Estimating Density Dependence, Environmental Variance, and Long-Term Selection on a Stage-Structured Life History.

AbstractA method for analyzing long-term demographic data on density-dependent stage-structured populations in a stochastic environment is derived to facilitate comparison of populations and species with different life histories. We assume that a weighted sum of stage abundances, N, exerts density dependence on stage-specific vital rates of survival and reproduction and that N has a small or moderate coefficient of variation. The dynamics of N are approximated as a univariate stochastic process governed by three key parameters: the density-independent growth rate, the net density dependence, and environmental variance in the life history. We show how to estimate the relative weighs of stages in N and the key parameters. Life history evolution represents a stochastic maximization of a simple function of the key parameters. The long-term selection gradient on the life history can be expressed as a vector of sensitivities of this function with respect to density-independent, density-dependent, and stochastic components of the vital rates. To illustrate the method, we analyze 38 years of demographic data on a great tit population, estimating the key parameters, which accurately predict the observed mean, coefficient of variation, and fluctuation rate of N; we also evaluate the long-term selection gradient on the life history.

The Regulatory Role of the Oral Commensal Streptococcus mitis on Human Monocytes.

Streptococcus mitis colonizes all niches of the human oral cavity from early infancy and throughout life. Monocytes patrol blood vessels, lymphoid and non-lymphoid tissues and migrate into infected tissue where they participate in the inflammatory cascade and immune regulation. Here, we studied the effect of S. mitis on monocytes. Transcriptome analysis of monocytes exposed to S. mitis (SmMo) revealed increased transcription of chemotactic factors (CCL2, CCL3, CCL20, CXCL1, CXCL2) and cytokines (IL1A, IL1B, IL6, IL23, IL36G, TNF), indicating that S. mitis may trigger recruitment of leucocytes and initiate inflammation. Increased transcription in SmMo of IL1B, IL6 and IL23 indicated that S. mitis may participate in the induction of Th17 responses and agreed with our earlier findings of S. mitis-mediated memory Th17 reactivity. Furthermore, S. mitis inhibited tetanus toxoid-specific CD4 T cell proliferation. This can be due to the increased secretion of IL-10 and expression of PD-L1 that was observed in SmMo. PGE2 can modulate IL-10 and PD-L1 expression, concomitant with that of CCR7, IL-12 and IL-23 that also were changed. This, along with increased SmMo transcription of PTGS2 (COX2) and PTGER4 (EP4), pointed to a role of PGE2. Measurement of PGE2 secretion by SmMo showed indeed a marked increase, and chemical inhibition of PGE2 production lowered the PD-L1 expression on SmMo. In conclusion, our findings show that S. mitis may trigger immune modulation by recruiting immune cells to the site of infection, while at the same time dampening the severity of the response through expression of IL-10, PGE2 and PD-L1.

Effective size of density-dependent two-sex populations: the effect of mating systems.

Density dependence in vital rates is a key feature affecting temporal fluctuations of natural populations. This has important implications for the rate of random genetic drift. Mating systems also greatly affect effective population sizes, but knowledge of how mating system and density regulation interact to affect random genetic drift is poor. Using theoretical models and simulations, we compare Ne in short-lived, density-dependent animal populations with different mating systems. We study the impact of a fluctuating, density-dependent sex ratio and consider both a stable and a fluctuating environment. We find a negative relationship between annual Ne /N and adult population size N due to density dependence, suggesting that loss of genetic variation is reduced at small densities. The magnitude of this decrease was affected by mating system and life history. A male-biased, density-dependent sex ratio reduces the rate of genetic drift compared to an equal, density-independent sex ratio, but a stochastic change towards male bias reduces the Ne /N ratio. Environmental stochasticity amplifies temporal fluctuations in population size and is thus vital to consider in estimation of effective population sizes over longer time periods. Our results on the reduced loss of genetic variation at small densities, particularly in polygamous populations, indicate that density regulation may facilitate adaptive evolution at small population sizes.

Estimating fluctuating selection in age-structured populations.

In age-structured populations, viability and fecundity selection of varying strength may occur in different age classes. On the basis of an original idea by Fisher of weighting individuals by their reproductive value, we show that the combined effect of selection on traits at different ages acts through the individual reproductive value defined as the stochastic contribution of an individual to the total reproductive value of the population the following year. The selection differential is a weighted sum of age-specific differentials that are the covariances between the phenotype and the age-specific relative fitness defined by the individual reproductive value. This enables estimation of weak selection on a multivariate quantitative character in populations with no density regulation by combinations of age-specific linear regressions of individual reproductive values on the traits. Demographic stochasticity produces random variation in fitness components in finite samples of individuals and affects the statistical inference of the temporal average directional selection as well as the magnitude of fluctuating selection. Uncertainties in parameter estimates and test power depend strongly on the demographic stochasticity. Large demographic variance results in large uncertainties in yearly estimates of selection that complicates detection of significant fluctuating selection. The method is illustrated by an analysis of age-specific selection in house sparrows on a fitness-related two-dimensional morphological trait, tarsus length and body mass of fledglings.

