Plant-soil Interactions: Ecological Aspects and Evolutionary Implications

Building on the concept of plants as ecosystem engineers, and on published information on effects of particular plant species on soils, we review the evidence that such effects can provide a positive feedback to such plants. Based on case studies involving dune formation by Marram grass, N supply by N2-fixing plants, depression of N availability by ericaceous plants, islands of fertility in deserts, mull- and mor-forming temperate forest trees, and formation of peatbogs, as well as similar other cases, we conclude that there is strong evidence for plant-soil feedbacks in a variety of ecosystems. We argue, moreover, that these feedbacks could have played a role in the evolution of the plant species in question. These ideas are based mainly on correlative observations, and need further testing.     

Probing Evolutionary Repeatability: Neutral and Double Changes and the Predictability of Evolutionary Adaptation

Background

The question of how organisms adapt is among the most fundamental in evolutionary biology. Two recent studies investigated the evolution of Escherichia coli in response to challenge with the antibiotic cefotaxime. Studying five mutations in the β-lactamase gene that together confer significant antibiotic resistance, the authors showed a complex fitness landscape that greatly constrained the identity and order of intermediates leading from the initial wildtype genotype to the final resistant genotype. Out of 18 billion possible orders of single mutations leading from non-resistant to fully-resistant form, they found that only 27 (1.5×10⁻⁷%) pathways were characterized by consistently increasing resistance, thus only a tiny fraction of possible paths are accessible by positive selection. I further explore these data in several ways.

Principal Findings

Allowing neutral changes (those that do not affect resistance) increases the number of accessible pathways considerably, from 27 to 629. Allowing multiple simultaneous mutations also greatly increases the number of accessible pathways. Allowing a single case of double mutation to occur along a pathway increases the number of pathways from 27 to 259, and allowing arbitrarily many pairs of simultaneous changes increases the number of possible pathways by more than 100 fold, to 4800. I introduce the metric ‘repeatability,’ the probability that two random trials will proceed via the exact same pathway. In general, I find that while the total number of accessible pathways is dramatically affected by allowing neutral or double mutations, the overall evolutionary repeatability is generally much less affected.

Conclusions

These results probe the conceivable pathways available to evolution. Even when many of the assumptions of the analysis of Weinreich et al. (2006) are relaxed, I find that evolution to more highly cefotaxime resistant β-lactamase proteins is still highly repeatable.     

双色FISH和DNA纤维FISH方法的建立与应用

在构建了含毛细胞白血病相关的结构性倒位inv (5) (p13.1q13.3)的细胞系后,为了确定该新建细胞系在建株过程中其倒位断裂点关键区遗传物质是否发生改变,以生物素或地高辛标记的cCI5-216 和cCI5-267黏粒DNA为探针,进行染色体中期、间期和DNA纤维3种双色荧光原位杂交的分析。结果表明：该新建细胞系的3种双色荧光原位杂交结果,均与该细胞系的原代细胞的完全相同,证实了该细胞系倒位断裂点关键区的遗传物质结构未发生改变。该细胞系是揭示毛细胞白血病发病的分子机理的重要研究材料。     

Life Stages: Interactions and Spatial Patterns

In many stage-structured species, different life stages often occupy separate spatial niches in a heterogeneous environment. Life stages of the giant flour beetle Tribolium brevicornis (Leconte), in particular adults and pupae, occupy different locations in a homogeneous habitat. This unique spatial pattern does not occur in the well-studied stored grain pests T. castaneum (Herbst) and T. confusum (Duval). We propose density dependent dispersal as a causal mechanism for this spatial pattern. We model and explore the spatial dynamics of T. brevicornis with a set of four density dependent integrodifference and difference equations. The spatial model exhibits multiple attractors: a spatially uniform attractor and a patchy attractor with pupae and adults spatially separated. The model attractors are consistent with experimental observations.     

