The evolution of virulence: A stochastic simulation model examining parasitism at individual and population levels

We modelled the evolution of virulence when co-infections were permitted and compared patterns generated by our modelling approach with those of other models. In support of current models, we found that strains with virulences above the maximum basic reproductive rate (Ro) were competitively superior, and that both high host density (as indexed by host encounter rate) and high parasite infectiousness favoured evolution of strains with high virulence. However, we found that co-existence typically did not continue indefinitely and that parasites with high virulences, and Ro values approaching unity, often did not persist. We examined the extent to which processes such as stochasticity and positive frequency dependence influenced patterns generated by our model. Also, we examined commonly used indices of parasite fitness [i.e. Ro and rate of spread (ROS)], and found that only ROS was positively related to competitive ability when co-infections were permitted. However, there was considerable variation in competitive ability that was not explained by variation in ROS. We conclude that our modelling approach can significantly influence patterns generated and that conclusions from single models or conclusions based on current indices of parasite fitness should be viewed with caution. We suggest empirical tests that distinguish our model from other models and further examine the impact of mechanisms such as positive frequency dependence on the evolution of virulence. This revised version was published online in July 2006 with corrections to the Cover Date.     

Density-dependent foraging in the harvester ant Messor ebeninus: two experiments

Harvester ants are important seed predators in many xeric environments, and their foraging choices can influence the composition of plant communities. Seed abundance has been cited as an important factor in determining such foraging preferences. Three seed types (sesame, millet, and flax) were experimentally introduced in differing proportions near nests of the ant Messor ebeninus near the Dead Sea, in territory administered by the state of Israel. Two experiments were designed to investigate the effects of this density conditioning on two stages of the ants' subsequent foraging behavior: recruitment to seed patches and selection of seeds from within a patch. When seeds were presented in small, single-species patches, experimentally common seeds were discovered and exploited significantly faster than rare seeds, especially among less preferred seed types. When seeds were presented in large, mixed patches, however, no consistent effect of density was observed.     

Calcium- and voltage-dependence of nematocyst discharge in Hydra vulgaris

In Hydra vulgaris, discharge of stenotele nematocysts was induced by contact with prey, electrical stimuli, or increase in the external potassium concentration. In each case 10^-4 M calcium was required in the culture medium. The results indicated a voltage- and calcium-dependent mechanism different from mechano- or chemoreception allowing calcium influx from the external medium. A threshold for activation was suggested by the steep increase of the rate of electrically induced discharge in external fields of 3.5 kV/m. Although organic antagonists for vertebrate calcium channels were ineffective in blocking the calcium-induced nematocyst discharge, inorganic divalent and trivalent cations competitively inhibited the process, with a sequence (Co²⁺ < Ni²⁺ < Cd²⁺ < La³⁺ < Gd³⁺) similar to that seen for antagonism of calcium influx through voltage-dependent channels. Magnesium, an intracellular calcium antagonist, decreased nematocyst discharge, while strontium replacing calcium supported the discharge at a lowered rate. It is concluded that in the nematocyte a voltage-activated influx of calcium through apical ion channels initiates the discharge of the nematocyst in an exocytotic process.     

PHYLOGENIES WITHOUT FOSSILS

Phylogenies that are reconstructed without fossil material often contain approximate dates for lineage splitting. For example, particular nodes on molecular phylogenies may be dated by known geographic events that caused lineages to split, thereby calibrating a molecular clock that is used to date other nodes. On the one hand, such phylogenies contain no information about lineages that have become extinct. On the other hand, they do provide a potentially useful testing ground for ideas about evolutionary processes. Here we first ask what such reconstructed phylogenies should be expected to look like under a birth-death process in which the birth and death parameters of lineages remain constant through time. We show that it is possible to estimate both the birth and death rates of lineages from the reconstructed phylogenies, even though they contain no explicit information about extinct lineages. We also show how such phylogenies can reveal mass extinctions and how their characteristic footprint can be distinguished from similar ones produced by density-dependent cladogenesis.     

