@misc{oai:ir.soken.ac.jp:00001222,
 author = {松井, 淳 and マツイ, アツシ and MATSUI, Atsushi},
 month = {2016-02-17},
 note = {Primate evolution draws special attention because of its direct relevance to the <br />human origins. Particularly, prosimians (tarsiers and strepsirrhini) are the first diverged <br />species among primates and have a close relation with the primate origin. In addition, <br />the adaptive radiation among prosimians of Madagascar provides an excellent model for <br />studies of evolutionary diversification. The phylogenetic relationships and divergence <br />times of primates have been of special interest to anthropologists and evolutionary <br />biologists. <br />　　　Chapter 1 presents the classification and the features of primates, especially <br />prosimians. <br />　　　In my study, complete mitochondrial DNA (mtDNA) sequences of primates <br />were used. I review the nature and characteristics of mtDNA in chapter 2. <br />　　　It is sometimes the most difficult step in such studies to get samples particularly <br />from endangered species. In chapter 3, I show a successful  amplification and <br />sequencing of mt-genome of Propithecus (sifaka) from feces sample, using the extract <br />method of Chelex-100 Phenol-Chloroform or QIAamp DNA Stool kit (Qiagen) in <br />combination with FTA cards (Whatmann). For biologists, such a noninvasive sampling <br />method should be an important resource that will provide greater opportunities to <br />collect and to use invaluable samples. By using the mt-genome sequence of sifaka <br />obtained by this work with other published sequences of primates, I estimated the <br />phylogeny of primates, and demonstrated that the evolutionary rate acceleration, <br />particularly in the amino acid level, occurred in the Anthropoids lineage after they <br />diverged from tarsier. <br />　　　Major lineages among anthropoidea are well represented by complete mtDNA <br />sequence data, but only one complete mtDNA sequence from a representative of each of <br />the infraorders in prosimians (<i>Nycticebus coucang</i> (lorisiformes), <i>Lemur catta</i> <br />(lemuriformes), <i>Tarsius bancanus</i> (tarsiiformes)) has been described. So, I determined <br />new complete mtDNA sequences from 6 lemurs (including the sifaka described in <br />chapter 3), 5 lorises and one platyrrhini and combined the data set with the 14 primates<br />sequences reported to the data base in order to carry out an extended study of the<br />prosimian relationships among primates. In chapter 4, I present the first systematic<br /> analyses using abundant complete mt genome data derived from 11 prosimians;, <br />representatives of three families out of five of lemuriformes, the Asian lorisidae (south <br />Asia, south-east Asia) and the African lorisidae and galagidae from lorisiformes, and <br />tarsiiformes. The purposes of this study are (1) to clarify problematic relationships <br />among prosimians based on mtDNA data and (2) to investigate the advantage of <br />mtDNA data in studying the phylogenetics of primates. The position of tarsiers among <br />primates and the question of the lorisidae monophyly could not be resolved by the <br />maximum likelihood (ML) and neibor-joining (NJ) analyses with several data sets. The <br />KH and SH tests indicated that the differences between several alternative trees are not<br />significant. As to the position of tarsiers, three alternative topologies (the monophyly of<br />haplorrhini, the monophyly of prosimians, and tarsiers being the basal position in<br />primates) were not rejected at the significance level of 5%, neither at the nucleotide nor<br /> at the amino acid level. As to lorisiformes, three distinct lineages (African lorisidae<br />(potto, <i>Perodicticus</i>), Asian lorisidae (<i>Loris</i> and <i>Nycticebus</i>), and monophyly galagidae<br />(<i>Galago</i> and <i>Otolemzur</i>)) were detected as well. In addition, the significant variations of<br /> C and T compositions were observed across primates. <br />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. <br />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. <br />　　　Although the phylogenetic relationships of living primate species are relatively <br />well established, the divergence times of living primates estimated by molecular data <br />and the biogeographic history of primates are still controversial. Furthermore, the <br />estimation of the divergence date of lemuriformes-lorisiformes and the adaptive <br />radiation among lemurs endemic to Madagascar was still problematic due to the lack of <br />terrestrial fossils from the Tertiary of Madagascar. In chapter 5, I estimate and discuss <br />the divergence dates among primates species. To estimates the speciation dates within <br />primates, particularly within