Density-dependent population dynamics in clonal organisms: a modelling approach

1. Density dependence may act at several stages in an organisms life-cycle (e.g. on mortality, fecundity, etc.), but not all density-dependent processes necessarily regulate population size. In this paper I use a density manipulation experiment to determine the effects of density on the transition rates between different size classes of the clonal zoanthid Palythoa caesia Dana 1846. I then formulate a density-dependent matrix model of population dynamics of Palythoa , and perform a series of sensitivity analyses on the model to determine at what stage in the life-cycle regulation acts.
2. Seven of the 16 transition probabilities decreased with density, most of them being shrinkage (due to loss of tissue or fission) and stasis (the self–self transition) of medium and large colonies. The only probability to increase was for the stasis of large colonies. Recruitment was quadratically dependent on density, peaking at intermediate densities.
3. Equilibrium cover in the model was 84% and was reached in ≈40 years. To determine which density-dependent transitions were involved in population regulation, the strength of density dependence was varied in each independently. This sensitivity analysis showed that only changes in the probabilities of large colonies remaining large and producing medium colonies, were regulating.
4. These results suggest that regulation is primarily acting on fission of large colonies to produce intermediate-sized colonies, in combination with size specific growth rates. Fission rates decrease greatly with density, resulting in a greater proportion of large colonies at high densities and large colonies grow more slowly than small. Overall, this behaviour is very similar to that of clonal plants which have a phalanx type life history.     

Density dependence at some time and place?

There appears to be widespread acceptance that for a population to persist, some demographic parameter must be density dependent at some place or time. In this paper, we question the veracity and heuristic value of treating this statement as a general principle of ecology. We also point out that some processes that have recently been defined as density dependent are, in fact, not. Taken in its original sense, density dependence implies a change in demographic rates based on biological (generally negative) feedback. Situations exist, however, in which demographic rates change in relation to density without negative biological feedback. For example, per capita recruitment in marine populations will decrease as local population size increases even as absolute numbers of arriving larvae do not change. The failure to separate these density-related processes from true density-dependent processes affects our understanding of population regulation and of the way in which the natural world functions. Furthermore, focusing solely on density-dependent processes and their role in population regulation neglects to address numerous density-independent processes like disturbance and climatic variation that may have important impacts in determining population size. Received: 20 January 1999 / Accepted: 12 January 2000     

Density dependence and stochastic variation in a newly established population of a small songbird

Models describing fluctuations in population size should include both density dependence and stochastic effects. We examine the relative contribution of variation in parameters of the expected dynamics as well as demographic and environmental stochasticity to fluctuations in a population of a small passerine bird, the pied flycatcher, that was newly established in a Dutch study area. Using the theta-logistic model of density regulation, we demonstrate that the estimated quasi-stationary distribution including demographic stochasticity is close to the stationary distribution ignoring demographic stochasticity, indicating a long expected time to extinction. We also show that the variance in the estimated quasi-stationary distribution is especially sensitive to variation in the density regulation function. Reliable population projections must therefore account for uncertainties in parameter estimates which we do by using the population prediction interval (PPI). After 2 years the width of the 90% PPI was already larger than the corresponding estimated range of variation in the quasi-stationary distribution. More precise prediction of future population size than can be derived from the quasi-stationary distribution could only be made for a time span less than about five years.     

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.     

Population density and module demography in Trapa natans (Trapaceae), an annual,clonal aquatic macrophyte

The effects of population density on module demography were studied in Trapa natans L., an annual aquatic macrophyte capable of extensive clonal propagation. At low density, the floating plants produced ten times as many ramets (clonal offshoots) as those at high density. Module mortality occurred at three levels: leaf, ramet (shoot), and genet (genetic individual). There was 100-fold variation in the size of nuts containing germinable seeds. In early summer there was a highly significant linear relationship between dry mass of nuts and the total mass of ramets that each had produced. In early summer most (73–83%) of the variation in total plant biomass was attributable to variation in initial nut size. However the significance of initial nut size was diminished later in the season. The great success of the exotic weed T. natans at colonizing and monopolizing an aquatic habitat is a function of its highly productive clonal growth response to low-density conditions, combined with greater proportional allocation of biomass to reproductive structures, resulting in greatly increased nut production at low initial density. The species appears able to develop and maintain a population at extremely high density: plant buoyancy and the production of large, well-protected nuts allow rapid early growth from the sediment each year and early pre-emption of the water surface.     

