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PubMed1980

Molecular evolution of mRNA: a method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application.

A method for estimating the evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences is presented. This method is applied to genes of phi X174 and G4 genomes, histone genes and beta-globin genes, for which homologous nucleotide sequences are available for comparison to be made. It is shown that the rates of synonymous substitutions are quite uniform among the non-overlapping genes of phi X174 and G4 and among histone genes H4, H2B, H3 and H2A. A comparison between phi X174 and G4 reveals that, in the overlapping segments of the A-gene, the rate of synonymous substitution is reduced more significantly than the rate of amino acid substitution relative to the corresponding rate in the non-overlapping segment. It is also suggested that, in the coding region surrounding the splicing points of intervening sequences of beta-globin genes, there exist rigid secondary structures. It is in only these regions that the beta-globin genes show the slowing down of evolutionary rates of both synonymous and amino acid substitutions in the primate line.

Amino Acid Sequence↗
PubMed1980

Amino acid diversity of immunoglobulins as a product of molecular evolution.

Based on population genetics theory of the evolution of multigene families, the sequence variability of the variable regions of immunoglobulins compiled by Kabat et al. (1976) has been analysed. An amino acid identity coefficient either within or between species is calculated separately for both the hypervariable and the framework regions. Under the somatic mutation hypothesis, the somatic component of amino acid diversity is in addition to the germ line component and should contribute an amount of change between the hypervariable and framework regions that is independent of the time since the divergence of any two immunoglobulin gene families. The relationship between the identity coefficient of the hypervariable region and that of the framework region is shown to be not in accord with such prediction. The result indicates that the rate of evolutionary accumulation of amino acid replacements in the hypervariable region is roughly three times more rapid than in the framework region and the hypervariability within a species is a necessary consequence of the high evolutionary rate.

Amino Acid Sequence↗
PubMed1980

Molecular evolution and subunit structure of cattle lens alpha crystallin.

The present studies were based on the premise that any common determinants in homologous proteins must have originated with the common ancestor of all of the taxonomic groups in which that determinant occurs. Cross-reacting antigenic determinants of lens alpha crystallin various classes of modern vertebrates were used to trace their evolutionary relationships. For quantitation of evolutionarily distinct determinants, equimolar amounts of alpha crystallin or its subunits, in either monomeric or reaggregated form, were bound to a matrix, then saturated with 125I-labeled Fab fragments of anti-cattle alpha crystallin antibodies having phylogenetically restricted specificities. This quantitative procedure has the important advantage of independence from variation in antibody responses to different determinants of the same antigenic molecule. The procedure is not impaired by steric hindrance. Both the SH-containing and SH-free subunits of cattle lens alpha crystallin were found to contain common antigenic determinants with the cyclostomata alpha crystallin. Such determinants originatd in evolution with the first vertebrates, the primitive agnatha. Antigenic determinants transferred from ancestral aquatic and land vertebrates to the mammals were found to constitute 93% of all determinants reactive in the monomeric SH-free subunits of cattle alpha crystallin. These determinants constitute only 76.5% of all determinants which are reactive in the SH-containing subunits. The antigenic determinants on both types of subunits were all found to be different. These findings indicate that evolutionary changes must have occurred more slowly in SH-free subunits than in SH-containing subunits. Significant decreases or increases were found in the content of various evolutionarily distinct determinants reactive in the reaggregated subunits as compared to the ones reactive in monomeric subunits. These differences can result from the formation of new conformational antigenic determinants during aggregation as well as from the burial or exposure of other determinants after aggregation. Different amounts of evolutionarily distinct antigenic determinants were found to be reactive in the molecules dissociated into subunits than in the intact molecules one of the reasons being that the intact molecules contain phylogenetically distinct determinants which depend on the quaternary structure of the protein molecule. The data obtained indicate that the quaternary structure of cattle alpha crystallin has, to a large degree, remained unchanged since the origin of vertebrates.

Alligators and Crocodiles↗
PubMed1976

The molecular evolution of cytochrome c in eukaryotes.

