{"_buckets": {"deposit": "98074b9d-accb-4940-a6ee-add1d9bea4ec"}, "_deposit": {"created_by": 1, "id": "884", "owners": [1], "pid": {"revision_id": 0, "type": "depid", "value": "884"}, "status": "published"}, "_oai": {"id": "oai:ir.soken.ac.jp:00000884", "sets": ["20"]}, "author_link": ["9822", "9823", "9824"], "item_1_biblio_info_21": {"attribute_name": "書誌情報（ソート用）", "attribute_value_mlt": [{"bibliographicIssueDates": {"bibliographicIssueDate": "1993-03-23", "bibliographicIssueDateType": "Issued"}, "bibliographic_titles": [{}]}]}, "item_1_creator_2": {"attribute_name": "著者名", "attribute_type": "creator", "attribute_value_mlt": [{"creatorNames": [{"creatorName": "近藤, るみ"}], "nameIdentifiers": [{"nameIdentifier": "9822", "nameIdentifierScheme": "WEKO"}]}]}, "item_1_creator_3": {"attribute_name": "フリガナ", "attribute_type": "creator", "attribute_value_mlt": [{"creatorNames": [{"creatorName": "コンドウ, ルミ"}], "nameIdentifiers": [{"nameIdentifier": "9823", "nameIdentifierScheme": "WEKO"}]}]}, "item_1_date_granted_11": {"attribute_name": "学位授与年月日", "attribute_value_mlt": [{"subitem_dategranted": "1993-03-23"}]}, "item_1_degree_grantor_5": {"attribute_name": "学位授与機関", "attribute_value_mlt": [{"subitem_degreegrantor": [{"subitem_degreegrantor_name": "総合研究大学院大学"}]}]}, "item_1_degree_name_6": {"attribute_name": "学位名", "attribute_value_mlt": [{"subitem_degreename": "博士（理学）"}]}, "item_1_description_1": {"attribute_name": "ID", "attribute_value_mlt": [{"subitem_description": "1993310", "subitem_description_type": "Other"}]}, "item_1_description_12": {"attribute_name": "要旨", "attribute_value_mlt": [{"subitem_description": "　　　This dissertation addresses the 4.9 kb (kilobases) nucleotide sequences of\u003cbr /\u003e mitochondrial (mt) DNAs from five hominoid species (common and pygmy\u003cbr /\u003echimpanzees, gorilla, orangutan and simang), and presents their detailed analyses,\u003cbr /\u003e together with the known human whole sequence, to assess the tempo and mode of\u003cbr /\u003e hominoid mtDNA evolution. Particular attention was paid to the rate of\u003cbr /\u003e synonymous substitutions in protein coding region as well as of silent substitutions\u003cbr /\u003e in other regions. This work was further extended to the whole mitochondrial\u003cbr /\u003e genomes of four hominoid species (human, common chimpanzee,′ gorilla and\u003cbr /\u003e orangutan) with additionally determined l0 to 12 kb mtDNAs from common\u003cbr /\u003e chimpanzee, goriIIa and orangutan. These hominoid mtDNAs revealed several\u003cbr /\u003e functionally and evolutionarily characteristic features and provided useful\u003cbr /\u003e information on the history of hominoid species. \u003cbr /\u003e　　　Most significant observations drawn from the present data are summarized as\u003cbr /\u003e follows.　First, comparsion of the base compositions in any specified region of\u003cbr /\u003e hominoid mtDNAs showed a strong base composition bias, as observed in other\u003cbr /\u003e vertebrate mtDNAs. The L-stand of hominoid mtDNAs is rich in A (adenine) and\u003cbr /\u003e C (cytosine) contents, but low in G (guanine) content. Base composition biases are\u003cbr /\u003e strongest at the third codon positions and are evident along the whole genome,\u003cbr /\u003eindependent of the genomic regions. Both codon usage and amino acid preference\u003cbr /\u003e of mitochondrial protein genes are in agreement with the base composition biases.\u003cbr /\u003e These observations suggested that there is a biased mutation pressure in mtDNA.\u003cbr /\u003e A possible cause may be differential diaminations of C residues owing to the\u003cbr /\u003e asymmetric replication of both L- and H-strands of mtDNA. It is possible that\u003cbr /\u003e diffferential deamination has resulted in the reduced number of C residues in the H-\u003cbr /\u003estrand,although there has been no clear evidence for this possibility in hominoid\u003cbr /\u003e mtDNAs.\u003cbr /\u003e　　　Second, there exist functionally important nucleotide sites over the genome.\u003cbr /\u003eTogether with information on tertiary structures of proteins, as Well as on\u003cbr /\u003e secondary structures of transfer (t) RNAs, ribosomal (r) RNA genes and noncoding\u003cbr /\u003e regions, the distributjon of variable sites among hominoid mtDNAs suggested that\u003cbr /\u003e some nucleotide sites have been playing important roles in peptide folding,\u003cbr /\u003e assembly of proteins, or interaction to some other proteins and regulatory elements.