Relative fitness can decrease in evolving asexual populations of S. cerevisiae

It is generally accepted from the darwinian theory of evolution that a progressive increase in population adaptation will occur in populations containing genetic variation in fitness, until a stable equilibrium is reached and/or the additive genetic variation is exhausted. However, the theoretical literature of population genetics documents exceptions where mean population fitness may decrease in response to evolutionary changes in gene frequency, due to varying selective coefficients, sexual selection or to epistatic interactions between loci. Until now, no examples of such exceptions have been documented from fitness estimates in either natural or experimental populations. We present here direct evidence that, as a result of epistatic interactions between adaptive mutations, mean population fitness can decrease in asexual evolving populations of the yeast Saccharomyces cerevisiae.     

Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein

The distribution of fitness effects of protein mutations is still unknown. Of particular interest is whether accumulating deleterious mutations interact, and how the resulting epistatic effects shape the protein's fitness landscape. Here we apply a model system in which bacterial fitness correlates with the enzymatic activity of TEM-1 beta-lactamase (antibiotic degradation). Subjecting TEM-1 to random mutational drift and purifying selection (to purge deleterious mutations) produced changes in its fitness landscape indicative of negative epistasis; that is, the combined deleterious effects of mutations were, on average, larger than expected from the multiplication of their individual effects. As observed in computational systems, negative epistasis was tightly associated with higher tolerance to mutations (robustness). Thus, under a low selection pressure, a large fraction of mutations was initially tolerated (high robustness), but as mutations accumulated, their fitness toll increased, resulting in the observed negative epistasis. These findings, supported by FoldX stability computations of the mutational effects, prompt a new model in which the mutational robustness (or neutrality) observed in proteins, and other biological systems, is due primarily to a stability margin, or threshold, that buffers the deleterious physico-chemical effects of mutations on fitness. Threshold robustness is inherently epistatic-once the stability threshold is exhausted, the deleterious effects of mutations become fully pronounced, thereby making proteins far less robust than generally assumed.     

Mutation and sex in a competitive world

How do deleterious mutations interact to affect fitness? The answer to this question has substantial implications for a variety of important problems in population biology, including the evolution of sex, the rate of adaptation and the conservation of small populations. Here we analyse a mathematical model of competition for food in which deleterious mutations affect competitive ability. We show that, if individuals usually compete in small groups, then competition can easily lead to a type of genetic interaction known as synergistic epistasis. This means that a deleterious mutation is most damaging in a genome that already has many other deleterious mutations. We also show that competition in small groups can produce a large advantage for sexual populations, both in mean fitness and in ability to resist invasion by asexual lineages. One implication of our findings is that experimental efforts to demonstrate synergistic epistasis may not succeed unless the experiments are redesigned to make them much more naturalistic.     

环境变化对山东苔类植物影响的研究

为了研究环境变化对山东苔类植物的影响,考察了1998年以前和2008年以后的山东苔类植物区系构成情况.经对比发现近10年以来山东苔类植物的种类明显减少.从温度、降水、海平面、植被、土壤、水和大气等自然环境因子的变化以及人为因素对苔类植物的影响进行了分析,以解释山东苔类植物减少的原因,从而唤起社会的环境保护意识.     

Fitness of RNA virus decreased by Muller's ratchet

Why sex exists remains an unsolved problem in biology. If mutations are on the average deleterious, a high mutation rate can account for the evolution of sex. One form of this mutational hypothesis is Muller's ratchet. If the mutation rate is high, mutation-free individuals become rare and they can be lost by genetic drift in small populations. In asexual populations, as Muller noted, the loss is irreversible and the load of deleterious mutations increases in a ratchet-like manner with the successive loss of the least-mutated individuals. Sex can be advantageous because it increases the fitness of sexual populations by re-creating mutation-free individuals from mutated individuals and stops (or slows) Muller's ratchet. Although Muller's ratchet is an appealing hypothesis, it has been investigated and documented experimentally in only one group of organisms--ciliated protozoa. I initiated a study to examine the role of Muller's ratchet on the evolution of sex in RNA viruses and report here a significant decrease in fitness due to Muller's ratchet in 20 lineages of the RNA bacteriophage phi 6. These results show that deleterious mutations are generated at a sufficiently high rate to advance Muller's ratchet in an RNA virus and that beneficial, backward and compensatory mutations cannot stop the ratchet in the observed range of fitness decrease.     

基于DSMC方法的涡轮分子泵跨流态抽气性能研究

基于直接模拟蒙特卡洛(DSMC)方法,可以计算获得涡轮分子泵叶列在不同稀薄气体流态下的抽气性能.通过改变涡轮叶列旋转速度、气体入口结构尺寸及被抽气体温度等参数,能够得到涡轮分子泵最大抽气效率和最大压缩比的变化情况.比较各参数在不同流态下对抽气性能的影响程度,并计算不同流态下涡轮叶列返流的变化.计算得出增大叶片速度在分子流态下对涡轮分子泵性能的提升最为明显,缩小气体入口面积可以提升涡轮分子泵压缩比等结论.从而为提升涡轮分子泵抽气性能提供了手段,拓展了涡轮分子泵的工作范围.     

