Population Structure Dynamics Research Articles

Population genetic structure and historical population dynamics of the South American sea lion, Otaria flavescens, in north-central Patagonia

The north-central Patagonian coast is the sea lions most abundant area in Argentina. As occurs along the entire Atlantic coast, the distribution of breeding colonies at this smaller geographical scale is also patchy, showing at least three areas with breeding activity. We study the genetic structure and historical population dynamics of the species in five colonies in this area, analysing a 508 base-pair segment of the D-loop control region. Otaria flavescens showed 10 haplotypes with 12 polymorphic sites. The genealogical relationship between haplotypes revealed a shallow pattern of phylogeographic structure. The analysis of molecular variance showed significant differences between colonies, however, pairwise comparisons only indicate significant differences between a pair of colonies belonging to different breeding areas. The pattern of haplotype differentiation and the mismatch distribution analysis suggest a possible bottleneck that would have occurred 64,000 years ago, followed by a demographic expansion of the three southernmost colonies. Thus, the historical population dynamics of O. flavescens in north-central Patagonia appears to be closely related with the dynamics of the Late Pleistocene glaciations.

Population and species boundaries in the South American subterranean rodent Ctenomys in a dynamic environment

Subterranean rodents of the genus Ctenomys are an interesting system to assess the effects of habitat instability on the genetic structure of populations. The perrensi group is a complex of three species (C. roigi, C. perrensi and C. dorbignyi) and several forms of uncertain taxonomic status, distributed in the vicinity of the Iberá wetland in Argentina. Because of limited availability of suitable dry habitat, Ctenomys populations are distributed patchily around a vast mosaic of marshes, swamps and lagoons and become connected or isolated over time, depending particularly on the precipitation regime. Genetic variation at 16 microsatellite loci in 169 individuals collected in the area revealed eight clusters of populations which are thought to be evolutionary units, but which do not fit previous species limits. We interpret this lack of congruence between taxonomy and genetic structure as the result of a dynamic population structure. Where populations become connected, hybridization is possible. Where populations become isolated, rapid genetic divergence may occur. In the perrensi group, it appears that both of these factors disrupt the association between different genetic and morphological characters. The study of multiple characters is crucial to the understanding of the recent evolutionary history for dynamic systems such as this.

Correction: Calculating Evolutionary Dynamics in Structured Populations

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Predicting invasion success in complex ecological networks

A central and perhaps insurmountable challenge of invasion ecology is to predict which combinations of species and habitats most effectively promote and prevent biological invasions. Here, we integrate models of network structure and nonlinear population dynamics to search for potential generalities among trophic factors that may drive invasion success and failure. We simulate invasions where 100 different species attempt to invade 150 different food webs with 15–26 species and a wide range (0.06–0.32) of connectance. These simulations yield 11 438 invasion attempts by non-basal species, 47 per cent of which are successful. At the time of introduction, whether or not the invader is a generalist best predicts final invasion success; however, once the invader establishes itself, it is best distinguished from unsuccessful invaders by occupying a lower trophic position and being relatively invulnerable to predation. In general, variables that reflect the interaction between an invading species and its new community, such as generality and trophic position, best predict invasion success; however, for some trophic categories of invaders, fundamental species traits, such as having the centre of the feeding range low on the theoretical niche axis (for non-omnivorous and omnivorous herbivores), or the topology of the food web (for tertiary carnivores), best predict invasion success. Across all invasion scenarios, a discriminant analysis model predicted successful and failed invasions with 76.5 per cent accuracy for properties at the time of introduction or 100 per cent accuracy for properties at the time of establishment. More generally, our results suggest that tackling the challenge of predicting the properties of species and habitats that promote or inhibit invasions from food web perspective may aid ecologists in identifying rules that govern invasions in natural ecosystems.