Population dynamical consequences of climate change for a small temperate songbird.

Predicting the effects of an expected climatic change requires estimates and modeling of stochastic factors as well as density-dependent effects in the population dynamics. In a population of a small songbird, the dipper (Cinclus cinclus), environmental stochasticity and density dependence both influenced the population growth rate. About half of the environmental variance was explained by variation in mean winter temperature. Including these results in a stochastic model shows that an expected change in climate will strongly affect the dynamics of the population, leading to a nonlinear increase in the carrying capacity and in the expected mean population size.

Capsule expression in Streptococcus mitis modulates interaction with oral keratinocytes and alters susceptibility to human antimicrobial peptides.

Streptococcus mitis is a colonizer of the oral cavity and the nasopharynx, and is closely related to Streptococcus pneumoniae. Both species occur in encapsulated and unencapsulated forms, but in S. mitis the role of the capsule in host interactions is mostly unknown. Therefore, the aim of this study was to examine how capsule expression in S. mitis can modulate interactions with the host with relevance for colonization. The S. mitis type strain, as well as two mutants of the type strain, an isogenic capsule deletion mutant, and a capsule switch mutant expressing the serotype 4 capsule of S. pneumoniae TIGR4, were used. Wild-type and capsule deletion strains of S. pneumoniae TIGR4 were included for comparison. We found that capsule production in S. mitis reduced adhesion to oral and lung epithelial cells. Further, exposure of oral epithelial cells to encapsulated S. mitis resulted in higher interleukin-6 and CXCL-8 transcription levels relative to the unencapsulated mutant. Capsule expression in S. mitis increased the sensitivity to human neutrophil peptide 1-3 but reduced the sensitivity to human ß-defensin-3 and cathelicidin. This was in contrast with S. pneumoniae in which capsule expression has been generally associated with increased sensitivity to human antimicrobial peptides (AMPs). Collectively, these findings indicate that capsule expression in S. mitis is important in modulating interactions with epithelial cells, and is associated with increased or reduced susceptibility to AMPs depending on the nature of the AMP.

Inferring patterns of migration from gene frequencies under equilibrium conditions.

A new maximum likelihood method to simultaneously estimate the parameters of any migration pattern from gene frequencies in stochastic equilibrium is developed, based on a model of multivariate genetic drift in a subdivided population. Motivated by simulations of this process in the simplified case of two subpopulations, problems related to the nuisance parameter q, the equilibrium gene frequency, are eliminated by conditioning on the observed mean gene frequency. The covariance matrix of this conditional distribution is calculated by constructing an abstract process that mimics the behavior of the original process in the subspace of interest. The approximation holds as long as there is limited differentiation between subpopulations. The bias and variance of estimates of long-range and short-range migration in a finite stepping stone model are evaluated by fitting the model to simulated data with known values of the parameters. Possible ecological extensions of the model are discussed.

Analysis of genetic structure and dispersal patterns in a population of sea beet.

A model of the migration pattern in a metapopulation of sea beet (Beta vulgaris L. ssp. maritima), based on the continuous distributions of seed and pollen movements, is fitted to gene frequency data at 12 isozyme and RFLP loci by maximum likelihood by using an approximation of the simultaneous equilibrium distribution of the gene frequencies generated by the underlying multivariate stochastic process of genetic drift in the population. Several alternative restrictions of the general model are fitted to the data, including the island model, a model of complete isolation, and a model in which the seed and pollen dispersal variances are equal. Several likelihood ratio tests between these alternatives are performed, and median bias in the estimated parameters is corrected by using parametric bootstrapping. To assess the fit of the selected model, the predicted covariances are compared with covariances computed from the data directly. The dependency of estimated parameters on the ratio between effective and absolute subpopulation sizes, which is treated as a known parameter in the analysis, is also examined. Finally, we note that the data also appear to contain some information about this ratio.

The short form of TSLP is constitutively translated in human keratinocytes and has characteristics of an antimicrobial peptide.