Ecological and Evolutionary Interactions between Wild Crucifers and Their Herbivorous Insects

Abstract Insects feeding on ten species of wild crucifer were investigated. Differences in host plant range and insect community structure were examined with regard to anti-herbivore defense mechanisms. Most of the crucifer species deterred insect herbivory by disappearing in the summer or by lowering their intrinsic quality as food for insects. Species with these defense mechanisms were exploited by only a few specialized herbivorous insects that seemed to have counter defenses. The plants without these defense mechanisms were used by many herbivorous insect species. Rorippa indica lacked direct defenses, but supported a low total density of herbivore individuals. This crucifer has an indirect defense mechanism: ants attracted to floral nectar defended the plant from deleterious herbivores. Crucifers that disappeared seasonally lacked other anti-herbivore defense mechanisms. This suggests that the phonological response is an alternative other responses to herbivore attack.     

Placental Type Interactions and Evolutionary Trends of Development of Uterus in Cestodes

In Proteocephalus thymalli and P. torulosus, a contact of the placental type in uterus was shown to be formed at two different levels. At the first level an interaction occurs between outgrowths of uterine epithelium and thin capsule of embryos closely adjacent to uterine wall. The next level is formation of contact between neighboring egg capsules, which allows distributing nutrients among fetuses present in the uterine cavity. Placental interactions in Clestobothrium acheilognathi are limited in time and space. First, a relatively small number of eggs are involved in interaction of the placental type in the uterine sac, while uterine duct is filled with freely lying eggs. Second, the closest contact is observed in eggs with non-sclerosed egg shell. One of the main evolutionary tendencies in cestodes has been shown to be a modification of uterus for formation of close interrelations with embryonic membranes in the course of transition from the extrauterine to the intrauterine type of embryonic development. Uterus in parasites with a polylecital type of the egg is suggested to serve to the greater extent as a reservoir, whereas in cestodes with oligolecital eggs, uterus performs its direct function—supply of developing embryos with nutrients. As a result, modifications of uterine epithelium are formed: from the appearance of the placental type interactions formed repeatedly in phylogenetically distant groups of cestodes to formation of branched outgrowths separating the uterine space into units or disintegration to actively functioning uterine capsules.     

Homologous and Heterologous Interactions between Hexokinase and Mitochondrial Porin: Evolutionary Implications

Binding of the Type I isozyme of mammalian hexokinase to mitochondria is mediated by the porin present in the outer mitochondrial membrane. Type I hexokinase from rat brain is avidly bound by rat liver mitochondria while, under the same conditions, there is no significant binding to mitochondria from S. cerevisiae. Previously published work demonstrates the lack of significant interaction of yeast hexokinase with mitochondria from either liver or yeast. Thus, structural features required for the interaction of porin and hexokinase must have emerged during evolution of the mammalian forms of these proteins. If these structural features serve no functional role other than facilitating this interaction of hexokinase with mitochondria, it seems likely that they evolved in synchrony since operation of selective pressures on the hexokinase–mitochondrial interaction would require the simultaneous presence of hexokinase and porin capable of at least minimal interaction, and be responsive to changes in either partner that affected this interaction. Recent studies have indicated that a second type of binding site, which may or may not involve porin, is present on mammalian mitochondria. There are also reports of hexokinase binding to mitochondria in plant tissues, but the nature of the binding site remains undefined.     

Establishment of DNA-DNA Interactions by the Cohesin Ring

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The Effects of Spatial Scale on Trophic Interactions

Food chain models have dominated empirical studies of trophic interactions in the past decades, and have lead to important insights into the factors that control ecological communities. Despite the importance of food chain models in instigating ecological investigations, many empirical studies still show a strong deviation from the dynamics that food chain models predict. We present a theoretical framework that explains some of the discrepancies by showing that trophic interactions are likely to be strongly influenced by the spatial configuration of consumers and their resources. Differences in the spatial scale at which consumers and their resources function lead to uncoupling of the population dynamics of the interacting species, and may explain overexploitation and depletion of resource populations. We discuss how changed land use, likely the most prominent future stress on natural systems, may affect food web dynamics by interfering with the scale of interaction between consumers and their resource.     

