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At least 541 records · Page 30Linked to original sources
PubMed2005

Sperm competition, mating rate and the evolution of testis and ejaculate sizes: a population model.

There are various ways to estimate ejaculate expenditure. Ejaculate size or sperm number (s) is an absolute number of units of ejaculate. Relative ejaculate expenditure (E) is the expenditure on the ejaculate as the proportion of the total expenditure on all aspects of the mating, including finding and acquiring a female, and so on. Relative testis size or gonadosomatic index (sigma) is testes mass divided by body mass; it is assumed to reflect the product of mating rate (M) and ejaculate mass (s). In a new model, where mating rate, sperm competition and sperm allocation interact, and where the female's inter-clutch interval is assumed to be independent of s or M, we show that sigma is directly proportional to the mean E for a species; across species sigma and E increase monotonically with sperm competition. However, the relation between s and sperm competition across species depends on the range of sperm competition (low risk or high intensity): s increases with sperm competition at low risk levels, but decreases with sperm competition at high intensity levels. This situation arises because s alpha E/M; both E and M increase with sperm competition, but E increases differently with sperm competition in its two ranges.

Animals↗
PubMed2005

Influences of nano-TiO2 on the chloroplast aging of spinach under light.

The effects of nano-TiO2 (rutile) on the chloroplast aging of spinach under light were studied. The results showed that when the chloroplasts were illuminated for 1, 5, and 10 min with 500 micromol/cm2/min light intensity, respectively, the evolution oxygen rate was rapidly increased; when the chloroplasts were treated for 20, 30, and 40 min with 500 micromol/cm2/min light intensity, respectively, the evolution oxygen rate was gradually decreased. While spinach was treated with 0.25% nano-TiO2, the rate of evolution oxygen of chloroplasts in different illumination times (1, 5, 10, 20, 30, and 40 min) was higher than that of control, and when the illumination time was over 10 min, the reduction of the evolution oxygen rate was lower than that of control. It suggested that nano-TiO2 treatment could protect chloroplasts from aging for long-time illumination. The mechanism researches indicated that nano-TiO2 treatment could significantly increase the activities of superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD), decrease accumulation of reactive oxygen free radicals and the level of malondialdehyde (MDA), and maintain stability of membrane structure of chloroplast under light.

Catalase↗
PubMed1998

Prion's progress: patterns and rates of molecular evolution in relation to spongiform disease.

Modification of the cellular prion protein has been correlated with the acquisition of several neurodegenerative diseases, including kuru, scrapie, bovine spongiform encephalopathy (BSE), and Creutzfeldt-Jakob disease (CJD). Sequence conservation and amino acid identity are known to influence the efficacy of interspecific transmission. We analyzed patterns of interspecific genetic variation with a view toward identifying features related to disease transmission. The reconstructed gene trees and amino acid tree were compared with the species tree, and all discordances observed were related to the species barrier of disease transmission. The rates of synonymous substitution, nonsynonymous substitution, and nucleotide content were determined for the protein-coding gene. Substitutions implicated in each of the prion diseases were found to occur in regions of the protein that are least variable across all species-opposite to the pattern of variability expected from interaction with an infectious pathogen. Amino acid residues related to the species barrier form a single cluster associated with the first alpha-helical domain of the protein. Residues related to sporadic and hereditary human prion disease form two separate clusters, associated with the second and third alpha-helical domains. Taken together, these results are consistent with the view that prion diseases arise from accidents in protein folding, rather than infection with an undiscovered virus-like particle. We speculate that the differences in disease phenotype between transmissable and hereditary forms could result from interactions between different parts of the protein during propagation.

Animals↗
PubMed1982

Evolution of developmental rate in mammals.

The allometric relationship between gestation period and body mass in terrestrial placental mammals was analyzed using data from 147 species. Important differences were found among the various orders. These differences can be explained if it were assumed that the order-specific lifestyle and environment in which the young are born has caused different selection pressures on the newborn young in the various orders and thus influenced the number of young per litter and duration of gestation. As proposed elsewhere, such evolutionary effects on embryonic development may have indirectly influenced the evolution of mammalian life span.

Adaptation, Physiological↗
PubMed1999

The dynamics of infinitesimally rare alleles, applied to the evolution of mutation rates and the expression of deleterious mutations.