Thymic stromal lymphopoietin (TSLP) has multifaceted immunological functions ranging from maintenance of tolerance to induction of disease. Two human transcript variants of TSLP are described: a long form (variant 1; lfTSLP) consisting of four exons and an alternative, short form (variant 2; sfTSLP) that lacks two exons compared with variant 1. SfTSLP has not been described at the protein level or functionally studied. Here, we demonstrate that the human sfTSLP is the predominant form of TSLP, constitutively expressed at the mRNA and protein level in keratinocytes of oral mucosa and skin and in salivary glands, is released in saliva, and is not regulated in the same manner as the long form. Compared with lfTSLP, sfTSLP exhibits a markedly stronger antibacterial activity. Synthetic sfTSLP did not activate signal transducer and activator of transcription 5 (STAT5) signaling in CD1c(+) dendritic cells nor interfered with STAT5 activation by lfTSLP. SfTSLP may, therefore, act as an antimicrobial peptide in the oral cavity and on the skin to create a defense barrier that aids in the control of both commensal and pathogenic microbes. The results show that the two translational products of the TSLP gene have a different expression and different biological properties, and emphasize the importance of analyzing the two TSLP isoforms separately.

Estimating density dependence from population time series using demographic theory and life-history data.

For populations with a density-dependent life history reproducing at discrete annual intervals, we analyze small or moderate fluctuations in population size around a stable equilibrium, which is applicable to many vertebrate populations. Using a life history having age at maturity alpha, with stochasticity and density dependence in adult recruitment and mortality, we derive a linearized autoregressive equation with time lags from 1 to alpha yr. Contrary to current interpretations, the coefficients corresponding to different time lags in the autoregressive dynamics are not simply measures of delayed density dependence but also depend on life-history parameters. The theory indicates that the total density dependence in a life history, D, should be defined as the negative elasticity of population growth rate per generation with respect to change in population size, [Formula: see text], where lambda is the asymptotic multiplicative growth rate per year, T is the generation time, and N is adult population size. The total density dependence in the life history, D, can be estimated from the sum of the autoregression coefficients. We estimate D in populations of seven vertebrate species for which life-history studies and unusually long time series of complete population censuses are available. Estimates of D were statistically significant and large, on the order of 1 or higher, indicating strong density dependence in five of the seven species. We also show that life history can explain the qualitative features of population autocorrelation functions and power spectra and observations of increasing empirical variance in population size with increasing length of time series.

Estimating the time to extinction in an island population of song sparrows.

We estimated and modelled how uncertainties in stochastic population dynamics and biases in parameter estimates affect the accuracy of the projections of a small island population of song sparrows which was enumerated every spring for 24 years. The estimate of the density regulation in a theta-logistic model (theta = 1.09 suggests that the dynamics are nearly logistic, with specific growth rate r1 = 0.99 and carrying capacity K = 41.54. The song sparrow population was strongly influenced by demographic (sigma2(d) = 0.66) and environmental (sigma2(d) = 0.41) stochasticity. Bootstrap replicates of the different parameters revealed that the uncertainties in the estimates of the specific growth rate r1 and the density regulation theta were larger than the uncertainties in the environmental variance sigma2(e) and the carrying capacity K. We introduce the concept of the population prediction interval (PPI), which is a stochastic interval which includes the unknown population size with probability (1 - alpha). The width of the PPI increased rapidly with time because of uncertainties in the estimates of density regulation as well as demographic and environmental variance in the stochastic population dynamics. Accepting a 10% probability of extinction within 100 years, neglecting uncertainties in the parameters will lead to a 33% overestimation of the time it takes for the extinction barrier (population size X = 1) to be included into the PPI. This study shows that ignoring uncertainties in population dynamics produces a substantial underestimation of the extinction risk.

Stochastic Dispersal Processes in Plant Populations

A dispersal model for airborne pollen based on assumptions about wind directionality, gravity, and a wind threshold at which pollen is taken by the wind is developed, using a three dimensional diffusion approximation. The bivariate probability distribution of pollen receipt by flowers at the same height as the pollen source is derived. Gravity, vertical random movements, and vegetation density turn out to have similar effects on this distribution. Maximum likelihood methods for estimating the combined parameters from data with multiple point or continuous pollen sources, and one or more plant varieties, are developed. Using an example data set from the literature, it is shown that our model gives a better fit than more traditional descriptive dispersal models of the form e-ar b. We also show that estimates of important properties of the dispersal distribution, such as the variances, become considerably smaller using our model than for the more traditional models. Finally, we discuss potential extensions and evolutionary implications of these types of models. Copyright 1997 Academic Press

Epidemiology of AIDS--statistical analyses.

