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PubMed1996

Evolutionary algorithms in computer-aided molecular design.

In recent years, search and optimisation algorithms inspired by evolutionary processes have been applied with marked success to a wide variety of problems in diverse fields of study. In this review, we survey the growing application of these 'evolutionary algorithms' in one such area: computer-aided molecular design. In the course of the review, we seek to summarise the work to date and to indicate where evolutionary algorithms have met with success and where they have not fared so well. In addition to this, we also attempt to discern some future trends in both the basic research concerning these algorithms and their application to the elucidation, design and modelling of chemical and biochemical structures.

Algorithms↗
PubMed1995

Evolutionary analysis of the picornavirus family.

An exhaustive evolutionary analysis of the picornavirus family has been carried out using the amino acid sequences of several proteins of the viruses including: the capsid proteins (1D, 1B, and 1C) situated at the 5' end of the genome and responsible for the serotype of the viruses, and the viral polymerase (3D), located at the 3' end of the genome. The evolutionary relationships found among the viruses studied support the new classification, recently suggested, in contrast to the classical one, and the existence of a new genus for the picornavirus family. In the new taxonomic organization, five genera form the picornavirus family: (1) aphthoviruses, (2) cardioviruses, (3) hepatoviruses (previously classified as enteroviruses), (4) renteroviruses (which mainly constitute a combination of the previous genera rhinovirus and enterovirus), and (5) a new genus, with a new and unique representative: the echovirus 22. Our analysis also allowed us, for the first time, to propose the most probable sequence of speciation events to have given rise to the current picornavirus family. The bootstrap procedure was used to check the reliability of the phylogenetic trees obtained. The application of the method of the statistical geometry in distance space to internal branches of the tree revealed a high degree of evolutionary "noise," which makes the resolution of some internal branching points difficult.

Capsid↗
PubMed1995

Analyses of ribosomal RNA sequences from glaucocystophyte cyanelles provide new insights into the evolutionary relationships of plastids.

Glaucocystophyte algae (sensu Kies, Berl. Deutsch. Bot. Ges. 92, 1979) contain plastids (cyanelles) that retain the peptidoglycan wall of the putative cyano-bacterial endosymbiont; this and other ultrastructural characters (e.g., unstacked thylakoids, phycobilisomes) have suggested that cyanelles are "primitive" plastids that may represent undeveloped associations between heterotrophic "host" cells (i.e., glaucocystophytes) and cyanobacteria. To test the monophyly of glaucocystophyte cyanelles and to determine their evolutionary relationship to other plastids, complete 16S ribosomal RNA sequences were determined for Cyanophora paradoxa, Glaucocystis nostochinearum, Glaucosphaera vacuolata, and Gloeochaete wittrockiana. Plastid rRNAs were analyzed with the maximum-likelihood, maximum-parsimony, and neighbor-joining methods. The phylogenetic analyses show that the cyanelles of C. paradoxa, G. nostochinearum, and G. wittrockiana form a distinct evolutionary lineage; these cyanelles presumably share a monophyletic origin. The rDNA sequence of G. vacuolata was positioned within the nongreen plastid lineage. This result is consistent with analyses of nuclear-encoded rRNAs that identify G. vacuolata as a rhodophyte and support is removal from the Glaucocystophyta. Results of a global search with the maximum-likelihood method suggest that cyanelles are the first divergence among all plastids; this result is consistent with a single loss of the peptidoglycan wall in plastids after the divergence of the cyanelles. User-defined tree analyses with the maximum-likelihood method indicate, however, that the position of the cyanelles is not stable within the rRNA phylogenies. Both maximum-parsimony and neighbor-joining analyses showed a close evolutionary relationship between cyanelles and non-green plastids; these phylogenetic methods were sensitive to inclusion/exclusion of the G. wittrockiana cyanelle sequence.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗
PubMed1995

The evolutionary divergence of neurotransmitter receptors and second-messenger pathways.

