IPMpack: an R package for integral projection models

Natural coral recovery despite negative population growth

Demographic processes that ensure the recovery and resilience of marine populations are critical as climate change sends an increasing proportion on a trajectory of decline. Yet for some populations, recovery potential remains high. We conducted annual monitoring over 9 years (2012-2020) to assess the recovery of coral populations belonging to the genus Pocillopora. These populations experienced a catastrophic collapse following a severe typhoon in 2009. From the start of the monitoring period, high initial recruitment led to the establishment of a juvenile population that rapidly transitioned to sexually mature adults, which dominated the population within 6 years after the disturbance. As a result, coral cover increased from 1.1% to 20.2% during this time. To identify key demographic drivers of recovery and population growth rates (λ), we applied kernel-resampled integral projection models (IPMs), constructing eight successive models to examine annual change. IPMs were able to capture reproductive traits as key demographic drivers over the initial 3 years, while individual growth was a continuous key demographic driver throughout the entire monitoring period. IPMs further detected a pulse of reproductive output subsequent to two further Category 5 typhoon events during the monitoring period, exemplifying key mechanisms of resilience for coral populations impacted by disturbance. Despite rapid recovery, (i.e., increased coral cover, individual colony growth, low mortality), IPMs estimated predominantly negative values of λ, indicating a declining population. Indeed, while λ translates to a change in the number of individuals, the recovery of coral populations can also be driven by an increase in the size of surviving colonies. Our results illustrate that accumulating long-term data on historical dynamics and applying IPMs to extract demographic drivers are crucial for future predictions that are based on comprehensive and robust understandings of ecological change.

Modelling the dynamics of Pinus sylvestris forests after a die-off event under climate change scenarios

In recent decades, die-off events in Pinus sylvestris populations have increased. The causes of these phenomena, which are usually related to local and regional extreme hot droughts, have been extensively investigated from a physiological viewpoint. However, the consequences of die-off process in terms of demography and vegetation dynamics have been less thoroughly addressed. Here, we projected P. sylvestris plot dynamics after a die-off event, under climate change scenarios, considering also their early demographic stages (i.e., seedlings, saplings and ingrowth from the sapling to adult class), to assess the resilience of P. sylvestris populations after such events. We used Integral Projection Models (IPMs) to project future plot structure under current climate, and under RCP4.5 and RCP8.0 climate scenarios, using climatic suitability - extracted from Species Distribution Models - as a covariable in the estimations of vital rates over time. Field data feeding IPMs were obtained from two successive surveys, at the end of the die-off event (2013) and four years later (2017), undertaken on populations situated across the P. sylvestris range of distribution in Catalonia (NE Spain). Plots affected by die-off experienced a loss of large trees, which causes that basal area, tree diameter and tree density will remain lower for decades relative to unaffected plots. After the event, this situation is partially counterbalanced in affected plots by a greater increase in basal area and seedling recruitment into tree stage, thus promoting resilience. However, resilience is delayed under the climate-change scenarios with warmer and drier conditions involving additional physiological stress, due to a reduced abundance of seedlings and a smaller plot basal area. The study shows lagged effect of drought-induced die-off events on forest structure, also revealing stabilizing mechanisms, such as recruitment and tree growth release, which enhance resilience. However, these mechanisms would be jeopardized by oncoming regional warming.

Projected Status of the Ghost Orchid (Dendrophylax lindenii) in Florida during the Next Decade Based on Temporal Dynamic Studies Spanning Six Years

The enigmatic ghost orchid, Dendrophylax lindenii (Lindley) Bentham ex Rolfe, is a showy leafless epiphyte restricted to low-lying forests in south Florida and western Cuba. Because of its appeal and reputation for being difficult to cultivate, D. lindenii remains vulnerable to poaching and environmental changes. About 2000 individuals are assumed to remain in Florida, most confined within water-filled cypress domes in the Fakahatchee Strand, but virtually no information exists on current population numbers throughout the region. This paper provides a preliminary summary of the ghost orchid’s projected status based on six continuous years of data collected within the Florida Panther National Wildlife Refuge (FPNWR) from 2015–2020. The orchids were clustered in seven different populations, each separated by ca. 5 km. Quantitative data were collected spanning three age classes (seedlings, juveniles, mature plants) for each population, and survival, flowering, and fruiting were noted. To estimate the temporal variability in the demographic rates, size-structured integral projection models (IPMs) were constructed for each annual transition (e.g., 2015–2016, 2016–2017). Results for all seven populations pooled suggest that D. lindenii numbers will decline by 20% during the next decade in the absence of external adverse factors. Seedling recruitment is not expected to keep pace with the projected decline. Only one population, which was also from the wettest location, continuously harbored spontaneous seedlings, suggesting that most populations within the FPNWR lack conditions suitable for reproduction.

