Physiological Characterization of Adaptive Clones in Evolving Populations of the Yeast, SACCHAROMYCES CEREVISIAE

Populations of a diploid strain of S. cerevisiae were grown in glucose-limited continuous culture for more than 260 generations. A series of seven sequential adaptive changes were identified by monitoring the frequency of cycloheximide resistance in these populations. Samples were taken from the continuous cultures following each adaptive shift and characterized physiologically to determine (1) the range of phenotypes that can be selected in a precisely defined constant environment and (2) the order and predictability of the occurrence of the adaptive mutations in evolving populations. The clones were characterized with respect to the growth parameters, maximum growth rate, saturation coefficient and yield, as well as for changes in cell size and geometry and rate of glucose uptake. The maximum growth rates of the seven adaptive clones were very similar, but in contrast the saturation coefficients differed substantially. Surprisingly, not all clones showed reductions in the saturation coefficients, in comparison to the immediately preceding clones, as would be predicted from classical continuous culture kinetics. In addition, yield estimates first increased and then decreased for later isolated adaptive clones. In general, the results suggest epistatic interactions between the adaptive clones, consistent with earlier published results. The rate of glucose uptake, as measured by 14C-xylose uptake, increased dramatically after the selection and fixation of seven adaptive clones. Progressive decreases in cell volume and changes in cell geometry, resulting in increased surface area to volume ratios, were also observed in the adaptive clones, but these changes were not always seen in other haploid and diploid yeast populations evolving under the same conditions. Such changes may be easily explainable in terms of the characteristics of the glucose-limited environment. The significance of the results to the evolution of microorganisms under nutrient-limiting conditions is discussed.     

Diversity of Arbuscular Mycorrhizal Fungus Populations in Heavy-Metal-Contaminated Soils

High concentrations of heavy metals have been shown to adversely affect the size, diversity, and activity of microbial populations in soil. The aim of this work was to determine how the diversity of arbuscular mycorrhizal (AM) fungi is affected by the addition of sewage-amended sludge containing heavy metals in a long-term experiment. Due to the reduced number of indigenous AM fungal (AMF) propagules in the experimental soils, several host plants with different life cycles were used to multiply indigenous fungi. Six AMF ecotypes were found in the experimental soils, showing consistent differences with regard to their tolerance to the presence of heavy metals. AMF ecotypes ranged from very sensitive to the presence of metals to relatively tolerant to high rates of heavy metals in soil. Total AMF spore numbers decreased with increasing amounts of heavy metals in the soil. However, species richness and diversity as measured by the Shannon-Wiener index increased in soils receiving intermediate rates of sludge contamination but decreased in soils receiving the highest rate of heavy-metal-contaminated sludge. Relative densities of most AMF species were also significantly influenced by soil treatments. Host plant species exerted a selective influence on AMF population size and diversity. We conclude based on the results of this study that size and diversity of AMF populations were modified in metal-polluted soils, even in those with metal concentrations that were below the upper limits accepted by the European Union for agricultural soils.     

Genetic Changes Accompanying Increased Fitness in Evolving Populations of Escherichia Coli

Two populations of Escherichia coli, each initiated with a single clone containing a derivative of the plasmid pBR322, were maintained for long periods in glucose-limited continuous culture. In both populations, after an extensive number of generations had elapsed, clones were isolated in which the transposon Tn3 from the plasmid had integrated into the bacterial chromosome. In both cases examined, the transpositions were shown to increase relative fitness approximately 6-7%, in the environment in which the populations were maintained. The loci of integration were mapped to approximately 13.2 min (population 1) and approximately 32.8 min (population 2).     

Genomewide Patterns of Substitution in Adaptively Evolving Populations of the RNA Bacteriophage MS2

Experimental evolution of bacteriophage provides a powerful means of studying the genetics of adaptation, as every substitution contributing to adaptation can be identified and characterized. Here, I use experimental evolution of MS2, an RNA bacteriophage, to study its adaptive response to a novel environment. To this end, three lines of MS2 were adapted to rapid growth and lysis at cold temperature for a minimum of 50 phage generations and subjected to whole-genome sequencing. Using this system, I identified adaptive substitutions, monitored changes in frequency of adaptive mutations through the course of the experiment, and measured the effect on phage growth rate of each substitution. All three lines showed a substantial increase in fitness (a two- to threefold increase in growth rate) due to a modest number of substitutions (three to four). The data show some evidence that the substitutions occurring early in the experiment have larger beneficial effects than later ones, in accordance with the expected diminishing returns relationship between the fitness effects of a mutation and its order of substitution. Patterns of molecular evolution seen here—primarily a paucity of hitchhiking mutations—suggest an abundant supply of beneficial mutations in this system. Nevertheless, some beneficial mutations appear to have been lost, possibly due to accumulation of beneficial mutations on other genetic backgrounds, clonal interference, and negatively epistatic interactions with other beneficial mutations.     

