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  • 1
    Electronic Resource
    Electronic Resource
    Renner–Teller splitting in the C 1s→π* excited states of CS2, OCS, and CO2 (1997)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 107 (1997), S. 4919-4926 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Fragment ions energetically emitted following the perpendicular (ΔΛ=+1) transitions of C 1s→π* of CS2, OCS, and CO2 are observed not only in the perpendicular (90°) direction but also in the parallel (0°) to the linear polarization; that is, ions have a momentum orthogonal to the linear molecule. This arises in the Renner–Teller (RT) vibronic coupling of bending vibrations in the C 1s→ in-plane π* excited state with a bent equilibrium geometry, though the RT splitting between the C 1s→ out-of-plane π* state with a linear geometry and the C 1s→ in-plane π* state is not visible directly due to the lifetime broadening. The 0° ion yield is relatively small in CS2 but is comparable to the 90° yield in CO2; in the latter the peak maximum at 0° is 0.06 eV lower than at 90° and the anisotropy parameter β is heavily dependent on the photon energy. In CO2 a great number of unresolved bending vibrations are coupled. The half-width at half-maximum on the lower energy side of the π* peak is much more sensitive to the RT splitting; 0.08, 0.11, and 0.29 eV for CS2, OCS, and CO2, compared with the full-width at half-maximum, 0.17, 0.39, and 0.64 eV. In CS2 the π* peak and β value are sharp and symmetric, indicating that the zero-point vibrational levels are only involved. In OCS three fine structures observed with separations of 0.21 eV are assigned to the ν3 mode, which is comparable to the stretching mode in CO. © 1997 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.474855
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  • 2
    Electronic Resource
    Electronic Resource
    Renner–Teller effect and Rydberg-valence mixing in the N and O K-edge photoabsorption spectra of N2O (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 102 (1995), S. 7369-7376 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We have measured high-resolution angle-resolved ion-yield spectra of the O and N 1s excited N2O molecules (Nt–Nc–O) and investigated them with the help of ab initio quantum chemical calculations. The peak width of the Nc 1s→π* transition is larger than that of the Nt 1s→π* one. This mainly arises from different populations of bending vibrations excited through the Renner–Teller effect, which breaks the degeneracy of the 1s→π* excited states by bending the linear molecule. The angular distribution of fragment ions emitted after the Auger decay is also affected by the Renner–Teller effect. That is, fragment ions significantly lose the information of the Π symmetry of the linear molecule. For the 1s→Rydberg excitations no Renner–Teller effect is observed and the angular distribution is directly related to the Σ and Π symmetries. Furthermore, it is found that the peak intensities of the O and Nt 1s→nsσ Rydberg transitions are unusually large. The N2O molecule has two σ* orbitals, σs*(8σ) and σp*(9σ), below and above the ionization threshold and the 1s→σs* excited states are mixed with the O and Nt 1s–nsσ Rydberg excited states; on the other hand, the Nc 1s→σs* transition is almost dipole-forbidden because of the orbital symmetry. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.469049
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  • 3
    Electronic Resource
    Electronic Resource
    High-resolution and symmetry-resolved N and O K-edge absorption spectra of NO (1992)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 97 (1992), S. 8842-8849 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: High-resolution electron-yield and "symmetry-resolved'' ion-yield spectra have been measured at the N and O K edges of a 2Π open-shell molecule, NO. Several Rydberg transitions converging to the 3Π and 1Π ionization thresholds are found. The core-to-valence and core-to-Rydberg transitions are interpreted with the help of ab initio self-consistent-field configuration-interaction and frozen-core calculations for the core-excited states with three open shells. It is found that the equivalent-core model (N*O=O2) breaks down in discussing the state ordering of the three N 1s–2pπ* excited states, 2Δ, 2Σ−, and 2Σ+. It is important to consider explicitly the core hole and the exchange repulsion between the core and π* electrons.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.463359
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  • 4
    Electronic Resource
    Electronic Resource
    The giant panda is closer to a bear, judged by α- and β-hemoglobin sequences (1993)
    Springer
    Journal of molecular evolution 36 (1993), S. 282-289 
    Details
    ISSN: 1432-1432