Members of the superfamily of G-protein-coupled neurotransmitter receptors have a conserved secondary structure, a moderate and reasonably steady rate of sequence change, and usually lack introns within the coding sequence. These properties are advantageous for evolutionary studies. The duplication and divergence of the genes in this gene family led to the formation of distinct neurotransmitter pathways and may have facilitated the evolution of complex nervous systems. I have analyzed this evolutionary divergence by quantitative multiple sequence alignment, bootstrap resampling, and statistical analysis of 49 adrenergic, muscarinic cholinergic, dopamine, and octopamine receptor sequences from 12 animal species. The results indicate that the first event to occur within this gene family was the divergence of the catecholamine receptors from the muscarinic acetylcholine receptors, which occurred prior to the divergence of the arthropod and vertebrate lineages. Subsequently, the ability to activate specific second-messenger pathways diverged independently in both the muscarinic and the catecholamine receptors. This appears to have occurred after the divergence of the arthropod and vertebrate lineages but before the divergence of the avian and mammalian lineages. However, the second-messenger pathways activated by adrenergic and dopamine receptors did not diverge independently. Rather, the ability of the catecholamine receptors to bind to specific ligands, such as epinephrine, norepinephrine, dopamine, or octopamine, was repeatedly modified in evolutionary history, and in some cases was modified after the divergence of the second-messenger pathways.

Adenylyl Cyclases↗
PubMed1994

Variable evolutionary rates in the molecular evolution of mammalian growth hormones.

In mammals pituitary growth hormone (GH) shows a slow basal rate of evolution (0.22 +/- 0.03 x 10(-9) substitutions/amino acid site/year) which appears to have increased by at least 25-50-fold on two occasions, during the evolution of primates (to at least 10.8 +/- 1.3 x 10(-9) substitutions/amino acid site/year) and artiodactyl ruminants (to at least 5.6 +/- 1.3 x 10(-9) substitutions/amino acid site/year). That these rate increases are real, and not due to inadvertent comparison of nonorthologous genes, was established by showing that features of the GH gene sequences that are not expressed as mature hormone do not show corresponding changes in evolutionary rate. Thus, analysis of non-synonymous substitutions in the coding sequence for the mature protein confirmed the rate increases seen in the primate and ruminant GHs, but analysis of nonsynonymous substitutions in the signal peptide sequence, synonymous substitutions in the coding sequence for signal peptide or mature protein, and 5' and 3' untranslated sequences showed no statistically significant changes in evolutionary rate. Evidence that the increases in evolutionary rate are probably due to positive selection is provided by the observation that in the cases of both ruminant and primate GHs the periods of rapid evolution were followed by a return to a slow rate similar to the basal rate seen in other mammalian GHs.(ABSTRACT TRUNCATED AT 250 WORDS)

Adaptation, Physiological↗
PubMed1994

Monte Carlo simulation in phylogenies: an application to test the constancy of evolutionary rates.

Monte Carlo simulation has commonly been used in phylogenetic studies to test different tree-reconstruction methods, and consequently, its application for testing evolutionary models can be considered as a natural extension of this usage. Repetitive simulation of a given evolutionary process, under the restrictions imposed by the model to be tested, along a determinate tree topology allow the estimate of probability distributions for the desired parameters. Next, the phylogenetic tree can be reconstructed again without the constraints of the model, and the parameter of interest, derived from this tree, can be compared to the corresponding probability distribution derived from the restricted, simulated trees. As an example we have used Monte Carlo simulation to test the constancy of evolutionary rates in a set of cytochrome-c protein sequences.

Animals↗
PubMed1987

Evolutionary relationships of the Chinese hamster X chromosome and autosomes: a comparison using solution hybridization techniques.

The evolutionary relationships of Chinese hamster X chromosome and autosome DNA sequences were compared by solution hybridization techniques. Chinese hamster X chromosome tracer was prepared by radiolabeling DNA from chromosomes isolated by fluorescence-activated sorting. Radiolabeled Chinese hamster total genomic DNA, approximately 90% of which is of autosome origin, was used as autosome tracer. Each tracer was mixed with excess driver DNA of Chinese hamster, Syrian hamster, rat, rabbit, cat, cow, or human origin. Reaction mixtures were melted and allowed to reassociate to an equivalent CoT of 12,000, under conditions which permitted 35% mismatch in DNA duplexes. Both the extent of duplex formation (the normalized percentage hybridization or NPH) and the average thermal stability of the duplexes formed (melting temperature or Tm) were measured; these values were used to compare the evolutionary relatedness of tracer and driver DNAs. The pattern of evolutionary relatedness revealed by comparing either the Tm or NPH values obtained with different drivers was the same for X chromosome and autosome DNA and was consistent with the phylogeny of the species examined. Although NPH and Tm values for X chromosome and autosome tracers differed, differences fell within the range of experimental error. The results of these studies provide no evidence for differential conservation of Chinese hamster X chromosome sequences, suggesting that the constraints on the mammalian X chromosome which act to maintain its gene linkage group intact do not markedly reduce the extent to which its sequences diverge during evolution.