Stabilizing Spatially-Structured Populations through Adaptive Limiter Control

Stabilizing the dynamics of complex, non-linear systems is a major concern across several scientific disciplines including ecology and conservation biology. Unfortunately, most methods proposed to reduce the fluctuations in chaotic systems are not applicable to real, biological populations. This is because such methods typically require detailed knowledge of system specific parameters and the ability to manipulate them in real time; conditions often not met by most real populations. Moreover, real populations are often noisy and extinction-prone, which can sometimes render such methods ineffective. Here, we investigate a control strategy, which works by perturbing the population size, and is robust to reasonable amounts of noise and extinction probability. This strategy, called the Adaptive Limiter Control (ALC), has been previously shown to increase constancy and persistence of laboratory populations and metapopulations of Drosophila melanogaster. Here, we present a detailed numerical investigation of the effects of ALC on the fluctuations and persistence of metapopulations. We show that at high migration rates, application of ALC does not require a priori information about the population growth rates. We also show that ALC can stabilize metapopulations even when applied to as low as one-tenth of the total number of subpopulations. Moreover, ALC is effective even when the subpopulations have high extinction rates: conditions under which another control algorithm had previously failed to attain stability. Importantly, ALC not only reduces the fluctuation in metapopulation sizes, but also the global extinction probability. Finally, the method is robust to moderate levels of noise in the dynamics and the carrying capacity of the environment. These results, coupled with our earlier empirical findings, establish ALC to be a strong candidate for stabilizing real biological metapopulations.     

嗜热毛壳菌内切β-葡聚糖酶的分离纯化及特性

探讨了液体发酵嗜热毛壳菌（Chaetomium thermophile)产生的内切β－葡聚糖酶的分离纯化及特性。粗酶液经硫酸铵分级沉淀,DEAE－Seplharose Fast Flow阴离子层析,Pheny1-Sepha-rose疏水层析,Sephacry1 S-100分子筛层析等步骤便可获得凝胶电泳均一的内切β－葡聚糖酶,经12．5％SDS－PAGE和凝胶过滤层析法分离纯化酶蛋白的分子量约为67．8kD的69．8kD。该酶反应的最适温度和pH分别为60℃和4．0－4．5在pH5.0条件下,该酶在60℃下稳定：70℃保温1h后,仍保留30％的活性;在80摄氏度的半衰期为25min,金属离子内切β－葡聚糖酶的活性影响较大,其中Na^ 对酶有激活作用;Fe^2 ,Ag^ ,Cu^2 ,Ba^2 ,Zn^2 等对酶有抑制作用。该酶对结晶纤维素有没水解能力。     

The Accuracy of Computerized Adaptive Testing in Heterogeneous Populations: A Mixture Item-Response Theory Analysis

Background

Computerized adaptive testing (CAT) utilizes latent variable measurement model parameters that are typically assumed to be equivalently applicable to all people. Biased latent variable scores may be obtained in samples that are heterogeneous with respect to a specified measurement model. We examined the implications of sample heterogeneity with respect to CAT-predicted patient-reported outcomes (PRO) scores for the measurement of pain.

Methods

A latent variable mixture modeling (LVMM) analysis was conducted using data collected from a heterogeneous sample of people in British Columbia, Canada, who were administered the 36 pain domain items of the CAT-5D-QOL. The fitted LVMM was then used to produce data for a simulation analysis. We evaluated bias by comparing the referent PRO scores of the LVMM with PRO scores predicted by a “conventional” CAT (ignoring heterogeneity) and a LVMM-based “mixture” CAT (accommodating heterogeneity).

Results

The LVMM analysis indicated support for three latent classes with class proportions of 0.25, 0.30 and 0.45, which suggests that the sample was heterogeneous. The simulation analyses revealed differences between the referent PRO scores and the PRO scores produced by the “conventional” CAT. The “mixture” CAT produced PRO scores that were nearly equivalent to the referent scores.