Informed dispersal, heterogeneity in animal dispersal syndromes and the dynamics of spatially structured populations

There is accumulating evidence that individuals leave their natal area and select a breeding habitat non-randomly by relying upon information about their natal and future breeding environments. This variation in dispersal is not only based on external information (condition dependence) but also depends upon the internal state of individuals (phenotype dependence). As a consequence, not all dispersers are of the same quality or search for the same habitats. In addition, the individual's state is characterized by morphological, physiological or behavioural attributes that might themselves serve as a cue altering the habitat choice of conspecifics. These combined effects of internal and external information have the potential to generate complex movement patterns and could influence population dynamics and colonization processes. Here, we highlight three particular processes that link condition-dependent dispersal, phenotype-dependent dispersal and habitat choice strategies: (1) the relationship between the cause of departure and the dispersers' phenotype; (2) the relationship between the cause of departure and the settlement behaviour and (3) the concept of informed dispersal, where individuals gather and transfer information before and during their movements through the landscape. We review the empirical evidence for these processes with a special emphasis on vertebrate and arthropod model systems, and present case studies that have quantified the impacts of these processes on spatially structured population dynamics. We also discuss recent literature providing strong evidence that individual variation in dispersal has an important impact on both reinforcement and colonization success and therefore must be taken into account when predicting ecological responses to global warming and habitat fragmentation.

The Finnish population structure. A genetic and genealogical study.

The distribution of both polymorphic and rare marker genes in the Finnish rural population showed evidence of the effect of genetic drift maintained by national and local isolation. The polymorphic genes belonged to nine loci, all representing blood or serum groups. Their distribution was studied from a weighted population sample and this was compared with the distribution at county, community and village level. Great differences were observed both at community and village level, which indicate that the breeding unit has been small up to the present time, consisting of hundreds rather than thousands of individuals. On the other hand, the distribution at county level showed great uniformity compatible with a uniform origin and lack of substantial later gene flow. The distribution of a variety of rare genes was compared with the dynamic population structure characterized by “isolation of population density”. Several examples of enrichment scattered all over the country covered usually an area of several communities which probably represent the very original large breeding units, “superisolates”. The national enrichment of these genes could hardly be explained without a primary enrichment among the first settlers. The distribution of the very rare genes, with an estimated frequency of .003 or less, was limited to the areas first settled during prehistoric times. This forms a piece of evidence showing that all the early Finns used the same route of immigration, i.e., over the Gulf of Finland, rather than a separate eastern and western route. “Finland is like England six hundred years ago” Arthur Mourant (during a visit to Finland in 1958)

A Finite‐State Continuous‐Time Approach for Inferring Regional Migration and Mortality Rates from Archival Tagging and Conventional Tag‐Recovery Experiments

Spatially structured population dynamics models are important management tools for harvested, highly mobile species and although conventional tag recovery experiments remain useful for estimation of various demographic parameters of these models, archival tagging experiments are becoming an important data source for analyzing migratory behavior of mobile marine species. We provide a likelihood-based approach for estimating the regional migration and mortality rate parameters intrinsic to these models that may use information obtained from conventional tag recovery and archival tagging experiments. Specifically, we assume that the regional location and survival of animals through time is a finite-state continuous-time stochastic process. The stochastic process is the basis of probability models for observations provided by the different types of tags. Results from application to simulated tagging experiments for western Atlantic bluefin tuna show that maximum likelihood estimators based on archival tagging observations and corresponding confidence intervals perform similar to conventional tagging observations for a given number of tag releases and releasing tags in each region can improve the behavior of maximum likelihood estimators regardless of tag type. We provide an example application with Atlantic bluefin tuna released with conventional tags in 1990-1992.