A new method is presented for analysing the dynamics of a classical model where infinitesimally rare alleles segregate at an infinite number of unlinked loci, and where the alleles at different loci have equivalent effects. The dynamics of the distribution of the number of rare alleles per individual (the "phenotypic distribution") can be followed without knowing the frequencies of individual genotypes. Meiosis and random union of gametes have a very simple effect on the factorial cumulants of the phenotypic distribution which are consequently the natural set of variables to follow. An exact solution is presented for the dynamics of rare alleles under mutation and multiplicative selection. This solution has a simple representation in terms of the factorial cumulants. Unlike the QLE (quasi-linkage equilibrium) solution, this solution applies even when the population is far from linkage equilibrium. This approach is extended to analyse the joint dynamics of infinitesimally rare alleles at an infinite number of unlinked loci, together with a locus (with arbitrary allele frequencies) with which they interact. This more general method is used to investigate (1) the joint dynamics of a modifier of the mutation rate, together with deleterious alleles under mutation and multiplicative selection, and (2) the fate of an allele that ameliorates or exacerbates the fitness effects of deleterious alleles. When a new modifier allele causes a large change in the mutation rate, strong linkage disequilibrium is generated during its progress. However, using this new approach based on factorial cumulants, it is found that a remarkably simple invasion condition applies to alleles at the modifier locus, even when strong linkage disequilibrium is generated.

Alleles↗
PubMed1998

Rate variation of DNA sequence evolution in the Drosophila lineages.

Rate constancy of DNA sequence evolution was examined for three species of Drosophila, using two samples: the published sequences of eight genes from regions of the normal recombination rates and new data of the four AS-C (ac, sc, l'sc and ase) and ci genes. The AS-C and ci genes were chosen because these genes are located in the regions of very reduced recombination in Drosophila melanogaster and their locations remain unchanged throughout the entire lineages involved, yielding less effect of ancestral polymorphism in the study of rate constancy. The synonymous substitution pattern of the three lineages was found to be erratic in both samples. The dispersion index for replacement substitution was relatively high for the per, G6pd and ac genes. A significant heterogeneity was found in the number of synonymous substitutions in the three lineages between the two samples of genes with different recombination rates. This is partly due to a lack of the lineage effect in the D. melanogaster and Drosophila simulans lineages in the AS-C and ci genes in contrast to Akashi's observation of genes in regions of normal recombination. The higher codon bias in Drosophila yakuba as compared with D. melanogaster and D. simulans was observed in the four AS-C genes, which suggests change(s) in action of natural selection involved in codon usage on these genes. Fluctuating selection intensity may also be responsible for the observed locus-lineage interaction effects in synonymous substitution.

Animals↗
PubMed2004

High rate of viral evolution associated with the emergence of carnivore parvovirus.

Canine parvovirus (CPV) is an emerging DNA virus that was first observed to cause disease in canines in 1978 and has since become a ubiquitous pathogen worldwide. CPV emerged from feline panleukopenia parvovirus (FPLV) or a closely related virus, differing at several key amino acid residues. Here we characterize the evolutionary processes underlying the emergence of CPV. Although FPLV has remained an endemic infection in its host populations, we show that, since the 1970s, the newly emerged CPV has undergone an epidemic-like pattern of logistic/exponential growth, effectively doubling its population size every few years. This rapid population growth was associated with a lineage of CPV that acquired a broader host range and greater infectivity. Recombination played no role in the emergence of CPV. Rather, any preexisting variation in the donor species and the subsequent rapid adaptation of the virus to canines were likely dependent on a high rate of mutation and the positive selection of mutations in the major capsid gene. Strikingly, although these single-stranded viruses have a DNA genome and use cellular replication machinery, their rate of nucleotide substitution is closer to that of RNA viruses than to that of double-stranded DNA viruses.

Animals↗
PubMed1986

Effect of Photon Fluence Rate on Oxygen Evolution and Uptake by Chlamydomonas reinhardtii Suspensions Grown in Ambient and CO(2)-Enriched Air.

