o List of Papers in the Last 10 Years

  1. M. Hasegawa, Y. Cao, and Z. Yang (1998) "Preponderance of slightly deleterious polymorphism in mitochondrial DNA: Nonsynonymous/synonymous rate ratio is much higher within species than between species" Mol. Biol. Evol., in press.
  2. Z. Yang, R. Nielsen, and M. Hasegawa (1998) "Models of amino acid substitution and applications to mitochondrial protein evolution" Mol. Biol. Evol., in press.
  3. Y. Cao, A. Janke, P.J. Waddell, M. Westerman, O. Takenaka, S. Murata, N. Okada, S. Paabo, and M. Hasegawa (1998) "Conflict amongst individual mitochondrial proteins in resolving the phylogeny of eutherian orders" J. Mol. Evol., in press.
  4. W. Martin, B. Stobe, V. Goremykin, S. Hansmann, M. Hasegawa, and K.V. Kowallik (1998) "Gene transfer to the nucleus and the evolution of chloroplasts" Nature, 393, 162-165.
  5. R. Zardoya, Y. Cao, M. Hasegawa, and A. Meyer (1998) "Searching for the closest living relative(s) of tetrapods through evolutionary analyses of mitochondrial and nuclear data" Mol. Biol. Evol., 15, 506-517.
  6. Y. Cao, J. Adachi, and M. Hasegawa (1998) "Comment on the quartet puzzling method for finding maximum-likelihood tree topologies" Mol. Biol. Evol., 15, 87-89.
  7. D. Penny and M. Hasegawa (1997) "The platypus put in its place", Nature, 387, 549-550.
  8. M. Hamada, Y. Kido, M. Himberg, J.D. Reist, Y. Cao, M. Hasegawa, and N. Okada (1997) "A newly isolated family of short interspersed repetitive elements (SINEs) in coregonid fishes (whitefish) with sequences that are almost identical to those of the SmaI family of repeats: possible evidence for the horizontal transfer of SINEs" Genetics, 146, 355-367.
  9. Y. Cao, N. Okada, and M. Hasegawa (1997) "Phylogenetic position of guinea-pigs revisited" Mol. Biol. Evol., 14, 461-464.
  10. M. Hasegawa, J. Adachi, and M.C. Milinkovitch (1997) "Novel phylogeny of whales supported by total molecular evidence" J. Mol. Evol., 44 (Suppl. 1), 117-120.
  11. A. Yamamoto, T. Hashimoto, E. Asaga, M. Hasegawa, and N. Goto (1997) "Phylogenetic position of mitochondrion-lacking protozoan, Trichomonas tenax, based on amino acid sequences of elongation factors 1alpha and 2" J. Mol. Evol., 44, 98-105.
  12. M. Aoshima, Y. Nishibe, M. Hasegawa, A. Yamagishi, and T. Oshima (1996) "Cloning and sequencing of a gene encoding 16S ribosomal RNA from a novel hyperthermophilic archaebacterium NC12" Gene, in press.
  13. M. Hasegawa and W.M. Fitch (1996) "Dating the cenancestor of organisms" Science, 274, 1750-1750.
  14. M.C. Milinkovitch, R.G. LeDuc, J. Adachi, F. Farnir, M. Georges, and M. Hasegawa (1996) "Effects of character weighting and species sampling on phylogeny reconstruction: a case study based on DNA sequence data in cetaceans" Genetics, 144, 1817-1833.
  15. T. Kamaishi, T. Hashimoto, Y. Nakamura, Y. Masuda, F. Nakamura, K. Okamoto, M. Shimizu, and M. Hasegawa (1996) "Complete nucleotide sequences of the genes encoding translation elongation factors 1alpha and 2 from a microsporidian parasite, Glugea plecoglossi: implications for the deepest branching of eukaryotes" J. Biochem., 120, 1095-1103.
  16. Y. Nakamura, T. Hashimoto, H. Yoshikawa, T. Kamaishi, F. Nakamura, K. Okamoto, and M. Hasegawa (1996) "Phylogenetic position of Blastocystis hominis that contains cytochrome-free mitochondria, inferred from the protein phylogeny of elongation factor 1alpha" Mol. Biochem. Parasit., 77, 241-245.
  17. T. Hashimoto and M. Hasegawa (1996) "Origin and early evolution of eukaryotes inferred from the amino acid sequences of translation elongation factors 1alpha/Tu and 2/G" Adv. Biophy., 32, 73-120.
  18. J. Adachi and M. Hasegawa (1996) "MOLPHY Version 2.3: Programs for Molecular Phylogenetics Based on Maximum Likelihood" Computer Science Monographs, 28, 1-150. Institute of Statistical Mathematics, Tokyo.
