Adaptive selection and coevolution at the proteins of the Polycomb repressive complexes in Drosophila

Polycomb group (PcG) proteins are important epigenetic regulatory proteins that modulate the chromatin state through posttranslational histone modifications. These interacting proteins form multimeric complexes that repress gene expression. Thus, PcG proteins are expected to evolve coordinately, which might be reflected in their phylogenetic trees by concordant episodes of positive selection and by a correlation in evolutionary rates. In order to detect these signals of coevolution, the molecular evolution of 17 genes encoding the subunits of five Polycomb repressive complexes has been analyzed in the Drosophila genus. The observed distribution of divergence differs substantially among and along proteins. Indeed, CAF1 is uniformly conserved, whereas only the established protein domains are conserved in other proteins, such as PHO, PHOL, PSC, PH-P and ASX. Moreover, regions with a low divergence not yet described as protein domains are present, for instance, in SFMBT and SU(Z)12. Maximum likelihood methods indicate an acceleration in the nonsynonymous substitution rate at the lineage ancestral to the obscura group species in most genes encoding subunits of the Pcl–PRC2 complex and in genes Sfmbt, Psc and Kdm2. These methods also allow inferring the action of positive selection in this lineage at genes E(z) and Sfmbt. Finally, the protein interaction network predicted from the complete proteomes of 12 Drosophila species using a coevolutionary approach shows two tight PcG clusters. These clusters include well-established binary interactions among PcG proteins as well as new putative interactions.     

Imbalance of predator and prey armament: geographic clines in phenotypic interface and natural selection

The escalation of defensive/offensive arms is ubiquitous in prey-predator evolutionary interactions. However, there may be a geographically varying imbalance in the armaments of participating species that affects the outcome of local interactions. In a system involving the Japanese camellia (Camellia japonica) and its obligate seed predator, the camellia weevil (Curculio camelliae), we investigated the geographic variation in physical defensive/offensive traits and that in natural selection on the plant's defense among 17 populations over a 700-km-wide area in Japan. The sizes of the plant defensive apparatus (pericarp thickness) and the weevil offensive apparatus (rostrum length) clearly correlated with each other across populations. Nevertheless, the balance in armaments between the two species was geographically structured. In the populations for which the balance was relatively advantageous for the plant's defense, natural selection on the trait was stronger because in the other populations, most plant individuals were too vulnerable to resist the attacks of the weevil, and their seeds were infested independent of pericarp thickness. We also found that the imbalance between the defensive/offensive armaments and the intensity of natural selection showed clear latitudinal clines. Overall, our results suggest that the imbalance of armament between sympatric prey and predator could determine the strength of local selection and that climatic conditions could affect the local and overall trajectory of coevolutionary arms races.     

Host-parasite coevolution and selection on sex through the effects of segregation

The advantage of producing novel variation to keep apace of coevolving species has been invoked as a major explanation for the evolution and maintenance of sex (the Red Queen hypothesis). Recent theoretical investigations of the Red Queen hypothesis have focused on the effects of recombination in haploid species, finding that species interactions rarely favor the evolution of sex unless selection is strong. Yet by focusing on haploids, these studies have ignored a potential advantage of sex in diploids: generating novel combinations of alleles at a particular locus through segregation. Here we investigate models of host-parasite coevolution in diploid species to determine whether the advantages of segregation might rescue the Red Queen hypothesis as a more general explanation for the evolution of sex. We find that the effects of segregation can favor the evolution of sex but only under some models of infection and some parameter combinations, almost always requiring inbreeding. In all other cases, the effects of segregation on selected loci favor reductions in the frequency of sex. In cases where segregation and recombination act in opposite directions, we found that the effects of segregation dominate as an evolutionary force acting on sex in diploids.     

