Population structure and evolutionary progress

Wright's shifting-balance theory is discussed as an example of a process that can cause species to evolve combinations of characters that could not evolve under natural selection alone. A review of the existing theory of peak shifts indicates that the conditions of extreme isolation that are necessary to permit genetic drift to alter the outcome of natural selection in local populations would make gene flow too weak to spread a new combination of genes to other populations in a reasonable time. Instead, it seems likely that major demographic changes must occur in a species for the shifting-balance process to work. A discussion of direct and indirect studies of gene flow in natural populations suggests that the current genetic structure of many species is likely to reflect past demographic events rather than ongoing gene flow. It is possible then that demographic processes could be responsible for spreading new traits in a species, but that would be true whether those new traits evolved only owing to natural selection or owing in addition to genetic drift and other forces.     

Population and evolutionary dynamics of phage therapy

Following a sixty-year hiatus in western medicine, bacteriophages (phages) are again being advocated for treating and preventing bacterial infections. Are attempts to use phages for clinical and environmental applications more likely to succeed now than in the past? Will phage therapy and prophylaxis suffer the same fates as antibiotics--treatment failure due to acquired resistance and ever-increasing frequencies of resistant pathogens? Here, the population and evolutionary dynamics of bacterial-phage interactions that are relevant to phage therapy and prophylaxis are reviewed and illustrated with computer simulations.     

Genomic and evolutionary comparisons of diazotrophic and pathogenic bacteria of the order Rhizobiales

Background

Species belonging to the Rhizobiales are intriguing and extensively researched for including both bacteria with the ability to fix nitrogen when in symbiosis with leguminous plants and pathogenic bacteria to animals and plants. Similarities between the strategies adopted by pathogenic and symbiotic Rhizobiales have been described, as well as high variability related to events of horizontal gene transfer. Although it is well known that chromosomal rearrangements, mutations and horizontal gene transfer influence the dynamics of bacterial genomes, in Rhizobiales, the scenario that determine pathogenic or symbiotic lifestyle are not clear and there are very few studies of comparative genomic between these classes of prokaryotic microorganisms trying to delineate the evolutionary characterization of symbiosis and pathogenesis.

Results

Non-symbiotic nitrogen-fixing bacteria and bacteria involved in bioremediation closer to symbionts and pathogens in study may assist in the origin and ancestry genes and the gene flow occurring in Rhizobiales. The genomic comparisons of 19 species of Rhizobiales, including nitrogen-fixing, bioremediators and pathogens resulted in 33 common clusters to biological nitrogen fixation and pathogenesis, 15 clusters exclusive to all nitrogen-fixing bacteria and bacteria involved in bioremediation, 13 clusters found in only some nitrogen-fixing and bioremediation bacteria, 01 cluster exclusive to some symbionts, and 01 cluster found only in some pathogens analyzed. In BBH performed to all strains studied, 77 common genes were obtained, 17 of which were related to biological nitrogen fixation and pathogenesis. Phylogenetic reconstructions for Fix, Nif, Nod, Vir, and Trb showed possible horizontal gene transfer events, grouping species of different phenotypes.

Conclusions

The presence of symbiotic and virulence genes in both pathogens and symbionts does not seem to be the only determinant factor for lifestyle evolution in these microorganisms, although they may act in common stages of host infection. The phylogenetic analysis for many distinct operons involved in these processes emphasizes the relevance of horizontal gene transfer events in the symbiotic and pathogenic similarity.     

黄山松种群结构与动态研究

以“空间代替时间”的方法,以种群径级结构代替年龄结构,采用静态生命表和生存分析的方法,探讨了天柱山国家森林公园黄山松种群结构和动态规律。结果表明,随海拔升高,黄山松种群密度增大,径级分布范围减小,种群存活曲线由Deevey-Ⅱ型之间过渡到Deevey—Ⅰ型,种群由稳定型过渡为增长型。表明由低海拔向高海拔,黄山松种群处于不同的演替和发展阶段。     

Population and evolutionary dynamics of Helitron transposable elements in Arabidopsis thaliana

Helitrons, a recently discovered superfamily of DNA transposons that capture host gene fragments, constitute up to 2% of the Arabidopsis thaliana genome. In this study, we identified 565 insertions of a family of nonautonomous Helitrons, known as Basho elements. We aligned subsets of these elements, estimated their phylogenetic relationships, and used branch lengths to yield insight into the age of each Basho insertion. The age distribution suggests that 87% of Bashos inserted within 5 Myr, subsequent to the divergence between A. thaliana and its sister species Arabidopsis lyrata. We screened 278 of these insertions for their presence or absence in a sample of 47 A. thaliana accessions. With both phylogenetic and population frequency data, we investigated the effects of gene density, recombination rate, and element length on Basho persistence. Our analyses suggested that longer Basho copies are less likely to persist in the genome, consistent with selection against the deleterious effects of ectopic recombination between Basho elements. Furthermore, we determined that 39% of Basho elements contain fragments of expressed protein-coding genes, but all of these fragments were explained by only 5 gene-capture events. Overall, the picture of A. thaliana Helitron evolution is one of rapid expansion, relatively few gene-capture events, and weak selection correlated with element length.     

