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PubMed2005

Patterns and localized structures in population dynamics.

Patterns, fronts, and localized structures of a prototypical model for population dynamics interaction are studied. The physical content of the model is the coexistence of a simple random walk for the motion of the individuals with a nonlinearity in the competitive struggle for resources which simultaneously stresses the Allee effect and interaction at a distance. Mathematically, the model is variational and exhibits coexistence between different stable extended states. Solutions are obtained, the phase diagram is constructed, and the emergence of localized structures is investigated.

Biophysics↗

PubMed2006

Characterizing population dynamics of Aedes sollicitans (Diptera: Culicidae) using meteorological data.

Numerous studies have investigated the role of weather on insect species. For mosquitoes, these studies have yielded mixed results. Although it is clear that weather impacts mosquito population dynamics, these investigations have failed to accurately characterize their fluctuations. We use a novel graphical method to examine large numbers of meteorological aggregations of varying lengths and lags simultaneously to establish relationships between these summary variables and mosquito counts, to gain a better understanding of the weather effects. Poisson regression models were developed to characterize the population dynamics of Aedes sollicitans (Walker) by using meteorological data and a 34-yr set of daily mosquito count data. The models accurately characterize mosquito dynamics over time and space. The aggregated meteorological variables included in the model were lowest minimum tides between days 27 and 14 before trapping, total precipitation between days 22 and 9, total precipitation on day 1 and the day of trapping, cooling degree-days on day 0, average minimum relative humidity between days 28 and 9, lowest stream flow from day 11 to day 0, and lowest minimum temperature between days 28 and 13.

Aedes↗

PubMed2005

Population dynamics of weeds in no-tillage and conventional crop systems.

Population dynamics of weeds in successive maize and bean crops were evaluated in two soil management systems (conventional and no-tillage), for two maize applications (grain and silage), and in four consecutive growing seasons. Every year, conventional tillage consisted in plowing and harrowing before sowing. In no-tillage, chemical weed desiccation was made with the mixture glyphosate + 2.4-D. To control weeds, the mixture fluazifop-p-butil + fomesafen was applied on the bean crop in all the planting seasons, and the herbicides nicosulfuron + atrazine on maize after crop emergence (1998--1999, 1999--2000, 2001--2002) and atrazine + metolachlor before emergence (2000--2001). Purple nutsedge (Cyperus rotundus) was the most important species under conventional soil tillage; while in no-tillage the dicotyledonous weed species (Amaranthus deflexus, Bidens pilosa, Euphorbia heterophylla, Galinsoga parviflora Ipomoea grandifolia) were the most relevant. Regardless of the maize use, the C. rotundus population and tuber bank, with prevailingly dormant tubers, was considerably reduced in no-tillage compared with the conventional system.

Agriculture↗

PubMed2004

Periodically varying externally imposed environmental effects on population dynamics.

Effects of externally imposed periodic changes in the environment on population dynamics are studied with the help of a simple model. The environmental changes are represented by the temporal and spatial dependence of the competition terms in a standard equation of evolution. Possible applications of the analysis are on the one hand to bacteria in Petri dishes and on the other to rodents in the context of the spread of the Hantavirus epidemic. The analysis shows that spatiotemporal structures emerge, with interesting features which depend on the interplay of separately controllable aspects of the externally imposed environmental changes.

Animals↗

PubMed1998

Population dynamics of phenol-degrading bacteria in activated sludge determined by gyrB-targeted quantitative PCR.

A method for quantifying bacterial populations introduced into an activated-sludge microbial community is described. The method involves extraction of DNA from activated sludge, appropriate dilution of the extracted DNA with DNA extracted from nonintroduced activated sludge, PCR amplification of a gyrB gene fragment from the introduced strain with a set of strain-specific primers, and quantification of the electrophoresed PCR product by densitometry. The adequacy of the method was examined by analyzing the population dynamics of two phenol-degrading bacteria, Pseudomonas putida BH and Comamonas sp. strain E6, that had been introduced into phenol-digesting activated sludge. The density of each of the two populations determined by the PCR method immediately after the introduction was consistent with the density estimated from a plate count of the inoculum. This quantitative PCR method revealed different population dynamics for the two strains in the activated sludge under different phenol-loading conditions. The behavior of both of these strains in the activated sludge reflected the growth kinetics of the strains determined in laboratory axenic cultures.