Some central questions concerning the epidemiology of AIDS are addressed by statistical analyses. Applying standard maximum likelihood theory to reported cases of transfusion-associated AIDS in the US, the mean and standard deviation of incubation time for AIDS are estimated to be about 60 and 19 months, respectively. If these parameters are applied to the data from the San Francisco CDC cohort study, we find a good correspondence between estimated and reported cases of AIDS when the probability factor p is 0.27-meaning that about 27% of those infected with HIV are expected to develop AIDS during a period of 8-10 years. Application of the incubation time model and the probability factor p to the data on transfusion-associated AIDS makes it possible to estimate the number of transfusion-associated infections with HIV from 1978 to 1984. These estimates give an exponential increase in the number of cases, with a relative increase of 2.74 each year. It seems reasonable to assume that this increase reflects the spread of the virus within this period.

Sexual mixing models: a comparison of analogue deterministic and stochastic models.

Models for sexual partner choice are discussed for the case of highly variable sexual activity in the population. It is demonstrated that the variances in the number of infected persons may be extremely large. For the random mixing model, higher order cumulants are also evaluated. On the basis of these results the applicability of deterministic models and models for expectations only are questioned. A general model is proposed for handling nonrandom, or correlated, mixing. The problem of inconsistency is overcome by considering the couples having sex as the natural unit in the model. In the case of s discrete homogeneous groups it is shown that only (s2) parameters defining the interaction between the groups can be chosen freely. Finally, the effect of correlation in partner choice is demonstrated by a bivariate lognormal model for partner choice.

A dynamic and spatial model with migration generating the log-Gaussian field of population densities.

A spatial version of a dynamic population model leading to the lognormal distribution is defined. The model establishes relations between the joint spatial and temporal autocorrelation and biological concepts like environmental stochasticity, migration and strength of local density-regulation. The model is generalized to describe communities of species leading to a dynamic and spatial lognormal species abundance model with migration.

Population dynamic models generating the lognormal species abundance distribution.

This paper deals with a new class of stochastic species abundance models where the abundances are the points of an inhomogeneous Poisson process. These models are the result of a dynamic approach in which the changes in abundances through time are described by a multivariate diffusion and speciation constitutes a homogeneous Poisson process. In particular, the lognormal model is generated by assuming that the density regulation within each species is given by the Gompertz curve and that the environmental variances are constant. A substantial generalization is obtained by introducing a general type of interspecific density regulation and correlated environmental noise. This more general mechanism also generates the lognormal species abundance distribution.

Asymmetric competition drives lake use of coexisting salmonids.

To what degree are population differences in resource use caused by competition and the occupation of adjacent positions along environmental gradients evidence of competition? Habitat use may be the result of a competitive lottery, or restricted by competition. We tested to what extent population differences in habitat use of two salmonids, cutthroat trout (Oncorhynchus clarki) and Dolly Varden charr (Salvelinus malma) were influenced by interspecific competition. We hypothesized that the depth distribution of Dolly Varden charr would be affected by competition from the more littoral and surface-oriented cutthroat trout, and that the depth distribution of cutthroat trout would be little affected by competition from Dolly Varden charr. Sympatric populations of cutthroat trout and Dolly Varden charr were created by reciprocal transfers of previously allopatric populations in two experimental lakes. We found evidence of asymmetric competition, as Dolly Varden charr were displaced from littoral habitats when sympatric with cutthroat trout, whereas cutthroat trout remained unaffected by the presence of Dolly Varden charr. Evolved differences between the species, and differences between experimental lakes, also contributed to population differences in habitat use, but asymmetric competition remained as the main driver of different depth distributions in sympatry.

The coverage of a random sample from a biological community.

A taxonomic group will frequently have a large number of species with small abundances. When a sample is drawn at random from this group, one is therefore faced with the problem that a large proportion of the species will not be discovered. A general definition of quantitative measures of "sample coverage" is proposed, and the problem of statistical inference is considered for two special cases, (1) the actual total relative abundance of those species that are represented in the sample, and (2) their relative contribution to the information index of diversity. The analysis is based on a extended version of the negative binomial species frequency model. The results are tabulated.

Age-specific optimal diets and optimal foraging tactics: a life-historic approach.

By linking optimal foraging theory and optimal life history theory, we demonstrate that optimal diets, in general, may depend on the individual's age even when everything else remains the same. Older individuals (i.e., individuals with lower reproductive values) are predicted to have diets composed of highly nutritious food types that are possibly dangerous to pursue.