{"created":"2023-06-20T13:21:07.378932+00:00","id":1222,"links":{},"metadata":{"_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":["2:431:23"]},"author_link":["0","0","0"],"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_12":{"attribute_name":"要旨","attribute_value_mlt":[{"subitem_description":" Primate evolution draws special attention because of its direct relevance to the
human origins. Particularly, prosimians (tarsiers and strepsirrhini) are the first diverged
species among primates and have a close relation with the primate origin. In addition,
the adaptive radiation among prosimians of Madagascar provides an excellent model for
studies of evolutionary diversification. The phylogenetic relationships and divergence
times of primates have been of special interest to anthropologists and evolutionary
biologists.
Chapter 1 presents the classification and the features of primates, especially
prosimians.
In my study, complete mitochondrial DNA (mtDNA) sequences of primates
were used. I review the nature and characteristics of mtDNA in chapter 2.
It is sometimes the most difficult step in such studies to get samples particularly
from endangered species. In chapter 3, I show a successful amplification and
sequencing of mt-genome of Propithecus (sifaka) from feces sample, using the extract
method of Chelex-100 Phenol-Chloroform or QIAamp DNA Stool kit (Qiagen) in
combination with FTA cards (Whatmann). For biologists, such a noninvasive sampling
method should be an important resource that will provide greater opportunities to
collect and to use invaluable samples. By using the mt-genome sequence of sifaka
obtained by this work with other published sequences of primates, I estimated the
phylogeny of primates, and demonstrated that the evolutionary rate acceleration,
particularly in the amino acid level, occurred in the Anthropoids lineage after they
diverged from tarsier.
Major lineages among anthropoidea are well represented by complete mtDNA
sequence data, but only one complete mtDNA sequence from a representative of each of
the infraorders in prosimians (Nycticebus coucang (lorisiformes), Lemur catta
(lemuriformes), Tarsius bancanus (tarsiiformes)) has been described. So, I determined
new complete mtDNA sequences from 6 lemurs (including the sifaka described in
chapter 3), 5 lorises and one platyrrhini and combined the data set with the 14 primates
sequences reported to the data base in order to carry out an extended study of the
prosimian relationships among primates. In chapter 4, I present the first systematic
analyses using abundant complete mt genome data derived from 11 prosimians;,
representatives of three families out of five of lemuriformes, the Asian lorisidae (south
Asia, south-east Asia) and the African lorisidae and galagidae from lorisiformes, and
tarsiiformes. The purposes of this study are (1) to clarify problematic relationships
among prosimians based on mtDNA data and (2) to investigate the advantage of
mtDNA data in studying the phylogenetics of primates. The position of tarsiers among
primates and the question of the lorisidae monophyly could not be resolved by the
maximum likelihood (ML) and neibor-joining (NJ) analyses with several data sets. The
KH and SH tests indicated that the differences between several alternative trees are not
significant. As to the position of tarsiers, three alternative topologies (the monophyly of
haplorrhini, the monophyly of prosimians, and tarsiers being the basal position in
primates) were not rejected at the significance level of 5%, neither at the nucleotide nor
at the amino acid level. As to lorisiformes, three distinct lineages (African lorisidae
(potto, Perodicticus), Asian lorisidae (Loris and Nycticebus), and monophyly galagidae
(Galago and Otolemzur)) were detected as well. In addition, the significant variations of
C and T compositions were observed across primates.
These 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.
In 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.
