Evolution and phylogeny of hominoids inferred from mitochondrial DNA sequences ミトコンドリアDNAを指標としたヒト上科の進化及び系統学的解析

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著者

    • 近藤, るみ コンドウ, ルミ

書誌事項

タイトル

Evolution and phylogeny of hominoids inferred from mitochondrial DNA sequences

タイトル別名

ミトコンドリアDNAを指標としたヒト上科の進化及び系統学的解析

著者名

近藤, るみ

著者別名

コンドウ, ルミ

学位授与大学

総合研究大学院大学

取得学位

博士 (理学)

学位授与番号

甲第48号

学位授与年月日

1993-03-23

注記・抄録

博士論文

   This dissertation addresses the 4.9 kb (kilobases) nucleotide sequences of<br /> mitochondrial (mt) DNAs from five hominoid species (common and pygmy<br />chimpanzees, gorilla, orangutan and simang), and presents their detailed analyses,<br /> together with the known human whole sequence, to assess the tempo and mode of<br /> hominoid mtDNA evolution. Particular attention was paid to the rate of<br /> synonymous substitutions in protein coding region as well as of silent substitutions<br /> in other regions. This work was further extended to the whole mitochondrial<br /> genomes of four hominoid species (human, common chimpanzee,′ gorilla and<br /> orangutan) with additionally determined l0 to 12 kb mtDNAs from common<br /> chimpanzee, goriIIa and orangutan. These hominoid mtDNAs revealed several<br /> functionally and evolutionarily characteristic features and provided useful<br /> information on the history of hominoid species. <br />   Most significant observations drawn from the present data are summarized as<br /> follows. First, comparsion of the base compositions in any specified region of<br /> hominoid mtDNAs showed a strong base composition bias, as observed in other<br /> vertebrate mtDNAs. The L-stand of hominoid mtDNAs is rich in A (adenine) and<br /> C (cytosine) contents, but low in G (guanine) content. Base composition biases are<br /> strongest at the third codon positions and are evident along the whole genome,<br />independent of the genomic regions. Both codon usage and amino acid preference<br /> of mitochondrial protein genes are in agreement with the base composition biases.<br /> These observations suggested that there is a biased mutation pressure in mtDNA.<br /> A possible cause may be differential diaminations of C residues owing to the<br /> asymmetric replication of both L- and H-strands of mtDNA. It is possible that<br /> diffferential deamination has resulted in the reduced number of C residues in the H-<br />strand,although there has been no clear evidence for this possibility in hominoid<br /> mtDNAs.<br />   Second, there exist functionally important nucleotide sites over the genome.<br />Together with information on tertiary structures of proteins, as Well as on<br /> secondary structures of transfer (t) RNAs, ribosomal (r) RNA genes and noncoding<br /> regions, the distributjon of variable sites among hominoid mtDNAs suggested that<br /> some nucleotide sites have been playing important roles in peptide folding,<br /> assembly of proteins, or interaction to some other proteins and regulatory elements.<br /> Noteworthy are two functionally distinct regions in the maior noncoding region (D-<br />loop). One is concerned with promoter sequences for transcripdon and the other is<br /> with three conserved blocks. Oranguan mtDNA sequence revealed unusual<br /> substitutions at both of these regions. This suggested that the replication and<br /> transcription machinery in orangutan mtDNA may differ from that of other<br /> hominoid mtDNAs.<br />   Third, comparsion of nucleotide differences observed among closely related<br /> hominoids revealed a remarkably biased mode of changes. Between human and<br /> chimpanzee, 70% of the observed nuculeotide differences are silent changes that<br /> occur mostly in the small noncoding regions or at the third codon positions of<br /> protein genes. Extensive deletions and additions are observed, but they are found<br /> only in the noncoding regions. Such observations suggested a conserved mode of<br /> the evolution of hominoid mtDNA genomes. There is also a strong preference to<br /> transitions over transversions. Out of 852 variable third positions of codons<br /> between the human and common chimpanzee mtDNAs, 93% account for<br /> transitions of which 66% are TC transitions (in the L-strand). Within the<br /> remaming 7% transversions, CA differences are most frequent while GT are least.