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PubMed1986

Ribosomal RNA phylogenies for the vibrio-enteric group of eubacteria.

Comparisons between the ribonucleotide sequences of 5S rRNAs of the Gram-negative eubacteria indicate that several families, namely Enterobacteriaceae, Vibrionaceae and Aeromonadaceae possess remarkably similar evolutionary histories. A study of the phylogenetic relationships among these groups, through cluster analysis and construction of evolutionary trees, suggests the existence of dissimilar rates of evolution along the several lineages. These dissimilarities are most evident in comparisons between the phylogenetic depths of the Enterobacteriaceae and Vibrionaceae. Detection of disparate rates of evolution, as well as their influence on the interpretation of the natural taxonomy of this group of bacteria, is discussed.

Aeromonas↗
PubMedDate not supplied

[Relation of fluctuations in the physiological traits of a continuous Saccharomyces cerevisiae culture to the cell division cycle].

Such physiological characteristics of a continuous Saccharomyces cerevisiae culture as the rate of O2 uptake and CO2 evolution, the rate at which the medium was acidified, were found to vary. When the flow rate was increased from 0.05 to 0.1 h-1, the period of variations also rose (from 3 to 33 h) and two maxima were detected in the quantity of budding cells within one 33-h period of the variations. These findings indicate that the variations do not depend on changes in the physiology of the cell in the course of its division cycle.

Cell Cycle↗
PubMedDate not supplied

[Characteristics of different growth stages of the blue-green alga Anacystis nidulans (Synechococcus)].

The rate of growth of the blue-green alga Anacystis nidulans is highest during the first 5--8 days but the number of the cells increases up to 30 days when the stationary phase takes place (30--60 days). The content of chlorophyll is almost constant during the first 20 days of growth while the content of phycocyanin increases; then the content of the both pigments decreases. The rate of O2 evolution and the rate of electron transport to ferricyanide decrease exponentionally during the first 10 days of growth. The rate of endogenous respiration and the rate of O2 absorption, induced by methylviologen in the light in the presence of DCMU decrease more slowly. At the same time, the rate of O2 absorption in the presence of methylviologen without DCMU and the rate of TTC reduction in the darkness increase and later decrease. The rate of TTC reduction in the light increases up to 30--40 days and then decreases. The rate of the cell death in the darkness decreases when the age of the "light" culture is 50 days. Addition to the medium of its main components does not increase the rate of growth of the culture after 10 days of its growth. Addition of CaCl2, glucose, and asparagic acid increases the rate of growth of the 3-day-old culture. Addition of phosphorus inhibits growth. Argon favours growth of the culture. The cells are rapidly discoloured in conditions of hampered gas exchange; they die rapidly also in the presence of DCMU, methylviologen, and KCN.

Chlorophyll↗
PubMedDate not supplied

Evolution of arginine kinase within the genus Drosophila.

The rate of evolution and extant levels of polymorphism for arginine kinase were examined in species of the genus Drosophila. Surveys of 11 species for electrophoretic variation revealed an average heterozygosity of 0.003. Using antisera prepared against arginine kinase purified from a representative of each of three major subdivisions of the genus, immunological distances were measured by microcomplement fixation (MC'F) assay for 20 species of Drosophila. These data are consistent with the broad outline of the phylogenetic relationships within the genus suggested by other kinds of data. The unit evolutionary period for Drosophila arginine kinase was estimated to be 59 million years (MY). This contrasts with an estimate of 30 MY as the unit evolutionary period for vertebrate creatine kinase. It is suggested that this difference in evolutionary rate arises because a single gene encodes Drosophila arginine kinase, whereas at least three different genes encode the various forms of vertebrate creatine kinase.

Animals↗
PubMed2006

Neutral theory, phylogenies, and the relationship between phenotypic change and evolutionary rates.

The neutral theory of molecular evolution predicts that rates of phenotypic change are largely independent from genotypic change. A recent study by Bromham et al. (2002) confirmed this expectation, finding no evidence for correlated phenotypic and molecular evolutionary rates in animals. We reevaluate this hypothesis, sampling at different taxonomic levels in plants and animals, using Bayesian inference to reconstruct phylogenetic trees and estimate rates of molecular evolution. We use independent contrasts in branch lengths to maximize the information extracted from each of the trees and nodal posterior probabilities to assess the influence of phylogenetic error. Our results indicate that in vascular plants between 2% and 11% of the variation in phenotypic rates of change can be explained by the rate of genotypic change. These results may be explained by the idea that processes that affect general evolutionary rates, such as body size, may also be expected to influence rates of morphological change.

Animals↗
PubMed1991

Extreme variations in the ratios of non-synonymous to synonymous nucleotide substitution rates in signal peptide evolution.