Population dynamics and evolutionary processes: the manifold roles of habitat selection

Summary Any character that has a substantial effect on a species' distribution and abundance can exert a variety of indirect effects on evolutionary processes. It is suggested that an organism's capacity for habitat selection is just such a character. Habitat selection can constrain the selective environment experienced by a population. Habitat selection can also indirectly influence the relative importance of natural selection, drift, and gene flow, through its effect on population size and growth rate. In many circumstances (but not all), habitat selection increases population size and growth rate, and thereby makes selection in a local environment more effective than drift and gene flow.     

Population structure inhibits evolutionary diversification under competition for resources

A model is presented that explores how population structure affects the evolutionary outcome of ecological competition for resources. The model assumes that competition for resources occurs within groups of a finite number of individuals (interaction groups), and that limited dispersal of individuals between groups (according to Wright's island model of population structure) results in genetic structuring of the population. It is found that both finite-sized interaction groups and limited dispersal can have substantial effects on the evolution of resource exploitation strategies as compared to models with a single, infinitely large, well-mixed interaction group. Both effects, in general, tend to select for less aggressive competitive strategies. Moreover, both effects also tend to reduce the likelihood of the evolutionary diversification of resource exploitation strategies that often occurs in models of resource competition with infinite populations. The results are discussed in the context of theories of the evolutionary diversification of resource exploitation strategies and speciation.     

濒危植物连香树种群结构与动态研究

以空间代替时间的方法调查了喇叭河自然保护区和宝兴县两个地区连香树种群的结构.绘制大小结构图,编制静态生命表,绘制存活曲线、消失率曲线和死亡率曲线,并进行种群动态谱分析.结果表明:两个地区连香树种群幼苗个体比例都比较大,但死亡率很高;存活曲线介于Deevey Ⅰ型和DeeveyⅡ型之间;消失率和死亡率曲线变化趋势一致;种群动态过程存在周期性,种群数量动态不仅受基波的影响,而且还显示出了小周期的波动.     

Population dynamics of nitrifying bacteria in an aquatic ecosystem.

In a space environment such as Space Shuttle or Space Station, animal experiments with aquatic species in a closed system pose a crucial problem in maintaining their water quality for a long term. In nature, ammonia as an animal wastes is converted by nitrifying bacteria to nitrite or nitrate compounds, which usually become nitrogen sources for plants. Thus an application of the biological reactor with such bacteria attached on some filters has been suggested and experimentally studied for efficient waste managements of ammonia. Although some successful results were reported (Kozu et al. 1995, Nagaoka et al. 1998, Nakamura et al. 1997, 1998) in the space applications, purely empirical approaches have so far been taken to develop a biological filter having a stable nitrifying activity. In this study, we constructed a mathematical model to deal with the dynamics of the ammonia nitrifying processes in a biological reactor. The model describes population dynamics of the ammonia-oxidizing bacteria and the nitrite-oxidizing bacteria cultivated on the same filter. We estimated parameters involved in the model using the experimental data. The result shows that these estimated parameters could be applied to general cases and that the two bacteria are in a symbiotic relationship; they can better perform when both coexist, as has been empirically recognized. Based on the model analysis, we discuss how to prepare a high performance biological filter.     

Population dynamics of type I and II methanotrophic bacteria in rice soils

Methane-oxidizing bacteria (methanotrophs) consume a significant but variable fraction of greenhouse-active methane gas produced in wetlands and rice paddies before it can be emitted to the atmosphere. Temporal and spatial dynamics of methanotroph populations in California rice paddies were quantified using phospholipid biomarker analyses in order to evaluate the relative importance of type I and type II methanotrophs with depth and in relation to rice roots. Methanotroph population fluctuations occurred primarily within the top 0-2 cm of soil, where methanotroph cells increased by a factor of 3-5 over the flooded rice-growing season. The results indicate that rice roots and rhizospheres were less important than the soil-water interface in supporting methanotroph growth. Both type I and type II methanotrophs were abundant throughout the year. However, only type II populations were strongly correlated with soil porewater methane concentrations and rice growth.     