  19. T. Kamaishi, T. Hashimoto, Y. Nakamura, F. Nakamura, S. Murata, N. Okada, K. Okamoto, M. Shimizu, and M. Hasegawa (1996) "Protein phylogeny of EF-1alpha suggests microsporidians are extremely ancient eukaryotes" J. Mol. Evol., 42, 257-263.
  20. M. Hasegawa and J. Adachi (1996) "Phylogenetic position of cetaceans relative to artiodactyls: Reanalysis of mitochondrial and nuclear sequences" Mol. Biol. Evol., 13, 710-717.
  21. J. Adachi and M. Hasegawa (1996) "Model of amino acid substitution in proteins encoded by mitochondrial DNA" J. Mol. Evol., 42, 459-468.
  22. J. Adachi and M. Hasegawa (1996) "Tempo and mode of synonymous substitutions in mitochondrial DNA of primates" Mol. Biol. Evol., 13, 200-208.
  23. Y. Nakamura, T. Hashimoto, T. Kamaishi, J. Adachi, F. Nakamura, K. Okamoto, and M. Hasegawa (1996) "Phylogenetic place of kinetoplastid protozoa inferred from protein phylogenies of elongation factors 1alpha and 2" J. Biochem., 119, 70-79
  24. T. Hashimoto, Y. Nakamura, T. Kamaishi, F. Nakamura, J. Adachi, K. Okamoto, and M. Hasegawa (1995) "Phylogenetic place of a mitochondrion-lacking protozoan, Giardia lamblia, inferred from amino acid sequences of elongation factor 2" Mol. Biol. Evol., 12, 782-793.
  25. T. Hashimoto, Y. Nakamura, T. Kamaishi, J. Adachi, F. Nakamura, K. Okamoto, and M. Hasegawa (1995) "Phylogenetic place of kinetoplastid protozoa inferred from a protein phylogeny of elongation factor 1alpha" Mol. Biochem. Parasitol., 70, 181-185.
  26. Y. Cao, J. Adachi, and M. Hasegawa (1994) "Eutherian phylogeny as inferred from mitochondrial DNA sequence data" Jpn. J. Genet., 69, 455-472.
  27. Y. Cao, J. Adachi, A. Janke, S. Paabo, and M. Hasegawa (1994) "Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: Instability of a tree based on a single gene" J. Mol. Evol., 39, 519-527.
  28. T. Shirakura, T. Hashimoto, Y. Nakamura, T. Kamaishi, Y. Cao, J. Adachi, M. Hasegawa, A. Yamamoto, and N. Goto (1994) "Phylogenetic place of a mitochondria-lacking protozoan, Entamoeba histolytica, inferred from amino acid sequences of elongation factor 2" Jpn. J. Genet., 69, 119-135.
  29. S. Yokobori, M. Hasegawa, T. Ueda, N. Okada, K. Nishikawa, and K. Watanabe (1994) "Relationship among coelacanths, lungfishes and tetrapods; a phylogenetic analysis based on mitochondrial cytochrome oxidase I gene sequences2" J. Mol. Evol., 38, 602-609.
  30. M. Hasegawa and H. Kishino (1994) "Accuracies of the simple methods for estimating the bootstrap probability of a maximum likelihood tree" Mol. Biol. Evol., 11, 142-145.
  31. T. Hashimoto, Y. Nakamura, F. Nakamura, T. Shirakura, J. Adachi, N. Goto, K. Okamoto, and M. Hasegawa (1993) "Protein phylogeny gives a robust estimation for early divergences of eukaryotes: phylogenetic place of a mitochondria-lacking protozoan, Giardia lamblia" Mol. Biol. Evol., 11, 65-71.
  32. M. Hasegawa and M. Fujiwara (1993) "Relative efficiencies of the maximum likelihood, maximum parsimony, and neighbor-joining methods for estimating protein phylogeny" Mol. Phyl. Evol., 2, 1-5.
  33. M. Hasegawa, A. Di Rienzo, T.D. Kocher, and A.C. Wilson (1993) "Toward a more accurate time scale for the human mitochondrial DNA tree" J. Mol. Evol., 37, 347-354.
  34. S. Kojima, T. Hashimoto, M. Hasegawa, S. Murata, S. Ohta, H. Seki, and N. Okada (1993) "Close phylogenetic relationship between Vestimentifera (tube worms) and Annelida revealed by the amino acid sequence of elongation factor-1alpha" J. Mol. Evol., 37, 66-70.
  35. M. Hasegawa and T. Hashimoto (1993) "Ribosomal RNA trees misleading?" Nature, 361, 23-23.
  36. M. Hasegawa, T. Hashimoto, J. Adachi, N. Iwabe, and T. Miyata (1993) "Early branchings in the evolution of eukaryotes: ancient divergence of Entamoeba that lacks mitochondria revealed by protein sequence data" J. Mol. Evol., 36, 380-388.
  37. T. Hashimoto, E. Otaka, J. Adachi, K. Mizuta, and M. Hasegawa (1993) "The giant panda is most close to a bear, judged by alpha- and beta-hemoglobin sequences" J. Mol. Evol., 36, 282-289.
