EXPERIMENTAL MOLECULAR EVOLUTION OF BACTERIOPHAGE T7

We present an analysis of molecular evolution in a laboratory-generated phylogeny of the bacteriophage T7, a virus of 40 kilo-base pairs of double-stranded DNA. The known biology of T7 is used in concert with observed changes in restriction sites and in DNA sequences to produce a model of restriction-site convergence and divergence in the experimental lineages. During laboratory propagation in the presence of a mutagen, the phage lineages changed an estimated 0.5%-1.5% in base pairs; most change appears to have been G → A or C → T, presumably because of the mutagen employed. Some classes of restriction-site losses can be explained adequately as simple outcomes of random processes, given the mutation rate and the bias in mutation spectrum. However, some other classes of sites appear to have undergone accelerated rates of loss, as though the losses were selectively favored. Overall, the wealth of knowledge available for T7 biology contributes only modestly to these explanations of restriction-site evolution, but rates of restriction-site gains remain poorly explained, perhaps requiring an even deeper understanding of T7 genetics than was employed here. Having measured these properties of molecular evolution, we programmed computer simulations with the parameter estimates and pseudo-replicated the empirical study, thereby providing a data base for statistical evaluation of phylogeny reconstruction methods. By these criteria, replicates of the experimental phylogeny would be correctly reconstructed over 97% of the time for the three methods tested, but the methods differed significantly both in their ability to recover the correct topology and in their ability to predict branch lengths. More generally, the study illustrates how analyses of experimental evolution in bacteriophage can be exploited to reveal relationships between the basics of molecular evolution and abstract models of evolutionary processes.     

SELECTION OF BENEVOLENCE IN A HOST–PARASITE SYSTEM

A paradigm for the evolution of cooperation between parasites and their hosts argues that the mode of parasite transmission is critical to the long-term maintenance of cooperation. Cooperation is not expected to be maintained whenever the chief mode of transmission is horizontal: a parasite's progeny infect hosts unrelated to their parent's host. Cooperation is expected to be maintained if the chief mode of transmission is vertical: a parasite's progeny infect only the parent's host or descendants of that host. This paradigm was tested using bacteria and filamentous bacteriophage (f1). When cells harboring different variants of these phage were cultured so that no infectious spread was allowed, ensuring that all parasite transmission was vertical, selection favored the variants that were most benevolent to the host—those that least harmed host growth rate. By changing the culture conditions so that horizontal spread of the phage was allowed, the selective advantage of the benevolent forms was lost. These experiments thus support the theoretical arguments that mode of transmission is a major determinant in the evolution of cooperation between a parasite and its host.     

分子系统学在微体古生物及相关领域中的应用

核酸（ＤＮＡ和ＲＮＡ）和蛋白等生物大分子（尤其是它们的序列资料）可作为重要的生物性状用于系统分类和演化等主题的研究。相对于形态学性状而言,分子性状不仅是前者的补充,而且具有许多前者无法比拟的优点;比如ＤＮＡ作为遗传信息的直接载体能较准确地反映生物类群之间的系统发生关系、信息量巨大、易于定量化和进行计算机分析等等。分子古生物研究包含两个方面：一、发掘化石生物分子,以提供历史生物界演化过程中的直接遗传学证据以及检验分子演化速率等方面的独特数据;二、利用现代分子生物学数据,探讨化石生物界的系统发生问题。上述两个研究方向均已成为当今演化生物学领域的热点。有孔虫等具有重要化石记录的微体生物的分子系统学研究已经开始。随着现生的和化石的生物分子资料的逐渐积累,预期在不久的将来,分子资料将成为微体古生物研究中不可缺少的重要数据之一。     

LIMITED DISPERSAL, BUDDING DISPERSAL, AND COOPERATION: AN EXPERIMENTAL STUDY

Numerous theoretical studies have investigated how limited dispersal may provide an explanation for the evolution of cooperation, by leading to interactions between relatives. However, despite considerable theoretical attention, there has been a lack of empirical tests. In this article, we test how patterns of dispersal influence the evolution of cooperation, using iron-scavenging in the bacterium Pseudomonas aeruginosa as our cooperative trait. We found that relatively limited dispersal does not favor cooperation. The reason for this is that although limited dispersal increases the relatedness between interacting individuals, it also leads to increased local competition for resources between relatives. This result supports Taylor's prediction that in the simplest possible scenario, the effects of increased relatedness and local competition exactly cancel out. In contrast, we show that one way for cooperation to be favored is if individuals disperse in groups (budding dispersal), because this maintains high relatedness while reducing local competition between relatives (relatively global competition).     

