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At least 1,081 records · Page 60Linked to original sources
PubMed1989

The chemical kinetics of molecular evolution.

This article describes a current view of the events that initiated the transition from the rich organic and inorganic chemistry of the primitive Earth to the earliest forms of life. It is a personal condensation of the basic ideas developed in the so-called Göttingen school. Most of these will be found in the seminal paper of Eigen and the other sources cited. A detailed exposition is given by Küppers.

Biological Evolution↗
PubMed1986

The molecular evolution of the immune response: idiotope-specific suppression indicates that B cells express germ-line-encoded V genes prior to antigenic stimulation.

Antibodies expressed by the immune B cell population are characterized by variable region amino acid substitutions resulting from somatic nucleotide replacement (somatic mutation). This is not true of antibodies expressed by the "naive" B cell population. It is at present unclear whether this discrepancy is due to the preferential clonal selection of a pre-existing subpopulation of naive B cells that express variable regions altered via nucleotide replacement, or whether the process of nucleotide replacement occurs only during the antigen-dependent stages of B cell differentiation. To address this question we have used anti-idiotypic suppression to functionally delete B cells that express particular variable-region structures from the antigen-responsive repertoire. Suppression of the major cross-reactive idiotype (IdCR) expressed in strain A mice in response to p-azophenylarsonate (Ars) was induced using the monoclonal anti-IdCR antibody AD8. The idiotope recognized by AD8 is easily destroyed by alteration of IdCR variable-region structure via nucleotide replacement. The IdCR anti-Ars immune repertoire is characterized by antibodies that lack the AD8-cognate idiotope due to nucleotide replacement. However, complete suppression of the IdCR could reproducibly be achieved by administration of AD8 prior to Ars immunization. This result indicates that all IdCR-expressing B cells also express the AD8-cognate idiotope prior to immunization. Thus, somatic nucleotide replacement must occur exclusively during the antigen-dependent stages of B cell differentiation in this system.

Animals↗
PubMed1994

Metabolic rate, generation time, and the rate of molecular evolution in birds.

A recent hypothesis suggests that resting metabolic rate, measured as energy expended per unit body mass per unit time, might be implicated in the rate of nucleotide substitution in animals. Using relative rate tests on DNA-DNA hybridization data from birds, we show that generation time is significantly correlated with genetic distance between members of an ingroup and an outgroup taxon, but that neither metabolic rate nor body mass explain variation consistent with the hypothesis, either alone or with generation time.

Age Factors↗
PubMed1990

Phylogeny and molecular evolution in primates.

Statistical methods for estimating the branching order and the branching dates from DNA sequence data, taking into account of the rate variation among lineages, are reviewed. An application of the methods to data from primates suggests that chimpanzee is the closest relative of man, and further suggests that these two species diverged about 4-5 million years ago.

Animals↗
PubMed1993

Remarkably high rate of molecular evolution of ruminant placental lactogens.

The sequences of ovine and bovine placental lactogens (based on published cDNA sequences) are remarkably different, indicating a very rapid rate of evolution. Analysis of the cDNA sequences indicates that the rate of nonsynonymous substitution in these proteins is considerably greater than the rate of synonymous substitution. This is an unusual situation, which suggests that the observed rapid rate of evolution is due to incorporation of adaptive rather than neutral mutations.

Animals↗
PubMed1995

Molecular evolution of transfer RNA from two precursor hairpins: implications for the origin of protein synthesis.

In this paper we are going to present a model for the coevolution of major components of the protein synthesis machinery in a primordial RNA world. We propose that the essential prerequisites for RNA-based protein synthesis, i.e., tRNA-like molecules, ribozymic charging catalysts, small-subunit(SSU) rRNA, and large-subunit(LSU) rRNA, evolved from the same ancestral RNA molecule. Several arguments are considered which suggest that tRNA-like molecules were derived by tandem joining of template-flanking hairpin structures involved in replication control. It is further argued that the ancestors of contemporary group I tRNA introns catalyzed such hairpin joining reactions, themselves also giving rise to the ribosomal RNAs. Our model includes a general stereochemical principle for the interaction between ribozymes and hairpin-derived recognition structures, which can be applied to such seemingly different processes as RNA polymerization, aminoacylation, tRNA decoding, and peptidyl transfer, implicating a common origin for these fundamental functions. These and other considerations suggest that generation and evolution of tRNA were coupled to the evolution of synthetases, ribosomal RNAs, and introns from the beginning and have been a consequence arising from the original function of tRNA precursor hairpins as replication and recombination control elements.

Animals↗
PubMed1994

Pattern generation in molecular evolution: exploitation of the variation in RNA landscapes.