Demographic effects of interacting species: exploring stable coexistence under increased climatic variability in a semiarid shrub community

Population persistence is strongly determined by climatic variability. Changes in the patterns of climatic events linked to global warming may alter population dynamics, but their effects may be strongly modulated by biotic interactions. Plant populations interact with each other in such a way that responses to climate of a single population may impact the dynamics of the whole community. In this study, we assess how climate variability affects persistence and coexistence of two dominant plant species in a semiarid shrub community on gypsum soils. We use 9 years of demographic data to parameterize demographic models and to simulate population dynamics under different climatic and ecological scenarios. We observe that populations of both coexisting species may respond to common climatic fluctuations both similarly and in idiosyncratic ways, depending on the yearly combination of climatic factors. Biotic interactions (both within and among species) modulate some of their vital rates, but their effects on population dynamics highly depend on climatic fluctuations. Our results indicate that increased levels of climatic variability may alter interspecific relationships. These alterations might potentially affect species coexistence, disrupting competitive hierarchies and ultimately leading to abrupt changes in community composition.

Integral Projection Models and Sustainable Forest Management of Agave inaequidens in Western Mexico

In México, at least 37 Agave species are extracted from wild populations for producing distilled spirits. This activity involves harvesting mature agaves just before producing their inflorescences, which cancels sexual reproduction of plants used. The increasing demand of agaves spirits in national and international markets is determining a strong pressure on wild populations, most of them lacking adequate management. In addition, the dynamics of agave populations may be affected by natural phenomena like oscillation of rainfall regimes, which affects the recruitment of agave seedlings, or the scarcity of pollinators that may affect seed production and general population dynamics. We studied the demography of wild populations of Agave inaequidens to analyze critical conditions for populations recovery, modelling the effects of rainfall trends on the demographic performance of this species, and exploring response of populations to hypothetical extraction regimes and reforestation efforts. Our study was performed in four well-conserved wild populations in Central Western Mexico, each population was sampled in a plot of about one hectare composed by 10 subplots 50 x 5 m (2500 m²). Populations were monitored yearly between 2011 and 2013, measuring plant size, reproductive individuals, and fecundity. Data were analyzed through integral projection models by using the IPMpack for R, to perform prospective analyses. We in addition constructed stochastic models to explore the possible influence of rainfall variation on species demography, using data for the drier and wetter years of the study period. Population growth varied from λ=1.003 to λ=0.899 among populations and years, and exceptionally λ=0.559 after a fire event. Low rainfall decreases λ values, indicating especial limitations to harvesting agaves during dry years whose frequency most probably will increase. In general, extraction rates from 10% to 30% of mature individuals are viable to maintain λ above 1, and these rates may be higher if new plants are introduced in populations. Depending on levels of extraction, our models suggest that it is necessary to carry out actions of reforestation, and in situ management according to the trends found in each site. This is one indispensable condition to maintain λ close to or greater than 1. Sustainable extraction of wild agaves is possible, some communities are already carrying out a repertoire of goods practices in this direction, but together with ecological criteria and good management techniques, strict regulations and social organization are needed to achieve it.

Forecasting species range dynamics with process-explicit models: matching methods to applications

Knowing where species occur is fundamental to many ecological and environmental applications. Species distribution models (SDMs) are typically based on correlations between species occurrence data and environmental predictors, with ecological processes captured only implicitly. However, there is a growing interest in approaches that explicitly model processes such as physiology, dispersal, demography and biotic interactions. These models are believed to offer more robust predictions, particularly when extrapolating to novel conditions. Many process-explicit approaches are now available, but it is not clear how we can best draw on this expanded modelling toolbox to address ecological problems and inform management decisions. Here, we review a range of process-explicit models to determine their strengths and limitations, as well as their current use. Focusing on four common applications of SDMs - regulatory planning, extinction risk, climate refugia and invasive species - we then explore which models best meet management needs. We identify barriers to more widespread and effective use of process-explicit models and outline how these might be overcome. As well as technical and data challenges, there is a pressing need for more thorough evaluation of model predictions to guide investment in method development and ensure the promise of these new approaches is fully realised.

