{"_buckets": {"deposit": "13ea87f3-5a6e-4384-afd6-e74f6ff2ce20"}, "_deposit": {"created_by": 1, "id": "1221", "owners": [1], "pid": {"revision_id": 0, "type": "depid", "value": "1221"}, "status": "published"}, "_oai": {"id": "oai:ir.soken.ac.jp:00001221", "sets": ["23"]}, "author_link": ["0", "0", "0"], "item_1_biblio_info_21": {"attribute_name": "書誌情報（ソート用）", "attribute_value_mlt": [{"bibliographicIssueDates": {"bibliographicIssueDate": "2006-03-24", "bibliographicIssueDateType": "Issued"}, "bibliographic_titles": [{}]}]}, "item_1_creator_2": {"attribute_name": "著者名", "attribute_type": "creator", "attribute_value_mlt": [{"creatorNames": [{"creatorName": "YANG, Zhong"}], "nameIdentifiers": [{"nameIdentifier": "0", "nameIdentifierScheme": "WEKO"}]}]}, "item_1_creator_3": {"attribute_name": "フリガナ", "attribute_type": "creator", "attribute_value_mlt": [{"creatorNames": [{"creatorName": "ヤン, ツォン"}], "nameIdentifiers": [{"nameIdentifier": "0", "nameIdentifierScheme": "WEKO"}]}]}, "item_1_date_granted_11": {"attribute_name": "学位授与年月日", "attribute_value_mlt": [{"subitem_dategranted": "2006-03-24"}]}, "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": "2006813", "subitem_description_type": "Other"}]}, "item_1_description_12": {"attribute_name": "要旨", "attribute_value_mlt": [{"subitem_description": "This thesis is a study of phylogenetic approaches and database system as well as\u003cbr /\u003etheir uses in bioinformatics. It focuses on three main　topics: (A) molecular\u003cbr /\u003ephylogenetic analysis as an effective tool to investigate the evolutionary relationships\u003cbr /\u003eand rates and adaptation of two important groups: the mangrove family\u003cbr /\u003eRhizophoraceae and the sere acute respiratory syndrome (SARS) coronavirus; (B)\u003cbr /\u003estatistical model and computer simulation approach for testing hybridization\u003cbr /\u003ehypotheses based on incongruent gene trees; and (C) a new data model and comparison\u003cbr /\u003emethod for interacting classifications and phylogenetic trees in a taxonomic database.\u003cbr /\u003e　　In Chapter 1 , I outlined the advances in today\u0027s biodiversity science and\u003cbr /\u003ebioinformatics, and in the studies of molecular evolution and phylogenetics. To meet\u003cbr /\u003ethe major needs for a newly formed cross-disciplinary between biodiversity science and\u003cbr /\u003ebioinformatics, \u003ci\u003ei. e.,\u003c/i\u003e biodiversity informatics, applications of phylogenetic approaches\u003cbr /\u003eand data models as well as taxonomic database systems in this field are needed.\u003cbr /\u003e　　In Chapter 2, I Investigated the phylogenetic relationships and evolutionary rate\u003cbr /\u003eheterogeneity of  the family Rhizophoraceae based on the sequences of chloroplast\u003cbr /\u003egenes \u003ci\u003emat\u003c/i\u003eK and \u003ci\u003erbcL\u003c/i\u003e, and ITS regions of nuclear ribosomal DNA.  Phylogenetic trees\u003cbr /\u003ewere constructed using the maximum parsimony (MP), neighbor-joining (NJ) and\u003cbr /\u003emaximum likelihood (ML) methods. The partition-homogeneity tests indicated that the\u003cbr /\u003edata sets were homogeneous, and the combined analysis showed that four mangrove\u003cbr /\u003egenera formed a monophyletic group and the terrestrial genus \u003ci\u003ePellacalyx\u003c/i\u003e was shown to\u003cbr /\u003ebe the basal clade.  Evolutionary rate heterogeneity for the plastid \u003ci\u003emat\u003c/i\u003eK and \u003ci\u003erbc\u003c/i\u003eL genes\u003cbr /\u003ein different species of the Rhizophoraceae was analyzed by means of the relative-rate\u003cbr /\u003etests. A number of significant rate differences at synonymous and non-synonymous\u003cbr /\u003esites were detected in the two genes. Two significant  contrasts are that the mangrove\u003cbr /\u003egenus \u003ci\u003eBruguiera\u003c/i\u003e has relatively slower substitution rates than the terrestrial genus\u003cbr /\u003e\u003ci\u003eCarallia\u003c/i\u003e at both synonymous and non-synonymous sites in the \u003ci\u003emat\u003c/i\u003eK sequences. The\u003cbr /\u003eMantel tests showed that the synonymous and non-synonymous relative･rate matrices\u003cbr /\u003eare correlated at the \u003ci\u003emat\u003c/i\u003eK gene, suggesting that selective constraint at non-synonymous\u003cbr /\u003esites is fairly constant among evolutionary lineages of the \u003ci\u003emat\u003c/i\u003eK locus. Second, there\u003cbr /\u003eare 13 significant contrasts at non-synonymous sites in the \u003ci\u003erbc\u003c/i\u003eL sequences.  