Nucleotide sequences encoding signal peptides from the precursors of alpha-amylase/trypsin inhibitors from cereals are homologous to those corresponding to the precursors of thaumatin II and of plastocyanins. Non-synonymous (KA) and synonymous (KS) rates of nucleotide substitutions have been calculated for all possible binary combinations. Extreme variation in KA/KS ratios has been observed; from the 0.167 average found within the plastocyanin family to an average of 1.90 calculated for the inhibitors/thaumatin II transition. A similar calculation has been carried out for the signal peptide sequences of thionins, which are unrelated to those of the alpha-amylase/trypsin inhibitor family, and an average KA/KS of 0.12 has been obtained. This variation can be largely explained in terms of an empirical index of stability related to amino acid composition and seems to be independent of functional constraints.

Amino Acid Sequence↗
PubMed1999

Calibrating bacterial evolution.

Attempts to calibrate bacterial evolution have relied on the assumption that rates of molecular sequence divergence in bacteria are similar to those of higher eukaryotes, or to those of the few bacterial taxa for which ancestors can be reliably dated from ecological or geological evidence. Despite similarities in the substitution rates estimated for some lineages, comparisons of the relative rates of evolution at different classes of nucleotide sites indicate no basis for their universal application to all bacteria. However, there is evidence that bacteria have a constant genome-wide mutation rate on an evolutionary time scale but that this rate differs dramatically from the rate estimated by experimental methods.

Bacteria↗
PubMedDate not supplied

Molecular evolution of X-linked accessory gland proteins in Drosophila pseudoobscura.

In Drosophila melanogaster and Drosophila simulans, positive Darwinian selection drives high rates of evolution of male reproductive genes, and accessory gland proteins (Acps) in particular. Here, we tested whether 13 X-linked male-specific genes, 4 Acps and 9 non-Acps, are under selective forces in the Drosophila pseudoobscura species group, much as those in the D. melanogaster group. We observed a statistically significant correlation in relative rates of nonsynonymous evolution between the two species groups tested. One Acp examined had a higher rate of nonsynonymous substitution than predicted by a neutral model in both species groups, suggesting its divergence was driven by positive Darwinian selection. To further test for the signature of selection, we examined polymorphism of three Acps within D. pseudoobscura. From this test, no Acp individually bore the signature of positive selection, but the 3 Acps together possessed an excess of nonsynonymous differences between species, relative to polymorphism within species. We conclude that faster evolution of Acps in the D. pseudoobscura group appears to be driven by positive selection, as previously suggested in the D. melanogaster group.

Animals↗
PubMed1999

Molecular epidemiology and evolution of enterovirus 71 strains isolated from 1970 to 1998.

Enterovirus 71 (EV71) (genus Enterovirus, family Picornaviridae), a common cause of hand, foot, and mouth disease (HFMD), may also cause severe neurological diseases, such as encephalitis and poliomyelitis-like paralysis. To examine the genetic diversity and rate of evolution of EV71, we have determined and analyzed complete VP1 sequences (891 nucleotides) for 113 EV71 strains isolated in the United States and five other countries from 1970 to 1998. Nucleotide sequence comparisons demonstrated three distinct EV71 genotypes, designated A, B, and C. The genetic variation within genotypes (12% or fewer nucleotide differences) was less than the variation between genotypes (16.5 to 19.7%). Strains of all three genotypes were at least 94% identical to one another in deduced amino acid sequence. The EV71 prototype strain, BrCr-CA-70, isolated in California in 1970, is the sole member of genotype A. Strains isolated in the United States and Australia during the period from 1972 to 1988, a 1994 Colombian isolate, and isolates from a large HFMD outbreak in Malaysia in 1997 are all members of genotype B. Although strains of genotype B continue to circulate in other parts of the world, none have been isolated in the United States since 1988. Genotype C contains strains isolated in 1985 or later in the United States, Canada, Australia, and the Republic of China. The annual rate of evolution within both the B and C genotypes was estimated to be approximately 1.35 x 10(-2) substitutions per nucleotide and is similar to the rate observed for poliovirus. The results indicate that EV71 is a genetically diverse, rapidly evolving virus. Its worldwide circulation and potential to cause severe disease underscore the need for additional surveillance and improved methods to identify EV71 in human disease.

Amino Acid Sequence↗
PubMed1997

Evolution of high mutation rates in experimental populations of E. coli.

Most mutations are likely to be deleterious, and so the spontaneous mutation rate is generally held at a very low value. Nonetheless, evolutionary theory predicts that high mutation rates can evolve under certain circumstances. Empirical observations have previously been limited to short-term studies of the fates of mutator strains deliberately introduced into laboratory populations of Escherichia coli, and to the effects of intense selective events on mutator frequencies in E. coli. Here we report the rise of spontaneously originated mutators in populations of E. coli undergoing long-term adaptation to a new environment. Our results corroborate computer simulations of mutator evolution in adapting clonal populations, and may help to explain observations that associate high mutation rates with emerging pathogens and with certain cancers.