Although the phylogenetic relationships of living primate species are relatively
well established, the divergence times of living primates estimated by molecular data
and the biogeographic history of primates are still controversial. Furthermore, the
estimation of the divergence date of lemuriformes-lorisiformes and the adaptive
radiation among lemurs endemic to Madagascar was still problematic due to the lack of
terrestrial fossils from the Tertiary of Madagascar. In chapter 5, I estimate and discuss
the divergence dates among primates species. To estimates the speciation dates within
primates, particularly within strepsirrhini, I used the new mt genome sequence data
from 12 primates together with those from 14 primates and 26 nonprimate mammals
available in the public databases. I used amino acid sequences of mtDNA for estimating
divergence times of distantly related species and employed a Bayesian method (Thorne
et al. 1998, Thorne and Kishino 2002). The Bayesian approach does not assume a
uniform clock and does not require prior specification of rates for branches and permits
the incorporation of multiple constraints from the fossil record. Seven calibration points,
including one calibration within the primate clade, were used based on paleontological
data. Divergence ages were estimated in this study for the following crown groups:
33.1±3.7 (26.2-40.8) million years ago (mya) for lorisidae, 20.6±3.1 (23.4-39.2) mya for
galagidae, 36.5±3.8 (29.3-44.4) mya for lorisiformes, 26.2±3.3 (20.2-33.0) mya for
lemuridae, 55.6±3.8 (48.1-63.2) mya for lemuriformes, 64.5±3.6 (57.5-71.7) mya for
strepsirrhini, 70.2±3.4 (63.5-77.2) mya for haplorrhini. and 76.0±3.3 (69.5-82.7) mya
for primates. The lorisiformes diverged 36.5±3.8 (29.3-44.4) mya into Galagidae and
Lorisidae which is well in agreement with the recently discovered fossils by Seiffert et
al. (2003) from the late Middle Eocene, which suggested that the basal divergence
between extant Galagidae and Lorisidae was under way by at least 38-40 mya.
In chapter 6, I reexamined the biogeographic scenarios proposed for the origin
of strepsirrhini (lemuriformes and lorisiformes) and dispersal of the lemuriformes and
lorisiformes with the data obtained by this study, as well as the fossil record and the
geological history of the relevant geographic areas. The enigmatic questions in
strepsirrhine evolution are when and how lemurs first arrived in Madagascar, when and
how lorises spread over Asia and Africa. By using the correlations between divergence
age and geological conditions, I hoped to gain a better understanding of the speciation
scenarios of lemuriformes and lorisiformes. The extant strepsirrhini colonize Africa,
Asia, and Madagascar. Where is the origin of strepsirrhini? In this study, two
hypotheses arise about dispersal and migration of strepsirrhini. One hypothesis is that
strepsirrhines originated in Africa and that Madagascar and Asia were colonized by
respective single immigration events. In agreement with paleocontinental data, the
molecular analyses suggest a crossing of the Mozambique Channel by rafting or
hopping island between the late Cretaceous and the middle Eocene, whereas Asia was
most likely colonized between the early Eocene and the middle Oligocene on a
continental route. Combining the colonization theories, it seems likely that the initial
separation between lemuriformes and lorisiformes occurred in Africa, followed by a
monophylic lemuriformes progenitor invading Madagascar. In Africa, the lorisiformes
subsequently underwent two major splitting events, with a first one separating galagidae
and lorisidae and a second one leading to two lorisidae lineages, of which one migrated
to Asia. Another hypothesis is that that strepsirrhini originally inhabited
Indo-Madagascar, rather than Africa, and that lemurs became isolated when Madagascar
separated from India, on which the ancestral lorisiformes evolved. Subsequently, lorises
could have migrated to Africa after India collided with Asia, reaching Africa during the
Eocene.The Indo-Madagascar continent split from the African mainland and reached its
current position 400 km east of Africa 121 mya. Later, 88 mya, the Indian subcontinent
split from Madagascar, drifting north-eastward and colliding with Asia 56-66 mya.
A later time of breakup between the Indian and Malagasy or an earlier divergence of
strepsirrhini might be compatible with this Indo-Madagascar origin hypothesis.
Bugtilemur fossil clearly enhances the critical role of the Indian subcontinent in the
early diversification of lemurs and constrains paleobiogeographic models of
strepsirrhine lemur evolution (Marivaux et al. 2001). However, this fossil suggested
another interpretation that Bugtilemur might alternatively be interpreted as a very
specialized adapiforms (Marivaux et al. 2006) and is needed more discussion. A similar
scenario (adapted from molecular data) has been suggested for the Indian frog (Biju and
Bossuyt 2003) and the ratites, large flightless birds (Cooper et al. 2001).
","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","filename":"甲1076_要旨.pdf","filesize":[{"value":"487.4 kB"}],"format":"application/pdf","licensetype":"license_11","mimetype":"application/pdf","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"],"pubdate":{"attribute_name":"公開日","attribute_value":"2010-02-22"},"publish_date":"2010-02-22","publish_status":"0","recid":"1222","relation_version_is_last":true,"title":["Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs"],"weko_creator_id":"1","weko_shared_id":1},"updated":"2023-06-20T15:55:22.631645+00:00"}