POPULATION STRUCTURE OF A CLONAL GORGONIAN CORAL: THE INTERPLAY BETWEEN CLONAL REPRODUCTION AND DISTURBANCE

Clonality is a common feature of plants and benthic marine organisms. In some cases clonal propagation results in a modest increase in population density, while in other cases dense populations may be generated by the propagation of only a few clones. We analyzed the population structure of the clonal gorgonian Plexaura kuna across several reef habitats with a range of disturbance regimes in the San Blas Islands, Panama, and the Florida Keys, U.S.A. Using multilocus DNA fingerprinting to distinguish clones, we estimated that clones ranged in size from single individuals to 500 colonies. The number of genotypes identified on nine reefs ranged from three to 25. Population density and clonal structure varied markedly among reefs with G_O:G_E ranging from 0.03 to 1.00. On some reefs vegetative reproduction transformed P. kuna from a rare species to the numerically most abundant gorgonian. The effect of clonal propagation on P. kuna population structure was dependent on interactions between fragmentation and the reef environment (disturbance regime, substratum). We present a generalized model relating population structure of clonal species to disturbance and the mode of vegetative propagation. Disturbance promotes colony propagation and skews the size-frequency distribution of clones among P. kuna and many species that propagate via fragmentation. Propagation of these species is promoted by disturbance (disturbance sensitive), and they tend to have clones that are dispersed across local sites. Species that fragment and have dispersed clones, have high genotypic diversity in habitats with low levels of disturbance. Genotypic diversity then decreases at intermediate disturbance and increases again at the highest disturbance levels. Clonal species that do not rely on disturbance for vegetative propagation (disturbance insensitive) generally do not disperse and form aggregated clones. Among these taxa disturbance has a greater affect on individual survival than on propagation. Genotypic diversity is directly related to the level of disturbance until very high levels of disturbance, at which time genotypic diversity declines.     

Climate, social factors and research disturbance influence population dynamics in a declining sociable weaver metapopulation

Population trends are determined by gains through reproduction and immigration, and losses through mortality and emigration. These demographic quantities and resulting population dynamics are affected by different external and internal drivers. We examined how these demographic quantities were affected by weather, research-induced disturbance, local density, colony site and year in a metapopulation of 17 sociable weaver (Philetairus socius) colonies over 17 years of study (4 years for reproduction). Most colonies declined, but at different rates. The four demographic quantities were related to different drivers. Survival strongly varied among years and colonies and was positively related to rainfall and negatively related to extreme temperature (together explaining 30 % of variation) and disturbance (measured as number of captures conducted at a colony; 7 %). There was a trend for a positive relationship between reproduction and rainfall (50 %). Movement was mainly related to local density: individuals were more likely to emigrate from small to large colonies and from colonies that were either well below or above their long-term mean. They were more likely to immigrate into colonies that were nearby, and below their mean size. We then quantified the effects of these relationships on metapopulation dynamics using a multi-site matrix projection model. Rainfall was potentially a strong driver of metapopulation dynamics. In addition, field-work disturbance might have contributed to the decline of this metapopulation but could not explain its full magnitude. Hence, through a combination of analytical methods we were able to obtain information on the main drivers affecting dynamics in a declining metapopulation.     