    Keywords: Ailuropoda melanoleuca ; Giant panda ; Carnivores ; Hemoglobin ; Maximum likelihood ; Protein phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Using α- and β-hemoglobin sequences, we made a maximum likelihood inference as to the phylogenetic relationship among carnivores, including the two pandas, giant and lesser. Molecular phylogenetic studies up to 1985 had consistently indicated that the giant panda is more closely related to the bear than to the lesser panda. In 1986, however, a contradictory tree was constructed, using hemoglobins and so on, in which the two pandas link together (Tagle et al. 1986). In contrast to that tree, our conclusion supports the close relationship between bear and giant panda. The surface impression of a close relationship between the two pandas drawn from pairwise amino acid differences is explained by a rapid rate of hemoglobin evolution in the bear compared to that in the two pandas.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00160484
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  • 5
    Electronic Resource
    Electronic Resource
    Model of Amino Acid Substitution in Proteins Encoded by Mitochondrial DNA (1996)
    Springer
    Journal of molecular evolution 42 (1996), S. 459-468 
    Details
    ISSN: 1432-1432
    Keywords: Key words: General reversible Markov model — Amino acid substitution — Maximum likelihood method
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Mitochondrial DNA (mtDNA) sequences are widely used for inferring the phylogenetic relationships among species. Clearly, the assumed model of nucleotide or amino acid substitution used should be as realistic as possible. Dependence among neighboring nucleotides in a codon complicates modeling of nucleotide substitutions in protein-encoding genes. It seems preferable to model amino acid substitution rather than nucleotide substitution. Therefore, we present a transition probability matrix of the general reversible Markov model of amino acid substitution for mtDNA-encoded proteins. The matrix is estimated by the maximum likelihood (ML) method from the complete sequence data of mtDNA from 20 vertebrate species. This matrix represents the substitution pattern of the mtDNA-encoded proteins and shows some differences from the matrix estimated from the nuclear-encoded proteins. The use of this matrix would be recommended in inferring trees from mtDNA-encoded protein sequences by the ML method.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00013324
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  • 6
    Electronic Resource
    Electronic Resource
    Plastid Genome Phylogeny and a Model of Amino Acid Substitution for Proteins Encoded by Chloroplast DNA (2000)
    Springer
    Journal of molecular evolution 50 (2000), S. 348-358 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Maximum likelihood — General reversible Markov model — Amino acid substitution — Chloroplast DNA — AA LogDet
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Maximum likelihood (ML) phylogenies based on 9,957 amino acid (AA) sites of 45 proteins encoded in the plastid genomes of Cyanophora, a diatom, a rhodophyte (red algae), a euglenophyte, and five land plants are compared with respect to several properties of the data, including between-site rate variation and aberrant amino acid composition in individual species. Neighbor-joining trees from AA LogDet distances and ML analyses are seen to be congruent when site rate variability was taken into account. Four feasible trees are identified in these analyses, one of which is preferred, and one of which is almost excluded by statistical criteria. A transition probability matrix for the general reversible Markov model of amino acid substitutions is estimated from the data, assuming each of these four trees. In all cases, the tree with diatom and rhodophyte as sister taxa was clearly favored. The new transition matrix based on the best tree, called cpREV, takes into account distinct substitution patterns in plastid-encoded proteins and should be useful in future ML inferences using such data. A second rate matrix, called cpREV*, based on a weighted sum of rate matrices from different trees, is also considered.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002399910038
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  • 7
    Electronic Resource
    Electronic Resource
    Early branchings in the evolution of eukaryotes: Ancient divergence of entamoeba that lacks mitochondria revealed by protein sequence data (1993)
    Springer
    Journal of molecular evolution 36 (1993), S. 380-388 
    Details
    ISSN: 1432-1432
    Keywords: Entamoeba histolytica ; Protozoa lacking mitochondria ; Eukaryotic kingdoms ; Elongation factor-1α ; Maximum likelihood ; Protein phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Phylogenetic analyses of ribosomal RNA sequences have played an important role in the study of early evolution of life. However, Loomis and Smith suggested that the ribosomal RNA tree is sometimes misleading—especially when G+C content differs widely among lineages—and that a protein tree from amino acid sequences may be more reliable. In this study, we analyzed amino acid sequence data of elongation factor-1α by a maximum likelihood method to clarify branching orders in the early evolution of eukaryotes. Contrary to Sogin et al.'s tree of small-subunit ribosomal RNA, a protozoan species, Entamoeba histolytica, that lacks mitochondria was shown to have diverged from the line leading to eukaryotes with mitochondria before the latter separated into several kingdoms. This indicates that Entamoeba is a living relic of the earliest phase of eukaryotic evolution before the symbiosis of protomitochondria occurred. Furthermore, this suggests that, among eukaryotic kingdoms with mitochondria, Fungi is the closest relative of Animalia, and that a cellular slime mold, Dictyostelium discoideum, had not diverged from the line leading to Plantae-Fungi-Animalia before these three kingdoms separated.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00182185