THE POPULATION GENETICS OF ADAPTATION: THE DISTRIBUTION OF FACTORS FIXED DURING ADAPTIVE EVOLUTION

We know very little about the genetic basis of adaptation. Indeed, we can make no theoretical predictions, however heuristic, about the distribution of phenotypic effects among factors fixed during adaptation nor about the expected “size” of the largest factor fixed. Study of this problem requires taking into account that populations gradually approach a phenotypic optimum during adaptation via the stepwise substitution of favorable mutations. Using Fisher's geometric model of adaptation, I analyze this approach to the optimum, and derive an approximate solution to the size distribution of factors fixed during adaptation. I further generalize these results to allow the input of any distribution of mutational effects. The distribution of factors fixed during adaptation assumes a pleasingly simple, exponential form. This result is remarkably insensitive to changes in the fitness function and in the distribution of mutational effects. An exponential trend among factors fixed appears to be a general property of adaptation toward a fixed optimum.     

人巨细胞病毒小鼠模型的建立

采用HCMV-AD_(169)株实验感染昆明系和BALB/C系小鼠,攻毒后感染急性期BALB/C系小鼠的死亡率(28.57％)高于昆明系小鼠(5.26％)。两种不同品系小鼠的临床症状和HCMV导致的病理损害脑钙化无明显差异。昆明小鼠的发病率(94.74％)高于BALB/C小鼠。     

野大豆种群转座子和转录因子的多样性和分子适应

对环境变化的适应机理一直是进化生物学和生态学长期争论的核心课题。根据适应逆境的生态学和分子生理的最新进展,设想逆境诱导转座子的转座,影响转录因子的表达,随即改变一系列抗性基因的表达水平,抗性种群快速适应形成;由此可能建立一个统一的进化理论。从黄河入海口野生大豆(Glycine soja)盐渍种群植株DNA扩增到一段干旱应答元件结合蛋白基因(DREB)序列,称为GsDREB1。克隆了一个全长的类Gypsy逆转录转座子整合酶基因序列,称为GsINT。种群内各植株该序列有多个拷贝,植株间存在限制片段长度多态性。根据所得的这两个序列,设计并合成包括GsINT 5'上游保守序列的Gs-1等若干引物,试图检测野大豆基因组中GsDREB1的5'上游是否存在逆转录转座子整合酶序列。将GsDREB1标记为探针,Southern杂交表明用Gs-1为正向引物GmDR1为逆向引物所扩增的产物既是多拷贝而又与GsDREB1高度同源。这一对引物扩增和部分测序的结果暗示逆转录转座子有的插入DREB的5'上游,种群内外植株间显现两基因间隔长度的多样性。据此提出抗性种群形成即适应进化分子机理的下列假说。正常种群主要由非抗性普通植株组成。当环境发生变化处于逆境条件时,种群内植株转座频率大大增加。转座子非定向地插入基因组。多数突变中性,不影响表型。少数插入到转录因子的5'上游或其编码区,可促进或阻抑其表达,由此引发转录因子所控制的抗性基因网络表达的增加或减少,抗性相应增加或降低。总的结果是在短时间内就能积累包括高抗性植株在内的有各种抗性水平的个体;对逆境敏感的个体不断地被自然选择所淘汰,但逆境不断诱导其产生,少数植株有可能利用逆境减弱的较短时间完成发育得以生存下来。此假说可以解释逆境条件下的植物种群为什么能快速形成而有更高的遗传多样性;又为什么抗性种群在高抗性植株产生的同时有时存在敏感植株。逆境促进的转座改变转录因子基因表达可能是植物生理和形态快速进化的一般分子机理。     

