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  • 1
    Electronic Resource
    Electronic Resource
    The Phylogenetic Position of the Pelobiont Mastigamoeba balamuthi Based on Sequences of rDNA and Translation Elongation Factors EF-1α and EF-2 (2002)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 49 (2002), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: . The taxonomic position and phylogenetic relationships of the Pelobionta, an amitochondriate amoeboflagellate group, are not yet completely settled. To provide more information, we obtained sequences for the large subunit rDNA gene, the gene for translation elongation factor la, and for a large part of the gene encoding translation elongation factor 2 from a representative of this group. Mastigamoeba balamuthi (formerly Phreatamoeba balamuthi). The gene for the large subunit rDNA was unusually large compared to those of other protists, a phenomenon that had previously been observed for the gene encoding the small subunit rDNA. Phylogenetic reconstruction using a maximum likelihood method was performed with these sequences, as well as the gene encoding the small subunit rDNA. When evaluated individually, the M. balamuthi genes for the small and large subunit rDNAs and elongation factor 1α had a most recent common ancestor with either the Mycetozoa (slime molds) or with Entamoeba histolytica. A clade formed by M. balamuthi, E. histolytica, and Mycetozoa was not rejected statistically for any of the sequences. A combined maximum likelihood analysis using 3,935 positions from all molecules suggested that these three taxonomic units form a robust clade. We were unable to resolve the closest group to this clade using the combined analysis. These findings support the notion, which had previously been proposed primarily on cytological evidence, that both M. balamuthi and E. histolytica are closely related to the Mycetozoa and that these three together represent a major eukaryotic lineage.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2002.tb00332.x
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  • 2
    Electronic Resource
    Electronic Resource
    Phylogenetic Position of Blastocystis hominis and of Stramenopiles Inferred from Multiple Molecular Sequence Data (2002)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 49 (2002), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: . Blastocystis hominis, a parasite of the human intestine, has recently been positioned within Stramenopiles by the small subunit rRNA phylogeny. To further confirm its phylogenetic position using multiple molecular sequence data, we determined the nucleotide sequences putatively encoding small subunit ribosomal RNA, cytosolic-type 70-kDa heat shock protein, translation elongation factor 2, and the non-catalytic ‘B’ subunit of vacuolar ATPase of B. hominis (HE87–1 strain). Moreover, we determined the translation elongation factor 2 sequence of an apicomplexan parasite, Plasmodium falciparum, that belongs to alveolates. The maximum likelihood analyses of small subunit rRNA and cytosolic-type 70-kDa heat shock protein clearly demonstrated that B. hominis (HE87–1 strain) is positioned within Stramenopiles, being congruent with the previous small subunit rRNA analysis, including the sequences of B. hominis (Nand strain) and a Blastocystis isolate from guinea pig. Although no clear resolution among major eukaryotic groups was obtained by the individual phytogenies based on the four molecules analyzed here, a combined analysis of various molecules, including these, clearly indicated that Blatocystis/stramenopiles are the closest relatives of alveolates.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2002.tb00339.x
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  • 3
    Electronic Resource
    Electronic Resource
    Role of a seasonally specialist bird Zosterops japonica on pollen transfer and reproductive success of Camellia japonica in a temperate area (2004)
    Melbourne, Australia : Blackwell Publishing Ltd.
