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.     

Population and evolutionary dynamics in spatially structured seasonally varying environments

Increasingly imperative objectives in ecology are to understand and forecast population dynamic and evolutionary responses to seasonal environmental variation and change. Such population and evolutionary dynamics result from immediate and lagged responses of all key life‐history traits, and resulting demographic rates that affect population growth rate, to seasonal environmental conditions and population density. However, existing population dynamic and eco‐evolutionary theory and models have not yet fully encompassed within‐individual and among‐individual variation, covariation, structure and heterogeneity, and ongoing evolution, in a critical life‐history trait that allows individuals to respond to seasonal environmental conditions: seasonal migration. Meanwhile, empirical studies aided by new animal‐tracking technologies are increasingly demonstrating substantial within‐population variation in the occurrence and form of migration versus year‐round residence, generating diverse forms of ‘partial migration’ spanning diverse species, habitats and spatial scales. Such partially migratory systems form a continuum between the extreme scenarios of full migration and full year‐round residence, and are commonplace in nature. Here, we first review basic scenarios of partial migration and associated models designed to identify conditions that facilitate the maintenance of migratory polymorphism. We highlight that such models have been fundamental to the development of partial migration theory, but are spatially and demographically simplistic compared to the rich bodies of population dynamic theory and models that consider spatially structured populations with dispersal but no migration, or consider populations experiencing strong seasonality and full obligate migration. Second, to provide an overarching conceptual framework for spatio‐temporal population dynamics, we define a ‘partially migratory meta‐population’ system as a spatially structured set of locations that can be occupied by different sets of resident and migrant individuals in different seasons, and where locations that can support reproduction can also be linked by dispersal. We outline key forms of within‐individual and among‐individual variation and structure in migration that could arise within such systems and interact with variation in individual survival, reproduction and dispersal to create complex population dynamics and evolutionary responses across locations, seasons, years and generations. Third, we review approaches by which population dynamic and eco‐evolutionary models could be developed to test hypotheses regarding the dynamics and persistence of partially migratory meta‐populations given diverse forms of seasonal environmental variation and change, and to forecast system‐specific dynamics. To demonstrate one such approach, we use an evolutionary individual‐based model to illustrate that multiple forms of partial migration can readily co‐exist in a simple spatially structured landscape. Finally, we summarise recent empirical studies that demonstrate key components of demographic structure in partial migration, and demonstrate diverse associations with reproduction and survival. We thereby identify key theoretical and empirical knowledge gaps that remain, and consider multiple complementary approaches by which these gaps can be filled in order to elucidate population dynamic and eco‐evolutionary responses to spatio‐temporal seasonal environmental variation and change.     

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 dynamics of bacteria in Arctic sea ice

The dynamics of bacterial populations in annual sea ice were measured throughout the vernal bloom of ice algae near Resolute in the Canadian Arctic. The maximum concentration of bacteria was 6.0·10¹¹ cells·m^–2 (about 2.0·10¹⁰ cells·l^–1) and average cell volume was 0.473 m³ in the lower 4 cm of the ice sheet. On average, 37% of the bacteria were epiphytic and were most commonly attached (70%) to the dominant alga,Nitzschia frigida (58% of total algal numbers). Bacterial population dynamics appeared exponential, and specific growth rates were higher in the early season (0.058 day^–1), when algal biomass was increasing, than in the later season (0.0247 day^–1), when algal biomass was declining. The proportion of epiphytes and the average number of epiphytes per alga increased significantly (P<0.05) through the course of the algal bloom. The net production of bacteria was 67.1 mgC·m^–2 throughout the algal bloom period, of which 45.5 mgC·m^–2 occurred during the phase of declining algal biomass. Net algal production was 1942 mgC·m^–2. Sea ice bacteria (both arctic and antarctic) are more abundant than expected on the basis of relationships between bacterioplankton and chlorophyll concentrations in temperate waters, but ice bacteria biomass and net production are nonetheless small compared with the ice algal blooms that presumably support them.     

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.     

Mitochondrial dynamics in the pathogenic mold Aspergillus fumigatus: therapeutic and evolutionary implications

Mitochondria within eukaryotic cells continuously fuse and divide. This phenomenon is called mitochondrial dynamics and crucial for mitochondrial function and integrity. We performed a comprehensive analysis of mitochondrial dynamics in the pathogenic mold Aspergillus fumigatus. Phenotypic characterization of respective mutants revealed the general essentiality of mitochondrial fusion for mitochondrial genome maintenance and the mold's viability. Surprisingly, it turned out that the mitochondrial rhomboid protease Pcp1 and its processing product, s‐Mgm,1 which are crucial for fusion in yeast, are dispensable for fusion, mtDNA maintenance and viability in A. fumigatus. In contrast, mitochondrial fission mutants show drastically reduced growth and sporulation rates and increased heat susceptibility. However, reliable inheritance of mitochondria to newly formed conidia is ensured. Strikingly, mitochondrial fission mutants show a significant and growth condition‐dependent increase in azole resistance. Parallel disruption of fusion in a fission mutant partially rescues growth and sporulation defects and further increases the azole resistance phenotype. Taken together, our results indicate an emerging dispensability of the mitochondrial rhomboid protease function in mitochondrial fusion, the suitability of mitochondrial fusion machinery as antifungal target and the involvement of mitochondrial dynamics in azole susceptibility.     