Among\u003cbr /\u003ethem, six indicate that the mangrove genera have relatively faster non-synonymous\u003cbr /\u003esubstitution rates than the related terrestrial groups. However, the terrestrial genus\u003cbr /\u003e\u003ci\u003eCarallia\u003c/i\u003e still shows a relatively faster non-synonymous rate than the mangrove genus\u003cbr /\u003e\u003ci\u003eKandelia.\u003c/i\u003e Moreover, the \u003ci\u003erbc\u003c/i\u003eL non-synonymous sites also exhibit rate heterogeneity\u003cbr /\u003eamong the terrestrial groups, regardless of their geographical distributions. The Mantel\u003cbr /\u003etests show that the \u003ci\u003erbc\u003c/i\u003eL rates at synonymous and non-synonymous sites are\u003cbr /\u003euncorrelated. The molecular evolutionary pattern of mangroves and their terrestrial\u003cbr /\u003erelatives in which non-synonymous and synonymous substitution rates are uncoupled\u003cbr /\u003esuggests that selection is probably an important influence on the rate variation.\u003cbr /\u003e　　　In Chapter 3, I detected the adaptive evolution in SARS coronavirus (SARS-CoV)\u003cbr /\u003egenome. First, 61 SARS coronavirus (SARS-CoV) genomic sequences derived from\u003cbr /\u003ethe early, middle, and late phases of the SARS epidemic were analyzed together with\u003cbr /\u003etwo viral sequences from palm civets. The neutral mutation rate of the viral genome\u003cbr /\u003ewas constant but the amino acid substitution rate of the coding sequences slowed\u003cbr /\u003eduring the course of the epidemic.   Between the sequences of the palm civets and each\u003cbr /\u003eof the human SARS-Co-V  sequences, the ratios of the rates of nonsynonymous to\u003cbr /\u003esynonymous changes (K\u003csmall\u003eA\u003c/small\u003e/ K\u003csmall\u003es\u003c/small\u003e) for the S gene sequences were always greater than 1,\u003cbr /\u003eindicating an overall positive selection pressure. However, pairwise  analysis of the K\u003csmall\u003eA\u003c/small\u003e/\u003cbr /\u003eK\u003csmall\u003es\u003c/small\u003e for the genotypes in each epidemic group shows that the average K\u003csmall\u003eA\u003c/small\u003e/ K\u003csmall\u003es\u003c/small\u003e for the\u003cbr /\u003e early phase was significantly larger than that for the middle phase, which in tum was\u003cbr /\u003esignificantly larger than the ratio for the late phase, which in fact was significantly less\u003cbr /\u003ethan 1. These data indicated that the S gene showed the strongest initial responses to\u003cbr /\u003epositive selection pressures, followed by subsequent purifying selection and eventual\u003cbr /\u003estabilization. Second, I further tested the hypothesis that radical amino acid\u003cbr /\u003ereplacements in the spike protein, favored by environmental selective pressure during\u003cbr /\u003ethe process of SARS-CoV interspecific  transmission. I investigated 108 complete\u003cbr /\u003esequences of the SARS-CoV S gene, and reconstructed the most recent common\u003cbr /\u003eancestor (MRCA) sequences of the S gene and detected the adaptive evolution in the\u003cbr /\u003espike protein. The results showed the simultaneous amino acid replacements in three\u003cbr /\u003esites, i.e., 360, 665 and 701. These sites led to the excess of observed radical\u003cbr /\u003esubstitution number over corresponding expectation under the assumption of selective\u003cbr /\u003eneutrality, indicative of potentially  important roles they played in the adaptive\u003cbr /\u003eevolution of the spike protein.