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  • 8
    Electronic Resource
    Electronic Resource
    Improved dating of the human/chimpanzee separation in the mitochondrial DNA tree: Heterogeneity among amino acid sites (1995)
    Springer
    Journal of molecular evolution 40 (1995), S. 622-628 
    Details
    ISSN: 1432-1432
    Keywords: Mitochondrial DNA ; Hominoidea ; Molecular clock ; Maximum likelihood ; Site heterogeneity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The internal branch lengths estimated by distance methods such as neighbor joining are shown to be biased to be short when the evolutionary rate differs among sites. The variable-invariable model for site heterogeneity fits the amino acid sequence data encoded by the mitochondrial DNA from Hominoidea remarkably well. By assuming the orangutan separation to be 13 or 16 Myr old, a maximum-likelihood analysis estimates a young date of 3.6 ± 0.6 or 4.4 ± 0.7 Myr (±1 SE) for the human/chimpanzee separation, and these estimates turn out to be robust against differences in the assumed model for amino acid substitutions. Although some uncertainties still exist in our estimates, this analysis suggests that humans separated from chimpanzees some 4–5 Myr ago.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00160510
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  • 9
    Electronic Resource
    Electronic Resource
    Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: Instability of a tree based on a single gene (1994)
    Springer
    Journal of molecular evolution 39 (1994), S. 519-527 
    Details
    ISSN: 1432-1432
    Keywords: Opossum ; Outgroup ; Branching order ; Mammalian evolution ; Maximum likelihood tree
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The phylogenetic relationships among Primates (human), Artiodactyla (cow), Cetacea (whale), Carnivora (seal), and Rodentia (mouse and rat) were estimated from the inferred amino acid sequences of the mitochondrial genomes using Marsupialia (opossum), Aves (chicken), and Amphibia (Xenopus) as an outgroup. The overall evidence of the maximum likelihood analysis suggests that Rodentia is an outgroup to the other four eutherian orders and that Cetacea and Artiodactyla form a clade with Carnivora as a sister taxon irrespective of the assumed model for amino acid substitutions. Although there remains an uncertainty concerning the relation among Artiodactyla, Cetacea, and Carnivora, the existence of a clade formed by these three orders and the outgroup status of Rodentia to the other eutherian orders seems to be firmly established. However, analyses of individual genes do not necessarily conform to this conclusion, and some of the genes reject the putatively correct tree with nearly 5% significance. Although this discrepancy can be due to convergent or parallel evolution in the specific genes, it was pointed out that, even without a particular reason, such a discrepancy can occur in 5% of the cases if the branching among the orders in question occurred within a short period. Due to uncertainty about the assumed model underlying the phylogenetic inference, this can occur even more frequently. This demonstrates the importance of analyzing enough sequences to avoid the danger of concluding an erroneous tree.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00173421
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  • 10
    Electronic Resource
    Electronic Resource
    Novel Phylogeny of Whales Supported by Total Molecular Evidence (1997)
    Springer
    Journal of molecular evolution 44 (1997), S. S117 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Cetacean evolution — Molecular phylogeny — Total evidence — Maximum likelihood — Sperm whale
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Given that the analysis of a single gene does not necessarily provide unambiguous phylogenetic information, it is important to scrutinize as many genes as possible. Using the maximum likelihood method, particularly suitable for a total evidence approach, we evaluated the phylogenetic information provided by the 12S and 16S rRNA, cytochrome b, and myoglobin sequence data in order to resolve one of the most debated phylogenetic questions: the relationships among the major groups of cetaceans. Our analysis strongly supports the hypothesis that sperm whales are closer to baleen whales than to dolphins.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00000062
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