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.     

Rapid evolutionary adaptation to elevated salt concentrations in pathogenic freshwater bacteria Serratia marcescens

Rapid evolutionary adaptions to new and previously detrimental environmental conditions can increase the risk of invasion by novel pathogens. We tested this hypothesis with a 133‐day‐long evolutionary experiment studying the evolution of the pathogenic Serratia marcescens bacterium at salinity niche boundary and in fluctuating conditions. We found that S. marcescens evolved at harsh (80 g/L) and extreme (100 g/L) salt conditions had clearly improved salt tolerance than those evolved in the other three treatments (ancestral conditions, nonsaline conditions, and fluctuating salt conditions). Evolutionary theories suggest that fastest evolutionary changes could be observed in intermediate selection pressures. Therefore, we originally hypothesized that extreme conditions, such as our 100 g/L salinity treatment, could lead to slower adaptation due to low population sizes. However, no evolutionary differences were observed between populations evolved in harsh and extreme conditions. This suggests that in the study presented here, low population sizes did not prevent evolution in the long run. On the whole, the adaptive potential observed here could be important for the transition of pathogenic S. marcescens bacteria from human‐impacted freshwater environments, such as wastewater treatment plants, to marine habitats, where they are known to infect and kill corals (e.g., through white pox disease).     

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.     

水稻体内细菌的动态研究

经过对水稻两品种(沈农319、中百4号)不同时期、不同组织内生细菌动态变化研究结果表明,根组织带菌量最高,其次是叶,茎最低。发育阶段以孕穗期带菌量显着增高,随着组织衰老而降低。对分离到的4个主要种群显着性检验结果表明,巨大芽孢杆菌为两品种体内细菌优势种。通过对水稻这一世界性粮食作物体内细菌的种类,以及随生育期、组织间菌体数量变化的探讨研究,为水稻害虫的生物防治,提供遗传改良工程杀虫细菌的有效载体菌。     

水稻体内细菌的动态研究

经过对水稻两品种（ 沈农３１９ 、中百４ 号） 不同时期、不同组织内生细菌动态变化研究结果表明,根组织带菌量最高,其次是叶,茎最低．发育阶段以孕穗期带菌量显著增高,随着组织衰老而降低．对分离到的４ 个主要种群显著性检验结果表明,巨大芽孢杆菌为两品种体内细菌优势种．通过对水稻这一世界性粮食作物体内细菌的种类,以及随生育期、组织间菌体数量变化的探讨研究,为水稻害虫的生物防治,提供遗传改良工程杀虫细菌的有效载体菌．     

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.     

濒危树种五莲杨种群结构与动态特征

五莲杨（Populus wulianensis）为山东特有种,属于极小种群野生植物。以昆嵛山国家级自然保护区内的五莲杨种群为研究对象,旨在通过建立静态生命表,绘制种群存活曲线来描述其种群的结构特征,使用4个生存函数进行种群的生存分析,运用数量动态指数定量描述种群的数量动态特征,并采用谱分析方法揭示种群年龄结构更替过程的周期性和结构的波动性。结果表明：（1）五莲杨种群龄级结构呈基部极宽顶部狭窄的金字塔形,种群存活曲线趋近于Deevey-Ⅲ型,幼龄个体数量丰富但存活率极低,种群增长性低;（2）死亡率和消失率曲线呈现"降低-增长-降低-增长"的复杂动态变化,种群在Ⅰ龄级死亡率最高;（3）生存分析表明该种群生存力低,具有前期锐减,中期和后期衰退的特点,呈现衰退特征;（4）种群数量动态指数显示种群呈增长趋势,但种群稳定性差且抗干扰能力弱;（5）谱分析表明该种群除受到基波影响外还受到个别小周期波动的显著影响。繁殖策略、有限的空间和资源是限制五莲杨种群增长的主要因素。建议对五莲杨种群进行原地保护的同时,通过输入实生苗防止种群在多个世代后因无性繁殖而导致抗性和遗传多样性降低。     

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.     

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.