Alteration in crossbridge kinetics caused by mutations in actin

The generation of force during muscle contraction results from the interaction of myosin and actin. The kinetics of this force generation vary between different muscle types and within the same muscle type in different species. Most attention has focused on the role of myosin isoforms in determining these differences. The role of actin isoforms has received little attention, largely because of the lack of a suitable cell type in which the myosin isoform remains constant yet the actin isoforms vary. An alternative approach would be to examine the effect of actin mutations, however, most of these cause such gross disruption of muscle structure that mechanical measurements are impossible. We have now identified two actin mutations which, despite involving conserved amino acids, can assemble into virtually normal myofibrils. These amino-acid changes in actin significantly affect the kinetics of force generation by muscle fibres. One of the mutations is not in the putative myosin-binding site, demonstrating the importance of long-range effects of amino acids on actin function.     

High plant diversity is needed to maintain ecosystem services

Biodiversity is rapidly declining worldwide, and there is consensus that this can decrease ecosystem functioning and services. It remains unclear, though, whether few or many of the species in an ecosystem are needed to sustain the provisioning of ecosystem services. It has been hypothesized that most species would promote ecosystem services if many times, places, functions and environmental changes were considered; however, no previous study has considered all of these factors together. Here we show that 84% of the 147 grassland plant species studied in 17 biodiversity experiments promoted ecosystem functioning at least once. Different species promoted ecosystem functioning during different years, at different places, for different functions and under different environmental change scenarios. Furthermore, the species needed to provide one function during multiple years were not the same as those needed to provide multiple functions within one year. Our results indicate that even more species will be needed to maintain ecosystem functioning and services than previously suggested by studies that have either (1) considered only the number of species needed to promote one function under one set of environmental conditions, or (2) separately considered the importance of biodiversity for providing ecosystem functioning across multiple years, places, functions or environmental change scenarios. Therefore, although species may appear functionally redundant when one function is considered under one set of environmental conditions, many species are needed to maintain multiple functions at multiple times and places in a changing world.     

The population genetics of ecological specialization in evolving Escherichia coli populations

When organisms adapt genetically to one environment, they may lose fitness in other environments. Two distinct population genetic processes can produce ecological specialization-mutation accumulation and antagonistic pleiotropy. In mutation accumulation, mutations become fixed by genetic drift in genes that are not maintained by selection; adaptation to one environment and loss of adaptation to another are caused by different mutations. Antagonistic pleiotropy arises from trade-offs, such that the same mutations that are beneficial in one environment are detrimental in another. In general, it is difficult to distinguish between these processes. We analysed the decay of unused catabolic functions in 12 lines of Escherichia coli propagated on glucose for 20,000 generations. During that time, several lines evolved high mutation rates. If mutation accumulation is important, their unused functions should decay more than the other lines, but no significant difference was observed. Moreover, most catabolic losses occurred early in the experiment when beneficial mutations were being rapidly fixed, a pattern predicted by antagonistic pleiotropy. Thus, antagonistic pleiotropy appears more important than mutation accumulation for the decay of unused catabolic functions in these populations.     

Fire as the dominant driver of central Canadian boreal forest carbon balance

Changes in climate, atmospheric carbon dioxide concentration and fire regimes have been occurring for decades in the global boreal forest, with future climate change likely to increase fire frequency--the primary disturbance agent in most boreal forests. Previous attempts to assess quantitatively the effect of changing environmental conditions on the net boreal forest carbon balance have not taken into account the competition between different vegetation types on a large scale. Here we use a process model with three competing vascular and non-vascular vegetation types to examine the effects of climate, carbon dioxide concentrations and fire disturbance on net biome production, net primary production and vegetation dominance in 100 Mha of Canadian boreal forest. We find that the carbon balance of this region was driven by changes in fire disturbance from 1948 to 2005. Climate changes affected the variability, but not the mean, of the landscape carbon balance, with precipitation exerting a more significant effect than temperature. We show that more frequent and larger fires in the late twentieth century resulted in deciduous trees and mosses increasing production at the expense of coniferous trees. Our model did not however exhibit the increases in total forest net primary production that have been inferred from satellite data. We find that poor soil drainage decreased the variability of the landscape carbon balance, which suggests that increased climate and hydrological changes have the potential to affect disproportionately the carbon dynamics of these areas. Overall, we conclude that direct ecophysiological changes resulting from global climate change have not yet been felt in this large boreal region. Variations in the landscape carbon balance and vegetation dominance have so far been driven largely by increases in fire frequency.     

