The impact of population dynamics on Y-chromosome microsatellite polymorphism. Mathematical modeling

In this article, we use mathematical modeling to study the impact of population dynamics on Y-chromosome STR-polymorphism accumulation in two independently evolving populations, namely, on the changes in genetic distance between the populations. Comparative analysis using two definitions of genetic distance—(δμ)² and ASD—shows that, in contrast to (δμ)², ASD is almost linearly dependent on time (except for sparse stationary populations, where deviations are observed). When the population numbers undergo oscillations, ASD proves to be smaller than that for stationary populations.     

Optimal harvesting of stochastically fluctuating populations

 We obtain the optimal harvesting plan to maximize the expected discounted number of individuals harvested over an infinite future horizon, under the most common (Verhulst-Pearl) logistic model for a stochastically fluctuating population. We also solve the problem for the standard variants of the model where there are constraints on the admissible harvesting rates. We use stochastic calculus to derive the optimal population threshold at which individuals are harvested as well as the overall value of the population in the sense of the model. We show that except under extreme conditions, the population is never depleted in finite time, but remains in a stationary distribution which we find explicitly. Needless to say, our results prove that any strategy which totally depletes the population is sub-optimal. These results are much more precise than those previously obtained for this problem. Received 24 June 1996; received in revised form 7 April 1997     

Short‐term and long‐term effects of acute kidney injury in chronic kidney disease patients: A longitudinal analysis

We use data from an ongoing cohort study of chronic kidney patients at Salford Royal NHS Foundation Trust, Greater Manchester, United Kingdom, to investigate the influence of acute kidney injury (AKI) on the subsequent rate of change of kidney function amongst patients already diagnosed with chronic kidney disease (CKD). We use a linear mixed effects modelling framework to enable estimation of both acute and chronic effects of AKI events on kidney function. We model the fixed effects by a piece‐wise linear function with three change‐points to capture the acute changes in kidney function that characterise an AKI event, and the random effects by the sum of three components: a random intercept, a stationary stochastic process with Matérn correlation structure, and measurement error. We consider both multivariate Normal and multivariate t versions of the random effects. For either specification, we estimate model parameters by maximum likelihood and evaluate the plug‐in predictive distributions of the random effects given the data. We find that following an AKI event the average long‐term rate of decline in kidney function is almost doubled, regardless of the severity of the event. We also identify and present examples of individual patients whose kidney function trajectories diverge substantially from the population‐average.     

The nature of laboratory domestication changes in freshly isolated Escherichia coli strains

Adaptation of environmental bacteria to laboratory conditions can lead to modification of important traits, what we term domestication. Little is known about the rapidity and reproducibility of domestication changes, the uniformity of these changes within a species or how diverse these are in a single culture. Here, we analysed phenotypic changes in nutrient‐rich liquid media or on agar of four Escherichia coli strains newly isolated through minimal steps from different sources. The laboratory‐cultured populations showed changes in metabolism, morphotype, fitness and in some phenotypes associated with the sigma factor RpoS. Domestication events and phenotypic diversity started to emerge within 2–3 days in replicate subcultures of the same ancestor. In some strains, increased amino acid usage and higher fitness under nutrient limitation resembled those in mutants with the GASP (growth advantage in stationary phase) phenotype. The domestication changes are not uniform across a species or even within a single domesticated population. However, some parallelism in adaptation within repeat cultures was observed. Differences in the laboratory environment also determine domestication effects, which differ between liquid and solid media or with extended stationary phase. Important lessons for the handling and storage of organisms can be based on these studies.     

Loss of genetic variability in social spiders: genetic and phylogenetic consequences of population subdivision and inbreeding