Base Sequence↗

PubMed1996

Spatially explicit models for the population dynamics of a species colonizing an island.

We construct reaction-diffusion models for the population dynamics of a species colonizing an island from a source population on a continent. We view the source population as inducing a density or flux of immigrants onto the island and interpret colonization as succeeding if the population on the island is predicted to persist even when immigration from the continent is stopped. To capture the observation that a sufficiently large population or density must be attained for colonization to succeed, we assume Allee (i.e., bistable) dynamics rather than logistic dynamics for the colonizing population. We consider the cases of colonization in both the absence and presence of a competitor. We use reaction-diffusion theory, especially comparison methods and sub- and supersolutions, to determine how parameters such as the distance from the continent to the island and the dispersal, birth and mortality rates, carrying capacity, and minimum viable population density of the colonizing species affect the outcome of the attempted colonization. In the case of colonization in the presence of a competitor we consider a number of scenarios involving different types and strengths of competition. Our analysis permits us to draw conclusions about the characteristics of a species that make it a good colonizer.

Animals↗

PubMed1999

Spatial population dynamics: analyzing patterns and processes of population synchrony.

The search for mechanisms behind spatial population synchrony is currently a major issue in population ecology. Theoretical studies highlight how synchronizing mechanisms such as dispersal, regionally correlated climatic variables and mobile enemies might interact with local dynamics to produce different patterns of spatial covariance. Specialized statistical methods, applied to large-scale survey data, aid in testing the theoretical predictions with empirical estimates. Observational studies and experiments on the demography of local populations are paramount to identify the true ecological mechanisms. The recent achievements illustrate the power of combining theory, observation and/or experimentation and statistical modeling in the ecological research protocol.

Journal Article↗

PubMed2006

Population dynamics and in situ kinetics of nitrifying bacteria in autotrophic nitrifying biofilms as determined by real-time quantitative PCR.

Population dynamics of ammonia-oxidizing bacteria (AOB) and uncultured Nitrospira-like nitrite-oxidizing bacteria (NOB) dominated in autotrophic nitrifying biofilms were determined by using real-time quantitative polymerase chain reaction (RTQ-PCR) and fluorescence in situ hybridization (FISH). Although two quantitative techniques gave the comparable results, the RTQ-PCR assay was easier and faster than the FISH technique for quantification of both nitrifying bacteria in dense microcolony-forming nitrifying biofilms. Using this RTQ-PCR assay, we could successfully determine the maximum specific growth rate (mu = 0.021/h) of uncultured Nitrospira-like NOB in the suspended enrichment culture. The population dynamics of nitrifying bacteria in the biofilm revealed that once they formed the biofilm, the both nitrifying bacteria grew slower than in planktonic cultures. We also calculated the spatial distributions of average specific growth rates of both nitrifying bacteria in the biofilm based on the concentration profiles of NH4+, NO2-, and O2, which were determined by microelectrodes, and the double-Monod model. This simple model estimation could explain the stratified spatial distribution of AOB and Nitrospira-like NOB in the biofilm. The combination of culture-independent molecular techniques and microelectrode measurements is a very powerful approach to analyze the in situ kinetics and ecophysiology of nitrifying bacteria including uncultured Nitrospira-like NOB in complex biofilm communities.

Bacteria↗

PubMed2006

Population dynamics of Bifidobacterium species in human feces during raffinose administration monitored by fluorescence in situ hybridization-flow cytometry.

