A global database of soil seed bank richness, density, and abundance.

A soil seed bank is the collective name for viable seeds that are stored naturally in the soil. At the species or population level, the ability to form a seed bank represents a strategy for (re)colonization following a disturbance or other change in the local environmental conditions. At the community level, seed banks are thought to buffer local diversity during periods of environmental change and are often studied in relation to the potential for passive habitat restoration.

Unclear relationships between mean survival rate and its environmental variance in vertebrates.

Current environmental changes may increase temporal variability of life history traits of species thus affecting their long-term population growth rate and extinction risk. If there is a general relationship between environmental variances (EVs) and mean annual survival rates of species, that relationship could be used as a guideline for analyses of population growth and extinction risk for populations, where data on EVs are missing. For this purpose, we present a comprehensive compilation of 252 EV estimates from 89 species belonging to five vertebrate taxa (birds, mammals, reptiles, amphibians and fish) covering mean annual survival rates from 0.

Partitioning variance in population growth for models with environmental and demographic stochasticity.

How demographic factors lead to variation or change in growth rates can be investigated using life table response experiments (LTRE) based on structured population models. Traditionally, LTREs focused on decomposing the asymptotic growth rate, but more recently decompositions of annual 'realized' growth rates using 'transient' LTREs have gained in popularity. Transient LTREs have been used particularly to understand how variation in vital rates translate into variation in growth for populations under long-term study.

Role of weather and other factors in the dynamics of a low-density insect population.

Insect population dynamics are the result of an interplay between intrinsic factors such as density dependence, trophic web interactions, and external forces such as weather conditions. We investigate potential mechanisms of population dynamics in a natural, low-density insect population. Eggs and larvae of the noctuid moth, , develop on its host plant during summer.

Temporal trends in opportunistic citizen science reports across multiple taxa.

Opportunistic reporting of species observations to online platforms provide one of the most extensive sources of information about the distribution and status of organisms in the wild. The lack of a clear sampling design, and changes in reporting over time, leads to challenges when analysing these data for temporal change in organisms. To better understand temporal changes in reporting, we use records submitted to an online platform in Sweden (Artportalen), currently containing 80 million records.

Cannot see the diversity for all the species: Evaluating inclusion criteria for local species lists when using abundant citizen science data.

Abundant citizen science data on species occurrences are becoming increasingly available and enable identifying composition of communities occurring at multiple sites with high temporal resolution. However, for species displaying temporary patterns of local occurrences that are transient to some sites, biodiversity measures are clearly dependent on the criteria used to include species into local species lists. Using abundant opportunistic citizen science data from frequently visited wetlands, we investigated the sensitivity of α- and β-diversity estimates to the use raw versus detection-corrected data and to the use of inclusion criteria for species presence reflecting alternative site use.

Why we should care about movements: Using spatially explicit integrated population models to assess habitat source-sink dynamics.

Assessing the source-sink status of populations and habitats is of major importance for understanding population dynamics and for the management of natural populations. Sources produce a net surplus of individuals (per capita contribution to the metapopulation > 1) and will be the main contributors for self-sustaining populations, whereas sinks produce a deficit (contribution < 1). However, making these types of assessments is generally hindered by the problem of separating mortality from permanent emigration, especially when survival probabilities as well as moved distances are habitat-specific.

Factors influencing plasticity in the arrival-breeding interval in a migratory species reacting to climate change.

Climate change is profoundly affecting the phenology of many species. In migratory birds, there is evidence for advances in their arrival time at the breeding ground and their timing of breeding, yet empirical studies examining the interdependence between arrival and breeding time are lacking. Hence, evidence is scarce regarding how breeding time may be adjusted via the arrival-breeding interval to help local populations adapt to local conditions or climate change.

Quantifying the links between land use and population growth rate in a declining farmland bird.

Land use is likely to be a key driver of population dynamics of species inhabiting anthropogenic landscapes, such as farmlands. Understanding the relationships between land use and variation in population growth rates is therefore critical for the management of many farmland species. Using 24 years of data of a declining farmland bird in an integrated population model, we examined how spatiotemporal variation in land use (defined as habitats with "Short" and "Tall" ground vegetation during the breeding season) and habitat-specific demographic parameters relates to variation in population growth taking into account individual movements between habitats.

New measures for evaluation of environmental perturbations using Before-After-Control-Impact analyses.

Before-After-Control-Impact (BACI) designs are powerful tools to derive inferences about environmental perturbations (e.g., hurricanes, restoration programs) when controlled experimental designs are unfeasible.

Exploiting opportunistic observations to estimate changes in seasonal site use: An example with wetland birds.

Nonsystematically collected, a.k.a.

Seed production and predation in a changing climate: new roles for resource and seed predator feedback?

Climate change may cause changes in the dynamics of populations beyond comparatively simple directional effects. To better understand complex effects on dynamics requires long-term studies of populations that experience changes in climatic conditions. We study the dynamics of a seed-production-seed-predation system, consisting of a perennial herb and its two seed predatory insects, over a 40-yr period during which climate change has caused the annual growing season to increase by 20 d.

Disentangling the effects of date, individual, and territory quality on the seasonal decline in fitness.