The consequences of population subdivision and inbreeding have been studied in many organisms, particularly in plants. However, most studies focus on the short‐term consequences, such as inbreeding depression. To investigate the consequences of both population fragmentation and inbreeding for genetic variability in the longer term, we here make use of a natural inbreeding experiment in spiders, where sociality and accompanying population subdivision and inbreeding have evolved repeatedly. We use mitochondrial and nuclear data to infer phylogenetic relationships among 170 individuals of Anelosimus spiders representing 23 species. We then compare relative mitochondrial and nuclear genetic variability of the inbred social species and their outbred relatives. We focus on four independently derived social species and four subsocial species, including two outbred–inbred sister species pairs. We find that social species have 50% reduced mitochondrial sequence divergence. As inbreeding is not expected to reduce genetic variability in the maternally inherited mitochondrial genome, this suggests the loss of variation due to strong population subdivision, founder effects, small effective population sizes (colonies as individuals) and lineage turnover. Social species have < 10% of the nuclear genetic variability of the outbred species, also suggesting the loss of genetic variability through founder effects and/or inbreeding. Inbred sociality hence may result in reduction in variability through various processes. Sociality in most Anelosimus species probably arose relatively recently (0.1–2 mya), with even the oldest social lineages having failed to diversify. This is consistent with the hypothesis that inbred spider sociality represents an evolutionary dead end. Heterosis underlies a species potential to respond to environmental change and/or disease. Inbreeding and loss of genetic variability may thus limit diversification in social Anelosimus lineages and similarly pose a threat to many wild populations subject to habitat fragmentation or reduced population sizes.     

The persistence of short‐term cold acclimation in Drosophila melanogaster (Diptera: Drosophilidae)

Daily and seasonal fluctuations in temperature present significant challenges for the survival of many ectothermic species that can be tempered via thermal acclimation. In the present study, we use multiple naturally derived genotypes of Drosophila melanogaster to determine the persistence of beneficial short‐term thermal acclimation on subsequent survival after cold shock. We found that the benefit of short‐term acclimation persisted for 2 h in most genotypes after a rapid cold hardening treatment. Genotype did not directly influence the persistence of short‐term acclimation benefits, indicating that environmental variation may be more important for the persistence of acclimation benefits rather than genetic capacity for acclimation. The present study extends the current understanding of the limits and importance of short‐term acclimation events, providing greater detail on the timing of the loss of short‐term acclimation benefits in a genetically variable natural population.     

SUBSTRATE COMPETITION BETWEEN A SALT MARSH DIATOM AND A BACTERIAL POPULATION1

Cylindrotheca closterium Ehrenberg, a benthic marine diatom, competes successfully with Aeromonas sp. a bacterium from the same environment, for low molecular weight organic substrates when they are presented at natural concentrations (1–10 μM). In short term (1 h) experiments, the uptake of mannose by C. closterium was enhanced in light. Seventy percent of the total uptake of mannose by both species was effected by C. closterium over a 1 h period in light. The diatom population was also competitive in darkness. The algal portion of glucose uptake over 1 h was 71% when both populations were given the substrate initially. Percentages of total amino acid uptake for C. closterium ranged from 33% glycine in light to 73% leucine in darkness when both species were given substrate initially. Cylindrotheca had smaller percentages of glucose and aspartic acid total uptake in competition experiments run to stationary phase (10 days).     

Convergence time to the Ewens sampling formula in the infinite alleles Moran model

In this paper, we establish an upper bound for time to convergence to stationarity for the discrete time infinite alleles Moran model. If M is the population size and μ is the mutation rate, this bound gives a cutoff time of log(M μ)/μ generations. The stationary distribution for this process in the case of sampling without replacement is the Ewens sampling formula. We show that the bound for the total variation distance from the generation t distribution to the Ewens sampling formula is well approximated by one of the extreme value distributions, namely, a standard Gumbel distribution. Beginning with the card shuffling examples of Aldous and Diaconis and extending the ideas of Donnelly and Rodrigues for the two allele model, this model adds to the list of Markov chains that show evidence for the cutoff phenomenon. Because of the broad use of infinite alleles models, this cutoff sets the time scale of applicability for statistical tests based on the Ewens sampling formula and other tests of neutrality in a number of population genetic studies.     

Shifting dynamic forces in fish stock fluctuations triggered by age truncation?

