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Akihito,
Akishinonomiya Fumihito,
Yuji Ikeda,
Masahiro Aizawa,
Takashi Makino,
Yumi Umehara,
Yoshiaki Kai, Yuriko Nishimoto,
Masami Hasegawa,
Tetsuji Nakabo,
Takashi Gojobori
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ABSTRACT: Pterogobius elapoides and Pterogobius zonoleucus are common free-swimming gobies found in rocky and weedy shores along the temperate coast of Japan. We collected individuals of both species from 23 locations around the coast of Japan and compared the mitochondrial nucleotide sequences of two gene regions, CytB and ND2. Phylogenetic trees constructed using the neighbor-joining, maximum parsimony, and maximum likelihood methods consistently indicated that all 125 samples of the two species, which are collected from a variety of locations in Japan, can be clearly divided into the following four clades: "Pacific P. elapoides" (Pa-ela), "Sea of Japan P. elapoides" (SJ-ela), "Pacific P. zonoleucus" (Pa-zon), and "Sea of Japan P. zonoleucus" (SJ-zon). These four monophyletic clades were supported with very high bootstrap values. Although Pa-ela and SJ-ela composed a monophyletic clade, it is noteworthy that the two clades of P. elapoides also formed a monophyletic group together with SJ-zon with a bootstrap value of 95% and 97% by the maximum likelihood and neighbor-joining methods, respectively. We observed several morphological differences between Pa-ela and SJ-ela, including; 1) six dark bands on the body in the former versus seven dark bands in the latter and 2) more pectoral-fin rays numbering 21-24 (mode 22) in the latter compared to the former (19-22, mode 21). Furthermore, the scatter plots of scores on principal components 1 and 2 based on the morphometric characters roughly separated the populations from each other. Moreover, we documented the following morphological differences between Pa-zon and SJ-zon for the first time; 1) six light bands on the body in the former versus five light bands in the latter and 2) the light bands from both eyes forming a complete U-shaped marking on the occipital region occurred in 55% of the specimens in the former versus 16% in the latter. However, no significant differences were found in the morphometric characters between the two populations of P. zonoleucus. The estimated divergence time of the two P. zonoleucus populations was 15.06+/-2.72 (mean+/-1 S.E.) times earlier than that of the two P. elapoides populations. However, the morphological differences between the two populations of the former were much smaller than those of the latter. An explanation for this obvious discrepancy between morphological and molecular features is proposed from an evolutionary point of view.
Gene 11/2008; 427(1-2):7-18. · 2.34 Impact Factor
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ABSTRACT: Unlike other eukaryotes, malaria parasites in the genus Plasmodium have structurally and functionally different paralogous copies of the cytosolic (cyto-) SSU rRNA (18S rRNA) gene that are expressed at different developmental stages. In P. falciparum, P. vivax, and P. berghei, A-type cyto-SSU rRNA is expressed in asexual stage, while S-type in sporozoite stage. A third type (O-type) has been described in P. vivax. It is expressed only in oocyst stage in the mosquito. Recently, it has been shown that the maintenance of heterogeneous cyto-SSU rRNAs in Plasmodium can be modeled as a birth-and-death process under strong purifying selection [Rooney, A.P., 2004. Mechanisms underlying the evolution and maintenance of functionally heterogeneous 18S rRNA genes in Apicomplexans. Mol. Biol. Evol. 21, 1704-1711]. In this study, we performed detailed phylogenetic analyses of Plasmodium cyto-SSU rRNAs with special emphasis on the evolution of multi-copy genes in simian Plasmodium species. We sequenced paralogous copies of the cyto-SSU rRNA genes from an African simian Plasmodium species, P. gonderi, and Asian simian Plasmodium species, P. fragile, P. coatneyi, P. inui, P. hylobati, P. fieldi, P. simiovale, and P. cynomolgi. Interestingly, all Asian simian Plasmodium species have a single S-type-like gene and several A-type-like genes. Alignment analysis demonstrated for the first time that an approximately 50-residue insertion in the V7 variable region near the stem 43 is shared exclusively by the S-type-like sequences of the Asian simian Plasmodium species and the S- and O-type sequences of P. vivax. We comprehensively analyzed all cyto-SSU rRNA sequences of the genus Plasmodium currently available in the database. Phylogenetic analyses of all publicly available cyto-SSU rRNA sequences for the genus Plasmodium clearly demonstrated that gene duplication events giving rise to A- and S-type-like sequences took place independently at least three times in the Plasmodium evolution, supporting the hypothesis that these genes evolve according to a birth-and-death model.