Using many more cytochrome sequences than previously available, we have confirmed: 1, the eukaryotic cytochrome c diverged from a common ancestor; 2, the ancestral eukaryotic cytochrome c was not greatly different in character from those present today; 3, fixations are non-randomly distributed among the codons, there being evidence for at least four classes of variability; 4, there are similar classes of variability when the data are considered according to the nucleotide position within the codon; 5, the number of covarions (concomitantly variable codons) in mammalian cytochrome c genes is about 12 and the same value has been obtained for dicotyledenous plants as well; 6, all of the hyper- and most highly variable codons are for external residues, nearly 60 per cent of the invariable codons are for internal residues and nearly half of the codons for internal residues are invariable; 7, the first nucleotide position of a codon is more likely and the second position less likely to fix mutations than would be expected on the basis of the number of ways that alternative amino acids can be reached; 8, the character of nucleotide replacements is enormously non-random, with G-A interchanges representing 42% of those observed in the first nucleotide position, but the observation does not stem from a bias in the DNA strand receiving the mutation, nor from the presence of a compositional equilibrium, nor from a bias in the frequency with which different nucleotides mutate, but rather from a bias in the acceptability of an alternative nucleotide as circumscribed by the functional acceptability of the new amino acid encoded; and 9, the unit evolutionary period is approximately 150 million years/observable (amino acid changing) nucleotide replacement/cytochrome c covarion in two diverging lines. Wherever non-randomness has been observed, it has always been consistent with the consideration that an alternative amino acid at any location is more likely to be acceptable the more closely it resembles the present amino acid in its physico-chemical properties. Finally, in no case did the a priori assumption of a biologically realistic phylogeny lead to any observations or conclusions that were in any way significantly different from those obtained when the phylogeny was based solely upon the sequences, proving that the earlier results were not a consequence of some internal circularity.

Amino Acid Sequence↗
PubMed1976

Molecular evolution as a process of message refinement.

Amino acid sequences are often said to code for proteins. Taking that statement literally, we propose a methodology in which protein sequences appear as messages and as such are amenable to the techniques of signal analysis. Not only does this view of amino acid sequences as messages appear to be tenable, but the clarity of expression of these sequences seems to increase, i.e., the noisiness decreases, consonant with notions of ascendancy in the hierarchy of morphological taxonomy.

Amino Acid Sequence↗
PubMed1977

Molecular evolution of snake venom toxins.

Phylogenetic trees were constructed for 62 venom toxins of snakes of Proteroglyphae suborder using matrix method. The resulting tree from Minimum Spanning Tree-Cluster Analysis technique had the lowest "percent deviation" (8.55). The taxonomic relationship of these toxins agrees very well with zoological opinions. However, the appearance of the tree did not directly provide a plausible evolutionary model for the toxins. A model was derived from nodal ancestral sequence calculations, comparisons between intra- and intergenerical rates of amino acid change, and generally held ideas about protein evolution. According to the model, short neurotoxin is the ancient form of snake venom toxins. The courses of evolution leading to the present intraspecific homologous toxins are explained by gene duplication and allelomorphism.

Amino Acid Sequence↗
PubMed1987

Nonuniformity of nucleotide substitution rates in molecular evolution: computer simulation and analysis of 5S ribosomal RNA sequences.

The effects of temporal (among different branches of a phylogeny) and spatial (among different nucleotide sites within a gene) nonuniformities of nucleotide substitution rates on the construction of phylogenetic trees from nucleotide sequences are addressed. Spatial nonuniformity may be estimated by using Shannon's (1948) entropy formula to measure the Relative Nucleotide Variability (RNV) at each nucleotide site in an aligned set of sequences; this is demonstrated by a comparative analysis of 5S rRNAs. New methods of constructing phylogenetic trees are proposed that augment the Unweighted Pair-Group Using Arithmetic Averages (UPGMA) algorithm by estimating and compensating for both spatial and temporal nonuniformity in substitution rates. These methods are evaluated by computer simulations of 5S rRNA evolution that include both kinds of nonuniformities. It was found that the proposed Reference Ratio Method improved both the ability to reconstruct the correct topology of a tree and also the estimation of branch lengths as compared to UPGMA. A previous method (Farris et al. 1970; Klotz et al. 1979; Li 1981) was found to be less successful in reconstructing topologies when there is high probability of multiple mutations at some sites. Phylogenetic analyses of 5S rRNA sequences support the endosymbiotic origins of both chloroplasts and mitochondria, even though the latter exhibit an accelerated rate of nucleotide substitution. Phylogenetic trees also reveal an adaptive radiation within the eubacteria and another within the eukaryotes for the origins of most major phyla within each group during the Precambrian era.

Animals↗
PubMed1988

Molecular evolution among some Drosophila species groups as indicated by two-dimensional electrophoresis.

The evolutionary and phylogenetic relationships of seven Drosophila species groups (represented by D. melanogaster, D. mulleri, D. mercatorum, D. robusta, D. virilis, D. immigrans, D. funebris, and D. melanica) were investigated by the use of two-dimensional electrophoresis. The resulting phylogeny is congruent with the current views of evolution among these groups based on morphological characters and immunological distances. Previous studies indicated that the ability of one-dimensional electrophoresis to resolve relationships between distantly related taxa extended to about the Miocene [25 million years (Myr) ago], but the present study demonstrates that two-dimensional electrophoresis is a useful indicator of phylogeny even back to the Paleocene (65 Myr ago). In addition, two-dimensional electrophoresis is shown to be a useful technique for detecting slowly evolving structural proteins such as actins and tropomyosins.