Multi-scale analysis of plant species richness in Serengeti grasslands

Aim To assess scale dependence between environmental factors and plant species richness. Additionally, we aimed to identify the scales at which niche relations and habitat heterogeneity, as hypothesized by A. Shmida & M.V. Wilson (1985) Journal of Biogeography, 12 , 1–20, operate in the savanna grasslands that were the focus of this study. Location Savanna grassland plant communities of Serengeti National Park, Tanzania. Methods Plant species richness was sampled in 102 modified Whittaker plots and tested for associations with two climate factors, mean annual rainfall (MAP) and potential evapotranspiration (PET), and two landscape variables, plot aspect (ASP) and topographic variation (TOPO), using multiple regressions. Scale dependence was assessed by conducting regressions after altering three aspects of spatial scale: grain, extent and focus. Grain was altered by analysing plant richness at 1, 10, 10² and 10³ m²; extent was investigated by restricting the maximum distance between samples to 75, 100, 125 and 150 km; and focus was manipulated by averaging samples spatially according to geographical land regions. Within the context of our data, we assumed that niche relations were represented by climate factors and habitat heterogeneity by landscape factors. Results Across all 102 plots, plant species richness between 1 and 10² m² had a negative relation to PET and a weak positive relation to MAP. Plant species richness at 10³ m² had a positive association with TOPO and weaker associations with climate factors. ASP stayed in the model between grains of 10 and 10³ m², but had a very weak positive association with richness. When the focus was changed to land regions, associations between plant species richness and explanatory variables strengthened, but were not qualitatively different. At spatial extents of 75 and 100 km, PET was the strongest correlate of plant species richness across all spatial grains. At spatial extents ≥ 125 km, PET explained the majority of the model variance at spatial grains ≤ 10² m², whereas TOPO explained equal amounts or more of the model variance at spatial grains of 10³ m². Main conclusions Both climate and topographic variation explained plant species richness in Serengeti grasslands, but specific patterns depended on grain, extent and, to a lesser degree, focus. Consistent with the ideas of Shmida & Wilson (1985) , determinants of plant species richness shifted from niche relations to habitat heterogeneity between spatial grains of 1 and 10³ m², although this occurred only at relatively large spatial extents (≥ 150 km). Finally, the signs, strength and shape of plant species richness relationships in Serengeti closely match those that describe macro‐scale patterns of woody plant species richness across the entire African continent.     

The unusual internal motion of the villin headpiece subdomain

The thermostable 36‐residue subdomain of the villin headpiece (HP36) is the smallest known cooperatively folding protein. Although the folding and internal dynamics of HP36 and close variants have been extensively studied, there has not been a comprehensive investigation of side‐chain motion in this protein. Here, the fast motion of methyl‐bearing amino acid side chains is explored over a range of temperatures using site‐resolved solution nuclear magnetic resonance deuterium relaxation. The squared generalized order parameters of methyl groups extensively spatially segregate according to motional classes. This has not been observed before in any protein studied using this methodology. The class segregation is preserved from 275 to 305 K. Motions detected in Helix 3 suggest a fast timescale of conformational heterogeneity that has not been previously observed but is consistent with a range of folding and dynamics studies. Finally, a comparison between the order parameters in solution with previous results based on solid‐state nuclear magnetic resonance deuterium line shape analysis of HP36 in partially hydrated powders shows a clear disagreement for half of the sites. This result has significant implications for the interpretation of data derived from a variety of approaches that rely on partially hydrated protein samples.     

Harvested populations are more variable only in more variable environments

The interaction between environmental variation and population dynamics is of major importance, particularly for managed and economically important species, and especially given contemporary changes in climate variability. Recent analyses of exploited animal populations contested whether exploitation or environmental variation has the greatest influence on the stability of population dynamics, with consequences for variation in yield and extinction risk. Theoretical studies however have shown that harvesting can increase or decrease population variability depending on environmental variation, and requested controlled empirical studies to test predictions. Here, we use an invertebrate model species in experimental microcosms to explore the interaction between selective harvesting and environmental variation in food availability in affecting the variability of stage‐structured animal populations over 20 generations. In a constant food environment, harvesting adults had negligible impact on population variability or population size, but in the variable food environments, harvesting adults increased population variability and reduced its size. The impact of harvesting on population variability differed between proportional and threshold harvesting, between randomly and periodically varying environments, and at different points of the time series. Our study suggests that predicting the responses to selective harvesting is sensitive to the demographic structures and processes that emerge in environments with different patterns of environmental variation.     

基于相关系数的水文相依性变异分级方法——以自回归模型为例

水文过程演变存在时间相依性,含有相依成分的水文序列无法满足水文计算中的一致性假设,给水问题研究带来诸多困难.针对水文序列相依性变异这一现象,以自相关模型为例,提出基于相关系数的水文相依性变异分级方法.该方法通过计算相依成分与原序列之间的相关系数,并选取合理的相关系数阈值,将相依性变异程度分为无变异、弱变异、中变异、强变异、巨变异.通过推导相关系数与序列各阶自相关系数之间的公式,说明相关系数主要取决于1阶到p阶自相关系数的大小,从而阐明分级方法的理论基础.以一阶和二阶自回归模型为例,利用统计试验验证了公式的合理性,并说明了相关系数和自相关系数的联系.将所提分级方法应用于3个实测径流序列进行分析,结果显示水文过程常常存在相依性与随机性并存的现象.