The seasonal timing of reproduction is a major fitness factor in many organisms. Commonly, individual fitness declines with time in the breeding season. We investigated three suggested but rarely tested hypotheses for this seasonal fitness decline: (1) time per se (date hypothesis), (2) late breeders are of lower quality than early ones (individual quality hypothesis), and (3) late breeders are breeding at poorer territories than early breeders (territory quality hypothesis).

Monte Carlo estimation of stage structured development from cohort data.

Cohort data are frequently collected to study stage-structured development and mortalities of many organisms, particularly arthropods. Such data can provide information on mean stage durations, among-individual variation in stage durations, and on mortality rates. Current statistical methods for cohort data lack flexibility in the specification of stage duration distributions and mortality rates.

An approximate Bayesian computation approach to parameter estimation in a stochastic stage-structured population model.

Complex population processes may require equally complex models, which can lead to analytically intractable estimation problems. Approximate Bayesian computation (ABC) is a computational tool for parameter estimation in situations where likelihoods cannot be computed. Instead of using likelihoods, ABC methods quantify the similarities between an observed data set and repeated simulations from a model.

The importance of individual developmental variation in stage-structured population models.

Population stage structure is fundamental to ecology, and models of this structure have proven useful in many different systems. Many ecological variables other than stage, such as habitat type, site occupancy and metapopulation status are also modelled using transitions among discrete states. Transitions among life stages can be characterised by the distribution of time spent in each stage, including the mean and variance of each stage duration and within-individual correlations among multiple stage durations.

Estimation of stage duration distributions and mortality under repeated cohort censuses.

Many processes in nature can be viewed as arising from subjects progressing through sequential stages and may be described by multistage models. Examples include disease development and the physiological development of plants and animals. We develop a multistage model for sampling designs where a small set of subjects is followed and the number of subjects in each stage is assessed repeatedly for a sequence of time points, but for which the subjects cannot be identified.

Using uncertainty estimates in analyses of population time series.

Recording and monitoring wildlife is crucial for the conservation of wild species and the protection of their environment. The most common type of information reported from a monitoring scheme is a time series of population abundance estimates, but the potential of such data for analyzing population dynamics is limited due to lack of information on sampling error. Recent work has shown that replicating the sampling process and analyzing replicates jointly in a dynamical model can considerably increase estimation efficiency compared to analyzing population estimates alone.

Estimating tree growth from complex forest monitoring data.

Understanding tree growth as a function of tree size is important for a multitude of ecological and management applications. Determining what limits growth is of central interest, and forest inventory permanent plots are an abundant source of long-term information but are highly complex. Observation error and multiple sources of shared variation (spatial plot effects, temporal repeated measures, and a mosaic of sampling intervals) make these data challenging to use for growth estimation.

Separating direct and indirect effects of global change: a population dynamic modeling approach using readily available field data.

Two sources of complexity make predicting plant community response to global change particularly challenging. First, realistic global change scenarios involve multiple drivers of environmental change that can interact with one another to produce non-additive effects. Second, in addition to these direct effects, global change drivers can indirectly affect plants by modifying species interactions.

Fitting complex population models by combining particle filters with Markov chain Monte Carlo.

We show how a recent framework combining Markov chain Monte Carlo (MCMC) with particle filters (PFMCMC) may be used to estimate population state-space models. With the purpose of utilizing the strengths of each method, PFMCMC explores hidden states by particle filters, while process and observation parameters are estimated using an MCMC algorithm. PFMCMC is exemplified by analyzing time series data on a red kangaroo (Macropus rufus) population in New South Wales, Australia, using MCMC over model parameters based on an adaptive Metropolis-Hastings algorithm.

Are patterns of density dependence in the Global Population Dynamics Database driven by uncertainty about population abundance?

Density dependence in population growth rates is of immense importance to ecological theory and application, but is difficult to estimate. The Global Population Dynamics Database (GPDD), one of the largest collections of population time series available, has been extensively used to study cross-taxa patterns in density dependence. A major difficulty with assessing density dependence from time series is that uncertainty in population abundance estimates can cause strong bias in both tests and estimates of strength.

Individual heterogeneity and senescence in silvereyes on Heron Island.

Individual heterogeneity and correlations between life history traits play a fundamental role in life history evolution and population dynamics. Unobserved individual heterogeneity in survival can be a nuisance for estimation of age effects at the individual level by causing bias due to mortality selection. We jointly analyze survival and breeding output from successful breeding attempts in an island population of Silvereyes (Zosterops lateralis chlorocephalus) by fitting models that incorporate age effects and individual heterogeneity via random effects.

On observation distributions for state space models of population survey data.

1. State space models are starting to replace more simple time series models in analyses of temporal dynamics of populations that are not perfectly censused. By simultaneously modelling both the dynamics and the observations, consistent estimates of population dynamical parameters may be obtained.

Effects of weather and climate on the dynamics of animal population time series.

Weather is one of the most basic factors impacting animal populations, but the typical strength of such impacts on population dynamics is unknown. We incorporate weather and climate index data into analysis of 492 time series of mammals, birds and insects from the global population dynamics database. A conundrum is that a multitude of weather data may a priori be considered potentially important and hence present a risk of statistical over-fitting.