Population structure and dynamics of the clonal dwarf-shrub Linnaea borealis

Abstract. The demography of the long-lived clonal dwarf-shrub Linnaea borealis was studied during four years in a coniferous forest in central Sweden. The main object was to infer patterns of temporal variation in population dynamics of this species. The shoot population is organized in fragments, i.e. physically connected systems of shoots partly covered by the moss carpet. The age and size structure of the fragment population is described, but shoots are more convenient units for a study of population dynamics. A stochastic model of shoot population dynamics was constructed, and simulations indicated a considerable temporal variation in population size and flowering. Hence, variability as such is an essential aspect of the dynamics of established populations of Linnaea. Simulations of extinction risks revealed that small-sized shoot populations (ca. 250 shoots) are likely to be long-lived when experiencing environmentally induced demographic variation of the range observed. Mortality agents for established genets, such as large-scale disturbances, were not incorporated in the models. Some implications of variable population growth rates in clonal plants in woodlands are discussed.     

Multi-species evolutionary dynamics

Dynamical attainability of an evolutionarily stable strategy (ESS) through the process of mutations and natural selection has mostly been addressed through the use of the continuously stable strategy (CSS) concept for species evolutionary games in which strategies are drawn from a continuum, and by the adaptive trait dynamics method. We address the issue of dynamical attainability of an ESS in coevolving species through the use of the concept of an ESNIS. It is shown that the definition of an ESNIS coalition for coevolving species is not in general equivalent to other definitions for CSS given in the literature. We show under some additional conditions that, in a dynamic system which involves the strategies of a dimorphic ESNIS coalition and at most two strategies that are not members of ESNIS coalition, the ESNIS coalition will emerge as the winner. In addition an ESNIS will be approached because of the invasion structure of strategies in its neighborhood. This proves that under the above conditions an ESNIS has a better chance of being attained than a strategy coalition which is a CSS. The theory developed is applied to a class of coevolutionary game models with Lotka–Volterra type interactions and we show that for such models, an ESS coalition will be dynamically attainable through mutations and natural selection if the ESS coalition is also an ESNIS coalition.Co-ordinating editor: Metz     

The multiplication dynamics of pathogenic bacteria in relation to the trophic and temperature cultivation conditions

The comparative study of the dynamics of multiplication of Listeria monocytogenes and Yersinia pseudotuberculosis in organic and synthetic media and in distilled water at temperatures of 37 degrees C and 6 degrees C was carried out. This study revealed that in organic media the multiplication of bacteria was good at 37 degrees C and 6 degrees C. In mineral media and distilled water their multiplication was observed only at 6 degrees C. Moreover, conditions necessary for the multiplication of pathogenic bacteria in distilled water were shown; these conditions depended on the inoculated dose, the number of autolyzed microbial cells and the state of the culture. Proofs of the multiplication of the bacteria under the conditions of minimum nutrition and low temperature were obtained with the use of labeled 3H-thymidine.     

Population structure and dynamics of wood mouse Apodemus sylvaticus in Iceland

Five-year-studies of two wood mouse populations (Apodemus sylvaticus L.) were carried out outside the village Vík. S. Iceland, and in a birch forest close to the lake Mývatn, N. Iceland. The population at Vík was studied on a 1.10 ha grid on a slope covered with Angelica archangelica L., the seeds of which constituted a major food resource for the mice. Altogether 948 individuals were caught, marked and followed during 1973–1978. No other free-living small mammals occur in Iceland, and predator pressure is low and considered non-existent on the Angelica slope. The population density was extremely high; highest autumn density recorded was 150 ind ha^?1. Like other Apodemus populations, the one at Vík showed a typical seasonal pattern in numbers: a winter decrease, relatively stable numbers in late summer, and an autumn peak. Breeding started in late April or early May and ended in late September; no winter breeding was observed. Three or four litters were produced, and the last litter(s) of the season greatly contributed to the autumn increase. The output of young per reproductive female throughout the year was negatively correlated with spring density, and autumn peak density with the number of females in August. Also overwinter success and weight changes appeared to be associated with population density (and weather). Survival rates did not vary much between years and seasons and were consistently rather high. Autumn survival of juveniles was positively correlated with mean minimum temperatures. Juvenile survival was, at least at times, negatively affected by the presence of adult males. Trapping outside the main grid did not indicate any marked dispersal, though some immigration to the grid must have occurred, especially in spring and early summer. Among the factors governing the population density and dynamics of wood mouse at Vík we emphasize the absence of interspecific competition and predation, the rich and dependable food resources (mainly Angelica seeds), the mild (though moist and windy) climate, the shelter of dense Angelica stands, the abundance of crevices (e.g. nest-sites), and the social interactions. The birch forest in northern Iceland was low productive and the wood mouse population differed from the Vík population by exhibiting low density, short breeding season, and high vagility; characteristics we consider to be representative for most Apodemus populations in Iceland.     