Animals↗
PubMed1984

A simple model for the evolutionary emergence of novel properties.

In contradistinction to classical theories quantum mechanics sharply distinguishes between potential and essential properties of a system. The potential properties of a quantal system are described by a set of observables. The subset of those observables that commute with all others is called the center of observables and represents the essential properties, i.e. the properties actualized in each state of the system. If a quantum system is open its time evolution can change the center and turn merely potential properties into essential ones and vice versa. The temporal behavior of such a system clearly shows the characteristics of evolutionary change; quantum mechanics can describe how novel properties emerge in the course of time. This is in clear contrast to the behavior of Turing- or Belousov-Zhabotinskii type models where the evolutionary change only produces a refinement of an existing essential property and not something really new. - As an illustration we present a simple model with non-trivial evolutionary behavior.

Biological Evolution↗
PubMed1986

An apparent progressive and recurrent evolutionary restriction in tissue expression of a gene, the lactate dehydrogenase-C gene, within a family of bony fish (Salmoniformes: Umbridae)

Unexpectedly large differences in the tissue patterns of lactate dehydrogenase-C (Ldh-C) gene regulation were observed among species of fish within the family Umbridae (Salmoniformes). Normally, all the species within a family or order of advanced fishes exhibit the same, tissue-restricted pattern of L-lactate dehydrogenase C4 isozyme synthesis--either eye- or liver-restricted expression, but not both. However, within the Umbridae the more anciently derived species had a more generalized (primitive) tissue expression, whereas the more recently derived species had a more tissue-restricted expression, predominating in the eye. Given the relative divergence times among the species estimated by genetic distance (using 51 protein-coding loci), divergence from the presumed primitive expression of the Ldh-C gene appears to have been proceeding more rapidly in some species lineages than others. This narrowing of Ldh-C gene tissue regulatory specificity within the family Umbridae is similar to the general trend observed over much greater evolutionary times within the class of bony fishes. The results support the hypothesis of repeated evolutionary canalizations of Ldh-C gene regulation from the generalized tissue expression in more primitive species to a predictable tissue-restricted expression (in either eye or liver) in advanced species. Furthermore, in the Umbridae, this progressive restriction of tissue expression of isozymes has taken place during the evolution of both the Ldh-C and Ldh-B genes. These evolutionary trends in the regulation of isozyme-locus tissue expression in the bony fishes are consistent with either an intrinsically conditioned trend of change in gene regulation or with a response to natural selection.

Animals↗
PubMed1982

Computer comparison of new and existing criteria for constructing evolutionary trees from sequence data.

Three new methods for constructing evolutionary trees from molecular sequence data are presented. These methods are based on a theory for correcting for non-constant evolutionary rates (Klotz et al. 1979; Klotz and Blanken 1981). Extensive computer simulations were run to compare these new methods to the commonly used criteria of Dayhoff (1978) and Fitch and Margoliash (1967). The results of these simulations showed that two of the new methods performed as well as Dayhoff's criterion, significantly better than that of Fitch and Margoliash, and as well as a simple variation of the latter (Prager and Wilson 1978) where any topology containing negative branch mutations is discarded. However, no method yielded the correct topology all of the time, which demonstrated the need to determine confidence estimates in a particular result when evolutionary trees are determined from sequence data.

Base Sequence↗
PubMed1990

Compositional statistics: an improvement of evolutionary parsimony and its application to deep branches in the tree of life.

We present compositional statistics, a new method of phylogenetic inference, which is an extension of evolutionary parsimony. Compositional statistics takes account of the base composition of the compared sequences by using nucleotide positions that evolutionary parsimony ignores. It shares with evolutionary parsimony the features of rate invariance and the fundamental distinction between transitions and transversions. Of the presently available methods of phylogenetic inference, compositional statistics is based on the fewest and mildest assumptions about the mode of DNA sequence evolution. It is therefore applicable to phylogenetic studies of the most distantly related organisms or molecules. This was illustrated by analyzing conservative positions in the DNA sequences of the large subunit of RNA polymerase from three archaebacterial groups, a eubacterium, a chloroplast, and the three eukaryotic polymerases. Internally consistent results, which are in accord with our knowledge of organelle origin and archaebacterial physiology, were achieved.