Accumulating evidence shows that environmental fluctuations and exploitation jointly affect marine fish populations, and understanding their interaction is a key issue for fisheries ecology. In particular, it has been proposed that age truncation induced by fisheries exploitation may increase the population's sensitivity to climate. In this study, we use unique long‐term abundance data for the Northeast Arctic stock of cod (Gadus morhua) and the Norwegian Spring‐Spawning stock of herring (Clupea harengus), which we analyze using techniques based on age‐structured population matrices. After identifying time periods with different age distributions in the spawning stock, we use linear models to quantify the relative effect of exploitation and temperature on the population growth rates. For the two populations, age truncation was found to be associated with an increasing importance of temperature and a relatively decreasing importance of exploitation, while the population growth rate became increasingly sensitive to recruitment variations. The results suggested that the removal of older age classes reduced the buffering capacity of the population, thereby making the population growth rate more dependent on recruitment than adult survival and increasing the effect of environmental fluctuations. Age structure appeared as a key characteristic that can affect the response of fish stocks to climate variations and its consequences may be of key importance for conservation and management.     

Extinction conditions for isolated populations affected by environmental stochasticity

We determine the critical patch size below which extinction occurs for populations living in one-dimensional habitats surrounded by completely hostile environments in the presence of environmental fluctuations. The population dynamics is reformulated in terms of a stochastic reaction–diffusion equation and is reduced to a deterministic equation that incorporates the systematic contributions of the noise. We obtain bifurcation diagrams and relations for the mean population density at the stationary state, the critical patch size, and the mean number of individuals in the habitat. The effect of the noise differs, depending on whether it affects the net growth rate or the intraspecific competition term. Fluctuations in the net growth rate decrease the critical patch size, whereas fluctuations in the competition term do not change the critical patch size. We compare our analytical results with numerical solutions of the stochastic partial differential equations and show that our procedure proves useful in dealing with reaction–diffusion equations with multiplicative noise.     

Analysis of the periodically fragmented environment model : I – Species persistence

This paper is concerned with the study of the stationary solutions of the equationwhere the diffusion matrix A and the reaction term f are periodic in x. We prove existence and uniqueness results for the stationary equation and we then analyze the behaviour of the solutions of the evolution equation for large times. These results are expressed by a condition on the sign of the first eigenvalue of the associated linearized problem with periodicity condition. We explain the biological motivation and we also interpret the results in terms of species persistence in periodic environment. The effects of various aspects of heterogeneities, such as environmental fragmentation are also discussed.     

Symbolic dynamics for identifying similarity between rhythms of ecological time series

Explaining the associations between animal populations or between population and environmental signals is an important challenge. The time series that quantify animal populations are often complex, nonlinear, noisy and non‐stationary. These characteristics may make it inappropriate to use traditional techniques when analysing these time series and their mutual dependencies. Here I propose to use symbolic dynamics and techniques from Information Theory to evaluate the degree of dynamic cohesion between time series fluctuations. The main idea is to check whether two (or more) signals tend to oscillate simultaneously, rising and falling together with the same rhythm. Based on synthetic and real time series, I demonstrate that this method is robust to the presence of noise and to the short length of the analysed time series and gives relevant information about the weak relationships between different series. Furthermore, this method appears as simple as classical cross‐correlation and outperforms it in the analysed examples.     

Prey diversity and prey identity affect herbivore performance on different time scales in a long term aquatic food‐web experiment

The question whether and how diversity‐mediated productivity at the base of food‐webs influences adjacent trophic levels is still unclear. Experiments revealed negative effects on consumers due to the increasing dominance of inedible species under grazing pressure, and positive effects due to a greater variety of prey resources. We experimentally investigate two more hypotheses, which have not been addressed in detail so far: first, more diverse primary producer communities potentially use limiting resources more efficiently, and are, therefore, more productive. This effect can be considered functionally similar to a direct enrichment with limiting resources, potentially resulting in a higher stochastic risk of herbivore extinction (‘paradox of enrichment’). Second, in a stable environment, enclosed primary producer communities should evolve towards a ‘climax state’, eventually dominated by one or few prey species. Therefore, long‐term diversity effects in producer communities should more likely result from the specific traits of the dominating species, than from complementarity. To address these hypotheses, we conducted long‐term laboratory experiments, exposing the freshwater grazer Daphnia magna to a gradient of algal species richness (1, 2, 4 or 8 edible chlorophyte species). The experiments were run in batch cultures, without exchange of growth medium after the start of the experiment. Six parameters related to Daphnia population demography, biomass accrual, and stability were followed and determined over a period of up to 263 days. Producer diversity exhibited strong positive effects on the short‐term performance of grazers (first reproduction, first population peak), and on grazer mean standing stocks. However, herbivore long‐term dynamics (day of extinction and temporal stability) depended on prey species identity, namely the presence of Chlamydomonas reinhardtii. Our experiments suggest that both prey diversity and identity can have positive effects on consumer performance, but act on different time scales.     