Animals↗
PubMed1990

Molecular evolution of human T-cell leukemia virus.

Phylogenetic trees for the human T-cell leukemia virus type I (HTLV-I) and its related viruses were constructed by use of nucleotide sequences of the long terminal repeat (LTR) and the tax gene. The trees showed that the viruses diverged from a common ancestral virus and that they are classified into two groups whose hosts are either primates or bovines. However, the topology of the trees for the viruses differed from that for the hosts. This suggests that HTLV-I and HTLV-I-related viruses evolved independently of host-species divergence and that interspecies transmission between human and monkeys occurred in the past. The nucleotide diversity of the tax genes of HTLV-I was estimated to be 0.025. This value is more than 10 times larger than that of human globin genes, but it is about 20 times smaller than that of hemagglutinin genes of influenza A viruses. Thus, the genetic variability of the HTLV-I genes seems to be higher than that of nuclear genes but much lower than the genes of typical RNA viruses. Furthermore, we examined functional constraints on the overlapping region of the rex and tax genes. The results obtained imply that for the overlapping region, the tax gene has much stronger constraints against amino acid changes than the rex gene.

Animals↗
PubMed1987

Molecular evolution of the Saccharomyces cerevisiae histone gene loci.

The core histone genes of Saccharomyces cerevisiae are arranged as duplicate nonallelic sets of specifically paired genes. The identity of structural organization between the duplicated gene pairs would have its simplest evolutionary origin in the duplication of a complete locus in a single event. In such a case, the time since the duplication of one of the genes should be identical to that since duplication of the gene adjacent to it on the chromosome. A calculation of the evolutionary distances between the coding DNA sequences of the histone genes leads to a duplication paradox: The extents of sequence divergence in the silent component of third-base positions for adjacent pairs of genes are not identical. Estimates of the evolutionary distance between the two H3-H4 noncoding intergene DNA sequences are large; the divergence between the two separate sequences is indistinguishable from the divergence between either of the regions and a randomly generated permutation of itself. These results suggest that the duplication event may have occurred much earlier than previously estimated. The potential age of the duplication, and the attractive simplicity of the duplication of both the H3-H4 and the H2A-H2B gene pairs having taken place in a single event, leads to the hypothesis that modern haploid S. cerevisiae may have evolved by diploidization or fusion of two ancient fungi.

Base Sequence↗
PubMed1987

Molecular evolution and phylogeny of the human AIDS viruses LAV, HTLV-III, and ARV.

A phylogenetic tree for the human lymphadenopathy-associated virus (LAV), the human T-cell lymphotrophic virus type III (HTLV-III), and the acquired immune deficiency syndrome (AIDS)-associated retrovirus (ARV) has been constructed from comparisons of the amino acid sequences of their gag proteins. A method is proposed for estimating the divergence times among these AIDS viruses and the rates of nucleotide substitution for their RNA genomes. The analysis indicates that the LAV and HTLV-III strains diverged from one another after 1977 and that their common ancestor diverged from the ARV virus no more than 10 years earlier. Hence, the evolutionary diversity among strains of the AIDS viruses apparently has been generated within the last 20 years. It is estimated that the genome of the AIDS virus has a nucleotide substitution rate on the order of 10(-3) per site per year, with the rate in the second half of the genome being double that in the first half.

Biological Evolution↗
PubMed1970

Molecular evolution of the neurohypophysial hormones: The active peptides of a primitive bony fish Polypterus bichir.

Neurohypophysial hormones have been so far identified in Neopterygii and Crossopterygii but not in species of the bird sub-class of bony fishes, the Palaeopterygii. Isolation and chemical characterization of the active principles of a primitive bony fish, Polypterus bichir, have been performed. Isotocin (Ser(4)-Ile(8)-oxytocin) and arginine vasotocin (Arg(8)-oxytocin) have been identified. Because the same peptides were found in the recent Neopterygii, it can be deduced that neurohypophysial hormones have displayed a peculiar stability in the course of the evolution of bony fishes. However isotocin and vasotocin are replaced by oxytocin and vasopressins in mammals and therefore might be regarded as "old" molecules.

Journal Article↗
PubMed1987

Molecular evolution of the calmodulin gene.

On the basis of the intron/exon organization and the intramolecular homology of DNA sequences, I propose a novel model for genesis of the calmodulin gene. A primordial calmodulin gene consisting of 51 base pairs (17 amino acids) was subjected to three-fold duplication to create modern calmodulin with four calcium-binding subdomains. The model elucidates the seemingly enigmatic positions of splice junctions observed in calmodulin genes.

Amino Acid Sequence↗