strepsirrhini, I used the new mt genome sequence data <br />from 12 primates together with those from 14 primates and 26 nonprimate mammals <br />available in the public databases. I used amino acid sequences of mtDNA for estimating<br /> divergence times of distantly related species and employed a Bayesian method (Thorne<br /> et al. 1998, Thorne and Kishino 2002). The Bayesian approach does not assume a<br />uniform clock and does not require prior specification of rates for branches and permits<br /> the incorporation of multiple constraints from the fossil record. Seven calibration points,<br /> including one calibration within the primate clade, were used based on paleontological<br /> data. Divergence ages were estimated in this study for the following crown groups:<br /> 33.1±3.7 (26.2-40.8) million years ago (mya) for lorisidae, 20.6±3.1 (23.4-39.2) mya for<br /> galagidae, 36.5±3.8 (29.3-44.4) mya for lorisiformes, 26.2±3.3 (20.2-33.0) mya for<br /> lemuridae, 55.6±3.8 (48.1-63.2) mya for lemuriformes, 64.5±3.6 (57.5-71.7) mya for<br /> strepsirrhini, 70.2±3.4 (63.5-77.2) mya for haplorrhini. and 76.0±3.3 (69.5-82.7) mya<br /> for primates. The lorisiformes diverged 36.5±3.8 (29.3-44.4) mya into Galagidae and<br /> Lorisidae which is well in agreement with the recently discovered fossils by Seiffert et<br /> al. (2003) from the late Middle Eocene, which suggested that the basal divergence<br /> between extant Galagidae and Lorisidae was under way by at least 38-40 mya. <br />　　　In chapter 6, I reexamined the biogeographic scenarios proposed for the origin <br />of strepsirrhini (lemuriformes and lorisiformes) and dispersal of the lemuriformes and <br />lorisiformes with the data obtained by this study, as well as the fossil record and the <br />geological history of the relevant geographic areas. The enigmatic questions in <br />strepsirrhine evolution are when and how lemurs first arrived in Madagascar, when and<br /> how lorises spread over Asia and Africa. By using the correlations between divergence <br /> age and geological conditions, I hoped to gain a better understanding of the speciation <br /> scenarios of lemuriformes and lorisiformes. The extant strepsirrhini colonize Africa, <br /> Asia, and Madagascar. Where is the origin of strepsirrhini? In this study, two <br />hypotheses arise about dispersal and migration of strepsirrhini. One hypothesis is that <br />strepsirrhines originated in Africa and that Madagascar and Asia were colonized by <br />respective single immigration events. In agreement with paleocontinental data, the <br />molecular analyses suggest a crossing of the Mozambique Channel by rafting or <br />hopping island between the late Cretaceous and the middle Eocene, whereas Asia was <br />most likely colonized between the early Eocene and the middle Oligocene on a <br />continental route. Combining the colonization theories, it seems likely that the initial <br />separation between lemuriformes and lorisiformes occurred in Africa, followed by a <br />monophylic lemuriformes progenitor invading Madagascar. In Africa, the lorisiformes <br />subsequently underwent two major splitting events, with a first one separating galagidae<br /> and lorisidae and a second one leading to two lorisidae lineages, of which one migrated<br /> to Asia. Another hypothesis is that that strepsirrhini originally inhabited <br />Indo-Madagascar, rather than Africa, and that lemurs became isolated when Madagascar<br /> separated from India, on which the ancestral lorisiformes evolved. Subsequently, lorises<br /> could have migrated to Africa after India collided with Asia, reaching Africa during the<br /> Eocene.The Indo-Madagascar continent split from the African mainland and reached its<br /> current position 400 km east of Africa 121 mya. Later, 88 mya, the Indian subcontinent<br /> split from Madagascar, drifting north-eastward and colliding with Asia 56-66 mya. <br />A  later time of breakup between the Indian and Malagasy or an earlier divergence of <br />strepsirrhini might be compatible with this Indo-Madagascar origin hypothesis. <br /><i>Bugtilemur</i> fossil clearly enhances the critical role of the Indian subcontinent in the <br />early diversification of lemurs and constrains paleobiogeographic models of <br />strepsirrhine lemur evolution (Marivaux et al. 2001). However, this fossil suggested <br />another interpretation that Bugtilemur might alternatively be interpreted as a very <br />specialized adapiforms (Marivaux et al. 2006) and is needed more discussion. A similar <br />scenario (adapted from molecular data) has been suggested for the Indian frog (Biju and <br /> Bossuyt 2003) and the ratites, large flightless birds (Cooper et al. 2001). <br />, 総研大甲第1076号},
 title = {Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs},
 year = {}
}