A theoretical study on the nucleotide changes under a definite functional constraint of forming stable base-pairs in the stem regions of ribosomal RNAs; its application to the phylogeny of eukaryotes

The large-scale evolution by generating new genes from gene duplication; similarity and difference between monoploid and diploid organisms

On the basis of the concept of biological activity, the large-scale evolution by generating new genes from gene duplication is theoretically compared between the monoploid organism and the diploid organism. The comparison is carried out not only for the process of generating one new gene but also for the process of generating two or more kinds of new genes from successive gene duplication. This comparison reveals the following difference in evolutionary pattern between the monoploids and diploids. The monoploid organism is more suitable to generate one or two new genes step by step but its successive gene duplication is obliged to generate smaller sizes of genes by the severer lowering of biological activity or self-reproducing rate. This is consistent with the evolutionary pattern of prokaryotes having steadily developed chemical syntheses, O₂-releasing photosynthesis and O₂-respiration in the respective lineages. On the other hand, the diploid organism with the plural number of homologous chromosome pairs has a chance to get together many kinds of new genes by the hybridization of variants having experienced different origins of gene duplication. Although this strategy of hybridization avoids the severe lowering of biological activity, it takes the longer time to establish the homozygotes of the more kinds of new genes. During this long period, furthermore different types of variants are accumulated in the population, and their successive hybridization sometimes yields various styles of new organisms. This evolutionary pattern explains the explosive divergence of body plans that has occasionally occurred in the diploid organisms, because the cell differentiation is a representative character exhibited by many kinds of genes and its evolution to the higher hierarchy constructs body plans.

Advanced formulation of base pair changes in the stem regions of ribosomal RNAs; its application to mitochondrial rRNAs for resolving the phylogeny of animals

The ribosomal RNAs (rRNAs) of animal mitochondria, especially those of arthropod mitochondria, have a higher content of G:U and U:G base pairs in their stem regions than the nuclear rRNAs. Thus, the theoretical formulation of base pair changes is extended to incorporate the faster base pair changes A:U<-->G:U<-->G:C and U:A<-->U:G<-->C:G into the previous formulation of the slower base pair changes between A:U, G:C, C:G and U:A. The relative base pair change probability containing the faster and slower base pair changes is theoretically derived to estimate the divergence time of rRNAs under the influence of selection for these base pairs. Using the cartilaginous fish-teleost fish divergence and the crustacean-insect divergence as calibration points, the present method successfully predicts the divergence times of the main branches of animals: Deuterostomia and Protostomia diverged 9.2 x 10(8) years ago, the divergence of Echinodermata, Hemichordata and Cephalochordata succeedingly occurred during the period from 8 x 10(8) to 6 x 10(8) years ago, while Arthropoda, Annelida and Mollusca diverged almost concomitantly about 7 x 10(8) years ago. The dating for the divergence of Platyhelminthes and Cnidaria is traced back to 1.2 x 10(9) years ago. This result is consistent with the fossil records in the Stirling Range Formation of southwestern Australia, the Ediacara and Avalon faunas and the Cambrian Burgess Shale. Thus, the present method may be useful for estimating the divergence times of animals ranging from 10(8) to 10(9) years ago, resolving the difficult problems, e.g. deviation from rate constancy and large sampling variances, in the usual methods of treating apparent change rates between individual bases and/or base pairs.

The influence of selection on the evolutionary distance estimated from the base changes observed between homologous nucleotide sequences