Adaptation, Physiological↗
PubMed2000

Molecular evolution of growth hormone and receptor in the guinea-pig, a mammal unresponsive to growth hormone.

Growth in the guinea-pig is completely unresponsive to endogenous or exogenous growth hormone, despite the fact that the guinea-pig produces normal to high levels of growth hormone and receptor. In primates and artiodactyls, growth hormone exhibits accelerated rates of evolution that appear to be correlated with changes in function. Surprisingly, both guinea-pig growth hormone and receptor exhibit slow rates of evolution similar to those seen in other mammals, implying that both proteins are as functionally conserved in the guinea-pig as in other mammals or that any loss or relaxation of functional constraint was very recent. However, the guinea-pig growth hormone and receptor both exhibit a single amino acid replacement at a site known to have functional significance. Nevertheless, it is unclear whether the aberrant nature of the guinea-pig growth hormone-growth hormone receptor axis is due to these replacements or whether it is due to a defect in post-receptor signalling.

Amino Acid Sequence↗
PubMed2000

Darwinian aspects of molecular evolution at sublinear propagation rates.

Mean fitness is non-decreasing in the symmetry sector of the frequency trajectory followed in competitive replication at sublinear propagation rates (parabolic time course). This sector contains the pairwise symmetric distribution of species frequencies and its neighboring states, and represents at least half the possible states of an evolving sublinear system. States is the non-symmetry sector produce a negative rate of change in mean fitness. The heterogeneous steady state attained in a finite sublinear system is destabilized by formation of a variant with above-threshold fitness. Evolution in the post-steady-state interval elevates the fitness threshold for coexistence. Contrary to the proposition that 'parabolic growth invariably results in the survival of all competing species', only species with sufficient fitness to avoid subthreshold fitness survive.

Evolution, Molecular↗
PubMed2001

Selection forces and constraints on retroviral sequence variation.

All retroviruses possess a highly error-prone reverse transcriptase, but the extent of the consequent sequence diversity and the rate of evolution differ greatly among retroviruses. Because of the high mutability of retroviruses, it is not the generation of new viral variants that limits the extent of diversity and the rate of evolution of retroviruses, but rather the selection forces that act on these variants. Here, we suggest that two selection forces--the immune response and the limited availability of appropriate target cells during transmission and persistence--are chiefly responsible for the observed sequence diversity in untreated retroviral infections. We illustrate these aspects of positive selection by reference to specific lentiviruses [human and simian immunodeficiency viruses (HIV and SIV)] and oncoviruses [feline leukemia virus (FeLV) and human T cell leukemia virus (HTLV)] that differ in their extent of variation and in disease outcomes.

Animals↗
PubMed1998

Sociality and the rate of rDNA sequence evolution in wasps (Vespidae) and honeybees (Apis).

Sequence data of mitochondrial 16S ribosomal DNA (mt-rDNA) and nuclear 28S ribosomal DNA (nuc-rDNA) were compared in two honeybee species (Apis mellifera and Apis dorsata) and a selection of 22 wasp species (Vespidae) with different levels of sociality. The averge substitution rates in mt-rDNA and nuc-rDNA were almost-equal in solitary species. In species with larger nests, however, the difference between the nuclear and the mitochondrial substitution rate significantly increased. The average substitution ratio, psi (nucleotide substitutions in mt-rDNA/nucleotide substitutions in nuc-rDNA) was 1.48 +/- 0.12 (SE) among the solitary Eumeninae, 3.70 +/- 0.15 among five primitive social Stenogastrinae species, 3.24 +/- 0.20 among five Polistinae species, 5.76 +/- 0.33 among nine highly eusocial Vespinae, and 12.7 in the two Apis species. The high egg-laying rate and the effective population size skew between the sexes may contribute to the rise of the substitution ratio in the highly eusocial species. Drift and bottleneck effects in the mitochondrial DNA pool during speciation events as well as polyandry may further enhance this phenomenon.

Animals↗
PubMed1985

H2, N2, and O2 metabolism by isolated heterocysts from Anabaena sp. strain CA.