Oscheius tipulae, a widespread hermaphroditic soil nematode, displays a higher genetic diversity and geographical structure than Caenorhabditis elegans

The nematode Oscheius tipulae belongs to the same family (Rhabditidae) as the model species Caenorhabditis elegans. Both species reproduce through self-fertilizing hermaphrodites and facultative males. Recent studies have shown that the self-fertile C. elegans and C. briggsae displayed a 20-fold lower genetic diversity than the male-female species C. remanei. Several explanations have been put forward to account for this difference, including their mode of reproduction and dynamic population structure. Here, we present the results of extensive worldwide sampling of O. tipulae, which we previously used as a laboratory organism for developmental genetics. We found that O. tipulae is much more widespread and common in soil throughout the world than Caenorhabditis species. We analysed 63 O. tipulae isolates from several continents using amplified fragment length polymorphism (AFLP). We found that O. tipulae harbours a 5-fold higher genetic diversity than C. elegans and C. briggsae. As in C. elegans, a high proportion of this diversity was found locally. Yet, we detected significant geographical differentiation, both at the worldwide scale with a latitudinal structure and between three localities in France. In summary, O. tipulae exhibited significantly higher levels of genetic diversity and large-scale geographical structure than C. elegans, despite their shared mode of reproduction. This species difference in genetic diversity may be explained by a number of other differences, such as population size, distribution, migration and dynamics. Due to its widespread occurrence and relatively high genetic diversity, O. tipulae may be a promising study species for evolutionary studies.

DENSITY DEPENDENCE AND THE SPREAD OF ANTHELMINTIC RESISTANCE

Variation in the strength of selection pressures acting upon different subpopulations may cause density-dependent regulatory processes to act differentially on particular genotypes and may influence the rate of selection of adaptive traits. Using host-helminth parasite systems as examples, we investigate the impact of different positive and negative density dependence on the potential spread of anthelmintic resistance. Following chemotherapy, the negative density-dependent processes restricting parasite population growth will be relaxed, increasing the genetic contribution of resistant parasites to the next generation. Simple deterministic models of directly transmitted nematodes that merge population dynamics and genetics show that the frequency of drug-resistant alleles may increase faster in species whose population size is down-regulated by density-dependent parasite fecundity than in species with density-dependent establishment or parasite mortality. A genetically structured population dynamics model of an indirectly transmitted nematode is used to highlight how population regulation will influence the resistance allele frequency in different parasite lifestages. Results indicate that surveys aimed at monitoring the evolution of drug resistance should consider carefully which life stage to sample, and the time following treatment samples should be collected. Anthelmintic resistance offers a good opportunity to apply fundamental evolutionary and ecological principles to the management of a potentially crucial public health problem.

Modelling of the age–sex–structured population dynamics with maternal care

We consider an age–sex–structured population dynamics model taking into account spatial diffusion, temporal pairs (for period of mating) and child care. All individuals have pre-reproductive, reproductive, and post-reproductive age intervals. Females of reproductive age are divided into single, fertilized and taking child care classes. Individuals of pre-reproductive age are divided into young (under maternal care) and juvenile groups. Juveniles can live without maternal care, but cannot reproduce. Separable solutions to this model and to the nondispersing population model are studied and numerical results are given.

STATE-DEPENDENT DELAYS ASSOCIATED TO THRESHOLD PHENOMENA IN STRUCTURED POPULATION DYNAMICS

The aim of this paper is to put in evidence the onset of state-dependent delays in threshold models for structured population dynamics. A unified approach to these models is provided, based on solving the corresponding balance law (hyperbolic P.D.E.) along the characteristic lines and showing the common underlying ideas. Size and age-structured models in different fields are presented: insect populations, cell proliferation and epidemics.

For which objective is birth process an optimal feedback in age structured population dynamics?

We consider the McKendrick linear model for the evolution of an age structured population. Usually the birth rate is given through a linear functional of the present population using the fertility rate. We are investigating the question of the existence of an objective function, depending on the control and some observation of the state, for which the associated optimal control problem using the birth rate as a control would yield the previous relation using the fertility rate as the optimal closed loop form. Then we consider adaption mechanisms that we model by including a desired value of the observation in the objective function. A modified fertility rate is derived.