Amino Acid Sequence↗
PubMed1984

Evolutionary implications of error amplification in the self-replicating and protein-synthesizing machinery.

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 in 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.

Animals↗
PubMed1996

Evolutionary dynamics of predator-prey systems: an ecological perspective.

Evolution takes place in an ecological setting that typically involves interactions with other organisms. To describe such evolution, a structure is needed which incorporates the simultaneous evolution of interacting species. Here a formal framework for this purpose is suggested, extending from the microscopic interactions between individuals--the immediate cause of natural selection, through the mesoscopic population dynamics responsible for driving the replacement of one mutant phenotype by another, to the macroscopic process of phenotypic evolution arising from many such substitutions. The process of coevolution that results from this is illustrated in the context of predator-prey systems. With no more than qualitative information about the evolutionary dynamics, some basic properties of predator-prey coevolution become evident. More detailed understanding requires specification of an evolutionary dynamic; two models for this purpose are outlined, one from our own research on a stochastic process of mutation and selection and the other from quantitative genetics. Much of the interest in coevolution has been to characterize the properties of fixed points at which there is no further phenotypic evolution. Stability analysis of the fixed points of evolutionary dynamical systems is reviewed and leads to conclusions about the asymptotic states of evolution rather different from those of game-theoretic methods. These differences become especially important when evolution involves more than one species.

Animals↗
PubMed1991

The evolutionary position of the rhodophyte Porphyra umbilicalis and the basidiomycete Leucosporidium scottii among other eukaryotes as deduced from complete sequences of small ribosomal subunit RNA.

The complete small ribosomal subunit RNA (srRNA) sequence was determined for the red alga Porphyra umbilicalis and the basidiomycete Leucosporidium scottii, representing two taxa for which no srRNA sequences were hitherto known. These sequences were aligned with other published complete srRNA sequences of 58 eukaryotes. Evolutionary trees were reconstructed by a matrix optimization method from a dissimilarity matrix based on sections of the alignment that correspond to structurally conservative areas of the molecule that can be aligned unambiguously. The overall topology of the eukaryotic tree thus constructed is as follows: first there is a succession of early diverging branches, leading to a diplomonad, a microsporidian, a euglenoid plus kinetoplastids, an amoeba, and slime molds. Later, a nearly simultaneous radiation seems to occur into a number of taxa comprising the metazoa, the red alga, the sporozoa, the higher fungi, the ciliates, the green plants, plus some other less numerous groups. Because the red alga diverges late in the evolutionary tree, it does not seem to represent a very primitive organism as proposed on the basis of morphological and 5S rRNA sequence data. Asco- and basidiomycetes do not share a common ancestor in our tree as is generally accepted on the basis of conventional criteria. In contrast, when all alignment positions, rather than the more conservative ones, are used to construct the evolutionary tree, higher fungi do form a monophyletic cluster. The hypothesis that higher fungi and red algae might have shared a common origin has been put forward. Although the red alga and fungi seem to diverge at nearly the same time, no such relationship can be detected. The newly determined sequences can be fitted into a secondary structure model for srRNA, which is now relatively well established with the exception of uncertainties in a number of eukaryote-specific expansion areas. A specific structural model featuring a pseudoknot is proposed for one of these areas.

Base Sequence↗
PubMed2005

Evolutionary ecology in silico: Does mathematical modelling help in understanding 'generic' trends?

Motivated by the results of recent laboratory experiments, as well as many earlier field observations, that evolutionary changes can take place in ecosystems over relatively short ecological time scales, several 'unified' mathematical models of evolutionary ecology have been developed over the last few years with the aim of describing the statistical properties of data related to the evolution of ecosystems. Moreover, because of the availability of sufficiently fast computers, it has become possible to carry out detailed computer simulations of these models. For the sake of completeness and to put these recent developments in perspective, we begin with a brief summary of some older models of ecological phenomena and evolutionary processes. However, the main aim of this article is to review critically these 'unified' models, particularly those published in the physics literature, in simple language that makes the new theories accessible to a wider audience.

Aging↗
PubMed1997

Evolutionary relationship of the ligand-gated ion channels and the avermectin-sensitive, glutamate-gated chloride channels.