The population dynamics of bifidobacteria in human feces during raffinose administration were investigated at the species level by using fluorescence in situ hybridization (FISH) coupled with flow cytometry (FCM) analysis. Although double-staining FISH-FCM using both fluorescein isothiocyanate (FITC) and indodicarbocyanine (Cy5) as labeling dyes for fecal samples has been reported, the analysis was interfered with by strong autofluorescence at the FITC fluorescence region because of the presence of autofluorescence particles/debris in the fecal samples. We circumvented this problem by using only Cy5 fluorescent dye in the FISH-FCM analysis. Thirteen subjects received 2 g of raffinose twice a day for 4 weeks. Fecal samples were collected, and the bifidobacterial populations were monitored using the established FISH-FCM method. The results showed an increase in bifidobacteria from about 12.5% of total bacteria in the prefeeding period to about 28.7 and 37.2% after the 2-week and 4-week feeding periods, respectively. Bifidobacterium adolescentis, the Bifidobacterium catenulatum group, and Bifidobacterium longum were the major species, in that order, at the prefeeding period, and these bacteria were found to increase nearly in parallel during the raffinose administration. During the feeding periods, indigenous bifidobacterial populations became more diverse, such that minor species in human adults, such as Bifidobacterium breve, Bifidobacterium bifidum, Bifidobacterium dentium, and Bifidobacterium angulatum, proliferated. Four weeks after raffinose administration was stopped, the proportion of each major bifidobacterial species, as well as that of total bifidobacteria, returned to approximately the original values for the prefeeding period, whereas that of each minor species appeared to differ considerably from its original value. To the best of our knowledge, these results provide the first clear demonstration of the population dynamics of indigenous bifidobacteria at the species level in response to raffinose administration.

Adult↗

PubMed2002

Phase-space transport of stochastic chaos in population dynamics of virus spread.

A general way to classify stochastic chaos is presented and applied to population dynamics models. A stochastic dynamical theory is used to develop an algorithmic tool to measure the transport across basin boundaries and predict the most probable regions of transport created by noise. The results of this tool are illustrated on a model of virus spread in a large population, where transport regions reveal how noise completes the necessary manifold intersections for the creation of emerging stochastic chaos.

Algorithms↗

PubMed2001

Demography and population dynamics of the mouse opossum (Thylamys elegans) in semi-arid Chile: seasonality, feedback structure and climate.

Here we present, to the authors' knowledge for the very first time for a small marsupial, a thorough analysis of the demography and population dynamics of the mouse opossum (Thylamys elegans) in western South America. We test the relative importance of feedback structure and climatic factors (rainfall and the Southern Oscillation Index) in explaining the temporal variation in the demography of the mouse opossum. The demographic information was incorporated into a stage-structured population dynamics model and the model's predictions were compared with observed patterns. The mouse opossum's capture rates showed seasonal (within-year) and between-year variability, with individuals having higher capture rates during late summer and autumn and lower capture rates during winter and spring. There was also a strong between-year effect on capture probabilities. The reproductive (the fraction of reproductively active individuals) and recruitment rates showed a clear seasonal and a between-year pattern of variation with the peak of reproductive activity occuring during winter and early spring. In addition, the fraction of reproductive individuals was positively related to annual rainfall, while population density and annual rainfall positively influenced the recruitment rate. The survival rates were negatively related to annual rainfall. The average finite population growth rate during the study period was estimated to be 1.011 +/- 0.0019 from capture-recapture estimates. While the annual growth rate estimated from the seasonal linear matrix models was 1.026, the subadult and adult survival and maturation rates represent between 54% (winter) and 81% (summer) of the impact on the annual growth rate.

Animals↗

PubMed2004

Modeling the population dynamics of Culex quinquefasciatus (Diptera: Culicidae), along an elevational gradient in Hawaii.