Adaptive variation in environmental and genetic sex determination in a fish

Two general mechanisms of sex determination have been identified among gonochoristic vertebrates: environmental sex determination where offspring become male or female in response to an environmental factor(s) during development (for example, some fishes and reptiles); and genetic sex determination where sex is determined by genotype at conception (as in birds and mammals). How do these sex-determining systems evolve? Direct evidence is virtually non-existent because the sex-determining systems of most species appear to have little genetic variation. Here we provide the first evidence of adaptive variation in environmental and genetic sex determination within a species. We show that in a fish with temperature-dependent sex determination, populations at different latitudes compensate for differences in thermal environment and seasonality by adjusting the response of sex ratio to temperature, and by altering the level of environmental as opposed to genetic control. The adjustments observed are precisely those predicted by adaptive sex ratio theory.     

苔藓和地衣对环境变化的响应和指示作用

隐花植物苔藓和地衣具有各类生境分布的广泛性、小范围内个体/种群/群落分布的稳定性、独特的生理特性及其对环境变化的生物敏感性,在环境变化响应与指示研究中已成为重要工具种。目前对隐花植物的监测指标包括:(1)物种生物量、种类组成及丰度指数等;(2)植株体内某元素积累量与环境含量间的相关性;(3)环境变化引起细胞代谢速率、光合速率、光合色素含量、各种酶含量及活性等的改变;(4)整合环境因子与监测种的生理生态指标间的相关性,构建监测模型。但不同物种对环境变化的响应存在差异性,选择合适的生物监测工具种及相应的监测指标,构建合理的"污染物类型-监测工具种-监测指标"的监测体系,将有利于进一步提升生物监测的可行性及可信度。     

The adaptive significance of temperature-dependent sex determination in a reptile

Understanding the mechanisms that determine an individual's sex remains a primary challenge for evolutionary biology. Chromosome-based systems (genotypic sex determination) that generate roughly equal numbers of sons and daughters accord with theory, but the adaptive significance of environmental sex determination (that is, when embryonic environmental conditions determine offspring sex, ESD) is a major unsolved problem. Theoretical models predict that selection should favour ESD over genotypic sex determination when the developmental environment differentially influences male versus female fitness (that is, the Charnov-Bull model), but empirical evidence for this hypothesis remains elusive in amniote vertebrates--the clade in which ESD is most prevalent. Here we provide the first substantial empirical support for this model by showing that incubation temperatures influence reproductive success of males differently than that of females in a short-lived lizard (Amphibolurus muricatus, Agamidae) with temperature-dependent sex determination. We incubated eggs at a variety of temperatures, and de-confounded sex and incubation temperature by using hormonal manipulations to embryos. We then raised lizards in field enclosures and quantified their lifetime reproductive success. Incubation temperature affected reproductive success differently in males versus females in exactly the way predicted by theory: the fitness of each sex was maximized by the incubation temperature that produces that sex. Our results provide unequivocal empirical support for the Charnov-Bull model for the adaptive significance of temperature-dependent sex determination in amniote vertebrates.     

冬春季节耕地与覆膜对地温影响的研究

通过对整个冬季春季土壤在3种处理条件下地温变化的动态观测，对照免耕裸地的地温变化，分析了3种处理条件对地温影响的差异，表明，耕地覆膜处理能加速冻土的解冻过程，使冻土提前解冻，迅速提高地温。     

使用共生机制对遗传算法的改进

自然界中，不同生物种群的个体通过交互作用可以弥补其自身的不足，获得更强的适应性。这种互利共生现象最终可以使种群获得通过遗传进化无法得到的新特性。文中使用人工生命方法建模仿真共生现象，结果表明，用共生方法改进过的遗传算法具有更快的收敛速度。     

Interference among deleterious mutations favours sex and recombination in finite populations

Sex and recombination are widespread, but explaining these phenomena has been one of the most difficult problems in evolutionary biology. Recombination is advantageous when different individuals in a population carry different advantageous alleles. By bringing together advantageous alleles onto the same chromosome, recombination speeds up the process of adaptation and opposes the fixation of harmful mutations by means of Muller's ratchet. Nevertheless, adaptive substitutions favour sex and recombination only if the rate of adaptive mutation is high, and Muller's ratchet operates only in small or asexual populations. Here, by tracking the fate of modifier alleles that alter the frequency of sex and recombination, we show that background selection against deleterious mutant alleles provides a stochastic advantage to sex and recombination that increases with population size. The advantage arises because, with low levels of recombination, selection at other loci severely reduces the effective population size and genetic variance in fitness at a focal locus (the Hill-Robertson effect), making a population less able to respond to selection and to rid itself of deleterious mutations. Sex and recombination reveal the hidden genetic variance in fitness by combining chromosomes of intermediate fitness to create chromosomes that are relatively free of (or are loaded with) deleterious mutations. This increase in genetic variance within finite populations improves the response to selection and generates a substantial advantage to sex and recombination that is fairly insensitive to the form of epistatic interactions between deleterious alleles. The mechanism supported by our results offers a robust and broadly applicable explanation for the evolutionary advantage of recombination and can explain the spread of costly sex.     