A closed system consisting of an assimilation chamber furnished with a membrane inlet from the liquid phase connected to a mass spectrometer was used to measure O(2) evolution and uptake by Chlamydomonas reinhardtii cells grown in ambient (0.034% CO(2)) or CO(2)-enriched (5% CO(2)) air. At pH = 6.9, 28 degrees C and concentrations of dissolved inorganic carbon (DIC) saturating for photosynthesis, O(2) uptake in the light (U(o)) equaled O(2) production (E(o)) at the light compensation point (15 micromoles photons per square meter per second). E(o) and U(o) increased with increasing photon fluence rate (PFR) but were not rate saturated at 600 micromoles photons per square meter per second, while net O(2) exchange reached a saturation level near 500 micromoles photons per square meter per second which was nearly the same for both, CO(2)-grown and air-grown cells. Comparison of the U(o)/E(o) ratios between air-grown and CO(2)-grown C. reinhardtii showed higher values for air-grown cells at light intensities higher than light compensation. For both, air-grown and CO(2)-grown algae the rates of mitochondrial O(2) uptake in the dark measured immediately before and 5 minutes after illumination were much lower than U(o) at PFR saturating for net photosynthesis. We conclude that noncyclic electron flow from water to NADP(+) and pseudocyclic electron flow via photosystem I to O(2) both significantly contribute to O(2) exchange in the light. In contrast, mitochondrial respiration and photosynthetic carbon oxidation cycle are regarded as minor O(2) consuming reactions in the light in both, air-grown and CO(2)-grown cells. It is suggested that the "extra" O(2) uptake by air-grown algae provides ATP required for the energy dependent CO(2)/HCO(3) (-) concentrating mechanism known to be present in these cells.

Journal Article↗
PubMed2002

Different types and rates of genome evolution detected by comparative sequence analysis of orthologous segments from four cereal genomes.

Orthologous regions in barley, rice, sorghum, and wheat were studied by bacterial artificial chromosome sequence analysis. General microcolinearity was observed for the four shared genes in this region. However, three genic rearrangements were observed. First, the rice region contains a cluster of 48 predicted small nucleolar RNA genes, but the comparable region from sorghum contains no homologous loci. Second, gene 2 was inverted in the barley lineage by an apparent unequal recombination after the ancestors of barley and wheat diverged, 11-15 million years ago (mya). Third, gene 4 underwent direct tandem duplication in a common ancestor of barley and wheat 29-41 mya. All four of the shared genes show the same synonymous substitution rate, but nonsynonymous substitution rates show significant variations between genes 4a and 4b, suggesting that gene 4b was largely released from the strong purifying selection that acts on gene 4a in both barley and wheat. Intergenic retrotransposon blocks, many of them organized as nested insertions, mostly account for the lower gene density of the barley and wheat regions. All but two of the retrotransposons were found in the regions between genes, while all but 2 of the 51 inverted repeat transposable elements were found as insertions in genic regions and outside the retrotransposon blocks.

Biological Evolution↗
PubMed1993

Rates of DNA evolution in Drosophila depend on function and developmental stage of expression.

DNA-sequence divergence of genes expressed in the embryonic stage was compared with the divergence of genes expressed in adults for 13 species of Drosophila representing various degrees of relatedness. DNA-DNA hybridization experiments were conducted using as tracers complementary DNA (cDNA) reversed transcribed from poly(A)+ mRNA isolated from different developmental stages. The results indicate: (1) cDNA is less diverged than total single-copy DNA; (2) cDNA sequences are not in the rapidly evolving fraction of the single-copy genome of Drosophila; (3) early in evolutionary divergence embryonic messages are about half as diverged as adult messages; sequence data from some of the species compared indicate this is likely due to differences in rates of silent substitutions in genes expressed at different stages of development; and (4) at greater evolutionary distance, the differences in embryonic and adult messages disappear; this could be due to lineage-specific shifts in codon usage.

Animals↗
PubMed1997

The Bag320 satellite DNA family in Bacillus stick insects (Phasmatodea): different rates of molecular evolution of highly repetitive DNA in bisexual and parthenogenic taxa.