RATES OF FLORAL EVOLUTION: ADAPTATION TO BUMBLEBEE POLLINATION IN AN ALPINE WILDFLOWER,POLEMONIUM VISCOSUM

Animal pollinators are thought to shape floral evolution, yet the tempo of this process has seldom been measured. I used the prediction equation of quantitative genetics, R = h²S , to predict the rate at which a change in pollinator abundance may have caused divergence in floral morphology of the alpine skypilot, Polemonium viscosum. A selection experiment determined the rate at which such divergence can actually proceed. Corolla flare in this species increases by 12% from populations pollinated by a wide assemblage of insect visitors to those pollinated only by bumblebees. To simulate the evolutionary process giving rise to this change, I used a pollinator selection experiment. Plants with broad flowers set significantly more seeds than plants with narrow flowers under bumblebee pollination but had equivalent fecundity when visited by other insects or hand-pollinated. Bumblebee-mediated selection for broad corolla flare intensified from 0.07 at seed set to 0.17 at progeny establishment. Maternal parent-offspring regression yielded a confidence interval of 0.22–1.00 for trait heritability. Given these parameter estimates, the prediction equation shows that broadly flared flowers of bumblebee-pollinated P. viscosum could have evolved from narrower ones in a single generation. This prediction is matched by an observed 9% increase in offspring corolla flare after a single bout of bumblebee-mediated selection, relative to offspring of unselected controls. Findings show that plant populations can adapt rapidly to abrupt changes in pollinator assemblages.     

EXPERIMENTAL EVOLUTION OF AN EMERGING PLANT VIRUS IN HOST GENOTYPES THAT DIFFER IN THEIR SUSCEPTIBILITY TO INFECTION

This study evaluates the extent to which genetic differences among host individuals from the same species condition the evolution of a plant RNA virus. We performed a threefold replicated evolution experiment in which Tobacco etch potyvirus isolate At17b (TEV‐At17b), adapted to Arabidopsis thaliana ecotype Ler‐0, was serially passaged in five genetically heterogeneous ecotypes of A. thaliana. After 15 passages we found that evolved viruses improved their fitness, showed higher infectivity and stronger virulence in their local host ecotypes. The genome of evolved lineages was sequenced and putative adaptive mutations identified. Host‐driven convergent mutations have been identified. Evidences supported selection for increased translational efficiency. Next, we sought for the specificity of virus adaptation by infecting all five ecotypes with all 15 evolved virus populations. We found that some ecotypes were more permissive to infection than others, and that some evolved virus isolates were more specialist/generalist than others. The bipartite network linking ecotypes with evolved viruses was significantly nested but not modular, suggesting that hard‐to‐infect ecotypes were infected by generalist viruses whereas easy‐to‐infect ecotypes were infected by all viruses, as predicted by a gene‐for‐gene model of infection.     

SUBSTITUTION PROCESSES IN MOLECULAR EVOLUTION. II. EXCHANGEABLE MODELS FROM POPULATION GENETICS

Substitution processes are of two sorts: origination processes record the times at which nucleotide mutations that ultimately fix in the population first appear, and fixation processes record the times at which they actually fix. Substitution processes may be generated by combining models of population genetics—here the symmetrical-neutral, overdominance, underdominance, TIM, and SAS-CFF models—with the infinite-sites, no-recombination model of the gene. This paper is mainly concerned with a computer simulation study of these substitution processes. The rate of substitution is shown to be remarkably insensitive to the strength of selection for models with strong balancing selection caused by the genealogical drift of mutations through alleles held in the population by selection. The origination process is shown to be more regular than Poisson for the overdominance, TIM, and SAS-CFF models but more clustered for the underdominance model. A class of point processes called Sawyer processes is introduced to help explain these observations as well as the observation that the times between successive originations are nearly uncorrelated. Fixation processes are shown to be more complex than origination processes, with regularly spaced bursts of multiple fixations. An approximation to the fixation process is described. One important conclusion is that protein evolution is not easily reconciled with any of these models without adding perturbations that recur on a time scale that is commensurate with that of molecular evolution.     

THE GENETICS OF ADAPTATION: THE GENETIC BASIS OF RESISTANCE TO WASP PARASITISM IN DROSOPHILA MELANOGASTER

There have been very few genetic analyses of “natural” adaptations, that is, those not involving artificial selection or responses to human disturbance. Here we analyze the genetic basis of geographic variation in Drosophila melanogaster's resistance to parasitism by a wasp, Asobara tabida. Our results suggest that population differences in ability to encapsulate parasitoid eggs have a fairly simple genetic basis: 60% of the D. melanogaster genome plays no role in differences between resistant and susceptible populations. Instead, resistance gene(s) are restricted to chromosome two, and may be further restricted to the centromeric region of this chromosome. This finding suggests that natural adaptations—like many responses to artificial selection and human disturbance—sometimes have a simple genetic basis.     