Establishing laboratory cultures and performing ecological and evolutionary experiments with the emerging model species Chironomus riparius

Chironomus riparius is a well‐established model organism in various fields such as ecotoxicology and ecology, and therefore, environmental preferences, ecological interactions and metabolic traits are well‐studied. With the recent publication of a high‐quality draft genome, as well as different population genetic parameters such as mutation and recombination rate, the species can be used as an alternative to the Drosophila models in experimental population genomics or molecular ecology. To facilitate access to this promising experimental model species for a wider range of researchers, we describe experimental methods to first create and sustain long‐term cultures of C. riparius and then use them to perform repeatable and comparable experiments for various research questions.     

Changes in pigmentation of phytoplankton species during growth and stationary phase — consequences for reliability of pigment-based methods of biomass determination

In applied water ecology several methods for estimating the biomass or activity of phytoplankton depend on the proportion of accessory pigments (xanthophylls) to chlorophyll a. Therefore, changes in pigmentation during growth and stationary phase were investigated in four different species (Amphidinium klebsii, Euglena gracilis, Prymnesium parvum, Cryptomonas ovata) typical representatives of the major algal groups. The ratios of the different xanthophylls to chlorophyll a depended not only on the growth phase, but also on the species. InAmphidinium andEuglena, the ratio of xanthophylls to chlorophyll rises continuously during the growth phase and declined during the stationary phase. InPrymnesium, quantitative pigmentation was found to be nearly independent of the growth phase. InCryptomonas, however, this ratio was relatively constant during growth, but increased in the stationary phase. In contrast to higher plants, in which the breakdown of chlorophylls occurs before that of the xanthophylls, in three of the species both pigment classes were reduced in parallel when the cultures were in the stationary phase. AgingCryptomonas, however, exhibited a pigment breakdown pattern similar to higher plants. The use of these findings for the widely applied biomass determination by chlorophyll fluorescence and for other pigment-based methods is discussed.     

Ecological change predicts population dynamics and genetic diversity over 120 000 years

While ecological effects on short‐term population dynamics are well understood, their effects over millennia are difficult to demonstrate and convincing evidence is scant. Using coalescent methods, we analysed past population dynamics of three lizard species (Psammodromus hispanicus, P. edwardsianus, P. occidentalis) and linked the results with climate change data covering the same temporal horizon (120 000 years). An increase in population size over time was observed in two species, and in P. occidentalis, no change was observed. Temporal changes in temperature seasonality and the maximum temperature of the warmest month were congruent with changes in population dynamics observed for the three species and both variables affected population density, either directly or indirectly (via a life‐history trait). These results constitute the first solid link between ecological change and long‐term population dynamics. The results moreover suggest that ecological change leaves genetic signatures that can be retrospectively traced, providing evidence that ecological change is a crucial driver of genetic diversity and speciation.     

Comparative breeding performance of Marsh Harriers Circus aeruginosus along a gradient of land‐use intensification and implications for population management

Assessing variation in breeding performance in relation to habitat characteristics may provide insights into predicting the consequences of land‐use change on species ecology and population dynamics. We compared four Marsh Harrier Circus aeruginosus populations subject to similar environmental conditions, but which differed in habitat composition, ranging from natural habitats to intensively cultivated areas. Using a 6‐year dataset, we characterized breeding habitat and diet in these four study sites, and analysed breeding performance in relation to this gradient of land‐use intensification. There was minimal variation in breeding performance between study years but consistent variation between study sites. Unexpectedly, Marsh Harriers breeding in intensively cultivated habitats had higher reproductive success than those breeding in more natural habitats, which, however, hosted higher breeding densities, so overall net population productivity (fledglings per unit area) was similar across sites. This resulted from combined effects of density‐dependence and different predation rates between study sites. The colonization of intensive farmland habitats may not necessarily impact negatively on population sustainability when breeding success and population density are traded against each other. However, our findings should not mask longer‐term conservation issues for populations breeding in these intensively managed areas, and further studies should assess potential long‐term negative effects of occupancy of human‐altered habitat.     