    Plant species biology 19 (2004), S. 0 
    Details
    ISSN: 1442-1984
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Camellia japonica is considered to be pollinated by birds, but to date no studies have clarified the contribution of birds to the seed production and reproductive success of this species. We conducted a pollinator exclusion experiment that showed that fruit set was sixfold greater in flowers visited by birds than in flowers without bird visitation. Field observations revealed that most of the visitations made by birds were of the species Zosterops japonica. Furthermore, the level of fruit set was found to be saturated after only five visitations by Z. japonica. These results demonstrate that Z. japonica is the most effective pollinator of C. japonica. Such a strong relationship between a plant and an omnivorous bird pollinator has rarely been reported in a temperate zone.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1442-1984.2004.00115.x
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  • 4
    Electronic Resource
    Electronic Resource
    Dating of the human-ape splitting by a molecular clock of mitochondrial DNA (1985)
    Springer
    Journal of molecular evolution 22 (1985), S. 160-174 
    Details
    ISSN: 1432-1432
    Keywords: Evolution of hominoids ; Phylogenetic position ofAustralopithecus afarensis ; Interspecies transfer of mitochondrial DNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A new statistical method for estimating divergence dates of species from DNA sequence data by a molecular clock approach is developed. This method takes into account effectively the information contained in a set of DNA sequence data. The molecular clock of mitochondrial DNA (mtDNA) was calibrated by setting the date of divergence between primates and ungulates at the Cretaceous-Tertiary boundary (65 million years ago), when the extinction of dinosaurs occurred. A generalized leastsquares method was applied in fitting a model to mtDNA sequence data, and the clock gave dates of 92.3±11.7, 13.3±1.5, 10.9±1.2, 3.7±0.6, and 2.7±0.6 million years ago (where the second of each pair of numbers is the standard deviation) for the separation of mouse, gibbon, orangutan, gorilla, and chimpanzee, respectively, from the line leading to humans. Although there is some uncertainty in the clock, this dating may pose a problem for the widely believed hypothesis that the bipedal creatureAustralopithecus afarensis, which lived some 3.7 million years ago at Laetoli in Tanzania and at Hadar in Ethiopia, was ancestral to man and evolved after the human-ape splitting. Another likelier possibility is that mtDNA was transferred through hybridization between a proto-human and a protochimpanzee after the former had developed bipedalism.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02101694
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  • 5
    Electronic Resource
    Electronic Resource
    Maximum likelihood inference of protein phylogeny and the origin of chloroplasts (1990)
    Springer
    Journal of molecular evolution 31 (1990), S. 151-160 
    Details
    ISSN: 1432-1432
    Keywords: Evolutionary tree ; Amino acid sequence ; Insertion/deletion ; Bootstrap probability ; psbA ; Prochlorothrix
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A maximum likelihood method for inferring protein phylogeny was developed. It is based on a Markov model that takes into account the unequal transition probabilities among pairs of amino acids and does not assume constancy of rate among different lineages. Therefore, this method is expected to be powerful in inferring phylogeny among distantly related proteins, either orthologous or parallogous, where the evolutionary rate may deviate from constancy. Not only amino acid substitutions but also insertion/deletion events during evolution were incorporated into the Markov model. A simple method for estimating a bootstrap probability for the maximum likelihood tree among alternatives without performing a maximum likelihood estimation for each resampled data set was developed. These methods were applied to amino acid sequence data of a photosynthetic membrane protein,psbA, from photosystem II, and the phylogeny of this protein was discussed in relation to the origin of chloroplasts.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02109483
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  • 6
    Electronic Resource
    Electronic Resource
    Molecular clock of silent substitution: At least six-fold preponderance of silent changes in mitochondrial genes over those in nuclear genes (1982)
    Springer
    Journal of molecular evolution 19 (1982), S. 28-35 
    Details
    ISSN: 1432-1432
    Keywords: Synonymous substitution ; Uniform Rate of Evolution ; Rapid Evolution of mtDNA ; Ck Gene of b4 Rabbit
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary For each of eleven different types of nuclear genes, comparisons of the protein coding sequences were made between human, mouse and rat pairwisely, and the evolutionary rate of silent substitution, v S nucl. , was estimated. It is shown that the v S nucl. is not only very high (=5.37×10−9/site/yr), but also approximately uniform for different genes regardless of the types, which confirms our previous results (Miyata et al. 1980b). This is in sharp contrast to the rate of protein evolution which differes greatly from protein to protein. Furthermore the v S nucl. is shown to be approximately constant with respect to different divergence times, at least within a short time period (≤75 Myr). Based on these observations, we propose a new molecular clock which has several advantages over a protein clock. Using this clock, we show that the rate of amino acid replacement in the immunoglobulin Ck gene of b4 rabbit is unexpectedly high, almost comparable to the rate of silent changes. This rate may be the highest one for protein evolution that we know so far. We further examine the rate of silent substitutions in mitochondrial genes comparing mouse and rat. Surprisingly the rate is extremely high (≥35×10−9/site/yr), at least 6-times as high as the corresponding rate of nuclear genes. Based on the estimate, we discuss a possible origin of the rapid rate found in mitochondrial DNA.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02100221
