Aim Despite unprecedented environmental change due to anthropogenic pressure, recent work has found increasing dissimilarity due to turnover but no overall trend in species diversity through time at the local scale. Functional diversity provides a potentially powerful alternative approach for understanding community composition by linking shifts in species identity to the characteristics that underpin ecosystem processes. Here...

Correlative species distribution models are widely used to quantify past shifts in ranges or communities, and to predict future outcomes under ongoing global change. Practitioners confront a wide range of potentially plausible models for ecological dynamics, but most specific applications only consider a narrow set. Here, we clarify that certain model structures can embed restrictive assumptions about key sources of forecast u...

Open‐population spatial capture–recapture (OPSCR) models use the spatial information contained in individual detections collected over multiple consecutive occasions to estimate not only occasion‐specific density, but also demographic parameters. OPSCR models can also estimate spatial variation in vital rates, but such models are neither widely used nor thoroughly tested. We developed a Bayesian OPSCR model that not only accou...

Spatial capture–recapture (SCR) is now routinely used for estimating abundance and density of wildlife populations. A standard SCR model includes sub‐models for the distribution of individual activity centers (ACs) and for individual detections conditional on the locations of these ACs. Both sub‐models can be expressed as point processes taking place in continuous space, but there is a lack of accessible and efficient tools to...

Disconnected habitat fragments are poor at supporting population and community persistence; restoration ecologists, therefore, advocate for the establishment of habitat networks across landscapes. Few empirical studies, however, have considered how networks of restored habitat patches affect metacommunity dynamics. Here, using a 10‐year study on restored hedgerows and unrestored field margins within an intensive agricultural l...

Climate and land‐use changes are thought to be the greatest threats to biodiversity, but few studies have directly measured their simultaneous impacts on species distributions. We used a unique historic resource—early 20th‐century bird surveys conducted by Joseph Grinnell and colleagues—paired with contemporary resurveys a century later to examine changes in bird distributions in California's Central Valley, one of the most in...

Climate niche models project that subalpine forest ranges will extend upslope with climate warming. These projections assume that the climate suitable for adult trees will be adequate for forest regeneration, ignoring climate requirements for seedling recruitment, a potential demographic bottleneck. Moreover, local genetic adaptation is expected to facilitate range expansion, with tree populations at the upper forest edge prov...

Biological communities are structured phylogenetically—closely related species are typically more likely to be found at the same sites. This may be, in part, because they respond similarly to environmental gradients. Accurately surveying biological communities is, however, made difficult by the fact that detection of species is not perfect. In recent years, numerous statistical methods have been developed that aim to overcome...

The interface between roots and soil, known as the rhizosphere, is a dynamic habitat in the soil ecosystem. Unraveling the factors that control rhizosphere community assembly is a key starting point for understanding the diversity of plant‐microbial interactions that occur in soil. The goals of this study were to determine how environmental factors shape rhizosphere microbial communities, such as local soil characteristics and...

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. In this paper, we present a ne...

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...

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. A practical obstacle to i...

Many ecological studies investigate how organisms use resources, such as habitats or foods, in relation to availability or other variables. Related statistical problems include analysis of proportions of species or genotypes in a community or population. These require statistical modeling of compositional count data: data on relative proportions of each category collected as counts. Common methods for analyzing compositional c...

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...

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...

Ecology Letters (2011) 14 : 17–23 Abstract 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 f...

Variation in organismal development is ubiquitous in nature but omitted from most age‐ and stage‐structured population models. I give a general approach for formulating and analyzing its role in density‐independent population models using the framework of integral projection models. The approach allows flexible assumptions, including correlated development times among multiple life stages. I give a new Monte Carlo numerical in...

A central problem in population ecology is to use time series data to estimate the form of density dependence in the per capita growth rate (pgr). This is often accomplished with phenomenological models such as the theta‐Ricker or generalized Beverton‐Holt. Using the theta‐Ricker model as a simple but flexible description of density dependence, we apply theory and simulations to show how multimodality and ridges in the likelih...

We investigate a recent proposal that invasive species display patterns of spatial “spread regulation” analogous to density‐dependent regulation of population abundances. While invasive species do offer valuable tests of ecological theories about spatial spread, we argue that the statistical approach used in the study is not useful, and that the proposed definition of “spread regulation” is likely to be confusing. While concep...