Natural selection, fitness entropy, and the dynamics of coevolution

The coevolutionary dynamics of interacting populations were studied by combining continuous time Lotka-Volterra models of population growth with single-locus genetic models of weak selection. The effects of natural selection on population growth were evaluated using Ginzburg's fitness entropy function as a measure of the deviation of a population's initial allele frequencies from their polymorphic equilibrium values. This entropy measure was used to relate the dynamics of a community composed of evolving populations to the dynamics of a "reference community" whose populations are initially in genetic equilibrium. Specifically, a quantity called the "selective difference area" was defined as the total difference between the population size trajectories of a reference and evolving population. The selective difference area represents the amount of extra life a species would realize if the entire community were at genetic equilibrium. It was shown that this selective difference area is a simple linear function of the initial fitness entropies of each species. This prediction is independent of the strength of selection and holds for any arbitrary set of initial population densities. Numerical examples were presented to illustrate the results. Under the assumption of weak selection, a generalization for arbitrary population growth models was outlined.     

Conformational selection during weak binding at the actin and myosin interface

The molecular mechanism of the powerstroke in muscle is examined by resonance energy transfer techniques. Recent models suggesting a pre-cocking of the myosin head involving an enormous rotation between the lever arm and the catalytic domain were tested by measuring separation distances among myosin subfragment-2, the nucleotide site, and the regulatory light chain in the presence of nucleotide transition state analogs. Only small changes (<0.5 nm) were detected that are consistent with internal conformational changes of the myosin molecule, but not with extreme differences in the average lever arm position suggested by some atomic models. These results were confirmed by stopped-flow resonance energy transfer measurements during single ATP turnovers on myosin. To examine the participation of actin in the powerstroke process, resonance energy transfer between the regulatory light chain on myosin subfragment-1 and the C-terminus of actin was measured in the presence of nucleotide transition state analogs. The efficiency of energy transfer was much greater in the presence of ADP-AlF(4), ADP-BeF(x), and ADP-vanadate than in the presence of ADP or no nucleotide. These data detect profound differences in the conformations of the weakly and strongly attached cross-bridges that appear to result from a conformational selection that occurs during the weak binding of the myosin head to actin.     

How selection affects phenotypic fluctuation

The large degree of phenotypic fluctuation among isogenic cells highlighted by recent studies on stochastic gene expression confers fitness on some individuals through a ‘bet‐hedging’ strategy, when faced with different selective environments. Under a single selective environment, the fluctuation may be suppressed through evolution, as it prevents maintenance of individuals around the fittest state and/or function. However, as fluctuation can increase phenotypic diversity, similar to mutation, it may contribute to the survival of individuals even under a single selective environment. To discuss whether the fluctuation increases over the course of evolution, cycles of mutation and selection for higher GFP fluorescence were carried out in Escherichia coli. Mutant genotypes possessing broad GFP fluorescence distributions with low average values emerged under strong selection pressure. These ‘broad mutants’ appeared independently on the phylogenetic tree and increased fluctuations in GFP fluorescence were attributable to the variance in mRNA abundance. In addition to the average phenotypic change by genetic mutation, the observed increase in phenotypic fluctuation acts as an evolutionary strategy to produce an extreme phenotype under severe selective environments.     

The importance of intraspecific frequency-dependent selection in modelling competitive coevolution

Summary The coevolution of competitors has been analyzed by two different types of fitness-maximization techniques; ESS methods (Lawlor and Maynard Smith, 1976), and CSS methods (Roughgarden, 1979). This paper argues that CSS methods generally do not predict the outcome of competitive coevolution. Even when there is relatively little variability within species, fitness maximization leads to an ESS rather than a CSS. A simple model is analyzed to show that ESS and CSS predictions about character displacement can differ qualitatively. Previous results of CSS analyses are discussed.     

Genetic and phenotypic models of natural selection

The following theorem is proposed: when two phenotypes differ in attributes affecting their relative fitness, selection will cease to cause further evolutionary change when the two phenotypes have the same fitness, provided that certain modes of inheritance apply; in particular, all genotypes specifying the same phenotype must have the same average fitness. If these conditions of “uniform fitness” patterns of inheritance are not met, particular genetic models of natural selection should replace an analysis of phenotypes. If the conditions are met, an analysis of the stationary conditions when the phenotypes have equal fitnesses permits quantitative statements about the outcome of selection without recourse to genetic models. Phenotypic analyses of natural selection are illustrated by models of sex ratios in plants, sexual versus asexual reproduction in plants, and parental investment by animals.     