The Bag320 satellite DNA (satDNA) family was studied in seven populations of the stick insects Bacillus atticus (parthenogenetic, unisexual) and Bacillus grandii (bisexual). It was characterized as widespread in all zymoraces of B. atticus and in all subspecies of B. grandii. The copy number of this satellite is higher in the bisexual B. grandii (15%-20% of the genome) than in the parthenogenetic B. atticus (2%-5% of the genome). The nucleotide sequences of 12 Bag320 clones from B. atticus and 17 from B. grandii differed at 13 characteristic positions by fixed nucleotide substitutions. Thus, nucleotide sequences from both species cluster conspecifically in phylogenetic dendrograms. The nucleotide sequences derived from B. grandii grandii could be clearly discriminated from those of B. grandii benazzii and B. grandii maretimi on the basis of 25 variable sites, although all taxa come from Sicily. In contrast, the Bag320 sequences from B. atticus could not be discriminated accordingly, although they derive from geographically quite distant populations of its three zymoraces (the Italian and Greek B. atticus atticus, the Greek and Turkish B. atticus carius, and the Cyprian B. atticus cyprius). The different rate of evolutionary turnover of the Bag320 satDNA in both species can be related to their different modes of reproduction. This indicates that meiosis and chromosome segregation affect processes in satDNA diversification.

Animals↗
PubMed2006

Pattern and rate of indel evolution inferred from whole chloroplast intergenic regions in sugarcane, maize and rice.

Microstructural changes such as insertions and deletions (=indels) are a major driving force in the evolution of non-coding DNA sequences. To better understand the mechanisms by which indel mutations arise, as well as the molecular evolution of non-coding regions, the number and pattern of indels and nucleotide substitutions were compared in the whole chloroplast genomes. Comparisons were made for a total of over 38 kb non-coding DNA sequences from 126 intergenic regions in two data sets representing species with different divergence times: sugarcane and maize and Oryza sativa var. indica and japonica. The main findings of this study are: (i) Approximately half of all indels are single nucleotide indels. This observation agrees with previous studies in various organisms. (ii) The distribution and number of indels was different between two data sets, and different patterns were observed for tandem repeat and non-repeat indels. (iii) Distribution pattern of tandem repeat indels showed statistically significant bias towards A/T-rich. (iv) The rate of indel mutation was estimated to be approximately 0.8 +/- 0.04 x 10(-9) per site per year, which was similar to previous estimates in other organisms. (v) The frequencies of nucleotide substitutions and indels were significantly lower in inverted repeat (IR).

Conserved Sequence↗
PubMed2005

Degeneration and domestication of a selfish gene in yeast: molecular evolution versus site-directed mutagenesis.

VDE is a homing endonuclease gene in yeasts with an unusual evolutionary history including horizontal transmission, degeneration, and domestication into the mating-type switching locus HO. We investigate here the effects of these features on its molecular evolution. In addition, we correlate rates of evolution with results from site-directed mutagenesis studies. Functional elements have lower rates of evolution than degenerate ones and higher conservation at functionally important sites. However, functionally important and unimportant sites are equally likely to have been involved in the evolution of new function during the domestication of VDE into HO. The domestication event also indicates that VDE has been lost in some species and that VDE has been present in yeasts for more than 50 Myr.

Evolution, Molecular↗
PubMed2006

Types and rates of sequence evolution at the high-molecular-weight glutenin locus in hexaploid wheat and its ancestral genomes.

The Glu-1 locus, encoding the high-molecular-weight glutenin protein subunits, controls bread-making quality in hexaploid wheat (Triticum aestivum) and represents a recently evolved region unique to Triticeae genomes. To understand the molecular evolution of this locus region, three orthologous Glu-1 regions from the three subgenomes of a single hexaploid wheat species were sequenced, totaling 729 kb of sequence. Comparing each Glu-1 region with its corresponding homologous region from the D genome of diploid wheat, Aegilops tauschii, and the A and B genomes of tetraploid wheat, Triticum turgidum, revealed that, in addition to the conservation of microsynteny in the genic regions, sequences in the intergenic regions, composed of blocks of nested retroelements, are also generally conserved, although a few nonshared retroelements that differentiate the homologous Glu-1 regions were detected in each pair of the A and D genomes. Analysis of the indel frequency and the rate of nucleotide substitution, which represent the most frequent types of sequence changes in the Glu-1 regions, demonstrated that the two A genomes are significantly more divergent than the two B genomes, further supporting the hypothesis that hexaploid wheat may have more than one tetraploid ancestor.

Base Sequence↗
PubMed2003

Effect of sodium dodecyl sulfate on the rate of hydrogen evolution at a cathode.