Variation across river channels in demographic dynamics of a riparian herb with threatened status: management and conservation implications

PREMISE

Gesneria pauciflora is a rare, threatened plant in riparian forests. Periodic disturbances, expected in this habitat, could influence demographic dynamics on plant populations, yet their impact may not be the same across the watershed. We hypothesized that differences in disturbances between the main channel and tributaries may lead to spatial dissimilarities in population growth rate (λ), structure, and fecundity.

METHODS

In the Maricao River Watershed in Puerto Rico, 1277 plants were tagged and monitored for 1.5 years. Every 6 months, we measured plant size and recorded survival, fecundity, and appearance of seedlings. These variables were used in integral projection models to assess the population status of G. pauciflora.

RESULTS

Plants in the main channel were smaller but more likely to flower and fruit than those in the tributaries. Overall mortality was greater in the main channel and greater during the rainy season. At both sites, λ ranged from 0.9114 to 0.9865, and survival/growth of larger plants had a greater effect on λ (>0.90) regardless of site.

CONCLUSIONS

Values for population growth rates suggest that G. pauciflora is declining across the watershed. Higher mortality rates in the main channel (more-perturbed sites) might drive G. pauciflora to reproduce at smaller sizes, while tributaries (less-perturbed sites) might be better for growth and lead to larger plant sizes. Extreme climatic events are expected to increase in the Caribbean and might decrease the population if the population is left unmanaged. Management strategies that reduce the time plants require to reach larger sizes might be necessary to increase λ, and reintroduction using cuttings might be a possible solution.

The devil is in the detail: Nonadditive and context-dependent plant population responses to increasing temperature and precipitation

In climate change ecology, simplistic research approaches may yield unrealistically simplistic answers to often more complicated problems. In particular, the complexity of vegetation responses to global climate change begs a better understanding of the impacts of concomitant changes in several climatic drivers, how these impacts vary across different climatic contexts, and of the demographic processes underlying population changes. Using a replicated, factorial, whole-community transplant experiment, we investigated regional variation in demographic responses of plant populations to increased temperature and/or precipitation. Across four perennial forb species and 12 sites, we found strong responses to both temperature and precipitation change. Changes in population growth rates were mainly due to changes in survival and clonality. In three of the four study species, the combined increase in temperature and precipitation reflected nonadditive, antagonistic interactions of the single climatic changes for population growth rate and survival, while the interactions were additive and synergistic for clonality. This disparity affects the persistence of genotypes, but also suggests that the mechanisms behind the responses of the vital rates differ. In addition, survival effects varied systematically with climatic context, with wetter and warmer + wetter transplants showing less positive or more negative responses at warmer sites. The detailed demographic approach yields important mechanistic insights into how concomitant changes in temperature and precipitation affect plants, which makes our results generalizable beyond the four study species. Our comprehensive study design illustrates the power of replicated field experiments in disentangling the complex relationships and patterns that govern climate change impacts across real-world species and landscapes.

Plastic Population Effects and Conservative Leaf Traits in a Reciprocal Transplant Experiment Simulating Climate Warming in the Himalayas

Climate warming poses considerable challenges for alpine plant species, especially for competitively inferior ones with resource-conservative adaptations to cold climates. The Himalayas are warming at rates considerably faster than the global average, so it is particularly important to assess how and through which mechanisms alpine plant species are affected there. We employed a demographic approach in a climate change experiment, where vegetation turfs were transplanted reciprocally between the central parts of the study species' (Viola biflora L. var. rockiana) range and the warmer range margin, with a temperature difference of ca. 1°C. In addition, turfs were also transplanted outside the range to warmer habitats, simulating two different scenarios of climate warming, +1 and +4°C. Transplanting to warmer sites negatively impacted population growth rates (λ), survival and clonality, but did not affect growth and fecundity, while the productivity of the plant community increased. The reciprocal transplants to the colder habitat showed the opposite effects, for both V. biflora and the plant community, indicating plastic responses of the study species, driven by changes in plant-plant competition. However, the leaf traits underlying the modeled population growth rates were origin-site specific and not affected by the climate-change treatments over the study period, suggesting local adaptation of growth form to competition in the warmer range margin, and to climate adversity in the colder range center. The transplants outside the present species' range showed consistently stronger reductions in population growth rate and survival, with mortality of 90-100% in the +4°C treatment. This illustrates that climatic changes beyond species' present climatic ranges pose a serious risk for range contraction and extinction for Himalayan alpine species in the near future. As V. biflora seems mostly limited by competition under warming, its persistence in a future climate may become increasingly dependent on keeping competitive effects from the surrounding community low, for instance by management interventions like grazing and mowing.