Evolution of RNA secondary structure is studied using simulation techniques and statistical analysis of fitness landscapes. The transition from RNA sequence to RNA secondary structure leads to fitness landscapes that have local variations in their "ruggedness." Evolution exploits these variations. In stable environments it moves the quasispecies toward relatively "flat" peaks, where not only the master sequence but also its mutants have a high fitness. In a rapidly changing environment, the situation is reversed; evolution moves the quasispecies to a region where the correlation between secondary structures of "neighboring" RNA sequences is relatively low. In selection for simple secondary structures the movement toward flat peaks leads to pattern generation in the RNA sequences. Patterns are generated at the level of polynucleotide frequencies and the distribution of purines and pyrimidines. The patterns increase the modularity of the sequence. They thereby prevent the formation of alternative secondary structures after mutations. The movement of the quasispecies toward relatively rugged parts of the landscape results in pattern generation at the level of the RNA secondary structure. The base-pairing frequency of the sequences increases. The patterns that are generated in the RNA sequences and the RNA secondary structures are not directly selected for and can be regarded as a side effect of the evolutionary dynamics of the system.

Animals↗
PubMed1976

Molecular evolution of 5S RNA.

Based on the comparative analyses of the primary structure of 5S RNAs from 19 organisms, a secondary structure model of 5S RNA is proposed. 5S RNA has essentially the same structure among all prokaryotic species. The same is true for eukaryotic 5S RNAs. Prokaryotic and eukaryotic 5S RNAs are also quite similar to each other, except for a difference in a specific region. By comparing the nucleotide alignment from the juxtaposed 5S RNA secondary structures, a phylogenic tree of nineteen organisms was constructed. The time of divergence between prokaryotes and eukaryotes was estimated to be 2.5 X 10(9) years ago (minimum estimate: 2.1 X 10(9).

Base Sequence↗
PubMed1982

Deoxyribonucleotide synthesis and the emergence of DNA in molecular evolution.

DNA replication requires monomeric deoxyribonucleotides, which cannot be regarded as primary products of organic syntheses on a primitive earth. However, the present biosynthetic pathway--reductive elimination of the 2'-OH group from ribonucleotides, catalyzed by ribonucleotide reductases and thioredoxins--suggests an early, polyphyletic combination of protein-nucleotide interactions and metal catalysis. That key process had to precede the upcome of RNA-DNA dualism on the way from RNA-protein protocells to true organisms.

Bacteria↗
PubMed1990

Chromosomal and molecular evolution in Asiatic wild asses.

Chromosomal studies of Tibetan wild ass, Equus kiang holdereri are reported for the first time. A Robertsonian polymorphism resulting in diploid numbers of 2n = 51 and 2n = 52 was identified. This polymorphism involves the same elements that participate in the polymorphic Robertsonian rearrangement producing diploid numbers of 54-56 in E. hemionus kulan and E. hemionus onager. Comparison of mitochondrial DNA restriction fragment patterns among three unrelated kiang individuals and between kiangs and a Transcaspian kulan, E. hemionus kulan, indicates an approximately 1% nucleotide sequence divergence of mitochondrial DNAs between the two taxa. The chromosomal divergence between E. hemionus and E. kiang probably originated less than 500,000 years ago. Studies of additional Asiatic wild ass taxa are indicated in order to gain further insights into the speciation and systematics of this threatened group of mammals.

Animals↗
PubMed1984

Dissimilar rates in molecular evolution.

In this work we present an evolutionary tree based on the differences in the physico-chemical properties involved in amino acid substitutions, instead of considering, for its construction, only the number of changes between species. Phylogenetic trees were constructed from the differences in bulkiness, refractivity index, hydrophobicity, polarity and optical rotation of 9 vertebrate calcitonins. A correlation of the form y = a xb was found between the number of changes (x) and the differences in any given physico-chemical property (y). This correlation implies that the evolutionary time can not be evaluated directly from the number of changes between species.

Amino Acid Sequence↗
PubMed1984

Domain structures and molecular evolution of class I and class II major histocompatibility gene complex (MHC) products deduced from amino acid and nucleotide sequence homologies.

Domain structures of class I and class II MHC products were analyzed from a viewpoint of amino acid and nucleotide sequence homologies. Alignment statistics revealed that class I (transplantation) antigen H chains consist of four mutually homologous domains, and that class II (HLA-DR) antigen beta and alpha chains are both composed of three mutually homologous ones. The N-terminal three and two domains of class I and class II (both beta and alpha) gene products, respectively, all of which being approximately 90 residues long, were concluded to be homologous to beta2-microglobulin (beta2M). The membrane-embedded C-terminal shorter domains of these MHC products were also found to be homologous to one another and to the third domain of class I H chains. Class I H chains were found to be more closely related to class II alpha chains than to class II beta chains. Based on these findings, an exon duplication history from a common ancestral gene encoding a beta2M-like primodial protein of one-domain-length up to the contemporary MHC products was proposed.

Amino Acid Sequence↗