Molecular Phylogenetics and Evolution 05/2008; 47(1):45-53. · 3.61 Impact Factor
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ABSTRACT: Similarly to other members of the Polyomaviridae family, BK virus (BKV) is thought to have co-evolved with its human host. BKV has four subtypes that are distinguishable by immunological reactivity, with two (subtypes I and IV) being most prevalent in human populations. Subtype I is the major subtype worldwide, whereas subtype IV is prevalent in East Asia and Europe but rare in Africa. The geographic distribution pattern of subtype IV BKV is in apparent disagreement with the hypothesis that BKV co-evolved with humans, since subtype IV rarely occurs in Africa. To elucidate the origin of subtype IV, 53 complete subtype IV sequences derived from East Asians and Europeans were subjected to a detailed phylogenetic analysis using the maximum-likelihood and neighbor-joining methods. We identified six subgroups (a1, a2, b1, b2, c1, and c2) that formed a tree represented by the formula: "(a1, a2), ((b1, b2), (c1, c2))." Interestingly, we found a close correlation between subtype IV subgroups and population geography; thus, all subgroups except c2 were prevalent in particular East Asian populations, with c2 occurring in both Europe and Northeast Asia. From these findings, we conclude that subtype IV of BKV now prevalent in modern humans is derived from a virus that infected ancestral Asians. We introduce two hypotheses to explain how ancestral Asians became infected with subtype IV BKV.
Journal of Molecular Evolution 08/2007; 65(1):103-11. · 2.27 Impact Factor
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Huai-Ying Zheng, Yuriko Nishimoto,
Qin Chen,
Masami Hasegawa,
Shan Zhong,
Hiroshi Ikegaya,
Norikazu Ohno,
Chie Sugimoto,
Tomokazu Takasaka,
Tadaichi Kitamura,
Yoshiaki Yogo
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ABSTRACT: BK polyomavirus (BKV) is ubiquitous in human populations, infecting children asymptomatically and then persisting in the kidney, in which it can cause nephropathy in renal transplant patients. BKV isolates are classified into four subtypes (I-IV) using serological or genotyping methods, and subtype I is further divided into four subgroups, Ia, Ib-1, Ib-2, and Ic, based on DNA sequence variations. To clarify whether there is an association between BK virus lineages and human populations, we examined BKV-positive urine samples collected from immunocompetent individuals at various locations in Europe, Africa, and Asia. Partial BKV DNA sequences (n=299) in these samples were determined and subjected to phylogenetic and single nucleotide polymorphism analysis to classify BKV isolates around the world. The validity of the classification was confirmed by analyses based on complete BKV DNA sequences. Subtype I was the major subtype throughout the studied regions, and subtype IV was prevalent only in Asia and Europe. Subtype-I subgroups showed close relationships to major geographical areas. It has recently been shown that JC virus (a human polyomavirus closely related to BKV) co-evolved with human populations, and the present study thus suggests that host-linked evolution is the general mode of polyomavirus evolution. Additionally, our results indicate certain unique aspects of the relationship between BKV and humans.
Microbes and Infection 03/2007; 9(2):204-13. · 3.10 Impact Factor
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ABSTRACT: The human polyomavirus BK virus (BKV) is ubiquitous in humans, infecting children asymptomatically. BKV is the only primate polyomavirus that has subtypes (I-IV) distinguishable by immunological reactivity. Nucleotide (nt) variations in a major capsid protein (VP1) gene region (designated the epitope region), probably responsible for antigenic diversity, have been used to classify BKV isolates into subtypes. Here, with all the protein-encoding gene sequences, we attempted to elucidate the evolutionary relationships among 28 BKV isolates belonging to subtypes I, III, and IV (no isolate belonging to subtype II, a minor one, was included). First, using the GTR + Gamma + I model, maximum likelihood trees were reconstructed for individual viral genes as well as for concatenated viral genes. On the resultant trees, the 28 BKV isolates were consistently divided into three clades corresponding to subtypes I, III, and IV, although bootstrap probabilities are not always high. Then we used more sophisticated likelihood models, one of which takes account of codon structure, to elucidate the phylogenetic relationships among BKV subtypes, but the phylogeny of the deep branchings remained ambiguous. Furthermore, the possibility of positive selection in the evolution of BKV was examined using the nonsynonymous/synonymous rate ratio as a measure of selection. An analysis based on entire genes could not detect any strong evidence for positive selection, but that based on the epitope region identified a few sites potentially under positive selection (these sites were among those showing subtype linked polymorphisms).
Journal of Molecular Evolution 10/2006; 63(3):341-52. · 2.27 Impact Factor
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ABSTRACT: We performed phylogenetic analyses of Fagopyrum species in the urophyllum group based on nucleotide sequences of two nuclear genes, FLORICAULA/LEAFY (FLO/LFY) and AGAMOUS (AG), and three segments of chloroplast DNA (cpDNA), rbcL-accD, trnK intron, and trnC-rpoB spacer. The FLO/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 a maximum-likelihood (ML) method, 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. gilesii, and F. jinshaense, whereas the former two species formed another monophyletic relation with the F. capillatum-F. gracilipes-F. gracilipedoides-F. rubifolium clade excluding F. jinshaense in the synthetic cpDNA phylogeny. In addition, two divergent sequences of FLO/LFY were found in F. rubifolium (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. rubifolium is possibly allotetraploid species.
Genes & Genetic Systems 05/2003; 78(2):139-53. · 0.95 Impact Factor