\u003cbr /\u003e Noteworthy are two functionally distinct regions in the maior noncoding region (D-\u003cbr /\u003eloop). One is concerned with promoter sequences for transcripdon and the other is\u003cbr /\u003e with three conserved blocks. Oranguan mtDNA sequence revealed unusual\u003cbr /\u003e substitutions at both of these regions. This suggested that the replication and\u003cbr /\u003e transcription machinery in orangutan mtDNA may differ from that of other\u003cbr /\u003e hominoid mtDNAs.\u003cbr /\u003e　　　Third, comparsion of nucleotide differences observed among closely related\u003cbr /\u003e hominoids revealed a remarkably biased mode of changes. Between human and\u003cbr /\u003e chimpanzee, 70% of the observed nuculeotide differences are silent changes that\u003cbr /\u003e occur mostly in the small noncoding regions or at the third codon positions of\u003cbr /\u003e protein genes. Extensive deletions and additions are observed, but they are found\u003cbr /\u003e only in the noncoding regions. Such observations suggested a conserved mode of\u003cbr /\u003e the evolution of hominoid mtDNA genomes. There is also a strong preference to\u003cbr /\u003e transitions over transversions. Out of 852 variable third positions of codons\u003cbr /\u003e between the human and common chimpanzee mtDNAs, 93% account for\u003cbr /\u003e transitions of which 66% are TC transitions (in the L-strand). Within the\u003cbr /\u003e remaming 7% transversions, CA differences are most frequent while GT are least.\u003cbr /\u003e These substitution biases correlate well with biased base compositions, particularly\u003cbr /\u003e the low G content of the L-strand. \u003cbr /\u003e　　　Fourth, owing to the outnumbered transitions and strong biases in the base\u003cbr /\u003e compositions, synonymous substitutions reach rapidly a rather low saturation\u003cbr /\u003e level. AG transitions attain a saturation level lower than TC transitions (in the L-\u003cbr /\u003estrand), and such a low ceiling is observed even between the human and\u003cbr /\u003e chimpanzee pair that diverged around five million years ago. At present,it seems\u003cbr /\u003e inevitable to select appropriate regions that have experienced theoretically tractable\u003cbr /\u003e numbers of substitutions.In the case of hominoid mtDNAs, candidates are all types\u003cbr /\u003e of changes in the tRNA and rRNA regions, transversions in the noncoding regions,\u003cbr /\u003e and nonsynonymous changes and synonymous transversions in the protein coding\u003cbr /\u003e regions.\u003cbr /\u003e　　　Fifth, rapidly evolving mtDNAs are potentially useful for addressing classical\u003cbr /\u003e issues in taxonomy, provided that each nucletide site has not undergone extensive\u003cbr /\u003e multiple-hit substitutions. From the Whole 16209 sites of mtDNAS compared\u003cbr /\u003e among the four hominoid specles, it appears that 12137 such sites are suitable to\u003cbr /\u003e phylogenetic use. The analysis strengthened the pattern and dating in hominoid\u003cbr /\u003e diversifjcation infened from the Previous analysis of 4.9 kb reglon in six homjnoid\u003cbr /\u003e species(among African apes,gorilla diverged first about 7.7 million years ago and\u003cbr /\u003e then chimpanzee and human became distinct about 4.7 million years ago).\u003cbr /\u003e　　　Finally, the synonymous and nonsynonymous substitution rates were\u003cbr /\u003e examined under the assumption of the gorilla divergence being 7.7 miIIion years\u003cbr /\u003eago.　The extent of the compositional biases differs from gene to gene. Such\u003cbr /\u003e differences in base compositions, even if small, can bring about considerable\u003cbr /\u003evariations in observed synonymous differences, and may result in the region-\u003cbr /\u003edependent estimate of the synonymous substitution rate.　A care should be taken\u003cbr /\u003e for heterogeneous transition and base composition biases as Well as different\u003cbr /\u003e saturation levels of transition changes. The synonymous substitution rate\u003cbr /\u003eestimated with this caution showed the uniformity over genes (2.37 \u0026plusmn; 0.11 x 10\u003csup\u003e-8\u003c/sup\u003e per\u003cbr /\u003e site per year) and the high transition rate, about 17 times faster than the\u003cbr /\u003e transversion rate. These synonymous and transition rates are comparable to the\u003cbr /\u003e silent substitution rate in the noncoding segments dispersed between genes. On the\u003cbr /\u003e other hand, the rate of nonsynonymous substitutions differs considerably from\u003cbr /\u003e gene to gene as expected under the neutral theory of molecular evolution. The\u003cbr /\u003e average differences in the gorilla - human and gorilla - chimpanzee comparisons\u003cbr /\u003e indicated that the lowest rate is 0.7 x 10\u003csup\u003e-9\u003c/sup\u003e per site per year for \u003ci\u003eCOI\u003c/i\u003e and that the\u003cbr /\u003e highest rate is 5.7 x 10\u003csup\u003e-9\u003c/sup\u003e for ATP\u003ci\u003ease 8\u003c/i\u003e.　