{"_buckets": {"deposit": "1726e0e4-3987-4251-8391-337c45cb5d93"}, "_deposit": {"created_by": 1, "id": "1222", "owners": [1], "pid": {"revision_id": 0, "type": "depid", "value": "1222"}, "status": "published"}, "_oai": {"id": "oai:ir.soken.ac.jp:00001222", "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": "2007-03-23", "bibliographicIssueDateType": "Issued"}, "bibliographic_titles": [{}]}]}, "item_1_creator_2": {"attribute_name": "著者名", "attribute_type": "creator", "attribute_value_mlt": [{"creatorNames": [{"creatorName": "松井, 淳"}], "nameIdentifiers": [{"nameIdentifier": "0", "nameIdentifierScheme": "WEKO"}]}]}, "item_1_creator_3": {"attribute_name": "フリガナ", "attribute_type": "creator", "attribute_value_mlt": [{"creatorNames": [{"creatorName": "マツイ, アツシ"}], "nameIdentifiers": [{"nameIdentifier": "0", "nameIdentifierScheme": "WEKO"}]}]}, "item_1_date_granted_11": {"attribute_name": "学位授与年月日", "attribute_value_mlt": [{"subitem_dategranted": "2007-03-23"}]}, "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（学術）"}]}, "item_1_description_1": {"attribute_name": "ID", "attribute_value_mlt": [{"subitem_description": "2007061", "subitem_description_type": "Other"}]}, "item_1_description_12": {"attribute_name": "要旨", "attribute_value_mlt": [{"subitem_description": "　　Primate evolution draws special attention because of its direct relevance to the \u003cbr /\u003ehuman origins. Particularly, prosimians (tarsiers and strepsirrhini) are the first diverged \u003cbr /\u003especies among primates and have a close relation with the primate origin. In addition, \u003cbr /\u003ethe adaptive radiation among prosimians of Madagascar provides an excellent model for \u003cbr /\u003estudies of evolutionary diversification. The phylogenetic relationships and divergence \u003cbr /\u003etimes of primates have been of special interest to anthropologists and evolutionary \u003cbr /\u003ebiologists. \u003cbr /\u003e　　　Chapter 1 presents the classification and the features of primates, especially \u003cbr /\u003eprosimians. \u003cbr /\u003e　　　In my study, complete mitochondrial DNA (mtDNA) sequences of primates \u003cbr /\u003ewere used. I review the nature and characteristics of mtDNA in chapter 2. \u003cbr /\u003e　　　It is sometimes the most difficult step in such studies to get samples particularly \u003cbr /\u003efrom endangered species. In chapter 3, I show a successful  amplification and \u003cbr /\u003esequencing of mt-genome of Propithecus (sifaka) from feces sample, using the extract \u003cbr /\u003emethod of Chelex-100 Phenol-Chloroform or QIAamp DNA Stool kit (Qiagen) in \u003cbr /\u003ecombination with FTA cards (Whatmann). For biologists, such a noninvasive sampling \u003cbr /\u003emethod should be an important resource that will provide greater opportunities to \u003cbr /\u003ecollect and to use invaluable samples. By using the mt-genome sequence of sifaka \u003cbr /\u003eobtained by this work with other published sequences of primates, I estimated the \u003cbr /\u003ephylogeny of primates, and demonstrated that the evolutionary rate acceleration, \u003cbr /\u003eparticularly in the amino acid level, occurred in the Anthropoids lineage after they \u003cbr /\u003ediverged from tarsier. \u003cbr /\u003e　　　Major lineages among anthropoidea are well represented by complete mtDNA \u003cbr /\u003esequence data, but only one complete mtDNA sequence from a representative of each of \u003cbr /\u003ethe infraorders in prosimians (\u003ci\u003eNycticebus coucang\u003c/i\u003e (lorisiformes), \u003ci\u003eLemur catta\u003c/i\u003e \u003cbr /\u003e(lemuriformes), \u003ci\u003eTarsius bancanus\u003c/i\u003e (tarsiiformes)) has been described. So, I determined \u003cbr /\u003enew complete mtDNA sequences from 6 lemurs (including the sifaka described in \u003cbr /\u003echapter 3), 5 lorises and one platyrrhini and combined the data set with the 14 primates\u003cbr /\u003esequences reported to the data base in order to carry out an extended study of the\u003cbr /\u003eprosimian relationships among primates. In chapter 4, I present the first systematic\u003cbr /\u003e analyses using abundant complete mt genome data derived from 11 prosimians;, \u003cbr /\u003erepresentatives of three families out of five of lemuriformes, the Asian lorisidae (south \u003cbr /\u003eAsia, south-east Asia) and the African lorisidae and galagidae from lorisiformes, and \u003cbr /\u003etarsiiformes. The purposes of this study are (1) to clarify problematic relationships \u003cbr /\u003eamong prosimians based on mtDNA data and (2) to investigate the advantage of \u003cbr /\u003emtDNA data in studying the phylogenetics of primates. The position of tarsiers among \u003cbr /\u003eprimates and the question of the lorisidae monophyly could not be resolved by the \u003cbr /\u003emaximum likelihood (ML) and neibor-joining (NJ) analyses with several data sets. The \u003cbr /\u003eKH and SH tests indicated that the differences between several alternative trees are