Maternal condition influences phenotypic selection on offspring

1. Environmentally induced maternal effects are known to affect offspring phenotype, and as a result, the dynamics and evolution of populations across a wide range of taxa. 2. In a field experiment, we manipulated maternal condition by altering food availability, a key factor influencing maternal energy allocation to offspring. We then examined how maternal condition at the time of gametogenesis affects the relationships among early life-history traits and survivorship during early development of the coral reef fish Pomacentrus amboinensis. 3. Maternal condition did not affect the number of embryos that hatched or the number of hatchlings surviving to a set time. 4. We found no significant difference in egg size in relation to the maternal physiological state. However, eggs spawned by supplemented mothers were provisioned with greater energy reserves (yolk-sac and oil globule size) than nonsupplemented counterparts, suggesting that provision of energy reserves rather than egg size more closely reflected the maternal environment. 5. Among offspring originating from supplemented mothers, those with larger yolk-sacs were more likely to successfully hatch and survive for longer periods after hatching. However, among offspring from nonsupplemented mothers, yolk-sac size was either inconsequential to survival or offspring with smaller yolk-sac sizes were favoured. Mothers appear to influence the physiological capacity of their progeny and in turn the efficiency of individual offspring to utilize endogenous reserves. 6. In summary, our results show that the maternal environment influences the relationship between offspring characteristics and survival and suggest that energy-driven selective mechanisms may operate to determine progeny viability.     

Estimation of phenotypic selection differentials for predicting genetic responses to ratio-based selection

Ratios of the phenotypic values of two traits may be used as selection criteria in animal and plant breeding to improve the ratio traits themselves or to effect changes in their two component (numerator and denominator) traits. Prediction of genetic responses to ratio-based selection would facilitate quantitative analysis and evaluation of selection based on ratios. Methods for predicting such responses are derived and presented here. They employ expressions for the truncation value of a ratio and for the phenotypic selection differentials of the numerator and denominator traits. The derivation of these expressions is based upon the assumption that the phenotypic values of each of these traits are normally distributed. Worked examples relating to livestock and crop improvement are included to demonstrate how responses to selection for ratios may be predicted.     

Phosphorylation at the interface

Proteomic studies have identified thousands of eukaryotic phosphorylation sites (phosphosites), but few are functionally characterized. Nishi et?al., in this issue of Structure, characterize phosphosites at protein-protein interfaces and estimate the effect of their phosphorylation on interaction affinity, by combining proteomics data with protein structures.     

Evolution of adaptive phenotypic traits without positive Darwinian selection

Recent evidence suggests the frequent occurrence of a simple non-Darwinian (but non-Lamarckian) model for the evolution of adaptive phenotypic traits, here entitled the plasticity-relaxation-mutation (PRM) mechanism. This mechanism involves ancestral phenotypic plasticity followed by specialization in one alternative environment and thus the permanent expression of one alternative phenotype. Once this specialization occurs, purifying selection on the molecular basis of other phenotypes is relaxed. Finally, mutations that permanently eliminate the pathways leading to alternative phenotypes can be fixed by genetic drift. Although the generality of the PRM mechanism is at present unknown, I discuss evidence for its widespread occurrence, including the prevalence of exaptations in evolution, evidence that phenotypic plasticity has preceded adaptation in a number of taxa and evidence that adaptive traits have resulted from loss of alternative developmental pathways. The PRM mechanism can easily explain cases of explosive adaptive radiation, as well as recently reported cases of apparent adaptive evolution over ecological time.     

毛茛状金莲花不同花期的花特征和访花昆虫的变化及表型选择

为了研究植物生长季内开花时间对花特征表型选择的影响,我们以青藏高原东缘高寒草地的毛茛状金莲花Trollius ranunculoides)为实验材料,在生长季内不同开花时间(花前期、花末期)测定花特征,观察访花昆虫的类群和访花频率,生长季结束后收集种子.根据昆虫访花的喜好和季节内类群与访花频率的变化,分析了不同开花时间毛茛状金莲花的花特征与昆虫的选择;并用种子产量表示雌性适合度,估计了毛茛状金莲花的花特征在不同开花时间所受的表型选择.结果表明:不同花期植物的花特征有显著差异,相应的访花昆虫的类群和频率也存在差异,不同类群昆虫访花喜好也不一样.蜂喜好花瓣和花萼较宽、花茎短和花茎数少的个体,这正符合花前期的特征,因而蜂的访花频率在花前期较高;蝇对花特征没有明显的偏好.而通过雌性适合度估计毛茛状金莲花花特征所受的表型选择则是:花前期,花茎较长和花茎数多的植株适合度大;花末期,花茎数多的植株适合度大.我们的研究表明:在植物生长季,花期的分化伴随着传粉昆虫活动的变化.不同花期,访花昆虫的变化可能对植物花特征的分化起了至关重要的作用.但是访花昆虫对花特征的选择与通过雌性适合度估计植物受到的选择不尽相同,这可能是由于其他因素造成的.     