Changes in seasonal climate outpace compensatory density‐dependence in eastern brook trout

Understanding how multiple extrinsic (density‐independent) factors and intrinsic (density‐dependent) mechanisms influence population dynamics has become increasingly urgent in the face of rapidly changing climates. It is particularly unclear how multiple extrinsic factors with contrasting effects among seasons are related to declines in population numbers and changes in mean body size and whether there is a strong role for density‐dependence. The primary goal of this study was to identify the roles of seasonal variation in climate driven environmental direct effects (mean stream flow and temperature) vs. density‐dependence on population size and mean body size in eastern brook trout (Salvelinus fontinalis). We use data from a 10‐year capture‐mark‐recapture study of eastern brook trout in four streams in Western Massachusetts, USA to parameterize a discrete‐time population projection model. The model integrates matrix modeling techniques used to characterize discrete population structures (age, habitat type, and season) with integral projection models (IPMs) that characterize demographic rates as continuous functions of organismal traits (in this case body size). Using both stochastic and deterministic analyses we show that decreases in population size are due to changes in stream flow and temperature and that these changes are larger than what can be compensated for through density‐dependent responses. We also show that the declines are due mostly to increasing mean stream temperatures decreasing the survival of the youngest age class. In contrast, increases in mean body size over the same period are the result of indirect changes in density with a lesser direct role of climate‐driven environmental change.     

Variation in reproductive characteristics of colonies of the freshwater bryozoan Cristatella mucedo

1. We studied relationships between different forms of reproduction and local variation in the reproductive state of colonies of a common freshwater bryozoan Cristatella mucedo Cuvier (Bryozoa: Phylactolaemata). Four sampling locations in central Finland, including both lotic and lentic habitats, were sampled by scuba diving. The traits studied were occurrence of sexual larvae, colony size, number of resting stages (statoblasts) and number of zooids. 2. While 76.9% of the sampled colonies carried statoblasts at the time of sampling, only 4.5% of the colonies were brooding sexual larvae. Most of the colonies were relatively small with a mean colony size of 16.6 mm. 3. In colonies brooding larvae, the number of statoblasts was positively correlated with the number of larvae. We did not detect a colony size threshold for sexual reproduction or formation of statoblasts. Colonies carrying statoblasts had a lower number of zooids per unit dry weight. 4. We found significant variation in reproductive traits of colonies among the sampling locations, and among lotic and lentic habitats. The observed phenotypic differences may reflect broadly distributed, phenotypically plastic clones. Differences in clonal composition of local populations cannot, however, be ruled out and factors that may provide clonal diversity are discussed.     

Carry-over effects,sequential density dependence and the dynamics of populations in a seasonal environment

Most animal populations have distinct breeding and non-breeding periods, yet the implications of seasonality on population dynamics are not well understood. Here, we introduce an experimental model system to study the population dynamics of two important consequences of seasonality: sequential density dependence and carry-over effects (COEs). Using a replicated seasonal population of Drosophila, we placed individuals at four densities in the non-breeding season and then, among those that survived, placed them to breed at three different densities. We show that COEs arising from variation in non-breeding density negatively impacts individual performance by reducing per capita breeding output by 29–77%, implying that non-lethal COEs can have a strong influence on population abundance. We then parametrized a bi-seasonal population model from the experimental results, and show that both sequential density dependence and COEs can stabilize long-term population dynamics and that COEs can reduce population size at low intrinsic rates of growth. Our results have important implications for predicting the successful colonization of new habitats, and for understanding the long-term persistence of seasonal populations in a wide range of taxa, including migratory organisms.     

Recruitment and local persistence of a freshwater bryozoan in stream riffles

Recruitment in clonal organisms often involves both sexual and asexual processes whereby new individuals are added to adult populations. During 1988–1990,1 examined local distribution and abundance patterns, substrate colonization, and recruitment in riffle populations of the freshwater bryozoan Plumatella emarginata. Abundance levels of P. emarginata at eight selected study sites were strongly dependent on substrate size but not on overall substrate availability or stream position. Colonization of large, P. emarginata-free substrates at one site resulted in an aggregated dispersion pattern of short-lived colonies and the production of locally persistent sessoblasts. Sessoblast production rates were dependent of colony size and number. However, the estimated single season rates of colonization and recruitment were insufficient to account for the high resident population on large substrates. I conclude that sessoblast persistence is essential for escaping mortality and promoting future recruitment and local population growth and that the population dynamics of P. emarginata are strongly nonequilibrial being influenced by unpredictable disturbances as well as by rates of recruitment which increase with local density.     