The degree of functional constraints\u003cbr /\u003e (measured by the ratio of the nonsynonymous to the synonymous substitution rate)\u003cbr /\u003e is 0.03 for COI and 0.24 for ATP\u003ci\u003ease 8\u003c/i\u003e. tRNA genes also showed variability in the\u003cbr /\u003e base content and thus in the extent of nucleotide differences as well. The\u003cbr /\u003e substitution rate averaged over 22 tRNAS is 5.6 x 10\u003csup\u003e-9\u003c/sup\u003e per site per year. The rate for\u003cbr /\u003e 12\u003ci\u003eS\u003c/i\u003e \u003ci\u003er\u003c/i\u003eRNA and 16\u003ci\u003eS\u003c/i\u003e \u003ci\u003er\u003c/i\u003eRNA is 4.1 x 10\u003csup\u003e-9\u003c/sup\u003e and 6.9 x 10\u003csup\u003e-9\u003c/sup\u003e per site per year. respectively.\u003cbr /\u003e All of these observations strongly suggested that mutations themselves occur more\u003cbr /\u003e or less with the same rate and compositional biases.", "subitem_description_type": "Other"}]}, "item_1_description_18": {"attribute_name": "フォーマット", "attribute_value_mlt": [{"subitem_description": "application/pdf", "subitem_description_type": "Other"}]}, "item_1_description_7": {"attribute_name": "学位記番号", "attribute_value_mlt": [{"subitem_description": "総研大甲第48号", "subitem_description_type": "Other"}]}, "item_1_select_14": {"attribute_name": "所蔵", "attribute_value_mlt": [{"subitem_select_item": "有"}]}, "item_1_select_8": {"attribute_name": "研究科", "attribute_value_mlt": [{"subitem_select_item": "生命科学研究科"}]}, "item_1_select_9": {"attribute_name": "専攻", "attribute_value_mlt": [{"subitem_select_item": "18 遺伝学専攻"}]}, "item_1_text_10": {"attribute_name": "学位授与年度", "attribute_value_mlt": [{"subitem_text_value": "1992"}]}, "item_1_text_20": {"attribute_name": "業務メモ", "attribute_value_mlt": [{"subitem_text_value": "（2018年2月19日）本籍など個人情報の記載がある旧要旨・審査要旨を個人情報のない新しいものに差し替えた。承諾書等未確認。要確認該当項目修正のこと。"}]}, "item_creator": {"attribute_name": "著者", "attribute_type": "creator", "attribute_value_mlt": [{"creatorNames": [{"creatorName": "KONDO, Rumi", "creatorNameLang": "en"}], "nameIdentifiers": [{"nameIdentifier": "9824", "nameIdentifierScheme": "WEKO"}]}]}, "item_files": {"attribute_name": "ファイル情報", "attribute_type": "file", "attribute_value_mlt": [{"accessrole": "open_date", "date": [{"dateType": "Available", "dateValue": "2016-02-17"}], "displaytype": "simple", "download_preview_message": "", "file_order": 0, "filename": "甲48_要旨.pdf", "filesize": [{"value": "380.3 kB"}], "format": "application/pdf", "future_date_message": "", "is_thumbnail": false, "licensetype": "license_11", "mimetype": "application/pdf", "size": 380300.0, "url": {"label": "要旨・審査要旨 / Abstract, Screening Result", "url": "https://ir.soken.ac.jp/record/884/files/甲48_要旨.pdf"}, "version_id": "bf3edd99-230f-4975-889e-7de00e0cf35f"}, {"accessrole": "open_date", "date": [{"dateType": "Available", "dateValue": "2016-02-17"}], "displaytype": "simple", "download_preview_message": "", "file_order": 1, "filename": "甲48_本文.pdf", "filesize": [{"value": "4.8 MB"}], "format": "application/pdf", "future_date_message": "", "is_thumbnail": false, "licensetype": "license_11", "mimetype": "application/pdf", "size": 4800000.0, "url": {"label": "本文", "url": "https://ir.soken.ac.jp/record/884/files/甲48_本文.pdf"}, "version_id": "e72c5874-01d4-4768-856c-13424a0e4072"}]}, "item_language": {"attribute_name": "言語", "attribute_value_mlt": [{"subitem_language": "eng"}]}, "item_resource_type": {"attribute_name": "資源タイプ", "attribute_value_mlt": [{"resourcetype": "thesis", "resourceuri": "http://purl.org/coar/resource_type/c_46ec"}]}, "item_title": "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", "item_titles": {"attribute_name": "タイトル", "attribute_value_mlt": [{"subitem_title": "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"}, {"subitem_title": "Evolution and phylogeny of hominoids inferred from mitochondrial DNA sequences", "subitem_title_language": "en"}]}, "item_type_id": "1", "owner": "1", "path": ["20"], "permalink_uri": "https://ir.soken.ac.jp/records/884", "pubdate": {"attribute_name": "公開日", "attribute_value": "2010-02-22"}, "publish_date": "2010-02-22", "publish_status": "0", "recid": "884", "relation": {}, "relation_version_is_last": true, "title": ["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"], "weko_shared_id": 1}