Competition and the Effect of Spatial Resource Heterogeneity on Evolutionary Diversification

A model is presented to explore how the form of selection arising from competition for resources is affected by spatial resource heterogeneity. The model consists of a single species occupying two patches connected by migration, where the two patches can differ in the type of resources that they contain. The main goal is to determine the conditions under which competition for resources results in disruptive selection (i.e., selection favoring a polymorphism) since it is this form of selection that will give rise to the evolutionary diversification of resource exploitation strategies. In particular, comparing the conditions giving rise to disruptive selection when the two patches are identical to the conditions when they contain different resources reveals the effect of spatial resource heterogeneity. Results show that when the patches are identical, the conditions giving rise to disruptive selection are identical to those that give rise to character displacement in previous models. When the patches are different, the conditions giving rise to disruptive selection can be either more or less stringent depending upon demographic parameters such as the intrinsic rate of increase and the migration rate. Surprisingly, spatial resource heterogeneity can actually make forms of evolutionary diversification such as character displacement less likely. It is also found that results are dependent on how the resource exploitation strategies and the spatial resource heterogeneity affect the population dynamics. One robust conclusion however, is that spatial resource heterogeneity always has a disruptive effect when the migration rate between patches is low.     

农作物种质资源调查数据标准制定与共享

系统提取并分析了农作物种质资源普查数据、调查数据、评价数据和保存数据等数据信息,采用基于数据元技术方法制定了农作物种质资源调查数据标准和数据元目录;定义了种质资源调查数据集以及对象和属性的映射关系;给出了基于XML数据标准存储及交换策略。标准的制定使农作物种质资源调查在"数据层"上达到统一,规范了数据库构建,促进了农作物种质资源调查数据的整合和共享。     

Social Interactions through the Eyes of Macaques and Humans

Group-living primates frequently interact with each other to maintain social bonds as well as to compete for valuable resources. Observing such social interactions between group members provides individuals with essential information (e.g. on the fighting ability or altruistic attitude of group companions) to guide their social tactics and choice of social partners. This process requires individuals to selectively attend to the most informative content within a social scene. It is unclear how non-human primates allocate attention to social interactions in different contexts, and whether they share similar patterns of social attention to humans. Here we compared the gaze behaviour of rhesus macaques and humans when free-viewing the same set of naturalistic images. The images contained positive or negative social interactions between two conspecifics of different phylogenetic distance from the observer; i.e. affiliation or aggression exchanged by two humans, rhesus macaques, Barbary macaques, baboons or lions. Monkeys directed a variable amount of gaze at the two conspecific individuals in the images according to their roles in the interaction (i.e. giver or receiver of affiliation/aggression). Their gaze distribution to non-conspecific individuals was systematically varied according to the viewed species and the nature of interactions, suggesting a contribution of both prior experience and innate bias in guiding social attention. Furthermore, the monkeys’ gaze behavior was qualitatively similar to that of humans, especially when viewing negative interactions. Detailed analysis revealed that both species directed more gaze at the face than the body region when inspecting individuals, and attended more to the body region in negative than in positive social interactions. Our study suggests that monkeys and humans share a similar pattern of role-sensitive, species- and context-dependent social attention, implying a homologous cognitive mechanism of social attention between rhesus macaques and humans.     

Fd : FNR Electron Transfer Complexes: Evolutionary Refinement of Structural Interactions

During the evolution of higher-plant root and leaf-type-specific Fd : FNR complexes from an original cyanobacterial type progenitor, rearrangement of molecular interaction has altered the relative orientation of prosthetic groups and there have been changes in complex induced conformational change. Selection has presumably worked on mutation of residues responsible for interaction between the two proteins, favoring optimized electron flow in a specific direction, and efficient dissociation following specific oxidation of leaf Fd and reduction of root Fd. Major changes appear to be: loss in both leaf and root complexes of a cyanobacterial mechanism that ensures Fd dissociation from the complex following change in Fd redox state, development of a structural rearrangement of Fd on binding to leaf FNR that results in a negative shift in Fd redox potential favorable to photosynthetic electron flow, creation of a vacant space in the root Fd:FNR complex that may allow access to the redox centers of other enzymes to ensure efficient channeling of heterotrophic reductant into bioassimilation. Further structural analysis is essential to establish how root type FNR distinguishes between Fd isoforms, and discover how residues not directly involved in intermolecular interactions may affect complex formation.     