We present a population model to understand the effects of temperature and rainfall on the population dynamics of the southern house mosquito, Culex quinquefasciatus Say, along an elevational gradient in Hawaii. We use a novel approach to model the effects of temperature on population growth by dynamically incorporating developmental rate into the transition matrix, by using physiological ages of immatures instead of chronological age or stages. We also model the effects of rainfall on survival of immatures as the cumulative number of days below a certain rain threshold. Finally, we incorporate density dependence into the model as competition between immatures within breeding sites. Our model predicts the upper altitudinal distributions of Cx. quinquefasciatus on the Big Island of Hawaii for self-sustaining mosquito and migrating summer sink populations at 1,475 and 1,715 m above sea level, respectively. Our model predicts that mosquitoes at lower elevations can grow under a broader range of rainfall parameters than middle and high elevation populations. Density dependence in conjunction with the seasonal forcing imposed by temperature and rain creates cycles in the dynamics of the population that peak in the summer and early fall. The model provides a reasonable fit to the available data on mosquito abundance for the east side of Mauna Loa, Hawaii. The predictions of our model indicate the importance of abiotic conditions on mosquito dynamics and have important implications for the management of diseases transmitted by Cx. quinquefasciatus in Hawaii and elsewhere.

Altitude↗

PubMed2001

Population dynamics of Pythium aphanidermatum in cucumber grown in closed systems.

Foot and root rot in cucumber, caused by Pythium aphanidermatum (Edson) Fitzp., is an economically important disease in soilless culture systems. Nevertheless, very few data are available on the populations of this pathogen. Therefore, two detection methods, nested PCR (polymerase chain reaction) and plating on a selective medium after concentration of samples, were optimised and evaluated. With both methods very low concentrations of P. aphanidermatum could be detected; i.e. the detection limits were around 0.05 CFU/ml nutrient solution. In addition, real-time quantitative PCR using a Molecular Beacon probe was designed and tested. The potential and limitations of the different detection methods are discussed. With these different detection techniques, the population dynamics of P. aphanidermatum in a cucumber crop was followed. The impact of different disinfection treatments was studied in a greenhouse experiment with a cucumber crop growing on rockwool slabs in 12 independent closed systems. The nutrient solution was recirculated without disinfection (control), after UV-irradiation (250 mJ/cm2), or after slow sand filtration treatment. Part of the crop was inoculated with an isolate of P. aphanidermatum. The non-inoculated part could only become infected through the recirculated nutrient solution. Disease symptoms (stem rot, wilt, and root rot) and the yield loss were recorded in addition to the population dynamics of the pathogen. Very clear differences in the spread of the pathogen and in disease symptoms were measured between the systems with and without disinfection. UV-irradiation and slow sand filtration were both effective in removing the pathogen and protected the crop from disease symptoms. Correlation indices between the final yield and the different measurements during the experiment were calculated.

Colony Count, Microbial↗

PubMed1997

A dynamic population model incorporating a variety of urban functions.

"This paper aims to investigate the theoretical background of Allen and Sanglier's model, slightly modifying it. We construct a dynamic two-city population model in which there are different types of urban functions in the cities. Population dynamics of both cities are expressed in terms of a system of differential equations of the logistic type, taking account of spatial interaction between them. For this model, both the existence condition and the globally asymptotic stability of the equilibrium state are theoretically explored. Then configurations of equilibrium population distribution that correspond to different combinations of the numbers of types of urban functions in two cities are also examined. Finally, some numerical simulations are done in order to supplement the theoretical considerations."

Demography↗

PubMed1998

Phase- and density-dependent population dynamics in Norwegian lemmings: interaction between deterministic and stochastic processes.

We analysed two 26-year long (1970-1995) time-series on annual population growth rates of Norwegian lemmings (Lemmus lemmus) from Finse, south Norway, using a threshold autoregressive (TAR) approach. We demonstrate that the population dynamics is both phase- and density-dependent. The phase-dependence accounts for the observed nonlinearity. We used the deduced stochastic model structure as a basis for evaluating the dynamic properties of this system. The dynamics is characterized either by limit cycles or chaos (the latter with a strong semi-periodic component). Stochasticity is seen to play an important role in the determination of the periodicity. The ecological implications of these statistical and mathematical results are discussed.

Animals↗

PubMed2005

Prevalence, intensity and aggregation of intestinal parasites in mountain hares and their potential impact on population dynamics.

