper Pages: S2 - S8

3. Role of random genetic drift in the evolution of interactive systems

   • Tomoko Ohta

   OriginalPaper Pages: S9 - S14

4. Positive darwinian selection on two homologous fertilization proteins: what is the selective pressure driving their divergence?

   • Victor D. Vacquier
   • Willie J. Swanson
   • Youn-Ho Lee

   OriginalPaper Pages: S15 - S22

5. The reason for as well as the consequence of the cambrian explosion in animal evolution

   • Susumu Ohno

   OriginalPaper Pages: S23 - S27

6. Evolutionary origin of cryptomonad microalgae: Two novel chloroplast/cytosol-specific GAPDH genes as potential markers of ancestral endosymbiont and host cell components

   • Marie-Françoise Liaud
   • Ulrike Brandt
   • Rüdiger Cerff

   OriginalPaper Pages: S28 - S37

7. Evolutionary motif and its biological and structural significance

   • Y. Tateno
   • K. Ikeo
   • T. Gojobori

   OriginalPaper Pages: S38 - S43

8. The major compositional transitions in the vertebrate genome

   • Giorgio Bernardi
   • Sandrine Hughes
   • Dominique Mouchiroud

   OriginalPaper Pages: S44 - S51

9. The 3′ ends of tRNA-derived SINEs originated from the 3’ ends of LINEs: A new example from the bovine genome

   • Norihiro Okada
   • Mitsuhiro Hamada

   OriginalPaper Pages: S52 - S56

10. Genome plasticity as a paradigm of eubacteria evolution

    • Hidemi Watanabe
    • Hirotada Mori
    • Takashi Gojobori

    OriginalPaper Pages: S57 - S64

11. Networks and viral evolution

    • Walter M. Fitch

    OriginalPaper Pages: S65 - S75

12. Molecular phylogeny of human T-cell leukemia virus type I and II of amerindians in Colombia and Chile

    • Tomoyuki Miura
    • Masahiro Yamashita
    • Masanori Hayami

    OriginalPaper Pages: S76 - S82

13. Constrained evolution with respect to gene overlap of hepatitis B virus

    • Masashi Mizokami
    • Etsuro Orito
    • Takashi Gojobori

    OriginalPaper Pages: S83 - S90

14. Molecular cloning of heterotrimeric G-protein α-subunits in chicken pineal gland

    • Toshiyuki Okano
    • Kazumitsu Yamazaki
    • Yoshitaka Fukada

    OriginalPaper Pages: S91 - S97

15. Phylogenetic reconstruction of the felidae using 16S rRNA and NADH-5 mitochondrial genes

    • Warren E. Johnson
    • Stephen J. O’Brien

    OriginalPaper Pages: S98 - S116

16. Novel phylogeny of whales supported by total molecular evidence

    • Masami Hasegawa
    • Jun Adachi
    • Michel C. Milinkovitch

    OriginalPaper Pages: S117 - S120

17. Molecular evidence from the nuclear genome for the time frame of human evolution

    • Simon Easteal
    • Genevierve Herbert

    OriginalPaper Pages: S121 - S132

18. A gene tree for β-globin sequences from melanesia

    • R. M. Harding
    • S. M. Fullerton
    • J. B. Clegg

    OriginalPaper Pages: S133 - S138

19. Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods

    • Jianzhi Zhang
    • Masatoshi Nei

    OriginalPaper Pages: S139 - S146

20. Genomic characterization of the region between HLA-B and TNF: Implications for the evolution of multicopy gene families

    • Silvana Gaudieri
    • Chanvit Leelayuwat
    • Roger L. Dawkins

    OriginalPaper Pages: S147 - S154

21. Adaptive amino acid replacements accompanied by domain fusion in reverse transcriptase

    • Tsuyoshi Shirai
    • Mitiko Gō

    OriginalPaper Pages: S155 - S162

22. Comparison of protein structures using 3D profile alignment

    • Mikita Suyama
    • Yo Matsuo
    • Ken Nishikawa

    OriginalPaper Pages: S163 - S173

23. Random structural models for double dynamic programming score evaluation

    • William R. Taylor

    OriginalPaper Pages: S174 - S180