Spatial Heterogeneity in Habitat Quality and Cross-Scale Interactions in Metapopulations

Abstract Integration of habitat heterogeneity into spatially realistic metapopulation approaches reveals the potential for key cross-scale interactions. Broad-scale environmental gradients and land-use practices can create autocorrelation of habitat quality of suitable patches at intermediate spatial scales. Patch occupancy then depends not only on habitat quality at the patch scale but also on feedbacks from surrounding neighborhoods of autocorrelated patches. Metapopulation dynamics emerge from how demographic and dispersal processes interact with relevant habitat heterogeneity. We provide an empirical example from a metapopulation of round-tailed muskrats (Neofiber alleni) in which habitat quality of suitable patches was spatially autocorrelated most strongly within 1,000 m, which was within the expected dispersal range of the species. After controlling for factors typically considered in metapopulation studies—patch size, local patch quality, patch connectivity—we use a cross-variogram analysis to demonstrate that patch occupancy by muskrats was correlated with habitat quality across scales ≤1,171 m. We also discuss general consequences of spatial heterogeneity of habitat quality for metapopulations related to potential cross-scale interactions. We focus on spatially correlated extinctions and metapopulation persistence, hierarchical scaling of source–sink dynamics, and dispersal decisions by individuals in relation to information constraints.     

Evolutionary dynamics of human retroviruses investigated through full-genome scanning

To test hypotheses on the differences in retroviral genetic diversity, we compared the evolutionary dynamics of the human immunodeficiency virus type 1 (HIV-1) group M and the primate T-cell lymphotropic virus (PTLV) using a full-genome analysis. Evolutionary rates and nonsynonymous/synonymous substitution rate ratios were estimated across the genome using a maximum likelihood sliding window approach, and molecular clock properties were investigated. We confirm a remarkable difference in genetic stability and selective pressure at the interhost level. While there is evidence for adaptive evolution in HIV-1, the evolution of PTLV is almost exclusively characterized by negative selection or nearly neutral processes. For both retroviruses, evolutionary rate estimates across the genome reflect the differential selective constraints. However, based on the relationship between evolutionary rate and selective pressure and based on the comparison of synonymous substitution rates, the differences in rate between HIV-1 and PTLV cannot be explained by selective forces only. Several evolutionary and statistical assumptions, examined using a Bayesian coalescent method, were shown to have little influence on our inference.     

Molecular Mechanisms of Tight Binding through Fuzzy Interactions

Many intrinsically disordered proteins (IDPs) form fuzzy complexes upon binding to their targets. Although many IDPs are weakly bound in fuzzy complexes, some IDPs form high-affinity complexes. One example is the nonstructural protein 1 (NS1) of the 1918 Spanish influenza A virus, which hijacks cellular CRKII through the strong binding affinity (K_d ～10 nM) of its proline-rich motif (PRM^NS1) to the N-terminal Src-homology 3 domain of CRKII. However, its molecular mechanism remains elusive. Here, we examine the interplay between structural disorder of a bound PRM^NS1 and its long-range electrostatic interactions. Using x-ray crystallography and NMR spectroscopy, we found that PRM^NS1 retains substantial conformational flexibility in the bound state. Moreover, molecular dynamics simulations showed that structural disorder of the bound PRM^NS1 increases the number of electrostatic interactions and decreases the mean distances between the positively charged residues in PRM^NS1 and the acidic residues in the N-terminal Src-homology 3 domain. These results are analyzed using a polyelectrostatic model. Our results provide an insight into the molecular recognition mechanism for a high-affinity fuzzy complex.