\u003cbr /\u003e　　In Chapter 4, I characterized certain distinctions between hybridization and other\u003cbr /\u003ebiological processes, including lineage sorting, paralogy, and lateral gene transfer,  that\u003cbr /\u003eare responsible for topological incongruence between gene trees. Consider two\u003cbr /\u003eincongruent gene trees with three taxa, A, B, and C, where B is a sister group of A on\u003cbr /\u003egene tree 1 but a sister group of C on gene tree 2. With a theoretical model based on the\u003cbr /\u003emolecular clock, we demonstrated that time of divergence of each gene between taxa A\u003cbr /\u003eand C is nearly equal in the case of hybridization (B is a hybrid) or lateral gene transfer,\u003cbr /\u003ebut differs significantly in the case of lineage sorting or paralogy.  After developing a\u003cbr /\u003ebootstrap test to test these altermative  hypotheses, we extended the model and test to\u003cbr /\u003eaccount for incongruent gene trees with numerous taxa.  Computer simulation studies\u003cbr /\u003esupported the validity of the theoretical model and bootstrap test when each gene\u003cbr /\u003eevolved at a constant rate.  The computer simulation also suggested that the model\u003cbr /\u003eremained valid as long as the rate heterogeneity was occurring proportionally in the\u003cbr /\u003esame taxa for both genes.\u003cbr /\u003e　　Finally, in Chapter 5, I described　an　information-theoretic view,\u003ci\u003e i. e.,\u003c/i\u003e taxon-view,\u003cbr /\u003ewhich can be applied to biological classification to capture taxonomic concepts as data\u003cbr /\u003eentities and to develop a system for managing these concepts and the lineage\u003cbr /\u003erelationships among them. A new data model and methodology for comparing\u003cbr /\u003einteracting classiflcations were outlined. On the basis of the data model and\u003cbr /\u003ecomparison and query methods, a prototype taxonomic database system called\u003cbr /\u003eHICLAS (Hierarchical CLAssification System)  was built to query classification data\u003cbr /\u003eand to compare interacting classifications and phylogenetic trees.", "subitem_description_type": "Other"}]}, "item_1_description_7": {"attribute_name": "学位記番号", "attribute_value_mlt": [{"subitem_description": "総研大乙第162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": "先導科学研究科"}]}, "item_1_select_9": {"attribute_name": "専攻", "attribute_value_mlt": [{"subitem_select_item": "21 生命体科学専攻"}]}, "item_1_text_10": {"attribute_name": "学位授与年度", "attribute_value_mlt": [{"subitem_text_value": "2005"}]}, "item_creator": {"attribute_name": "著者", "attribute_type": "creator", "attribute_value_mlt": [{"creatorNames": [{"creatorName": "YANG, Zhong", "creatorNameLang": "en"}], "nameIdentifiers": [{"nameIdentifier": "0", "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": "乙162_要旨.pdf", "filesize": [{"value": "330.0 kB"}], "format": "application/pdf", "future_date_message": "", "is_thumbnail": false, "licensetype": "license_11", "mimetype": "application/pdf", "size": 330000.0, "url": {"label": "要旨・審査要旨", "url": "https://ir.soken.ac.jp/record/1221/files/乙162_要旨.pdf"}, "version_id": "a6a30fcd-326b-4fa4-9157-b1fa56961e65"}]}, "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": "Bioinformatics for the study of biodiversity", "item_titles": {"attribute_name": "タイトル", "attribute_value_mlt": [{"subitem_title": "Bioinformatics for the study of biodiversity"}, {"subitem_title": "Bioinformatics for the study of biodiversity", "subitem_title_language": "en"}]}, "item_type_id": "1", "owner": "1", "path": ["23"], "permalink_uri": "https://ir.soken.ac.jp/records/1221", "pubdate": {"attribute_name": "公開日", "attribute_value": "2010-02-22"}, "publish_date": "2010-02-22", "publish_status": "0", "recid": "1221", "relation": {}, "relation_version_is_last": true, "title": ["Bioinformatics for the study of biodiversity"], "weko_shared_id": -1}