Mountain hare Lepus timidus populations show unstable dynamics and since hares carry a significant helminth infection and host-parasite interactions are known to be destabilising, they have been proposed as a possible causal mechanism for the observed instability. We assessed the prevalence, intensity of infection and aggregation of the helminth parasites Graphidium strigosum and Trichostrongylus retortaeformis recovered from 589 mountain hares culled from 30 Scottish sporting estates in 1999 and 2000. Graphidium strigosum showed low prevalence and intensity of infection and was highly aggregated. In contrast, T. retortaeformis showed high prevalence and intensity of infection and a low degree of aggregation. Differences in body condition of the hares were best explained by a model including sex and month of collection and interaction terms for sex-month and intensity of infection of T. retortaeformis-month. The low degree of aggregation of T. retortaeformis and the significant negative effect of intensity of infection on body condition are in accordance with the hypothesis that the host-parasite interaction is the causative destabilising mechanism for mountain hare dynamics.

Animals↗

PubMed1987

Population dynamics of Pomphorhynchus bulbocolli in Gammarus pseudolimnaeus.

The population dynamics of larval Pomphorhynchus bulbocolli were studied in the amphipod intermediate host, Gammarus pseudolimnaeus. Amphipods were collected monthly from April 1982 to March 1983 from a study site at the West Fork of Drake's Creek, Simpson Co., Kentucky. The number of infected amphipods per m2 was lowest (0.6) in May and highest (27.3) in November. A total of 2,502 amphipods was examined; 1,575 (62.9%) were infected with P. bulbocolli. Infection intensity ranged from 1 to 12 with a mean of 1.83 +/- 0.03. Single and multiple worm infections were found in 800 (50.8%) and 775 (49.2%) amphipods, respectively. Female amphipods had higher prevalence and intensity of infections than males but differences were not significant. Prevalence in the monthly samples was lowest in May (5.1%) and highest in October (88.1%). The monthly mean intensity of infection was lowest in July (1.10 +/- 0.04) and highest in November (2.02 +/- 0.08). Amphipods in length classes 3 through 15 were infected with P. bulbocolli. In late summer and fall, amphipods in all length classes were infected, while in late winter and spring only large amphipods were infected. Recruitment of P. bulbocolli into amphipods was seasonal and the total infrapopulation within an amphipod was usually acquired at one time. There was little correlation between size and number of larvae present.

Acanthocephala↗

PubMed2006

Application of fluorescence in situ hybridisation (FISH) to the analysis of yeast population dynamics in winery and laboratory grape must fermentations.

To analyse the yeast population diversity during wine fermentations, specific fluorescein-labelled oligonucleotide probes targeted to the D1/D2 region of the 26S rRNA of different yeast species known to occur frequently in this environment were designed and tested with reference strains. The probes were then used to identify wine must isolates and to follow, in combination with plate counts, the evolution of yeast populations in two winery fermentations of white and red grape musts. In both cases, a high diversity of non-Saccharomyces yeast species was detected, including Candida stellata, Hanseniaspora uvarum, H. guilliermondii, Kluyveromyces marxianus, K. thermotolerans and Torulaspora delbrueckii. Some of these species (e.g., K. marxianus, K. thermotolerans and T. delbrueckii) were present in significant amounts during the tumultuous fermentation stage, despite the predominance of Saccharomyces cerevisiae cells following the inoculation of the wine musts with a starter strain. To further clarify the yeast population dynamics at the late phase of the fermentations, and because winery conditions do not allow a reliable control of experimental variables, strains isolated from the industrial musts were used to conduct two laboratory microvinifications in synthetic grape juice, using different ratios of S. cerevisiae/non-Saccharomyces in the inocula. Under these conditions, the results were similar to those obtained in the winery, showing a yeast profile with mixed species throughout the first fermentation stage, i.e. until about 40-50% of the total sugar was consumed. Non-Saccharomyces yeasts were outgrown by S. cerevisiae only after ethanol reached concentrations around 4-5% (v/v), which argues in favour of a potential important role of non-Saccharomyces in the final organoleptic characteristics of the wine.

Coculture Techniques↗