Conclusion

Bias in PRO scores based on latent variable models may result when population heterogeneity is ignored. Improved accuracy could be obtained by using CATs that are parameterized using LVMM.     

Variable Mutation Rates as an Adaptive Strategy in Replicator Populations

For evolving populations of replicators, there is much evidence that the effect of mutations on fitness depends on the degree of adaptation to the selective pressures at play. In optimized populations, most mutations have deleterious effects, such that low mutation rates are favoured. In contrast to this, in populations thriving in changing environments a larger fraction of mutations have beneficial effects, providing the diversity necessary to adapt to new conditions. What is more, non-adapted populations occasionally benefit from an increase in the mutation rate. Therefore, there is no optimal universal value of the mutation rate and species attempt to adjust it to their momentary adaptive needs. In this work we have used stationary populations of RNA molecules evolving in silico to investigate the relationship between the degree of adaptation of an optimized population and the value of the mutation rate promoting maximal adaptation in a short time to a new selective pressure. Our results show that this value can significantly differ from the optimal value at mutation-selection equilibrium, being strongly influenced by the structure of the population when the adaptive process begins. In the short-term, highly optimized populations containing little variability respond better to environmental changes upon an increase of the mutation rate, whereas populations with a lower degree of optimization but higher variability benefit from reducing the mutation rate to adapt rapidly. These findings show a good agreement with the behaviour exhibited by actual organisms that replicate their genomes under broadly different mutation rates.     

植物居群的基因流动态及其相关适应进化的研究进展

生物自然居群间的基因流不但可以阻止遗传分化以维持物种的完整性, 而且也能积极响应生物多样化的进程。理解与基因流相关的适应性进化及其内在机理将有助于我们更好地认识生物物种形成和多样化的原始动力以及真正原因。该文通过对植物种内和种间居群基因流动态进行讨论, 阐述了近年来有关植物基因流动态的一些重要理论观念和研究进展, 以期为相关领域动态及趋势研究提供参考。     

植物居群的基因流动态及其相关适应进化的研究进展

生物自然居群间的基因流不但可以阻止遗传分化以维持物种的完整性,而且也能积极响应生物多样化的进程。理解与基因流相关的适应性进化及其内在机理将有助于我们更好地认识生物物种形成和多样化的原始动力以及真正原因。该文通过对植物种内和种间居群基因流动态进行讨论,阐述了近年来有关植物基因流动态的一些重要理论观念和研究进展,以期为相关领域动态及趋势研究提供参考。     

Differential Susceptibility of Two Melolontha Populations to Infections by the Fungus Beauveria brongniartii

The susceptibility of second-instar larvae of the European cockchafer, Melolontha melolontha L., originating from two different geographical locations was investigated with eight isolates of the insect pathogenic fungus Beauveria brongniartii (Sacc.) Petch. 77-94% of larvae from northern Italy (Auer, South Tyrolia) succumbed to mycosis with an average survival time (AST) of 22.9-40.1 days. Infections in larvae from south-western Switzerland (Bramois, Valais) were 28-72% and the ASTs varied between 34.7-56.4 days. Differences in susceptibility between the two host populations may be explained by the historical ages of the two populations and the presence of B. brongniartii resulting in a coevolution of tolerance between the host and pathogen. The Italian population is occasionally infected by B. brongniartii; in comparison, the Swiss population has existed for at least 50 years and regular infections by the pathogen are observed. Coevolution between B. brongniartii and M. melolontha from Switzerland may explain the apparent resistance of the host towards this pathogen in laboratory assays.     

On the Prospect of Identifying Adaptive Loci in Recently Bottlenecked Populations

Identifying adaptively important loci in recently bottlenecked populations – be it natural selection acting on a population following the colonization of novel habitats in the wild, or artificial selection during the domestication of a breed – remains a major challenge. Here we report the results of a simulation study examining the performance of available population-genetic tools for identifying genomic regions under selection. To illustrate our findings, we examined the interplay between selection and demography in two species of Peromyscus mice, for which we have independent evidence of selection acting on phenotype as well as functional evidence identifying the underlying genotype. With this unusual information, we tested whether population-genetic-based approaches could have been utilized to identify the adaptive locus. Contrary to published claims, we conclude that the use of the background site frequency spectrum as a null model is largely ineffective in bottlenecked populations. Results are quantified both for site frequency spectrum and linkage disequilibrium-based predictions, and are found to hold true across a large parameter space that encompasses many species and populations currently under study. These results suggest that the genomic footprint left by selection on both new and standing variation in strongly bottlenecked populations will be difficult, if not impossible, to find using current approaches.     