ENVIRONMENTAL VISCOSITY DOES NOT AFFECT THE EVOLUTION OF COOPERATION DURING EXPERIMENTAL EVOLUTION OF COLICIGENIC BACTERIA

Cooperation should be favored under environmental conditions allowing the preferential interaction of cooperators among themselves and limiting interactions with defectors. Bacteria cooperating to kill competitors by secreting a toxin evolved during several hundred generations in two environments: a viscous environment that should promote cooperator assortment, and a nonviscous environment that should not allow such preferential interaction. A quantitative decrease in cooperation was observed in all populations, but as expected, cooperation was maintained at a higher level in the viscous environment. Mutants that are resistant against but not producing the toxin were identified at a low frequency in a few populations from the viscous environment and at a high frequency in all the populations from the nonviscous environment. The underlying mutations were identified. Relative fitness of the cooperator and mutant genotypes were obtained with bacteria that were isogenic, except for the identified mutations. Competition experiments indicated that cooperation is not favored by environmental viscosity as imposed in our system and suggested that when it comes to cooperation, environmental viscosity should be considered not only in terms of individual movement, but also in terms of the distribution of the public good.     

THE COMPLEX EVOLUTIONARY HISTORY OF SEEING RED: MOLECULAR PHYLOGENY AND THE EVOLUTION OF AN ADAPTIVE VISUAL SYSTEM IN DEEP‐SEA DRAGONFISHES (STOMIIFORMES: STOMIIDAE)

The vast majority of deep‐sea fishes have retinas composed of only rod cells sensitive to only shortwave blue light, approximately 480–490 nm. A group of deep‐sea dragonfishes, the loosejaws (family Stomiidae), possesses far‐red emitting photophores and rhodopsins sensitive to long‐wave emissions greater than 650 nm. In this study, the rhodopsin diversity within the Stomiidae is surveyed based on an analysis of rod opsin‐coding sequences from representatives of 23 of the 28 genera. Using phylogenetic inference, fossil‐calibrated estimates of divergence times, and a comparative approach scanning the stomiid phylogeny for shared genotypes and substitution histories, we explore the evolution and timing of spectral tuning in the family. Our results challenge both the monophyly of the family Stomiidae and the loosejaws. Despite paraphyly of the loosejaws, we infer for the first time that far‐red visual systems have a single evolutionary origin within the family and that this shift in phenotype occurred at approximately 15.4 Ma. In addition, we found strong evidence that at approximately 11.2 Ma the most recent common ancestor of two dragonfish genera reverted to a primitive shortwave visual system during its evolution from a far‐red sensitive dragonfish. According to branch‐site tests for adaptive evolution, we hypothesize that positive selection may be driving spectral tuning in the Stomiidae. These results indicate that the evolutionary history of visual systems in deep‐sea species is complex and a more thorough understanding of this system requires an integrative comparative approach.     

昆虫分子生物学的一些进展：杀虫剂抗性的分子基础

昆虫分子生物学的一些进展：杀虫剂抗性的分子基础翟启慧（中国科学院动物研究所北京１０００８０）昆虫对杀虫剂的中毒,在药物动力学上包括三种不同水平上的作用：穿透表皮组织,在体内组织中的分布、贮存和代谢,以及对最终靶部位的作用。因此,已经公认的抗性机理包括...     

ADAPTATION TO DIFFERENT RATES OF ENVIRONMENTAL CHANGE IN CHLAMYDOMONAS

We investigate how different rates of environmental change affect adaptive outcomes and dynamics by selecting Chlamydomonas populations for over 200 generations in environments where the rate of change varies. We find that slower rates of environmental change result in end populations that grow faster and pay a lower cost of adaptation than populations that adapt to a sudden change of the same magnitude. We detected partial selective sweeps in adapting populations by monitoring changes in marker frequency in each population. Although populations adapting to a sudden environmental change showed evidence of mutations of large effect segregating early on, populations adapting to slow rates of change showed patterns that were consistent with mutations of relatively small effect occurring at less predictable times. This work suggests that rates of environmental change may fundamentally alter adaptive dynamics and outcomes of adaptation by changing the size and timing of fitness increases. We suggest that using mutations of smaller effect during adaptation may result in lower levels of pleiotropy and historical constraints, which could in turn result in higher fitness by the end of the experiment.     