not\u003cbr /\u003esignificant. As to the position of tarsiers, three alternative topologies (the monophyly of\u003cbr /\u003ehaplorrhini, the monophyly of prosimians, and tarsiers being the basal position in\u003cbr /\u003eprimates) were not rejected at the significance level of 5%, neither at the nucleotide nor\u003cbr /\u003e at the amino acid level. As to lorisiformes, three distinct lineages (African lorisidae\u003cbr /\u003e(potto, \u003ci\u003ePerodicticus\u003c/i\u003e), Asian lorisidae (\u003ci\u003eLoris\u003c/i\u003e and \u003ci\u003eNycticebus\u003c/i\u003e), and monophyly galagidae\u003cbr /\u003e(\u003ci\u003eGalago\u003c/i\u003e and \u003ci\u003eOtolemzur\u003c/i\u003e)) were detected as well. In addition, the significant variations of\u003cbr /\u003e C and T compositions were observed across primates. \u003cbr /\u003eThese variations of base composition could sort primates to three groups. The first group is catarrhini, higher primates involving human, having a high percentage of C. The second group consists of platyrrhini, tarsiiformes, and lemuriformes having a low percentage of C. The third group is lorisiformes having an intermediate percentage of C between the above 2 groups. These variations of base composition across primates were found some significant correlation to codon and amino acid bias and they might affect the phylogenetic analyses. Furthermore, I used AGY data sets for phylogenetic analyses in order to retain information from transitions between purines and to remove the effect of transition between pyrimidines. As to the analyses of protein-encoding region, the support value of the position of tarsiers branching off first among primates were decreased from 85% to 60% with the HKY + Γ model, from 88% to 57% with the GTR + Γ model using data excluding third codon positions and decreased as well using all codon position data. The rRNA data sets yielded the topology, with tarsier and the anthropoids forming a monophyletic group where bootstrap support increased from 34% to 57% with the HKY + Γ model and from 36% to 60% with the GTR + Γ model. \u003cbr /\u003eIn this study, the ML analyses could not give a fu11y resolved and reasonable inference about the problematic taxa, that is, tarsiers and potto. The analyses of AGY data sets, however, provided a medium support for the monophyly of haplorhini. I feel that the monophyly of haplorhini might be screened by the variation in base composition of mtDNA across species. \u003cbr /\u003e　　　Although the phylogenetic relationships of living primate species are relatively \u003cbr /\u003ewell established, the divergence times of living primates estimated by molecular data \u003cbr /\u003eand the biogeographic history of primates are still controversial. Furthermore, the \u003cbr /\u003eestimation of the divergence date of lemuriformes-lorisiformes and the adaptive \u003cbr /\u003eradiation among lemurs endemic to Madagascar was still problematic due to the lack of \u003cbr /\u003eterrestrial fossils from the Tertiary of Madagascar. In chapter 5, I estimate and discuss \u003cbr /\u003ethe divergence dates among primates species. To estimates the speciation dates within \u003cbr /\u003eprimates, particularly within strepsirrhini, I used the new mt genome sequence data \u003cbr /\u003efrom 12 primates together with those from 14 primates and 26 nonprimate mammals \u003cbr /\u003eavailable in the public databases. I used amino acid sequences of mtDNA for estimating\u003cbr /\u003e divergence times of distantly related species and employed a Bayesian method (Thorne\u003cbr /\u003e et al. 1998, Thorne and Kishino 2002). The Bayesian approach does not assume a\u003cbr /\u003euniform clock and does not require prior specification of rates for branches and permits\u003cbr /\u003e the incorporation of multiple constraints from the fossil record. Seven calibration points,\u003cbr /\u003e including one calibration within the primate clade, were used based on paleontological\u003cbr /\u003e data. Divergence ages were estimated in this study for the following crown groups:\u003cbr /\u003e 33.1±3.7 (26.2-40.8) million years ago (mya) for lorisidae, 20.6±3.1 (23.4-39.2) mya for\u003cbr /\u003e galagidae, 36.5±3.8 (29.3-44.4) mya for lorisiformes, 26.2±3.3 (20.2-33.0) mya for\u003cbr /\u003e lemuridae, 55.6±3.8 (48.1-63.2) mya for lemuriformes, 64.5±3.6 (57.5-71.7) mya for\u003cbr /\u003e strepsirrhini, 70.2±3.4 (63.5-77.2) mya for haplorrhini. and 76.0±3.3 (69.5-82.7) mya\u003cbr /\u003e for primates. The lorisiformes diverged 36.5±3.8 (29.3-44.4) mya into Galagidae and\u003cbr /\u003e Lorisidae which is well in agreement with the recently discovered fossils by Seiffert et\u003cbr /\u003e al. (2003) from the late Middle Eocene, which suggested that the basal divergence\u003cbr /\u003e between extant Galagidae and Lorisidae was under way by at least 38-40 mya. \u003cbr /\u003e　　　In chapter 6, I reexamined the biogeographic scenarios proposed for the origin \u003cbr /\u003eof strepsirrhini (lemuriformes and lorisiformes) and dispersal of the lemuriformes and \u003cbr /\u003elorisiformes with the data obtained by this study, as well as the fossil record and the \u003cbr /\u003egeological history of the relevant geographic areas. The enigmatic questions in \u003cbr /\u003estrepsirrhine evolution are when and how lemurs first arrived in Madagascar, when and\u003cbr /\u003e how lorises spread over Asia and Africa. By using the correlations between divergence \u003cbr /\u003e age and geological conditions, I hoped to gain a better understanding of the speciation \u003cbr /\u003e scenarios of lemuriformes and lorisiformes. The extant strepsirrhini colonize Africa, \u003cbr /\u003e Asia, and Madagascar. Where is the origin of strepsirrhini? In this study, two \u003cbr /\u003ehypotheses arise about dispersal and migration of strepsirrhini. One hypothesis is that \u003cbr /\u003estrepsirrhines originated in Africa and that Madagascar and Asia were colonized by \u003cbr /\u003erespective single immigration events. In agreement with paleocontinental data, the \u003cbr /\u003emolecular analyses suggest a crossing of the Mozambique Channel by rafting or \u003cbr /\u003ehopping island between the late Cretaceous and the middle Eocene, whereas Asia was \u003cbr /\u003emost likely colonized between the early Eocene and the middle Oligocene on a \u003cbr /\u003econtinental route. Combining the colonization theories, it seems likely that the initial \u003cbr /\u003eseparation between lemuriformes and lorisiformes occurred in Africa, followed by a \u003cbr /\u003emonophylic lemuriformes progenitor invading Madagascar. In Africa, the lorisiformes \u003cbr /\u003esubsequently underwent two major splitting events, with a first one separating galagidae\u003cbr /\u003e and lorisidae and a second one leading to two lorisidae lineages, of which one migrated\u003cbr /\u003e to Asia. Another hypothesis is that that strepsirrhini originally inhabited \u003cbr /\u003eIndo-Madagascar, rather than Africa, and that lemurs became isolated when Madagascar\u003cbr /\u003e separated from India, on which the ancestral lorisiformes evolved. Subsequently, lorises\u003cbr /\u003e could have migrated to Africa after India collided with Asia, reaching Africa during the\u003cbr /\u003e Eocene.The Indo-Madagascar continent split from the African mainland and reached its\u003cbr /\u003e current position 400 km east of Africa 121 mya. Later, 88 mya, the Indian subcontinent\u003cbr /\u003e split from Madagascar, drifting north-eastward and colliding with Asia 56-66 mya. \u003cbr /\u003eA  later time of breakup between the Indian and Malagasy or an earlier divergence of \u003cbr /\u003estrepsirrhini might be compatible with this Indo-Madagascar origin hypothesis. \u003cbr /\u003e\u003ci\u003eBugtilemur\u003c/i\u003e fossil clearly enhances the critical role of the Indian subcontinent in the \u003cbr /\u003eearly diversification of lemurs and constrains paleobiogeographic models of \u003cbr /\u003estrepsirrhine lemur evolution (Marivaux et al. 2001). However, this fossil suggested \u003cbr /\u003eanother interpretation that Bugtilemur might alternatively be interpreted as a very \u003cbr /\u003especialized adapiforms (Marivaux et al. 2006) and is needed more discussion. A similar \u003cbr /\u003escenario (adapted from molecular data) has been suggested for the Indian frog (Biju and \u003cbr /\u003e Bossuyt 2003) and the ratites, large flightless birds (Cooper et al. 2001). \u003cbr /\u003e", "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1076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": "2006"}]}, "item_creator": {"attribute_name": "著者", "attribute_type": "creator", "attribute_value_mlt": [{"creatorNames": [{"creatorName": "MATSUI, Atsushi", "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": "甲1076_要旨.pdf", "filesize": [{"value": "487.4 kB"}], "format": "application/pdf", "future_date_message": "", "is_thumbnail": false, "licensetype": "license_11", "mimetype": "application/pdf", "size": 487400.0, "url": {"label": "要旨・審査要旨", "url": "https://ir.soken.ac.jp/record/1222/files/甲1076_要旨.pdf"}, "version_id": "63e858fe-3278-45ac-8085-51c8bfcc8f4f"}]}, "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": "Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs", "item_titles": {"attribute_name": "タイトル", "attribute_value_mlt": [{"subitem_title": "Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs"}, {"subitem_title": "Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs", "subitem_title_language": "en"}]}, "item_type_id": "1", "owner": "1", "path": ["23"], "permalink_uri": "https://ir.soken.ac.jp/records/1222", "pubdate": {"attribute_name": "公開日", "attribute_value": "2010-02-22"}, "publish_date": "2010-02-22", "publish_status": "0", "recid": "1222", "relation": {}, "relation_version_is_last": true, "title": ["Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs"], "weko_shared_id": 1}