Landscape‐scale redistribution of a highly mobile threatened species,Pteropus conspicillatus (Chiroptera,Pteropodidae), in response to Tropical Cyclone Larry

Abstract Severe category 4 Tropical Cyclone Larry, which crossed north‐east Queensland on 20 March 2006, provided a unique opportunity to examine the short‐term impacts of a major disturbance event on the population of a highly mobile threatened species, Pteropus conspicillatus. As we had recorded, the species’ population distribution in colonial roosts (camps) across the region each month for almost 2 years prior to Cyclone Larry, we continued monthly surveying of P. conspicillatus camp‐sites for a year post‐cyclone. Here we report on how P. conspicillatus responded and redistributed immediately after the cyclone, and over the subsequent year. Post‐cyclone, P. conspicillatus typically roosted in smaller camps than pre‐cyclone, suggesting that these animals had largely dispersed to locate available blossoms and fruit. For 6 months after Cyclone Larry, up to 90% of the pre‐cyclone P. conspicillatus population (ca. 250 000) was unaccounted for across the region. Information provided by the general public assisted us in locating six small camps of P. conspicillatus at ‘new’ locations, but contributed little to increase our overall population estimate for the species at this time. After November 2006, the number of P. conspicillatus built up at located camp‐sites until a post‐cyclone peak of 209 000 at the end of the study in March 2007, comparable with the population estimates in March 2005 and 2006. There is no evidence that the cyclone caused significant direct mortality among P. conspicillatus, although there may yet be longer‐term and indirect effects on population size. We suggest that redistribution by P. conspicillatus makes sense ecologically in the face of major habitat disturbance and short‐ to long‐term food resource limitation, and is not unlike the response of other Australian mainland Pteropus species to seasonal changes in food availability.     

Random effects in population models with hereditary effects

This paper discusses the influence of environmental noise on the dynamics of single species population models with hereditary effects. A detailed analysis is carried out for the logistic equation with discrete delay in the resource limitation term (Hutchinson's equation). When the system undergoes Hopf bifurcation, we find the stationary probability density distribution for the amplitude of the periodic solution by means of an averaged Fokker-Planck equation. Finally, we estimate the persistence time of the species when the population density has a lower bound beyond which it goes extinct.     

Survival,site fidelity,and the population dynamics of Piping Plovers in Saskatchewan

ABSTRACT To conserve threatened species, managers require predictions about the effects of natural and anthropogenic factors on population growth that in turn require accurate estimates of survival, birth, and dispersal rates, and their correlation with natural and anthropogenic factors. For Piping Plovers (Charadrius melodus), fledging rate is often more amenable to management than adult survival, and population models can be used to estimate the productivity (young produced per breeding female) necessary to maintain or increase populations for given levels of survival. We estimated true survival and site fidelity of adult and subadult (from fledging to second year) Piping Plovers breeding in Saskatchewan using mark‐resight data from 2002 to 2009. By estimating true survival rather than apparent survival (which is confounded with permanent emigration), we were able to provide more accurate projections of population trends. Average adult and subadult survival rates during our study were 0.80 and 0.57, respectively. Adult survival declined over time, possibly due in part to the loss of one breeding site to flooding. Average adult and subadult site fidelity were 0.86 and 0.46, respectively. Adult site fidelity declined during our study at two study sites, most strongly at the flooded site. Male and female Piping Plovers had similar survival rates, but males had greater site fidelity than females in some years. Based on our survival estimates, productivity needed for a stationary population was 0.75, a benchmark used for plover management on the Atlantic Coast, but not previously estimated for Prairie Canada. In stochastic simulations incorporating literature‐based variation in survival rates, productivity needed for a stationary population increased to 0.86, still lower than that previously estimated for western populations. Mean productivity for our study sites ranged from 0.87 to 0.96 fledged young per pair. Our results suggest that fledging rates of Piping Plovers in Saskatchewan were sufficient to ensure a stationary or increasing population during our study period. However, large‐scale habitat changes such as drought or anthropogenic flooding may lead to dispersal of breeding adults and possibly mortality that will increase the fledging rate needed for a stationary population.