Individual‐based modelling of resource competition to predict density‐dependent population dynamics: a case study with white storks

Density regulation influences population dynamics through its effects on demographic rates and consequently constitutes a key mechanism explaining the response of organisms to environmental changes. Yet, it is difficult to establish the exact form of density dependence from empirical data. Here, we developed an individual‐based model to explore how resource limitation and behavioural processes determine the spatial structure of white stork Ciconia ciconia populations and regulate reproductive rates. We found that the form of density dependence differed considerably between landscapes with the same overall resource availability and between home range selection strategies, highlighting the importance of fine‐scale resource distribution in interaction with behaviour. In accordance with theories of density dependence, breeding output generally decreased with density but this effect was highly variable and strongly affected by optimal foraging strategy, resource detection probability and colonial behaviour. Moreover, our results uncovered an overlooked consequence of density dependence by showing that high early nestling mortality in storks, assumed to be the outcome of harsh weather, may actually result from density dependent effects on food provision. Our findings emphasize that accounting for interactive effects of individual behaviour and local environmental factors is crucial for understanding density‐dependent processes within spatially structured populations. Enhanced understanding of the ways animal populations are regulated in general, and how habitat conditions and behaviour may dictate spatial population structure and demographic rates is critically needed for predicting the dynamics of populations, communities and ecosystems under changing environmental conditions.     

Sexual reproduction, clonal diversity and genetic differentiation in patchily distributed populations of the temperate forest herb Paris quadrifolia (Trilliaceae)

Clonal plant species have been shown to adopt different strategies to persist in heterogeneous environments by changing relative investments in sexual reproduction and clonal propagation. As a result, clonal diversity and genetic variation may be different along environmental gradients. We examined the regional and local population structure of the clonal rhizomatous forest herb Paris quadrifolia in a complex of forest fragments in Voeren (Belgium). Relationships between population size (the number of shoots), shoot density (the number of shoots per m²) and local growth conditions were investigated for 47 populations. Clonal diversity and genetic variation within and among 19 populations were investigated using amplified fragment length polymorphism markers. To assess the importance of sexual reproduction, seed set, seed weight and germination success were determined in 18 populations. As predicted, local growth conditions largely affected population distribution, size and density of P. quadrifolia. Populations occurring in moist and relatively productive sites contained significantly more shoots. Here, shoots were also much more sparsely distributed compared to populations occurring in dry and relatively unproductive sites, where shoots showed a strongly aggregated distribution pattern. Clonal diversity was relatively high, compared with other clonal species (G/N ratio = 0.43 and Simpson’s D=0.81). Clonal diversity significantly (P<0.01) decreased with increasing shoot density while molecular genetic variation was significantly (P<0.01) affected by population size and local environmental conditions. Lack of recruitment and out-competition of less-adapted genotypes may explain the decreased genetic variation in dry sites. Analysis of molecular variance revealed significant genetic variation among populations (Φ _ST=0.42, P<0.001), whereas pairwise genetic distances were not correlated to geographic distances, suggesting that gene flow among populations is limited. Finally, the number of generative shoots, the number of seeds per fruit and seed weight were significantly and positively related to population size and local growth conditions. We conclude that under stressful conditions populations of clonal forest plant species can slowly evolve into remnant populations characterized by low levels of genetic variation and limited sexual reproduction. Conservation of suitable habitat conditions is therefore a prerequisite for effective long-term conservation of clonal forest plant species.     

Effective size of density‐dependent populations in fluctuating environments

Reliable estimates of effective population size are of central importance in population genetics and evolutionary biology. For populations that fluctuate in size, harmonic mean population size is commonly used as a proxy for (multi‐) generational effective size. This assumes no effects of density dependence on the ratio between effective and actual population size, which limits its potential application. Here, we introduce density dependence on vital rates in a demographic model of variance effective size. We derive an expression for the ratio in a density‐regulated population in a fluctuating environment. We show by simulations that yearly genetic drift is accurately predicted by our model, and not proportional to as assumed by the harmonic mean model, where N is the total population size of mature individuals. We find a negative relationship between and N. For a given N, the ratio depends on variance in reproductive success and the degree of resource limitation acting on the population growth rate. Finally, our model indicate that environmental stochasticity may affect not only through fluctuations in N, but also for a given N at a given time. Our results show that estimates of effective population size must include effects of density dependence and environmental stochasticity.     