秦岭巴山冷杉(Abies fargesii)种群结构与动态

为了阐明秦岭巴山冷杉(Abies fargesii)种群的结构特征和动态规律,对位于秦岭中段南坡佛坪保护区内不同海拔分布的巴山冷杉种群的年龄结构、生命表以及存活曲线等进行了研究.结果表明: 在海拔2350、2500和2700 m,巴山冷杉种群都表现为衰退型,种群个体主要聚集在中龄级,幼龄级的个体都极度缺乏.在各海拔巴山冷杉种群生命表中,死亡量(dx)、死亡率(qx)和消失率(Kx)都为负值,反映了种群幼龄个体的缺乏程度.随着海拔的升高,幼龄级个体数量增加而大龄级个体数量减少.巴山冷杉种群生命表和存活曲线的分析表明,巴山冷杉种群个体存活量最多的年龄级和出现最大死亡率的年龄级都随着海拔的降低而依次后推.随着海拔的升高,巴山冷杉种群的分布格局由随机分布类型过渡为聚集分布类型.     

麦田捕食性昆虫群落、结构与动态研究

【目的】探究小麦捕食性昆虫群落结构以及动态规律,为小麦害虫的生物防治提供科学依据。【方法】试验采用了网捕法、陷阱法、黄盘法和马氏网法定期采集地表、小麦植株上的捕食性昆虫,并将其带回实验室进行鉴定、计数和数据分析。【结果】两年共采集捕食性昆虫1 479头,属于4目7科22种,其中龟纹瓢虫Propylaea japonica(Thunberg,1781)为优势种;小麦拔节期之前几乎没有捕食性昆虫,抽穗期和扬花期捕食性昆虫个体数和物种数逐渐增加,灌浆期和乳熟期物种数继续增加、个体数则迅速增多;捕食性昆虫群落的Shannon-wiener多样性指数H′、均匀度指数E,均随时间整体呈现低-高-低-高的变化趋势,而优势集中性指数C和优势度B则整体呈现高-低-高-低的变化趋势。【结论】该研究结果对小麦害虫的生物防治具有指导意义。     

Functional genomics of pathogenic bacteria

Microbial diseases remain the commonest cause of global mortality and morbidity. Automated-DNA sequencing has revolutionized the investigation of pathogenic microbes by making the immense fund of information contained in their genomes available at reasonable cost. The challenge is how this information can be used to increase current understanding of the biology of commensal and virulence behaviour of pathogens with particular emphasis on in vivo function and novel approaches to prevention. One example of the application of whole-genome-sequence information is afforded by investigations of the pathogenic role of Haemophilus influenzae lipopolysaccharide and its candidacy as a vaccine.     

Evolutionary genomics of pathogenic bacteria

Complete genome sequences are now available for multiple strains of several bacterial pathogens and comparative analysis of these sequences is providing important insights into the evolution of bacterial virulence. Recently, DNA microarray analysis of many strains of several pathogenic species has contributed to our understanding of bacterial diversity, evolution and pathogenesis. Comparative genomics has shown that pathogens such as Escherichia coli, Helicobacter pylori and Staphylococcus aureus contain extensive variation in gene content whereas Mycobacterium tuberculosis nucleotide divergence is very limited. Overall, these approaches are proving to be a powerful means of exploring bacterial diversity, and are providing an important framework for the analysis of the evolution of pathogenesis and the development of novel antimicrobial agents.     

IgA-specific proteins of pathogenic bacteria

Data on structure and specificity of bacterial IgA receptors (IgA-binding M-like proteins Arp4 and Sir22 from hemolytic streptococci of serogroup A, β-antigen from hemolytic streptococci of serogroup B, and SSL family proteins from Staphylococcus aureus) are surveyed in this review. The principal conclusion derived from comparison is the fact that all bacterial receptors bind the same site in the IgA molecule overlapping with the binding site of endogenous human IgA receptor CD89. We assume that this site, consisting of spatially close amino acid strands Leu257-Gly259 in domain Cα2 and Pro440-Phe443 in domain Cα3, is subject to conformational rearrangement induced by the binding of antigen in the IgA active site.