Reduction of Banana Weevil Populations Using Different Formulations of the Entomopathogenic Fungus Beauveria bassiana

One of the major constraints for banana production in Uganda is the banana weevil, Cosmopolites sordidus (Germar), (Coleoptera: Curculionidae). Investigations were carried out to evaluate the efficacy of maize, soil-based and oil formulations of an indigenous isolate of Beauveria bassiana for the control of the banana weevil. Weekly trapping of weevils over a 9-month monitoring period showed significant reduction in unmarked and marked weevil population in B. bassiana treated plots. Application of maize formulation at 2 ×10 15 conidia ha -1 proved most effective, reducing the weevil populations by 63-72% within 8 weeks after a single application. The soil based formulation at 2 ×10 14 conidia ha -1 was intermediate while the oil formulation at 6 ×10 15 conidial ha -1 was least effective. Trapping efficiency declined in B. bassiana treated and untreated banana plots but was greatest in the latter.     

Assessment of Sensitivities to Anilinopyrimidine- and Strobilurin-fungicides in Populations of the Apple Scab Fungus Venturia inaequalis

The sensitivity of Venturia inaequalis populations to the anilinopyrimidine fungicides pyrimethanil and cyprodinil was analysed by microscopic in vivo analysis of conidiophore formation. The sensitivity to the strobilurin kresoxim-methyl was analysed using an in vitro germination assay and by determination of the diseased leaf area and conidia produced in vivo. Baseline sensitivities were determined with V. inaequalis populations from control orchards that had never been treated with fungicides. Comparison of the baseline sensitivities with sensitivities of populations obtained from orchards that had received 43 anilinopyrimidine treatments over 4 years, or from an orchard with 54 kresoxim-methyl treatments over 6 years indicated that no resistance to these fungicides has developed at the sites sampled.     

Effects of Management Practices on Nematode and Fungus Populations and Cucumber Yield

Three crops of cucumber were grown in succession in beds by use of trickle irrigation, plastic film mulch, and soil chemical treatments over a 17-month period, including a fallow winter season. Total yield for the three crops was highest (1208 quintals/ha) in film-mulched plots treated with MBR-CP, and next-highest in film-mulched plots treated with DD-MENCS (1094 quintals/ha); total yield was only 456 quintals/ha in film-mulched control (untreated) plots. Yield in untreated film-mulched plots was 256% of that in untreated unmulched plots (178 quintals/ha). Plant growth and yields were greatest when populations of nematodes and soil-borne fungi were suppressed to very low levels. The residual control by soil treatments lasted longest on Meloidogyne incognita and Fusarium solani.     

Genet Distribution of Ectomycorrhizal Fungus Suillus grevillei Populations in Two Larix kaempferi Stands over Two Years

Suillus grevillei in two Larix kaempferi stands was determined over two years by inter-simple sequence repeat (ISSR) polymorphism analysis using primers, (GTG)₅, (GCC)₅ and (GACA)₄. Thirty-five genets were identified from 67 sporocarps at the older stand (stand A in which the distribution of S. grevillei genet in 1997 was analyzed previously) in 1998, and 14 genets from 52 sporocarps at the younger stand (stand B) in 1997 and 1998. The characteristics of S. grevillei genets in stand A in 1998 were similar to those in 1997. A single genet was represented by 1.8 and 3.7 sporocarps on average in stands A and B, respectively. In stand A, 42 out of 61 genets, i.e., about 70% were represented by individual sporocarps compared to five out of 14 genets, i.e., about 35% in stand B. The largest and the average genet sizes was 6.8 m and less than 1 m in stand A, and 11 m and 2.3 m in stand B, respectively. A t-test showed the genet size in stand A to be significantly smaller than that in stand B. The above results indicate that the smaller genets of the S. grevillei population in stand A might be due to environmental conditions not genetic traits specific to this species. Observations over two years showed that although some genets formed sporocarps in both 1997 and 1998, many formed sporocarps only in one of the two years. Emerging positions of sporocarps in 1997 and 1998, which belonged to the same genet, were similar but not identical, about 2 m apart, suggesting mobility in the subterranean parts of ECM fungal genets. Received 10 April 2000/ Accepted in revised form 31 August 2000