{"created":"2023-06-20T13:20:49.802906+00:00","id":884,"links":{},"metadata":{"_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":["2:430:20"]},"author_link":["9822","9823","9824"],"item_1_creator_2":{"attribute_name":"著者名","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"近藤, るみ"}],"nameIdentifiers":[{}]}]},"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":[{}]}]},"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_12":{"attribute_name":"要旨","attribute_value_mlt":[{"subitem_description":" This dissertation addresses the 4.9 kb (kilobases) nucleotide sequences of
mitochondrial (mt) DNAs from five hominoid species (common and pygmy
chimpanzees, gorilla, orangutan and simang), and presents their detailed analyses,
together with the known human whole sequence, to assess the tempo and mode of
hominoid mtDNA evolution. Particular attention was paid to the rate of
synonymous substitutions in protein coding region as well as of silent substitutions
in other regions. This work was further extended to the whole mitochondrial
genomes of four hominoid species (human, common chimpanzee,′ gorilla and
orangutan) with additionally determined l0 to 12 kb mtDNAs from common
chimpanzee, goriIIa and orangutan. These hominoid mtDNAs revealed several
functionally and evolutionarily characteristic features and provided useful
information on the history of hominoid species.
Most significant observations drawn from the present data are summarized as
follows. First, comparsion of the base compositions in any specified region of
hominoid mtDNAs showed a strong base composition bias, as observed in other
vertebrate mtDNAs. The L-stand of hominoid mtDNAs is rich in A (adenine) and
C (cytosine) contents, but low in G (guanine) content. Base composition biases are
strongest at the third codon positions and are evident along the whole genome,
independent of the genomic regions. Both codon usage and amino acid preference
of mitochondrial protein genes are in agreement with the base composition biases.
These observations suggested that there is a biased mutation pressure in mtDNA.
A possible cause may be differential diaminations of C residues owing to the
asymmetric replication of both L- and H-strands of mtDNA. It is possible that
diffferential deamination has resulted in the reduced number of C residues in the H-
strand,although there has been no clear evidence for this possibility in hominoid
mtDNAs.
Second, there exist functionally important nucleotide sites over the genome.
Together with information on tertiary structures of proteins, as Well as on
secondary structures of transfer (t) RNAs, ribosomal (r) RNA genes and noncoding
regions, the distributjon of variable sites among hominoid mtDNAs suggested that
some nucleotide sites have been playing important roles in peptide folding,
assembly of proteins, or interaction to some other proteins and regulatory elements.
Noteworthy are two functionally distinct regions in the maior noncoding region (D-
loop). One is concerned with promoter sequences for transcripdon and the other is
with three conserved blocks. Oranguan mtDNA sequence revealed unusual
substitutions at both of these regions. This suggested that the replication and
transcription machinery in orangutan mtDNA may differ from that of other
hominoid mtDNAs.
Third, comparsion of nucleotide differences observed among closely related
hominoids revealed a remarkably biased mode of changes. Between human and
chimpanzee, 70% of the observed nuculeotide differences are silent changes that
occur mostly in the small noncoding regions or at the third codon positions of
protein genes. Extensive deletions and additions are observed, but they are found
only in the noncoding regions. Such observations suggested a conserved mode of
the evolution of hominoid mtDNA genomes. There is also a strong preference to
transitions over transversions. Out of 852 variable third positions of codons
between the human and common chimpanzee mtDNAs, 93% account for
transitions of which 66% are TC transitions (in the L-strand). Within the
remaming 7% transversions, CA differences are most frequent while GT are least.
These substitution biases correlate well with biased base compositions, particularly
the low G content of the L-strand.
Fourth, owing to the outnumbered transitions and strong biases in the base
compositions, synonymous substitutions reach rapidly a rather low saturation
level. AG transitions attain a saturation level lower than TC transitions (in the L-
strand), and such a low ceiling is observed even between the human and
chimpanzee pair that diverged around five million years ago. At present,it seems
inevitable to select appropriate regions that have experienced theoretically tractable
numbers of substitutions.In the case of hominoid mtDNAs, candidates are all types
of changes in the tRNA and rRNA regions, transversions in the noncoding regions,
and nonsynonymous changes and synonymous transversions in the protein coding
regions.
Fifth, rapidly evolving mtDNAs are potentially useful for addressing classical
issues in taxonomy, provided that each nucletide site has not undergone extensive
multiple-hit substitutions. From the Whole 16209 sites of mtDNAS compared
among the four hominoid specles, it appears that 12137 such sites are suitable to
phylogenetic use. The analysis strengthened the pattern and dating in hominoid
diversifjcation infened from the Previous analysis of 4.9 kb reglon in six homjnoid
species(among African apes,gorilla diverged first about 7.7 million years ago and
then chimpanzee and human became distinct about 4.7 million years ago).
Finally, the synonymous and nonsynonymous substitution rates were
examined under the assumption of the gorilla divergence being 7.7 miIIion years
ago. The extent of the compositional biases differs from gene to gene. Such
differences in base compositions, even if small, can bring about considerable
variations in observed synonymous differences, and may result in the region-
dependent estimate of the synonymous substitution rate. A care should be taken
for heterogeneous transition and base composition biases as Well as different
saturation levels of transition changes. The synonymous substitution rate
estimated with this caution showed the uniformity over genes (2.37 ± 0.11 x 10-8 per
site per year) and the high transition rate, about 17 times faster than the
transversion rate. These synonymous and transition rates are comparable to the
silent substitution rate in the noncoding segments dispersed between genes. On the
other hand, the rate of nonsynonymous substitutions differs considerably from
gene to gene as expected under the neutral theory of molecular evolution. The
average differences in the gorilla - human and gorilla - chimpanzee comparisons
indicated that the lowest rate is 0.7 x 10-9 per site per year for COI and that the
highest rate is 5.7 x 10-9 for ATPase 8. The degree of functional constraints
(measured by the ratio of the nonsynonymous to the synonymous substitution rate)
is 0.03 for COI and 0.24 for ATPase 8. tRNA genes also showed variability in the
base content and thus in the extent of nucleotide differences as well. The
substitution rate averaged over 22 tRNAS is 5.6 x 10-9 per site per year. The rate for
12S rRNA and 16S rRNA is 4.1 x 10-9 and 6.9 x 10-9 per site per year. respectively.
All of these observations strongly suggested that mutations themselves occur more
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_creator":{"attribute_name":"著者","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"KONDO, Rumi","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48_要旨.pdf","filesize":[{"value":"380.3 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/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","filename":"甲48_本文.pdf","filesize":[{"value":"4.8 MB"}],"format":"application/pdf","licensetype":"license_11","mimetype":"application/pdf","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"],"pubdate":{"attribute_name":"公開日","attribute_value":"2010-02-22"},"publish_date":"2010-02-22","publish_status":"0","recid":"884","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_creator_id":"1","weko_shared_id":1},"updated":"2023-06-20T14:43:29.736160+00:00"}