Structured population dynamics: continuous size and discontinuous stage structures

A nonlinear stochastic model for the dynamics of a population with either a continuous size structure or a discontinuous stage structure is formulated in the Eulerian formalism. It takes into account dispersion effects due to stochastic variability of the development process of the individuals. The discrete equations of the numerical approximation are derived, and an analysis of the existence and stability of the equilibrium states is performed. An application to a copepod population is illustrated; numerical results of Eulerian and Lagrangian models are compared.

The genetic structure of Australasian green turtles (Chelonia mydas): exploring the geographical scale of genetic exchange

Ecological and genetic studies of marine turtles generally support the hypothesis of natal homing, but leave open the question of the geographical scale of genetic exchange and the capacity of turtles to shift breeding sites. Here we combine analyses of mitochondrial DNA (mtDNA) variation and recapture data to assess the geographical scale of individual breeding populations and the distribution of such populations through Australasia. We conducted multiscale assessments of mtDNA variation among 714 samples from 27 green turtle rookeries and of adult female dispersal among nesting sites in eastern Australia. Many of these rookeries are on shelves that were flooded by rising sea levels less than 10 000 years (c. 450 generations) ago. Analyses of sequence variation among the mtDNA control region revealed 25 haplotypes, and their frequency distributions indicated 17 genetically distinct breeding stocks (Management Units) consisting either of individual rookeries or groups of rookeries in general that are separated by more than 500 km. The population structure inferred from mtDNA was consistent with the scale of movements observed in long-term mark-recapture studies of east Australian rookeries. Phylogenetic analysis of the haplotypes revealed five clades with significant partitioning of sequence diversity (Phi = 68.4) between Pacific Ocean and Southeast Asian/Indian Ocean rookeries. Isolation by distance was indicated for rookeries separated by up to 2000 km but explained only 12% of the genetic structure. The emerging general picture is one of dynamic population structure influenced by the capacity of females to relocate among proximal breeding sites, although this may be conditional on large population sizes as existed historically across this region.

Larval dynamics and recruitment modelling of the Moroccan Atlantic coast sardine ( Sardina pilchardus)

An age structured population dynamics model of the Moroccan Atlantic coast sardine is presented. The model focuses essentially on the larval phase which is composed of two stages: endogenous and exogenous stages called, respectively, S 1 and S 2. The entrance in stage S 2, here called pre-recruitment, is characterized by yolk resorption and mouth opening. At the beginning of stage S 2, there is a short but critical period when larvae have consumed their vitelline reserves but are not yet able to move enough in quest of food. The recruitment in the juvenile phase occurs when the larva reaches a threshold size related to a certain amount of food it has to ingest during the whole stage S 2. Larval mortality and feeding are density-dependent. A function ω ( t , X ) is introduced to take implicitly into account the impact of environmental and hydrographic conditions variability (upwelling, enrichment, retention, … , etc.) on pre-recruitment.

Global attractivity of a positive periodic solution for a nonautonomous stage structured population dynamics with time delay and diffusion

By employing the continuation theorem of coincidence degree theory, the existence of a positive periodic solution for a nonautonomous stage structured population dynamics with time delay and diffusion is established. Further, by constructing a Lyapunov functional and using the result of the existence of positive periodic solution, the attractivity of a positive periodic solution for above system is obtained.

Genetic Diversity in Australian Populations of Puccinia graminis f. sp. avenae

ABSTRACT Sequence-tagged microsatellite profiling was used to develop 110 microsatellites for Puccinia graminis f. sp. tritici (causal agent of wheat stem rust). Low microsatellite polymorphism was exhibited among 10 pathogenically diverse P. graminis f. sp. tritici isolates collected from Australian cereal growing regions over a period of at least 70 years, with two polymorphic loci detected, each revealing two alleles. Limited cross-species amplification was observed for the wheat rust pathogens, P. triticina (leaf rust) and P. striiformis f. sp. tritici (stripe rust). However, very high transferability was revealed with P. graminis f. sp. avenae (causal agent of oat stem rust) isolates. A genetic diversity study of 47 P. graminis f. sp. avenae isolates collected from an Australia-wide survey in 1999, and a historical group of 16 isolates collected from Australian cereal growing regions from 1971 to 1996, revealed six polymorphic microsatellite loci with a total of 15 alleles. Genetic analysis revealed the presence of several clonal lineages and subpopulations in the pathogen population, and wide dispersal of identical races and genotypes throughout Australian cereal-growing regions. These findings demonstrated the dynamic population structure of this pathogen in Australia and concur with the patterns of diversity observed in pathogenicity studies.