  38. J. Adachi, Y. Cao, and M. Hasegawa (1993) "Tempo and mode of mitochondrial DNA evolution in vertebrates at the amino acid sequence level: rapid evolution in warm-blooded vertebrates" J. Mol. Evol., 36, 270-281.
  39. M. Hasegawa, Y. Cao, J. Adachi, and T. Yano (1992) "Rodent polyphyly?" Nature, 355, 595-595.
  40. J. Adachi and M. Hasegawa (1992) "MOLPHY: Programs for Molecular Phylogenetics, I. --PROTML: Maximum Likelihood Inference of Protein Phylogeny" Computer Science Monographs, 27, 1-77. Institute of Statistical Mathematics, Tokyo
  41. J. Adachi and M. Hasegawa (1992) "Amino acid substitution of proteins coded for in mitochondrial DNA during mammalian evolution" Jpn. J. Genet., 67, 187-197.
  42. M. Hasegawa (1991) "Molecular phylogeny and man's place in Hominoidea" J. Anthrop. Soc. Nippon, 99, 49-61.
  43. N. Iwabe, K. Kuma, H. Kishino, M. Hasegawa, and T. Miyata (1991) "Evolution of RNA polymerases and branching patterns of the three major groups of archaebacteria" J. Mol. Evol., 32, 70-78.
  44. M. Hasegawa and S. Horai (1991) "Time of the deepest root for polymorphism in human mitochondrial DNA" J. Mol. Evol., 32, 37-42.
  45. Y. Mukohata, K. Ihara, H. Kishino, M. Hasegawa, N. Iwabe, and T. Miyata (1990) "Close evolutionary relatedness of archaebacteria with eukaryotes" Proc. Japan Acad., 66B, 63-67.
  46. M. Hasegawa (1990) "Phylogeny and molecular evolution in primates" Jpn. J. Genet., 65, 243-265.
  47. M. Hasegawa, N. Iwabe, Y. Mukohata, and T. Miyata (1990) "Close evolutionary relatedness of archaebacteria, Methanococcus and Halobacterium, to eukaryotes demonstrated by composite phylogenetic trees of elongation factors EF-Tu and EF-G: eocyte tree is unlikely" Jpn. J. Genet., 65, 109-114.
  48. N. Iwabe, H. Kishino, M. Hasegawa, and T. Miyata (1990) "Compartmentalized isozyme genes and the origin of introns" J. Mol. Evol., 31, 205-210.
  49. M. Hasegawa, H. Kishino, K. Hayasaka, and S. Horai (1990) "Mitochondrial DNA evolution in primates: transition rate has been extremely low in lemur" J. Mol. Evol., 31, 113-121.
  50. H. Kishino and M. Hasegawa (1990) "Converting distance to time: an application to human evolution" Methods in Enzymology, 183, 550-570.
  51. H. Kishino, T. Miyata, and M. Hasegawa (1990) "Maximum likelihood inference of protein phylogeny and the origin of chloroplasts" J. Mol. Evol., 30, 151-160.
  52. N. Iwabe, K. Kuma, M. Hasegawa, S. Osawa, and T. Miyata (1989) "Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes" Proc. Natl. Acad. Sci. USA, 86, 9355-9359.
  53. H. Kishino and M. Hasegawa (1989) "Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea" J. Mol. Evol., 29, 170-179.
  54. M. Hasegawa, H. Kishino, and T. Yano (1989) "Estimation of branching dates among primates by molecular clocks of nuclear DNA which slowed down in Hominoidea" J. Human Evol., 18, 461-476.
  55. M. Hasegawa and H. Kishino (1989) "Heterogeneity of tempo and mode of mitochondrial DNA evolution among mammalian orders" Jpn. J. Genet., 64, 243-258.
  56. M. Hasegawa and H. Kishino (1989) "Confidence limits on the maximum-likelihood estimate of the hominoid tree from mitochondrial-DNA sequences" Evolution, 43, 672-677.

o List of Books

  1. M. Hasegawa and H. Kishino (1996) "Molecular Phylogenetics (in Japanese)" Iwanami Publ., Tokyo
  2. M. Hasegawa (1992) "What Genes Tell about Your Ancestors (in Japanese)" Asunaro Shobou, Tokyo
  3. M. Hasegawa (1991) "Evolutionary History of Humans Inscribed on the DNA (in Japanese)" Iwanami Publ., Tokyo
  4. M. Hasegawa and M. Tanemura (1986) "Ecology of Territory -- Ecological Models and Statistics of Spatial Patterns (in Japanese)" Tokai Univ. Press, Tokyo
  5. M. Hasegawa (1984) "Origin and evolution of Humans as Inferred from DNA (in Japanese)" Kaimeisha Publ., Tokyo


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