<br /> These substitution biases correlate well with biased base compositions, particularly<br /> the low G content of the L-strand. <br />   Fourth, owing to the outnumbered transitions and strong biases in the base<br /> compositions, synonymous substitutions reach rapidly a rather low saturation<br /> level. AG transitions attain a saturation level lower than TC transitions (in the L-<br />strand), and such a low ceiling is observed even between the human and<br /> chimpanzee pair that diverged around five million years ago. At present,it seems<br /> inevitable to select appropriate regions that have experienced theoretically tractable<br /> numbers of substitutions.In the case of hominoid mtDNAs, candidates are all types<br /> of changes in the tRNA and rRNA regions, transversions in the noncoding regions,<br /> and nonsynonymous changes and synonymous transversions in the protein coding<br /> regions.<br />   Fifth, rapidly evolving mtDNAs are potentially useful for addressing classical<br /> issues in taxonomy, provided that each nucletide site has not undergone extensive<br /> multiple-hit substitutions. From the Whole 16209 sites of mtDNAS compared<br /> among the four hominoid specles, it appears that 12137 such sites are suitable to<br /> phylogenetic use. The analysis strengthened the pattern and dating in hominoid<br /> diversifjcation infened from the Previous analysis of 4.9 kb reglon in six homjnoid<br /> species(among African apes,gorilla diverged first about 7.7 million years ago and<br /> then chimpanzee and human became distinct about 4.7 million years ago).<br />   Finally, the synonymous and nonsynonymous substitution rates were<br /> examined under the assumption of the gorilla divergence being 7.7 miIIion years<br />ago. The extent of the compositional biases differs from gene to gene. Such<br /> differences in base compositions, even if small, can bring about considerable<br />variations in observed synonymous differences, and may result in the region-<br />dependent estimate of the synonymous substitution rate. A care should be taken<br /> for heterogeneous transition and base composition biases as Well as different<br /> saturation levels of transition changes. The synonymous substitution rate<br />estimated with this caution showed the uniformity over genes (2.37 &plusmn; 0.11 x 10<sup>-8</sup> per<br /> site per year) and the high transition rate, about 17 times faster than the<br /> transversion rate. These synonymous and transition rates are comparable to the<br /> silent substitution rate in the noncoding segments dispersed between genes. On the<br /> other hand, the rate of nonsynonymous substitutions differs considerably from<br /> gene to gene as expected under the neutral theory of molecular evolution. The<br /> average differences in the gorilla - human and gorilla - chimpanzee comparisons<br /> indicated that the lowest rate is 0.7 x 10<sup>-9</sup> per site per year for <i>COI</i> and that the<br /> highest rate is 5.7 x 10<sup>-9</sup> for ATP<i>ase 8</i>. The degree of functional constraints<br /> (measured by the ratio of the nonsynonymous to the synonymous substitution rate)<br /> is 0.03 for COI and 0.24 for ATP<i>ase 8</i>. tRNA genes also showed variability in the<br /> base content and thus in the extent of nucleotide differences as well. The<br /> substitution rate averaged over 22 tRNAS is 5.6 x 10<sup>-9</sup> per site per year. The rate for<br /> 12<i>S</i> <i>r</i>RNA and 16<i>S</i> <i>r</i>RNA is 4.1 x 10<sup>-9</sup> and 6.9 x 10<sup>-9</sup> per site per year. respectively.<br /> All of these observations strongly suggested that mutations themselves occur more<br /> or less with the same rate and compositional biases.