POPULATION GENETICS OF A PARASITIC CHROMOSOME: EXPERIMENTAL ANALYSIS OF PSR IN SUBDIVIDED POPULATIONS

Nasonia vitripennis is a parasitoid wasp that harbors several non-Mendelian sex-ratio distorters. These include MSR (Maternal Sex Ratio), a cytoplasmic element that causes nearly all-female families, and PSR (Paternal Sex Ratio), a supernumerary chromosome that causes all-male families. As in other hymenoptera, N. vitripennis has haplodiploid sex determination. Normally, unfertilized (haploid) eggs develop into males and fertilized (diploid) eggs develop into females. The PSR chromosome violates this normal pattern; it is inherited through sperm, but then causes destruction of the paternal chromosomes (except itself), thus converting diploid fertilized eggs (normally females) into haploid eggs that develop into PSR-bearing males. PSR is an extreme example of “parasitic” or “selfish” DNA. Because N. vitripennis has a highly subdivided population structure in nature, population-level selection may be important in determining the dynamics of PSR in natural populations. A theoretical analysis shows that subdivided population structure reduces PSR frequency, whereas high fertilization proportion (such as produced by the MSR element) increases PSR frequency. Population experiments using two deme sizes (3- and 12-foundress groups) and strains producing two fertilization proportions [wild-type (LabII)–57–67% female, and MSR (MI)–90–93% female] confirm these predictions. PSR achieved frequencies over 0.90 in 12–foundress group MSR populations in contrast to 0.20–0.40 in wild-type 12–foundress populations. PSR was selected against in wild-type populations composed of three-foundress groups. In MSR populations with three-foundress groups, presence of PSR selected against the MSR cytoplasmic element, eventually leading to low frequencies of both PSR and MSR. Complicated dynamics may occur when these two sex-ratio distorters are both present in highly subdivided populations. The existence of PSR in natural populations may depend on the presence of MSR. Results indicate that population subdivision could be important in determining the frequency of sex ratio distorters in N. vitripennis.     

MOLECULAR EVOLUTION OF GLUTAMINE SYNTHETASE II AND III IN THE CHROMALVEOLATES1

Glutamine synthetase (GS) is encoded by three distinct gene families (GSI, GSII, and GSIII) that are broadly distributed among the three domains of life. Previous studies established that GSII and GSIII isoenzymes were expressed in diatoms; however, less is known about the distribution and evolution of the gene families in other chromalveolate lineages. Thus, GSII cDNA sequences were isolated from three cryptophytes (Guillardia theta D. R. A. Hill et Wetherbee, Cryptomonas phaseolus Skuja, and Pyrenomonas helgolandii Santore), and GSIII was sequenced from G. theta. Red algal GSII sequences were obtained from Bangia atropurpurea (Mertens ex Roth) C. Agardh; Compsopogon caeruleus (Balbis ex C. Agardh) Mont.; Flintiella sanguinaria F. D. Ott and Porphyridium aerugineum Geitler; Rhodella violacea (Kornmann) Wehrmeyer and Dixoniella grisea (Geitler) J. L. Scott, S. T. Broadwater, B. D. Saunders, J. P. Thomas et P. W. Gabrielson; and Stylonema alsidii (Zanardini) K. M. Drew. In Bayesian inference and maximum‐likelihood (ML) phylogenetic analyses, chromalveolate GSII sequences formed a weakly supported clade that nested among sequences from glaucophytes, red algae, green algae, and plants. Red algal GSII sequences formed two distinct clades. The largest clade contained representatives from the Cyanidiophytina and Rhodophytina and grouped with plants and green algae. The smaller clade (C. caeruleus, Porphyra yezoensis, and S. alsidii) nested within the chromalveolates, although its placement was unresolved. Chromalveolate GSIII sequences formed a well‐supported clade in Bayesian and ML phylogenies, and mitochondrial transit peptides were identified in many of the sequences. There was strong support for a stramenopile‐haptophyte‐cryptophyte GSIII clade in which the cryptophyte sequence diverged from the deepest node. Overall, the evolutionary history of the GS gene families within the algae is complex with evidence for the presence of orthologous and paralogous sequences, ancient and recent gene duplications, gene losses and replacements, and the potential for both endosymbiotic and lateral gene transfers.