Dynamics of human populations

This study expands on earlier findings of racial/ethnic and education–allostatic load associations by assessing whether racial/ethnic differences in allostatic load persist across all levels of educational attainment. This study used data from four recent waves of the National Health and Nutrition Survey (NHANES). Results from this study suggest that allostatic load differs significantly by race/ethnicity and educational attainment overall, but that the race/ethnicity association is not consistent across education level. Analysis of interactions and education-stratified models suggest that allostatic load levels do not differ by race/ethnicity for individuals with low education; rather, the largest allostatic load differentials for Mexican Americans (p < .01) and non-Hispanic blacks (p < .001) are observed for individuals with a college degree or more. These findings add to the growing evidence that differences in socioeconomic opportunities by race/ethnicity are likely a consequence of differential returns to education, which contribute to higher stress burdens among minorities compared to non-Hispanic whites.     

Dynamics of natural rotifer populations

New tools for analyzing ecological time series have permitted the construction of rigorous models from relatively short series. We have applied these techniques to abundance data for nine natural rotifer populations to construct realistic models of their dynamics. Species included are Asplanchna girodi, Filinia pejleri, Keratella tropica, Monostyla bulla, Brachionus rotundiformis, and four other Brachionus species. The overall shapes of the time series were similar with an initial peak followed by oscillations of varying amplitude around a mean of lower population density. Auto correlation functions (ACF) for all populations were positive at small time lags and decayed rapidly to zero. This suggest that these are stationary, exponentially damped time series, fluctuating arround a constant mean with constant variance. The rapid decay of the ACFs indicates that the effect of a perturbation on these populations is quickly removed in one or two days. Phase portrait plots of log current population density vs log lagged density indicate that the time series are stable and non-chaotic. One type of model yielded the highest R² for four of the nine species and was designated the consensus model. The mean R² of this model for all nine species was 0.53 with a coefficient of variation of 38%. Lyapanov exponents were strongly negative, indicating that these populations rapidly return to equilibrium after an exogenous perturbation. Rotifer populations appear to be tracking very recent perturbations and their dynamics cannot be predicted from perturbations in the more distant past. We investigated the effects of increasing the level of stochasticity in the consensus model on the length of the growing season and resting egg production. Increasing stochastic variance increased the probability of extremely low population densities, shortening the growing season. In shorter growing seasons, fewer resting eggs were produced, other factors being equal. Counteracting this negative effect, was an increased probability of extremely high populations densities which increased mixis and resting egg production. Constructing models accurately depicting the dynamics of natural zooplankton populations should improve aquatic ecosystem models. This revised version was published online in July 2006 with corrections to the Cover Date.     

Mutation-selection balance in mixed mating populations

An approximation to the average number of deleterious mutations per gamete, Q, is derived from a model allowing selection on both zygotes and male gametes. Progeny are produced by either outcrossing or self-fertilization with fixed probabilities. The genetic model is a standard in evolutionary biology: mutations occur at unlinked loci, have equivalent effects, and combine multiplicatively to determine fitness. The approximation developed here treats individual mutation counts with a generalized Poisson model conditioned on the distribution of selfing histories in the population. The approximation is accurate across the range of parameter sets considered and provides both analytical insights and greatly increased computational speed. Model predictions are discussed in relation to several outstanding problems, including the estimation of the genomic deleterious mutation rates (U), the generality of "selective interference" among loci, and the consequences of gametic selection for the joint distribution of inbreeding depression and mating system across species. Finally, conflicting results from previous analytical treatments of mutation-selection balance are resolved to assumptions about the life-cycle and the initial fate of mutations.     

Dynamics of protein distributions in cell populations

A population of cells exhibits wide phenotypic variation even if it is genetically homogeneous. In particular, individual cells differ from one another in the amount of protein they express under a given regulatory system under fixed conditions. Here we study how protein distributions in a population of the yeast S. cerevisiae are shaped by a balance of processes: protein production--an intracellular process--and protein dilution due to cell division--a population process. We measure protein distributions by employing reporter green fluorescence protein (gfp) under the regulation of the yeast GAL system under conditions where it is metabolically essential. Cell populations are grown in chemostats, thus allowing control of the environment and stable measurements of distribution dynamics over many generations. Despite the essential functional role of the GAL system in a pure galactose medium, steady-state distributions are found to be universally broad, with exponential tails and a large standard-deviation-to-mean ratio. Under several different perturbations the dynamics of the distribution is observed to be asymmetric, with a much longer time to build a wide expression distribution from below compared with a fast relaxation of the distribution toward steady state from above. These results show that the main features of the protein distributions are largely determined by population effects and are less sensitive to the intracellular biochemical noise.     