Optimization of recurrent selection on the phenotypic value of doubled haploid lines

Summary Three methods of recurrent selection using doubled haploids (DH) are compared with the same resources: individual line selection (with one DH line per plant), selection between and within families, and selection index of family and line within family values. It seems that for low heritabilities at the individual level, the selection index method is the most efficient method, followed by the selection between and within families. Because of the difficulty in optimizing selection intensities, the selection between and within families can be less efficient than individual line selection. For very low heritabilities, it will be better to use selection index with a relatively low number of lines per haploidized plant, to minimize the rate of decrease of the effective population size. For a large range of situations, recurrent selection with only one DH line per plant seems one of the more efficient and the simpler methods.     

Dynamin at the actin-membrane interface

Many important cellular processes such as phagocytosis, cell motility and endocytosis require the participation of a dynamic and interactive actin cytoskeleton that acts to deform cellular membranes. The extensive family of non-traditional myosins has been implicated in linking the cortical actin gel with the plasma membrane. Recently, however, the dynamins have also been included in these cell processes as a second family of mechanochemical enzymes that self-associate and hydrolyze nucleotides to perform 'work' while linking cellular membranes to the actin cytoskeleton. The dynamins are believed to form large helical polymers from which extend many interactive proline-rich tail domains, and these domains bind to a variety of SH3-domain-containing proteins, many of which appear to be actin-binding proteins. Recent data support the concept that the dynamin family might act as a 'polymeric contractile scaffold' at the interface between biological membranes and filamentous actin.     

A general model of the relation between phenotypic selection and genetic response

The phenotypic view of selection assumes that genetic responses can be predicted from selective forces and heritability — or in the classical quantitative genetic equation: R = h²S. However, data on selection in bird populations show that often no selection responses is found, despite consistent selective forces on phenotypes and significant heritable variation. Such discrepancies may arise due to the assumption that selection only acts on observed phenotypes. We derive a general selection equation that takes into account the possibility that some relevant (internal or external) traits are not measured. This equation shows that the classic equation applies if selection directly acts on the measured, phenotypic traits. This is not the case when, for instance, there are unknown internal genetic trade-offs, or unknown common environmental factors affecting both trait and fitness. In such cases, any relationship between phenotypic selection and genetic response is possible. Fortunately, the classical model can be tested by comparing phenotypic and genetic covariances between traits and fitness; an indication that important internal or external traits are missing can thus be obtained. Such an analysis was indeed found in the literature; for selection on fledging weight in Great Tits it yielded valuable extra information.     

Phytochemicals at the plant-insect interface

Opportunities for genetic engineering of natural products are increasing, while discovery and development of synthetic insecticides and developmental regulators are declining. However, discovery and potential applications of natural compounds are constrained by present ecological knowledge and theory. Biochemistry offers additional perspective to chemical interaction across the interface between plant and herbivore. Phytochemical effects on an insect herbivore may be determined by physical, chemical, and biotic characteristics of the microenvironment during phytochemical transfer between plant and insect. The midgut lumen is often overlooked as part of this microenvironment. It initially determines rates of metabolism and uptake of phytochemicals into hemolymph, and ultimately the quantity of a compound seen by affected tissues. Additive processes such as absorption, binding, and transport by proteins in hemolymph may ultimately prove more crucial to toxication than subtractive processes such as metabolism and excretion. Uptake and transport of coumarins in hemolymph are being studied in larvae of the citrus root weevil Diaprepes abbreviatus. Studies with synthetic 7-amino-3-phenyl coumarin (coumarin-10) have preceded studies with natural coumarins. The fluorescence properties of coumarin-10 have enabled determination of absorption and binding to hemolymph proteins.