目次

  1. TABLE OF CONTENTS / p2 (0005.jp2)
  2. CHAPTER ONE:INTRODUCTION / p1 (0008.jp2)
  3. Mitochondrion / p2 (0009.jp2)
  4. Organization of mammalian mtDNA / p3 (0009.jp2)
  5. Transcription of mammalian mtDNA / p6 (0011.jp2)
  6. Hominoid phylogeny / p7 (0011.jp2)
  7. Evolutionary studies of mtDNA / p8 (0012.jp2)
  8. Questions to be addressed / p10 (0013.jp2)
  9. CHAPTER TWO:MATERIALS AND METHODS / p11 (0013.jp2)
  10. Abbreviations / p11 (0013.jp2)
  11. Sample sources / p12 (0014.jp2)
  12. Reagents / p12 (0014.jp2)
  13. Extraction and cloning of mtDNA / p13 (0014.jp2)
  14. Amplification of mtDNA segments / p13 (0014.jp2)
  15. Cloning from the PCR product / p18 (0017.jp2)
  16. Isolation of single-stranded DNA from phage / p18 (0017.jp2)
  17. Preparing single-stranded template for direct sequencing / p19 (0017.jp2)
  18. DNA sequencing / p21 (0018.jp2)
  19. Sequencing gel electrophoresis / p22 (0019.jp2)
  20. Recipes / p23 (0019.jp2)
  21. CHAPTER THREE:BASE COMPOSITIONS AND REPLICATION IN MITOCHONDRIAL DNA / p27 (0021.jp2)
  22. Base composition biases in animals / p27 (0021.jp2)
  23. General features of base composition biases in hominoids / p30 (0023.jp2)
  24. Base composition biases and asymmetric replication / p38 (0027.jp2)
  25. Conclusions / p46 (0031.jp2)
  26. CHAPTER FOUR:STRUCTURAL AND FUNCTIONAL PROPERTIES OF MITOCHONDRIAL GENES / p47 (0031.jp2)
  27. Protein genes / p47 (0031.jp2)
  28. tRNA genes / p66 (0041.jp2)
  29. rRNA genes / p74 (0045.jp2)
  30. Control regions / p76 (0046.jp2)
  31. Conclusions / p82 (0049.jp2)
  32. CHAPTER FIVE:NUCLEOTIDE DIFFERENCES AND MODE OF EVOLUTION / p83 (0049.jp2)
  33. Nucleotide differences in protein genes / p86 (0051.jp2)
  34. Nucleotide differences in tRNA and rRNA genes / p87 (0051.jp2)
  35. Nucleotide differences in the noncoding regions / p96 (0056.jp2)
  36. Conclusions / p97 (0056.jp2)
  37. CHAPTER SIX:HOMINOID PHYLOGENY / p99 (0057.jp2)
  38. Resolution of trichotomy and the estimation of divergence times / p99 (0057.jp2)
  39. Phylogenetic analysis of the whole mitochondrial genome / p100 (0058.jp2)
  40. Conclusions / p106 (0061.jp2)
  41. CHAPTER SEVEN:CONSIDERATION OF THE CORRECTION METHODS / p108 (0062.jp2)
  42. Nucleotide substitutions in a stationary Markov model. / p109 (0062.jp2)
  43. Simulation of nucleotide substitutions in mtDNA / p112 (0064.jp2)
  44. Estimation of synonymous sites / p116 (0066.jp2)
  45. Multiple hit corrections / p120 (0068.jp2)
  46. Conclusions / p121 (0068.jp2)
  47. CHAPTER EIGHT:ESTIMATION OF SUBSTITUTION RATES / p122 (0069.jp2)
  48. Substitution rates of protein genes / p122 (0069.jp2)
  49. Substitution rates of tRNA and rRNA genes / p124 (0070.jp2)
  50. Substitution rates in the noncoding region / p124 (0070.jp2)
  51. Conclusions / p125 (0070.jp2)
  52. CHAPTER NINE:CONCLUSIONS AND PROSPECTS / p127 (0071.jp2)
  53. LITERATURE CITED / p129 (0072.jp2)
  54. APPENDIX I:Calculations / p139 (0077.jp2)
  55. APPENDIX II:Evolution of hominoid mitochondrial DNA with special reference to the silent substitution rate over the genome,by R.Kondo,S.Horai,Y.Satta,and N.Takahata / p144 (0080.jp2)
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  • NII論文ID(NAID)
    500000099295
  • NII著者ID(NRID)
    • 8000000099525
  • DOI(NDL)
  • 本文言語コード
    • eng
  • NDL書誌ID
    • 000000263609
  • データ提供元
    • 機関リポジトリ
    • NDL-OPAC
    • NDLデジタルコレクション
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