{"created":"2023-06-20T13:21:06.768221+00:00","id":1208,"links":{},"metadata":{"_buckets":{"deposit":"f3b15f84-f88f-4360-9d35-b24c32c7026b"},"_deposit":{"created_by":1,"id":"1208","owners":[1],"pid":{"revision_id":0,"type":"depid","value":"1208"},"status":"published"},"_oai":{"id":"oai:ir.soken.ac.jp:00001208","sets":["2:431:23"]},"author_link":["10202","10200","10201"],"item_1_creator_2":{"attribute_name":"著者名","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"西本, 由利子"}],"nameIdentifiers":[{}]}]},"item_1_creator_3":{"attribute_name":"フリガナ","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"ニシモト, ユリコ"}],"nameIdentifiers":[{}]}]},"item_1_date_granted_11":{"attribute_name":"学位授与年月日","attribute_value_mlt":[{"subitem_dategranted":"2003-09-30"}]},"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_12":{"attribute_name":"要旨","attribute_value_mlt":[{"subitem_description":"Molecular phylogenetic analyses using multiple sequence data were performed by maximum likelihood (ML) methods for attempts to reach a consensus on tree topology in order to reconstruct a reliable tree and to estimate divergence dates for the urophyllum group in the genus Fagopyrum (Polygonaceae).  In Chapter 1, nucleotide sequences of rbcL-accD, tri intron, and trnC-rpoB spacer region in chloroplast DNA (cpDNA) and the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA) available from GenBank database were re-examined for phylogenetic inference and tree topologies estimated from these different genes were compared.  A statistical analysis by the Kishino-Hasegawa (KH) test indicated that the tree topologies might be different between the nuclear and chloroplast DNA phylogenies, although insufficient taxon sampling in the nrDNA ITS sequence data did not allow me to decide whether the topological incongruence is real.  Topological incongruence among gene trees may include important issues on evolution, and therefore confirmation by the other evidence is needed.  For this purpose, in Chapter 2, two novel nuclear genes:  FLORICAUIA/LEAFY (FLU/LFY) and AGAMOUS (AG) were isolated from all the Fagopyrum species.  The FLU/LFY and AG sequences turned out to be phylogenetically more informative at the intrageneric level than the cpDNA sequences. Congruence among these gene trees, inferred by the KH-test, demonstrated that topologies were partially incongruent between the nuclear and chloroplast DNA phylogenies.  The nuclear DNA sequence data supported a monophyletic relation of F. statice, F. leptopodum, F.  gilesii, and F. jinshaense, whereas the former two species formed another monophyletic relation with the F. capillatum-F. gracilipes-F. gracilipedoides-F. rubfolium clade excluding F. jinshaense in the synthetic cpDNA phylogeny.  In addition, two divergent sequences of FLO/LFY were found in F. rubfolium (tetraploid).  One of these was sister to F. gracilipedoides and another was sister to F. statice, and a monophyletic relation of these two genes was rejected by a bootstrap analysis.  These results suggest that hybridization may have occurred during diversification of Fagopyrum species in the urophyllum group, and that F. rubfolium is possibly allotetraploid species.  In Chapter 3 and Chapter 4, molecular dating was performed in order to have another insight into Fagopyrum evolution.  Because conflict over time scale has been explained by potential sources of error and bias in estimations based on molecular clock methods, these factors that affect dating should be considered accurately.  In Chapter 3, I performed date estimation by a Bayesian approach that can evaluate heterogeneity in the evolutionary rate among lineages in the framework of land plants, using fossil data to yield constraints on some node times.  Dates estimated from different genes (atpB, rbcL, and 18S rDNA) were fairly consistent but they were sensitive to the number of calibrations involved.  The best estimate derived from rbcL calibrated with five fossil dates showed a reasonable time scale for angiosperm evolution, suggesting that the improved technique of molecular date estimation may provide evolutionary implications, especially for lineages for which sufficient fossil information is not available, such as Fagopyrum.  The date for divergence between Polygonum and Fagopyrum was estimated to be 30 MYA.  The date for separation between the two Fagopyrum subgroups was estimated to be 20 MYA.  In Chapter 4, using the 20 MYA date for the Fagopyrum subgroup separation as a reference, divergence dates among Fagopyrum species were estimated with FLU/LFY and AG by the ML method that assumed local molecular clocks.  Divergence dates of each Fagopyrum subgroup were estimated to be 9.6 MYA for the cymosum group and 8.2 MYA for the urophyllum group.<br />  The primary object of this thesis is to reconstruct phylogenetic trees, in which various phylogenetic and evolutionary questions should be addressed by using multiple sequence data.  In alternative methods of maximum parsimony (MP), neighbor joining (NJ), and maximum likelihood (ML), the ML method is the most helpful to deal with a number of sequence data for investigating topological differences among the gene trees and for synthesizing these results into total evidence.  By comparing likelihood scores, the ML method provides comprehensive ways for testing specific hypotheses.  Therefore, I mainly used the ML method in order to elucidate hypothetical issues on topological incongruence.  The second object of my study is to estimate divergence date of Fagopyrum.  Because the molecular clock assumption for the land plant lineages was rejected by the ML method (the KH test), I used the Bayesian approach that explicitly models molecular evolution.  This method has advantages of putting several constraints on node times at once and of estimating confidence interval.  Additionally, I used the ML method with assuming local molecular clocks for date estimation in Fagopyrum.  In this thesis, I discussed Fagopyrum evolution particularly for the urophyllum group, highlighting the occurrence of hybridization and allopolyploidization and the time scale of evolution potentially related to the uplift of the Tibetan plateau on the basis of the multiple gene analysis.","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730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":"2003"}]},"item_creator":{"attribute_name":"著者","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"NISHIMOTO, Yuriko","creatorNameLang":"en"}],"nameIdentifiers":[{}]}]},"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","filename":"甲730_要旨.pdf","filesize":[{"value":"312.6 kB"}],"format":"application/pdf","licensetype":"license_11","mimetype":"application/pdf","url":{"label":"要旨・審査要旨 / Abstract, Screening Result","url":"https://ir.soken.ac.jp/record/1208/files/甲730_要旨.pdf"},"version_id":"c02dbc58-521c-43c0-ab22-9dfbfd1a28c6"}]},"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 phylogenetic analysis of the urophyllum  group in the genus Fagopyrum by the maximum  likelihood method.","item_titles":{"attribute_name":"タイトル","attribute_value_mlt":[{"subitem_title":"Molecular phylogenetic analysis of the urophyllum  group in the genus Fagopyrum by the maximum  likelihood method."},{"subitem_title":"Molecular phylogenetic analysis of the urophyllum  group in the genus Fagopyrum by the maximum  likelihood method.","subitem_title_language":"en"}]},"item_type_id":"1","owner":"1","path":["23"],"pubdate":{"attribute_name":"公開日","attribute_value":"2010-02-22"},"publish_date":"2010-02-22","publish_status":"0","recid":"1208","relation_version_is_last":true,"title":["Molecular phylogenetic analysis of the urophyllum  group in the genus Fagopyrum by the maximum  likelihood method."],"weko_creator_id":"1","weko_shared_id":1},"updated":"2023-06-20T14:39:40.254930+00:00"}