Dynamics of genome rearrangement in bacterial populations

Genome structure variation has profound impacts on phenotype in organisms ranging from microbes to humans, yet little is known about how natural selection acts on genome arrangement. Pathogenic bacteria such as Yersinia pestis, which causes bubonic and pneumonic plague, often exhibit a high degree of genomic rearrangement. The recent availability of several Yersinia genomes offers an unprecedented opportunity to study the evolution of genome structure and arrangement. We introduce a set of statistical methods to study patterns of rearrangement in circular chromosomes and apply them to the Yersinia. We constructed a multiple alignment of eight Yersinia genomes using Mauve software to identify 78 conserved segments that are internally free from genome rearrangement. Based on the alignment, we applied Bayesian statistical methods to infer the phylogenetic inversion history of Yersinia. The sampling of genome arrangement reconstructions contains seven parsimonious tree topologies, each having different histories of 79 inversions. Topologies with a greater number of inversions also exist, but were sampled less frequently. The inversion phylogenies agree with results suggested by SNP patterns. We then analyzed reconstructed inversion histories to identify patterns of rearrangement. We confirm an over-representation of "symmetric inversions"-inversions with endpoints that are equally distant from the origin of chromosomal replication. Ancestral genome arrangements demonstrate moderate preference for replichore balance in Yersinia. We found that all inversions are shorter than expected under a neutral model, whereas inversions acting within a single replichore are much shorter than expected. We also found evidence for a canonical configuration of the origin and terminus of replication. Finally, breakpoint reuse analysis reveals that inversions with endpoints proximal to the origin of DNA replication are nearly three times more frequent. Our findings represent the first characterization of genome arrangement evolution in a bacterial population evolving outside laboratory conditions. Insight into the process of genomic rearrangement may further the understanding of pathogen population dynamics and selection on the architecture of circular bacterial chromosomes.     

Dynamics of size structure in plant populations

The size structure of populations is important for the study of the life histories and evolution of plant species. Many aspects of the dynamics of size structure as affected by species characteristics and environmental conditions have been interpreted well by recent models.     

Transposable element number in mixed mating populations

Theoretical population genetic studies of transposable elements focus almost exclusively on random mating species, whereas many plants reproduce through partial or substantial self-fertilization. Here I develop computer simulation and analytic approximations of simplified element dynamics (transposition balanced by selective elimination) in partially self-fertilizing populations, using Ty1-copia elements for biological inspiration. Under the most plausible models and parameter values, element numbers decrease with self-fertilization when element insertions are deleterious, but may increase when ectopic exchange regulates element number. Conclusions for models of ectopic exchange depend in part on parameters for which little firm empirical evidence is available. Small changes in selfing rate can lead to abrupt changes in element number when homozygous and heterozygous elements have markedly different fitness effects. Equilibrium element numbers can be sensitive to population size, especially at high selfing rates. Elements are frequently lost in small highly selfing populations under the deleterious insertion model. In contrast, small highly selfing populations can accumulate very large numbers of elements under ectopic exchange. Empirical data on element number and localization in plants with different mating systems suggests that deleterious insertion, rather than ectopic exchange, may regulate element number. Limitations to available empirical data, especially the lack of comparison between closely related species differing in mating system, mean that this conclusion is tentative.     

Dynamics of yeast metabolism and regulation

The dynamic behavior of yeasts is discussed on the basis of transient experiments, such as pulses and shifts in continuous culture, and of oscillating synchronized cultures. The minimal elements of a structured model are evaluated and extensions by regulatory mechanisms are proposed. Segregation of a population in cell classes reflecting the position of a cell in the cell cycle, its individual age, is shown to be necessary in order to account for the spontaneous synchronization of continuous S. cerevisisae cultures.     