Time to cut: population models reveal how to mow invasive common ragweed cost-effectively

Roadsides are an important habitat for invasive common ragweed, Ambrosiaartemisiifolia L., by facilitating seed dispersal. Reducing the size of roadside populations is therefore essential for confining this highly allergenic species. Here, we aim to determine the cost-effectiveness of mowing regimes varying in frequency and timing, by analysing population-level effects and underlying demographic processes. We constructed population models of A.artemisiifolia parameterised by demographic data for four unmanaged reference populations across Europe in two years. We integrated the effects of four experimental mowing regimes along Austrian road sides on plant performance traits of five years and experimental data on seed viability after cutting. All four experimental regimes reduced the projected intrinsic population growth rates (r) compared to the unmanaged controls by reducing plant height and seed viability, thereby counteracting increased size-dependent fecundity. The prevailing 2-cut regime in Austria (cutting during vegetative growth, here in June and just before seed ripening, here in September) performed least well and the reduction in r was mainly due to reduced seed viability after the second cut. The efficacy of the two best experimental regimes (alternative schemes for 2 or 3 cuts) was mainly due to cutting just before female flowering (here in August) by decreasing final adult plant height dramatically and thereby reducing seed numbers. Patterns were consistent across reference populations and years. Whether regimes reduced r below replacement level, however, varied per population, year and the survival rate of the seeds in the soil bank. Our model allowed projecting effects of five theoretical mowing regimes with untested combinations of cuts on r. By plotting r-cost relationships for all regimes, we identified the most cost-effective schemes for each cutting frequency (1–3 cuts). They all included the cut just before female flowering, highlighting the importance of cutting at this moment (here in August). Our work features i) the suitability of a modelling approach for the demography of an annual species with a seed bank, ii) the importance of seed viability in assessing mowing effects, iii) the use of population models in designing cost-effective mowing regimes.

Delivering the promises of trait-based approaches to the needs of demographic approaches, and vice versa

Few facets of biology vary more than functional traits and life-history traits. To explore this vast variation, functional ecologists and population ecologists have developed independent approaches that identify the mechanisms behind and consequences of trait variation.Collaborative research between researchers using trait-based and demographic approaches remains scarce. We argue that this is a missed opportunity, as the strengths of both approaches could help boost the research agendas of functional ecology and population ecology.This special feature, which spans three journals of the British Ecological Society due to its interdisciplinary nature, showcases state-of-the-art research applying trait-based and demographic approaches to examine relationships between organismal function, life history strategies and population performance across multiple kingdoms. Examples include the exploration of how functional trait × environment interactions affect vital rates and thus explain population trends and species occurrence; the coordination of seed traits and dispersal ability with the pace of life in plants; the incorporation of functional traits in dynamic energy budget models; or the discovery of linkages between microbial functional traits and the fast-slow continuum.Despite their historical isolation, collaborative work between functional ecologists and population ecologists could unlock novel research pathways. We call for an integrative research agenda to evaluate which and when traits are functional, as well as their ability to describe and predict life history strategies and population dynamics. We highlight promising, complementary research avenues to overcome current limitations. These include a more explicit linkage of selection gradients in the context of functional trait-vital rate relationships, and the implementation of standardised protocols to track changes in traits and vital rates over time at the same location and individuals, thus allowing for the explicit incorporation of trade-offs in analyses of covariation of functional traits and life-history traits.