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  • 7
    Electronic Resource
    Electronic Resource
    Evolutionary implications of error amplification in the self-replicating and protein-synthesizing machinery (1984)
    Springer
    Journal of molecular evolution 20 (1984), S. 77-85 
    Details
    ISSN: 1432-1432
    Keywords: Error cascade ; Evolutionary rate ; tRNA ; Ribosomal protein ; Mitochondria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Evolutionary constraints operating on animal mitochondrial tRNA were estimated to be reduced to about 1/30 of those that apply to cytoplasmic tRNA. In the nuclear-cytoplasmic system, an effect of a mutation tRNA is likely to be amplified through positive feedback loops consisting of DNA polymerases, RNA polymerases, ribosomal proteins, aminoacyl-tRNA synthetases, tRNA processing enzymes, and others. This amplification phenomenon is called an “error cascade” and the loops that cause it are called “error loops.” The freedom of evolutionary change of cytoplasmic tRNA is expected to be severely restricted to avoid the error cascade. In fact, cytoplasmic tRNA is highly conserved during evolution. On the other hand, in the animal mitochondrial system, all of the proteins involved in error loops are coded for in the nuclear genome and imported from the cytoplasm, and accordingly the system is free from the error cascade. The difference in constraints operating on animal tRNA between cytoplasm and mitochondria is attributed to the presence or absence of error loops. It is shown that the constraints on mitochondrial tRNA in fungi are not as relaxed as those in animals. This observation is attributed to the presence of an error loop in fungal mitochondria, since at least one protein of the mitochondrial ribosome is coded for in the mitochondrial genome of fungi. The evolutionary rates of proteins involved in the processing of genetic information are discussed in relation to the error cascade.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02101989
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  • 8
    Electronic Resource
    Electronic Resource
    Phylogenetic relationships among eukaryotic kingdoms inferred from ribosomal RNA sequences (1985)
    Springer
    Journal of molecular evolution 22 (1985), S. 32-38 
    Details
    ISSN: 1432-1432
    Keywords: Ribosomal RNA ; Eukaryotic kingdoms ; Phylogeny ; Maximum-likelihood method
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Phylogenetic trees among eukaryotic kingdoms were inferred for large- and small-subunit rRNAs by using a maximum-likelihood method developed by Felsenstein. Although Felsenstein's method assumes equal evolutionary rates for transitions and transversions, this is apparently not the case for these data. Therefore, only transversiontype substitutions were taken into account. The molecules used were large-subunit rRNAs fromXenopus laevis (Animalia), rice (Plantae),Saccharomyces cerevisiae (Fungi),Dictyostelium discoideum (Protista), andPhysarum polycephalum (Protista); and small-subunit rRNAs from maize (Plantae),S. cerevisiae, X. laevis, rat (Animalia), andD. discoideum. Only conservative regions of the nucleotide sequences were considered for this study. In the maximum-likelihood trees for both large- and small-subunit rRNAs, Animalia and Fungi were the most closely related eukaryotic kingdoms, and Plantae is the next most closely related kingdom, although other branching orders among Plantae, Animalia, and Fungi were not excluded by this work. These three eukaryotic kingdoms apparently shared a common ancestor after the divergence of the two species of Protista,D. discoideum andP. polycephalum. These two species of Protista do not form a clade, andP. polycephalum diverged first andD. discoideum second from the line leading to the common ancestor of Plantae, Animalia, and Fungi. The sequence data indicate that a drastic change occurred in the nucleotide sequences of rRNAs during the evolutionary separation between prokaryote and eukaryote.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02105802
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  • 9
    Electronic Resource
    Electronic Resource
    The broken-stick model for amino acid composition in proteins (1980)
    Springer
    Journal of molecular evolution 16 (1980), S. 69-72 
    Details
    ISSN: 1432-1432
    Keywords: Broken-stick model ; Amino acid composition
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The relative abundances among the amino acids, which are functionally similar to one another, were explained by random partition of a unit interval.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01732070
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  • 10
    Electronic Resource
    Electronic Resource
    Erratum (1980)
    Springer
    Journal of molecular evolution 16 (1980), S. 151-151 
    Details
    ISSN: 1432-1432
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01731584
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