Mechanisms controlling virulence thresholds of mixed viral populations

The propensity of RNA viruses to revert attenuating mutations contributes to disease and complicates vaccine development. Despite the presence of virulent revertant viruses in some live-attenuated vaccines, disease from vaccination is rare. This suggests that in mixed viral populations, attenuated viruses may limit the pathogenesis of virulent viruses, thus establishing a virulence threshold. Here we examined virulence thresholds using mixtures of virulent and attenuated viruses in a transgenic mouse model of poliovirus infection. We determined that a 1,000-fold excess of the attenuated Sabin strain of poliovirus was protective against disease induced by the virulent Mahoney strain. Protection was induced locally, and inactivated virus conferred protection. Treatment with a poliovirus receptor-blocking antibody phenocopied the protective effect of inactivated viruses in vitro and in vivo, suggesting that one mechanism controlling virulence thresholds may be competition for a viral receptor. Additionally, the type I interferon response reduces poliovirus pathogenesis; therefore, we examined virulence thresholds in mice lacking the alpha/beta interferon receptor. We found that the attenuated virus was virulent in immunodeficient mice due to the enhanced replication and reversion of attenuating mutations. Therefore, while the type I interferon response limits the virulence of the attenuated strain by reducing replication, protection from disease conferred by the attenuated strain in immunocompetent mice can occur independently of replication. Our results identified mechanisms controlling the virulence of mixed viral populations and indicate that live-attenuated vaccines containing virulent virus may be safe, as long as virulent viruses are present at levels below a critical threshold.     

混播草地不同种群再生性的研究

在不同刈割频率和时间尺度下 ,对混播草地多年生黑麦草 (Lolium perenne)分蘖数和叶片生长、白三叶 (Trifoliumrepens)分枝数和匍匐茎生长及不同种群年产量和组分进行了连续 3年的监测研究 .结果表明 ,刈割能刺激黑麦草叶片、白三叶匍匐茎生长和分枝数发生 ,保持混播草地黑麦草和白三叶的适宜比和稳定共存 ,提高草地年生产力 ,但不同刈割频率和刈割时间对其影响差异不显著 (P >0 .0 5 ) .黑麦草叶片生长对 6月刈割效果比 8月明显 ,而白三叶匍匐茎生长则与之相反 ,黑麦草产量主要取决于叶片生长 ,白三叶产量主要取决于匍匐茎分枝数 .刈割的黑麦草、白三叶产量组分比分别为 5 0 %、15 % ,比试验前约低 10 %、5 % ,而CK为 39%、6 % .     

Dynamics of populations on the verge of extinction

Theoretical considerations suggest that extinction in dispersal-limited populations is necessarily a threshold-like process that is analogous to a critical phase transition in physics. We use this analogy to find robust, common features in the dynamics of extinctions, and suggest early warning signals which may indicate that a population is endangered. As the critical threshold of extinction is approached, the population spontaneously fragments into discrete subpopulations and, consequently, density regulation fails. The population size declines and its spatial variance diverges according to scaling laws. Therefore, we can make robust predictions exactly in the range where prognosis is vital, on the verge of extinction.     

Dynamics of maturing populations and their asymptotic behaviour

Summary It is well known that the partial differential equation of the traditional model describing the dynamics of an age-dependent population is of the first order hyperbolic type. An equation of that type cannot simultaneously accommodate a renewal type birth boundary condition and a death boundary condition by old age (accumulation of aging injury) and thus lacks biological realism (mortality by old age). In this paper a governing equation of a parabolic type is derived to represent the expected size of a stochastically maturing population. Using techniques well known for the solution of parabolic partial differential and Volterra integral equations, the asymptotic behaviour of such a maturing population is discussed. Due to a non-local boundary condition, the boundary value problem encountered appears to be new.     

Dynamics of dsRNA mycoviruses in black Aspergillus populations

Approximately 10% of all examined 668 representatives of black Aspergillus species, independent of worldwide location, were infected with double-stranded RNA (dsRNA) mycoviruses. These isometric viruses (25-40 nm diameter) contained a variety of often multiple segments of different dsRNA sizes ranging from 0.8 to 4.4 kb in size. In one strain the virus shows clear visible effects on its host with non-sporulating sectors. We quantified the fitness costs of these and more 'cryptic' virus infections on mycelial growth rate and spore production, and on competitive ability with respect to other strains under different growth conditions. Mycovirus infection proved detrimental in all these measures. The reduced success in interference competition due to mycovirus infection belies co-evolution of mycovirus and host to a mutually beneficial symbiosis, like in killer virus systems in yeast and smut and agrees more to recent infections. For a stable virus infection frequency in the black Aspergillus population, fitness costs and spontaneous loss should be balanced with new infections. Implications of even small viral fitness effects combined with the observed transmission limits for host and mycovirus are discussed.     

Evolutionary stability in the dynamics of populations having short reproduction periods

A special class of models of competition (D-systems) were constructed in which the coefficients of population growth are periodic delta-functions. Effective methods for the analysis of the global dynamics of D-systems were proposed. In the framework of this model system, the problem of the existence of evolutionarily stable parameters, the periods of reproduction of populations in a variable medium, was studied. Using analytical methods and the data of computer-assisted experiments, open sets of evolutionarily stable parameters were found.