The effect of H(2) evolution on the mass-transfer coefficient of cathode reduction of potassium ferricyanide at a mercury cathode was studied with the aim of (i) comparing the mass transfer behavior at a Hg cathode with that at solid electrodes under gas-evolving conditions and (ii) testing the effect of anionic surface-active agent on the mass transfer behavior of an H(2)-evolving Hg cathode. It is found that the mass transfer coefficient at the Hg cathode was much higher than the value at a solid cathode. The mass transfer coefficient at H(2)-evolving Hg was found to decrease in the presence of sodium dodecyl sulfate (SDS) surfactant by an amount ranging from 58.8 to 76%, depending on the H(2) discharge rate and the SDS concentrations.

Journal Article↗
PubMed2006

Rate of viral evolution and risk of losing future drug options in heavily pretreated, HIV-infected patients who continue to receive a stable, partially suppressive treatment regimen.

BACKGROUND: Many treatment-experienced, HIV-infected patients who have limited therapeutic options for complete viral suppression continue to receive a partially suppressive treatment regimen pending the availability of at least 2 new antiretroviral drugs. The major risk of this approach is ongoing viral evolution and the loss of future drug options. METHODS: Antiretroviral-treated subjects with incomplete viral suppression were sampled from a clinic-based cohort. Inclusion criteria were receipt of a stable treatment regimen for > or = 120 days, a plasma HIV RNA load of > 500 copies/mL, and > or = 1 resistance mutation. Phenotypic and genotypic resistance testing was performed every 4 months. RESULTS: The 106 patients who were eligible for the study had a median of 3 observations during a median of 11.3 months. An estimated 23% and 18% developed at least 1 new nucleoside analogue and 1 new protease inhibitor mutation at 1 year, respectively. An estimated 30% lost the phenotypic equivalent of 1 susceptible drug at 1 year. A lower number of total mutations at baseline was a significant predictor of developing a new nucleoside analogue mutation (P=.01). At 1 year, the probability that an existing mutation would become undetectable using population-based sequencing was 32%. There was a higher rate of change at nonresistance codons than at codons known to be associated with drug resistance. CONCLUSIONS: Heavily pretreated patients with HIV infection who remain on a partially suppressive regimen have a measurable risk of losing future drug options, particularly those patients who have few baseline mutations. Resistance mutations vary over time, which suggests that the results of any single resistance test may not be representative of all mutations selected by a given treatment regimen.

Anti-HIV Agents↗
PubMed1999

The approach to mutation-selection balance in an infinite asexual population, and the evolution of mutation rates.

A method is described for calculating the dynamics of the distribution of fitness in an infinite asexual population which is subject to unconditionally deleterious mutations with independent effects. This method is applied to the problem of calculating the frequency of a mutator subpopulation, at equilibrium between mutation and indirect selection due to association with deleterious mutations. Many mutator alleles are produced by loss-of-function mutations in polymerase or mismatch repair genes. Previous calculations have ignored the fact that this creates a flux of higher fitness individuals into the mutator subpopulation. This flux raises the mean fitness of the mutator subpopulation, and when this factor is taken into account, the frequency of the mutator may be more than an order of magnitude greater than recent theoretical work has suggested.

Alleles↗
PubMed2024

Evolution of homologous recombination rates across bacteria.

Bacteria are nonsexual organisms but are capable of exchanging DNA at diverse degrees through homologous recombination. Intriguingly, the rates of recombination vary immensely across lineages where some species have been described as purely clonal and others as "quasi-sexual." However, estimating recombination rates has proven a difficult endeavor and estimates often vary substantially across studies. It is unclear whether these variations reflect natural variations across populations or are due to differences in methodologies. Consequently, the impact of recombination on bacterial evolution has not been extensively evaluated and the evolution of recombination rate-as a trait-remains to be accurately described. Here, we developed an approach based on Approximate Bayesian Computation that integrates multiple signals of recombination to estimate recombination rates. We inferred the rate of recombination of 162 bacterial species and one archaeon and tested the robustness of our approach. Our results confirm that recombination rates vary drastically across bacteria; however, we found that recombination rate-as a trait-is conserved in several lineages but evolves rapidly in others. Although some traits are thought to be associated with recombination rate (e.g., GC-content), we found no clear association between genomic or phenotypic traits and recombination rate. Overall, our results provide an overview of recombination rate, its evolution, and its impact on bacterial evolution.

Bacteria↗