Two cDNAs, GluClalpha and GluClbeta, encoding glutamate-gated chloride channel subunits that represent targets of the avermectin class of antiparasitic compounds, have recently been cloned from Caenorhabditis elegans (Cully et al., Nature, 371, 707-711, 1994). Expression studies in Xenopus oocytes showed that GluClalpha and GluClbeta have pharmacological profiles distinct from the glutamate-gated cation channels as well as the gamma-aminobutyric acid (GABA)- and glycine-gated chloride channels. Establishing the evolutionary relationship of related proteins can clarify properties and lead to predictions about their structure and function. We have cloned and determined the nucleotide sequence of the GluClalpha and GluClbeta genes. In an attempt to understand the evolutionary relationship of these channels with the members of the ligand-gated ion channel superfamily, we have performed gene structure comparisons and phylogenetic analyses of their nucleotide and predicted amino acid sequences. Gene structure comparisons reveal the presence of several intron positions that are not found in the ligand-gated ion channel superfamily, outlining their distinct evolutionary position. Phylogenetic analyses indicate that GluClalpha and GluClbeta form a monophyletic subbranch in the ligand-gated ion channel superfamily and are related to vertebrate glycine channels/receptors. Glutamate-gated chloride channels, with electrophysiological properties similar to GluClalpha and GluClbeta, have been described in insects and crustaceans, suggesting that the glutamate-gated chloride channel family may be conserved in other invertebrate species. The gene structure and phylogenetic analyses in combination with the distinct pharmacological properties demonstrate that GluClalpha and GluClbeta belong to a discrete ligand-gated ion channel family that may represent genes orthologous to the vertebrate glycine channels.

Animals↗
PubMed1997

Structural and evolutionary relationships among chitinases of flowering plants.

The analysis of nuclear-encoded chitinase sequences from various angiosperms has allowed the categorization of the chitinases into discrete classes. Nucleotide sequences of their catalytic domains were compared in this study to investigate the evolutionary relationships between chitinase classes. The functionally distinct class III chitinases appear to be more closely related to fungal enzymes involved in morphogenesis than to other plant chitinases. The ordering of other plant chitinases into additional classes mainly relied on the presence of auxiliary domains-namely, a chitin-binding domain and a carboxy-terminal extension-flanking the main catalytic domain. The results of our phylogenetic analyses showed that classes I and IV form discrete and well-supported monophyletic groups derived from a common ancestral sequence that predates the divergence of dicots and monocots. In contrast, other sequences included in classes I* and II, lacking one or both types of auxiliary domains, were nested within class I sequences, indicating that they have a polyphyletic origin. According to phylogenetic analyses and the calculation of evolutionary rates, these chitinases probably arose from different class I lineages by relatively recent deletion events. The occurrence of such evolutionary trends in cultivated plants and their potential involvement in host-pathogen interactions are discussed.

Amino Acid Sequence↗
PubMed1999

Molecular phylogeny of phi29-like phages and their evolutionary relatedness to other protein-primed replicating phages and other phages hosted by gram-positive bacteria.

The phi29-like phage genus of Podoviridae family contains phages B103, BS32, GA-1, M2, Nf, phi15, phi29, and PZA that all infect Bacillus subtilis. They have very similar morphology and their genomes consist of linear double-stranded DNA of approximately 20 kb. The nucleotide sequences of individual genomes or their parts determined thus far show that these phages evolved from a common ancestor. A terminal protein (TP) that is covalently bound to the DNA 5'-end primes DNA replication of these phages. The same mechanism of DNA replication is used by the Cp-1 related phages (also members of the Podoviridae family) and by the phage PRD1 (member of the Tectoviridae family). Based on the complete or partial genomic sequence data of these phages it was possible to analyze the evolutionary relationship within the phi29-like phage genus as well as to other protein-primed replicating phages. Noncoding regions containing origins of replication were used in the analysis, as well as amino acid sequences of DNA polymerases, and with the phi29-like phages also amino acid sequences of the terminal proteins and of the gene 17 protein product, an accessory component of bacteriophage DNA replicating machinery. Included in the analysis are also results of a comparison of these phage DNAs with the prophages present in the Bacillus subtilis genome. Based on this complex analysis we define and describe in more detail the evolutionary branches of phi29-like phages, one branch consisting of phages BS32, phi15, phi29, and PZA, the second branch composed of phages B103, M2, and Nf, and the third branch having phage GA-1 as its sole member. In addition, amino acid sequences of holins, proteins involved in phage lysis were used to extend the evolutionary study to other phages infecting Gram-positive bacteria. The analysis based on the amino acid sequences of holins showed several weak points in present bacteriophage classification.

Amino Acid Sequence↗