Metabolically active heterocysts isolated from wild-type Anabaena sp. strain CA showed high rates of light-dependent acetylene reduction and hydrogen evolution. These rates were similar to those previously reported in heterocysts isolated from the mutant Anabaena sp. strain CA-V possessing fragile vegetative cell walls. Hydrogen production was observed with isolated heterocysts. The ratio of C2H4 to H2 produced ranged from 0.9 to 1.2, and H2 production exhibited unique biphasic kinetics consisting of a 1 to 2-min burst of hydrogen evolution followed by a lower, steady-state rate of hydrogen production. This burst was found to be dependent upon the length of the dark period immediately preceding illumination and may be related to dark-to-light ATP transients. The presence of 100 nM NiCl2 in the growth medium exerted an effect on both acetylene reduction and hydrogen evolution in the isolated heterocysts from strain CA. H2-stimulated acetylene reduction was increased from 2.0 to 3.2 mumol of C2H4 per mg (dry weight) per h, and net hydrogen production was abolished. A phenotypic Hup- mutant (N9AR) of Anabaena sp. strain CA was isolated which did not respond to nickel. In isolated heterocysts from N9AR, ethylene production rates were the same under both 10% C2H2-90% Ar and 10% C2H2-90% H2 with or without added nickel, and net hydrogen evolution was not affected by the presence of 100 nM Ni2+. Isolated heterocysts from strain CA were shown to have a persistent oxygen uptake of 0.7 mumol of O2 per mg (dry weight) per h, 35% of the rate of whole filaments, at air saturating O2 levels, indicating that O2 impermeability is not a requirement for active heterocysts.

Acetylene↗
PubMed2006

Behavioural trade-offs between growth and mortality explain evolution of submaximal growth rates.

1. The importance of body size and growth rate in ecological interactions is widely recognized, and both are frequently used as surrogates for fitness. However, if there are significant costs associated with rapid growth rates then its fitness benefits may be questioned. 2. In replicated whole-lake experiments, we show that a domestic strain of rainbow trout (artificially selected for maximum intrinsic growth rate) use productive but risky habitats more than wild trout. Consequently, domestic trout grow faster in all situations, experience greater survival in the absence of predators, but have lower survival in the presence of predators. Therefore, rapid growth rates are selected against due to increased foraging effort (or conversely, lower antipredator behaviour) that increases vulnerability to predators. In other words, there is a behaviourally mediated trade-off between growth and mortality rates. 3. Whereas rapid growth is beneficial in many ecological interactions, our results show the mortality costs of achieving it are large in the presence of predators, which can help explain the absence of an average phenotype with maximized growth rates in nature.

Animals↗
PubMed1981

[Intercellular serine proteinases from spore-forming bacilli].

Some physico-chemical properties, immunological reactions, structural, functional and evolutionary features of intracellular serine proteinases from spore-forming bacilli were studied. These enzymes belong to an individual subfamily of serine proteinases and in terms of their structure and evolution are most closely related to secretory subtilisins. Intracellular serine proteinases are found in a wide variety of microorganisms--from the spore-forming bacilli to Escherichia coli and are characterized by a higher (as compared to secretory subtilisins) rate of evolution due to a more rigid selective control of the structure and function of intracellular enzymes. Active intracellular proteinases have a unique dimeric structure, which allows to exclude random proteolysis of native proteins in vivo. Secretory subtilisins and intracellular bacillary serine proteinases are coded by separate closely related structural genes, whose presence in the bacillary genome can be explained by duplication of the precursor gene. The existence of duplicated genes of serine proteinases provides sufficient evidence for the marked structural divergence and a high rate of evolution of secretory subtilisins.

Amino Acid Sequence↗
PubMed2002

Sequence and phylogenetic analysis of the L and VP1 genes of foot-and-mouth disease virus serotype Asia1.

Most of the molecular epidemiological studies of foot-and-mouth disease virus (FMDV) are based on comparison of VP1 gene sequence. In this report, we determine the nucleotide (nt) sequence of the L (603 nt) and VP1 (633 nt) genes of 27 FMDV serotype Asia 1 isolates recovered from different outbreaks in India, and compared with each other and the vaccine strain, IND 63/72, used in the country. Independent phylogenetic analyses on both the aligned gene sequences identified two major lineages (designated A & B) in the Asia 1 isolates. Both L- and VP1-based trees were congruent with respect to the major branching pattern of the isolates. The lineage A is represented by the isolates of 1986-2000 including the vaccine strain IND 63/72, whereas, lineage B appeared to be dominant and responsible for most of the recent outbreaks. A correlation was observed between the clustering of the isolates in the phylogenetic tree and the amino acid changes at many of the positions in VP1 as well as in L protein. The annual rate of evolution in L and VP1 genes was found similar and estimated to be 4.0 x 10(-3) and 3.8 x 10(-3) substitutions per nucleotide, respectively. Our result, largely from the congruence in phylogenetic trees and the rate of evolution in both the genes, suggests the possibility for the use of L gene sequence in phylogenetic comparison of FMDV.

Amino Acid Sequence↗