不同管理条件下永久性草地样方的生长型谱和多样性(英文)

相当一段时间以来,人们对于永久样方中植被所做工作主要集中于对其一定时间范围之中区系成分变化的研究.例如用不同的管理方法所产生效果的对比.根据植被中物种的多样性,本文将着重探讨在老的稳定草地群落之中的一系列样方生长型谱的变化情况.植被的结构由植物的生长型决定,而植被结构对于萌发过程和新个体的定居是极为重要的,因此与区系成分就密切相关.把注意力放在植物生长型、植被结构与成分上,将扩大我们对植物群落是怎样行使其功能这一问题的理解.按照Barkman(1979)的方法,我区分出了植被结构与植被质地,认为植被质地是关于不同形态要素的质量和数量组成,不考虑其排列情况,而植被结构是这些要素的空间(水平和垂直)的排列.本文运用在一石灰质的草地上永久样方中14—15年的研究.指出了植物种的多样性和不同生长型的显著性的关系,研究中采用了如下几种方法:放羊、(扌弃)荒、割草,而后两种处理方法又分别采用了施肥与不施肥的处理.从显花植物之中区分出了十个不同的生长型,且用种的估计盖度百分比所得的生长型谱与用地上植物量所测的生长型谱极相符合,某些生长型(高禾草、爬缘双子草植物和高灌木)的显著度与种的多样性下降显著相关,而另外一些生长型(丛生植物、花茎上无叶)的显著性并不表现出与种多样     

Generation of prion transmission barriers by mutational control of amyloid conformations

Self-propagating beta-sheet-rich protein aggregates are implicated in a wide range of protein-misfolding phenomena, including amyloid diseases and prion-based inheritance. Two properties have emerged as common features of amyloids. Amyloid formation is ubiquitous: many unrelated proteins form such aggregates and even a single polypeptide can misfold into multiple forms--a process that is thought to underlie prion strain variation. Despite this promiscuity, amyloid propagation can be highly sequence specific: amyloid fibres often fail to catalyse the aggregation of other amyloidogenic proteins. In prions, this specificity leads to barriers that limit transmission between species. Using the yeast prion [PSI+], we show in vitro that point mutations in Sup35p, the protein determinant of [PSI+], alter the range of 'infectious' conformations, which in turn changes amyloid seeding specificity. We generate a new transmission barrier in vivo by using these mutations to specifically disfavour subsets of prion strains. The ability of mutations to alter the conformations of amyloid states without preventing amyloid formation altogether provides a general mechanism for the generation of prion transmission barriers and may help to explain how mutations alter toxicity in conformational diseases.     

沙区人工固沙植物水分适宜度模糊数学模型及应用

以固沙植物油蒿和柠条为研究对象，探讨了样区土壤水分变化的模糊属性特征；运用模糊数学方法，建立了水分适宜度的概念及其模型，并进行实例计算与分析．结果表明：柠条在单播情况下随着营林密度的升高，其适宜度值呈现下降趋势；混播比单播具有较高的适宜度值，其中以5000株/hm^2混播下适宜度最高，植被覆盖率最大，是值得推广的一种营林方式．试验条件下，植被覆盖率高者，其适宜度亦高，二者呈现出一致性．文中分析了油蒿与柠条对水分竞争与共存的机理，有关结论为人工固沙林稳定发展提供了科学依据．     

Theory predicts the uneven distribution of genetic diversity within species

Global efforts to conserve species have been strongly influenced by the heterogeneous distribution of species diversity across the Earth. This is manifest in conservation efforts focused on diversity hotspots. The conservation of genetic diversity within an individual species is an important factor in its survival in the face of environmental changes and disease. Here we show that diversity within species is also distributed unevenly. Using simple genealogical models, we show that genetic distinctiveness has a scale-free power law distribution. This property implies that a disproportionate fraction of the diversity is concentrated in small sub-populations, even when the population is well-mixed. Small groups are of such importance to overall population diversity that even without extrinsic perturbations, there are large fluctuations in diversity owing to extinctions of these small groups. We also show that diversity can be geographically non-uniform--potentially including sharp boundaries between distantly related organisms--without extrinsic causes such as barriers to gene flow or past migration events. We obtained these results by studying the fundamental scaling properties of genealogical trees. Our theoretical results agree with field data from global samples of Pseudomonas bacteria. Contrary to previous studies, our results imply that diversity loss owing to severe extinction events is high, and focusing conservation efforts on highly distinctive groups can save much of the diversity.