In most studies of molecular evolution, the nucleotide base at a site is assumed to change with the apparent rate under functional constraint, and the comparison of base changes between homologous genes is thought to yield the evolutionary distance corresponding to the site-average change rate multiplied by the divergence time. However, this view is not sufficiently successful in estimating the divergence time of species, but mostly results in the construction of tree topology without a time-scale. In the present paper, this problem is investigated theoretically by considering that observed base changes are the results of comparing the survivals through selection of mutated bases. In the case of weak selection, the time course of base changes due to mutation and selection can be obtained analytically, leading to a theoretical equation showing how the selection has influence on the evolutionary distance estimated from the enumeration of base changes. This result provides a new method for estimating the divergence time more accurately from the observed base changes by evaluating both the strength of selection and the mutation rate. The validity of this method is verified by analysing the base changes observed at the third codon positions of amino acid residues with four-fold codon degeneracy in the protein genes of mammalian mitochondria; i.e. the ratios of estimated divergence times are fairly well consistent with a series of fossil records of mammals. Throughout this analysis, it is also suggested that the mutation rates in mitochondrial genomes are almost the same in different lineages of mammals and that the lineage-specific base-change rates indicated previously are due to the selection probably arising from the preference of transfer RNAs to codons.

RNA sequence evolution with secondary structure constraints: comparison of substitution rate models using maximum-likelihood methods

We test models for the evolution of helical regions of RNA sequences, where the base pairing constraint leads to correlated compensatory substitutions occurring on either side of the pair. These models are of three types: 6-state models include only the four Watson-Crick pairs plus GU and UG; 7-state models include a single mismatch state that combines all of the 10 possible mismatches; 16-state models treat all mismatch states separately. We analyzed a set of eubacterial ribosomal RNA sequences with a well-established phylogenetic tree structure. For each model, the maximum-likelihood values of the parameters were obtained. The models were compared using the Akaike information criterion, the likelihood-ratio test, and Cox's test. With a high significance level, models that permit a nonzero rate of double substitutions performed better than those that assume zero double substitution rate. Some models assume symmetry between GC and CG, between AU and UA, and between GU and UG. Models that relaxed this symmetry assumption performed slightly better, but the tests did not all agree on the significance level. The most general time-reversible model significantly outperformed any of the simplifications. We consider the relative merits of all these models for molecular phylogenetics.

Cirripede phylogeny using a novel approach: molecular morphometrics

We present a new method using nucleic acid secondary structure to assess phylogenetic relationships among species. In this method, which we term "molecular morphometrics," the measurable structural parameters of the molecules (geometrical features, bond energies, base composition, etc.) are used as specific characters to construct a phylogenetic tree. This method relies both on traditional morphological comparison and on molecular sequence comparison. Applied to the phylogenetic analysis of Cirripedia, molecular morphometrics supports the most recent morphological analyses arguing for the monophyly of Cirripedia sensu stricto (Thoracica + Rhizocephala + Acrothoracica). As a proof, a classical multiple alignment was also performed, either using or not using the structural information to realign the sequence segments considered in the molecular morphometrics analysis. These methods yielded the same tree topology as the direct use of structural characters as a phylogenetic signal. By taking into account the secondary structure of nucleic acids, the new method allows investigators to use the regions in which multiple alignments are barely reliable because of a large number of insertions and deletions. It thus appears to be complementary to classical primary sequence analysis in phylogenetic studies.

An evaluation of rDNA variation in Lolium species (ryegrass)

Species of the genus Lolium are important fodder and turf grasses for agricultural and amenity use world-wide. Difficulties currently exist regarding the taxonomy of Lolium species and also in the demarcation between Lolium and the genus Festuca, with the debate focusing on the status of Festuca pratensis and its relations. The diversity in ribosomal DNA (rDNA) in Lolium was investigated. Cloned probes for rDNA, derived from the intergenic spacer (IGS-M) and transcribed regions (COD-M) of mustard (Sinapis alba) were used to investigate species relationships. Genomic DNA from seven Lolium taxa, F. pratensis, and xFestulolium braunii, were assessed for variation in rDNA by RFLP. Data support continued recognition of existing Lolium species' demarcations, and provided more taxonomic insight between allogamous Lolium taxa and F. pratensis. The COD-M and IGS-M probes grouped taxa by reproductive mode. The IGS-M probe distinguished all species as unique entities and established that hybrids, xFestulolium braunii and Lolium xboucheanum, had rDNA phenotypes that were composites of their parental species. The evolution of the ribosomal repeat unit is discussed and the potential for further rDNA taxonomic study in Lolium is considered.Key words: Lolium, variation, ribosomal, rDNA, RFLP.