Asymptotic behaviour of solutions to abstract logistic equations

We analyze the asymptotic behaviour of solutions of the abstract differential equation u′( t) = Au( t) − F( u( t)) u( t) + f. Our results are applicable to models of structured population dynamics in which the state space consists of population densities with respect to the structure variables. In the equation the linear term A corresponds to internal processes independent of crowding, the nonlinear logistic term F corresponds to the influence of crowding, and the source term f corresponds to external effects. We analyze three separate cases and show that for each case the solutions stabilize in a way governed by the linear term. We illustrate the results with examples of models of structured population dynamics – a model for the proliferation of cell lines with telomere shortening, a model of proliferating and quiescent cell populations, and a model for the growth of tumour cord cell populations.

Extinction dynamics in experimental metapopulations

Metapopulation theory provides a framework for understanding population persistence in fragmented landscapes and as such has been widely used in conservation biology to inform management of fragmented populations. However, classical metapopulation theory [Levins, R. (1970) Lect. Notes Math. 2, 75-107] ignores metapopulation structure and local population dynamics, both of which may affect extinction dynamics. Here, we investigate metapopulation dynamics in populations that are subject to different migration rates by using experimental metapopulations of the annual plant Cardamine pensylvanica. As predicted by classical metapopulation theory, connected populations persisted longer than did isolated populations, but the relationship between migration and persistence time was nonlinear. Extinction risk sharply increased as the distance between local populations increased above a threshold value that was consistent with stochastic simulations and calculation of metapopulation capacity [Hanski, I. & Ovaskainen, O. (2000) Nature 404, 755-758]. In addition, the most connected metapopulations did not have the highest persistence levels. Stochastic simulations indicated an increase in extinction risk with the highest migration rates. Moreover, calculation of population coherence [Earn, D. J. D., Levin, S. A. & Rohani, P. (2000) Science 290, 1360-1364], a metric that predicts synchronous cycles, indicated that continuous populations should cycle in phase, resulting in an increased extinction risk. Determining empirically the optimal migration level to improve survival chances will be challenging for any natural population. Migration rates that would not increase migration above the threshold value would be ineffectual, but migration rates that would homogenize local densities could increase the risk of coherent oscillations and enhance extinction risk.

A stochastic model for the dynamics of a stage structured population

A stochastic model for the dynamics of a single species of a stagestructured population is presented. The model (in Lagrangian orMonte Carlo formulation) describes the life history of an individualassumed completely determined by the biological processes ofdevelopment, mortality and reproduction. The dynamics of the overallpopulation is obtained by the time evolution of the number of theindividuals and of their physiological age. No other assumption isrequested on the structure of the biological cycle and on theinitial conditions of the population. Both a linear and a nonlinearmodels have been implemented. The nonlinearity takes into accountthe feedback of the population size on the mortality rate of theoffsprings. For the linear case, i.e. when the population growthswithout any feedback dependent on the population size, the balanceequations for the overall population density are written in theEulerian formalism (equations of Von Foerster type in thedeterministic case and of Fokker-Planck type in the stochasticcase). The asymptotic solutions to these equations, for sufficientlylarge time, are in good agreement with the results of the numericalsimulations of the Lagrangian model. As a case study the model isapplied to simulate the dynamics of the greenhouse whitefly, Trialeurodes vaporarioum (Westwood), a highly polyphagous pestinsect, on tomato host plants.