Quantifying density dependence in a bird population using human disturbance

Although density dependence has long been recognised as vital to population regulation, there have been relatively few studies demonstrating it spatially in wildlife populations, often due to the confounding effects of variation in habitat quality. We report on a study of woodlarks Lullula arborea, a species of European conservation concern, breeding on lowland heath in Dorset, England. We take the novel approach of utilising the birds’ response to human disturbance, which resulted in much of the variation in density but had no direct impact on demographic rates. Within years, in sites with greater density there were smaller mean chick masses, lower post-fledging survival, and higher rates of nestling mortality attributed to starvation. The effects on clutch size and fledging success were confounded by the area of grassland within a site. There was no effect on brood size. Density dependence also operated within sites between years: as density increased there were reductions in mean chick mass and post-fledging survival, while nestling mortality attributed to starvation increased. Density-dependent effects on clutch size were only weakly regulatory, whereas density-dependent starvation and post-fledging mortality rates contributed strongly to differences in overall breeding output. Heavier chicks (when 7 days old) were significantly more likely to fledge and less likely to starve. Broods with heavier chicks were more likely to supply recruits to the breeding population. Nestling mass was not a factor in survival in the immediate post-fledging period, suggesting that density-dependent processes act independently on this stage. We conclude that the number of birds per hectare of suitable habitat is a valid means of expressing density, and that habitat acts as a surrogate for food abundance through which density dependence operates on the woodlark population.     

Genotyping the clonal structure of a gorgonian coral, Junceella juncea (Anthozoa: Octocorallia), using microsatellite loci

The identification of different clones is fundamental to the study of population structure among organisms with mixed reproductive modes such as cnidarians. However, due to the low genetic variation of coral mtDNA and contamination by zooxanthellate DNA, very few molecular markers are available for studying the clonal structure of cnidarians. Herein we used four polymorphic loci of microsatellite DNA isolated from a zooxanthellae-free octocoral, Junceella juncea, to study its clonal structure in seven populations collected from three localities in Taiwan. In total, 40 multilocus genotypes were found among 152 colonies, and the number of genotypes (clones) identified in the seven populations ranged from 2 to 16. Each of the 40 multilocus genotypes was restricted to a single population, even where adjacent populations were only 100 m distant. The ratio of observed to expected genotypic diversity (G_o:G_e) ranged from 0.217 to 0.650, and G_o showed a significant departure from G_e (p<0.05) at each site indicating that asexual fragmentation may play a major role in the maintenance of established populations. Mean relatedness (R) values showed that genotypes within reefs were more closely related than those between regions. The results indicate that microsatellites are useful for discerning the clonal structures among and within populations at different spatial scales. Electronic supplement: Unique multilocus genotypes (clones) revealed by 4 polymorphic loci for Junceella juncea colonies collected from Xiashuijui (Reefs A, B, C, Transplant, Transect), Nanwan and Shicheng     

cloncase: Estimation of sex frequency and effective population size by clonemate resampling in partially clonal organisms

Inferring reproductive and demographic parameters of populations is crucial to our understanding of species ecology and evolutionary potential but can be challenging, especially in partially clonal organisms. Here, we describe a new and accurate method, cloncase , for estimating both the rate of sexual vs. asexual reproduction and the effective population size, based on the frequency of clonemate resampling across generations. Simulations showed that our method provides reliable estimates of sex frequency and effective population size for a wide range of parameters. The cloncase method was applied to Puccinia striiformis f.sp. tritici, a fungal pathogen causing stripe/yellow rust, an important wheat disease. This fungus is highly clonal in Europe but has been suggested to recombine in Asia. Using two temporally spaced samples of P. striiformis f.sp. tritici in China, the estimated sex frequency was 75% (i.e. three‐quarter of individuals being sexually derived during the yearly sexual cycle), indicating strong contribution of sexual reproduction to the life cycle of the pathogen in this area. The inferred effective population size of this partially clonal organism (N_c = 998) was in good agreement with estimates obtained using methods based on temporal variations in allelic frequencies. The cloncase estimator presented herein is the first method allowing accurate inference of both sex frequency and effective population size from population data without knowledge of recombination or mutation rates. cloncase can be applied to population genetic data from any organism with cyclical parthenogenesis and should in particular be very useful for improving our understanding of pest and microbial population biology.     

Factors controlling the colonial structure of <Emphasis Type="Italic">Pediastrum tetras</Emphasis> (Chlorophyceae)

Accounting for morphological plasticity in phytoplankton populations is relevant for taxonomy, systematic/evolutionary, and ecological studies. In this work, the green alga Pediastrum tetras (Ehrenberg) Ralfs was used to describe the variation in population size structure over its growth cycle and to analyze responses to changes in biotic and abiotic factors. Pediastrum cultures reached a final stable concentration in approximately 10 days. This density (8 × 10⁵ cells ml⁻¹) remained stable for at least another 13 days and the intrinsic growth rate was 0.24 ± 0.01 day⁻¹. In the exponential phase, the relative number of single cells and the proportion of large cells (with vesicles inside) within colonies increased. When density peaked, a relative increase of single cells as well as small cells in new colonies took place. Finally, during the stationary phase, the trend reversed: fewer single cells and a larger cell size (without vesicles) were observed. Results indicated that nutrient supply could affect population structure, diminishing the proportion of eight-cell colonies. Daphnia magna Straus significantly reduced the Pediastrum population density due to predation, and this led to a significant decrease in the density of the largest colonies. In addition, info-chemicals induced a slight increase in the density of the largest colonies compared to the control treatment. Our study suggests a possible trade-off in P. tetras colonial size in natural environments: during the stationary growth period in a lake, Pediastrum populations tend to increase in size for efficient use of nutrients, while they decrease in size in the presence of herbivores. Handling editor: J. Padisak     

Rodent population cycles: life history adjustments to age-specific dispersal strategies and intrinsic time lags

Summary Multi-annual population cycles can be generated by life history responses to density dependent changes in adult and pre-reproductive survival. The proximate mechanism linking population dynamics and demography of cycling rodents appears to be high pre-reproductive dispersal at peak density, or during periods of population increase. This model is similar to the Chitty hypothesis which can best be viewed as a special case of demographic control on population size. Normally, this control should be selfreinforcing and lead to damped oscillations toward a stable population density. Intrinsic time lags induced by variation in the length of the breeding season modify the dependence of demography on population size, and enable the cycles to persist.     

Factors influencing reproductive success in the clonal moss, Hylocomium splendens

Female reproductive success in the unisexual perennial clonal moss Hylocomium splendens was examined by recording, if the segment was reproductive [produced sporophyte(s)] or not, together with several distance-to-male and male density variables, and segment size. This was done for every female segment in a population over a 5 year study period. A high fraction of the population could be sexed because we monitored the population in situ for 5 years, and thereafter harvested the population for electrophoretic analysis from which the clonal identity and expressed sex could be deduced. Fertilization distances in H. splendens were short, indicated by the fact that as many as 85% of the female segments with sporophytes were situated within a distance of 5.0 cm from the nearest male. The longest distance measured between a sporophytic female and the closest male was 11.6 cm. However, analysed within a generalized linear modelling (GLM) framework, the year was the best single predictor for the presence of H. splendens sporophyte although female-segment size and distance to the closest situated male were also strongly significant. The two latter factors explained larger fractions of variation in sporophyte presence in a GLM model with three predictors than in single-predictor models. This is because (i) the large variation in sporophyte production among years partly obscures the strong general increase in sporophyte production with increasing female-segment size and vitality, and (ii) the between-year variation and the size obscure the effect of the distance to the most proximate male. To our knowledge, this study is the first to incorporate into one model the relative importance of several factors for bryophyte reproductive success. Our results demonstrate the value of multiple-predictor approaches in studies of reproductive success.