Implications of clonality for ageing research

Senescence, an organismal performance decline with age, has historically been considered a universal phenomenon by evolutionary biologists and zoologist. Yet, increasing fertility and survival with age are nothing new to plant ecologists, among whom it is common knowledge that senescence is not universal. Recently, these two realities have come into a confrontation, begging for the rephrasing of the classical question that has led ageing research for decades: “why do we senesce?” to a more practical “what are the mechanisms by which some organisms escape from senescence?” Plants are amenable to examining this question because of their rich repertoire of life history strategies. These include the existence of permanent seed banks, vegetative dormancy and ability to produce clones, among others. Here, I use a large number of high resolution demographic models from 181 species that reflect life history strategies and their trade-offs among herbaceous perennials, succulents and shrubs measured under field conditions worldwide to examine whether senescence rates of ramets from clonal plants differ from those of whole plants reproducing either strictly sexually, or with a combination of sexual and clonal mechanisms. Contrary to the initial expectation from the mutation accumulation theory of senescence, ramets of clonal plants were more likely to exhibit senescence than those species employing sexual reproduction. I discuss why these comparisons between ramets and genets are useful, as well as its implications and future directions for ageing research.

Fitting state-space integral projection models to size-structured time series data to estimate unknown parameters

Integral projection models (IPMs) have a number of advantages over matrix-model approaches for analyzing size-structured population dynamics, because the latter require parameter estimates for each age or stage transition. However, IPMs still require appropriate data. Typically they are parameterized using individual-scale relationships between body size and demographic rates, but these are not always available. We present an alternative approach for estimating demographic parameters from time series of size-structured survey data using a Bayesian state-space IPM (SSIPM). By fitting an IPM in a state-space framework, we estimate unknown parameters and explicitly account for process and measurement error in a dataset to estimate the underlying process model dynamics. We tested our method by fitting SSIPMs to simulated data; the model fit the simulated size distributions well and estimated unknown demographic parameters accurately. We then illustrated our method using nine years of annual surveys of the density and size distribution of two fish species (blue rockfish, Sebastes mystinus, and gopher rockfish, S. carnatus) at seven kelp forest sites in California. The SSIPM produced reasonable fits to the data, and estimated fishing rates for both species that were higher than our Bayesian prior estimates based on coast-wide stock assessment estimates of harvest. That improvement reinforces the value of being able to estimate demographic parameters from local-scale monitoring data. We highlight a number of key decision points in SSIPM development (e.g., open vs. closed demography, number of particles in the state-space filter) so that users can apply the method to their own datasets.

Sex-specific responses to climate change in plants alter population sex ratio and performance

Males and females are ecologically distinct in many species, but whether responses to climate change are sex-specific is unknown. We document sex-specific responses to climate change in the plant Valeriana edulis (valerian) over four decades and across its 1800-meter elevation range. Increased elevation was associated with increased water availability and female frequency, likely owing to sex-specific water use efficiency and survival. Recent aridification caused male frequency to move upslope at 175 meters per decade, a rate of trait shift outpacing reported species' range shifts by an order of magnitude. This increase in male frequency reduced pollen limitation and increased seedset. Coupled with previous studies reporting sex-specific arthropod communities, these results underscore the importance of ecological differences between the sexes in mediating biological responses to climate change.

From facilitation to competition: temperature-driven shift in dominant plant interactions affects population dynamics in seminatural grasslands

Biotic interactions are often ignored in assessments of climate change impacts. However, climate-related changes in species interactions, often mediated through increased dominance of certain species or functional groups, may have important implications for how species respond to climate warming and altered precipitation patterns. We examined how a dominant plant functional group affected the population dynamics of four co-occurring forb species by experimentally removing graminoids in seminatural grasslands. Specifically, we explored how the interaction between dominants and subordinates varied with climate by replicating the removal experiment across a climate grid consisting of 12 field sites spanning broad-scale temperature and precipitation gradients in southern Norway. Biotic interactions affected population growth rates of all study species, and the net outcome of interactions between dominants and subordinates switched from facilitation to competition with increasing temperature along the temperature gradient. The impacts of competitive interactions on subordinates in the warmer sites could primarily be attributed to reduced plant survival. Whereas the response to dominant removal varied with temperature, there was no overall effect of precipitation on the balance between competition and facilitation. Our findings suggest that global warming may increase the relative importance of competitive interactions in seminatural grasslands across a wide range of precipitation levels, thereby favouring highly competitive dominant species over subordinate species. As a result, seminatural grasslands may become increasingly dependent on disturbance (i.e. traditional management such as grazing and mowing) to maintain viable populations of subordinate species and thereby biodiversity under future climates. Our study highlights the importance of population-level studies replicated under different climatic conditions for understanding the underlying mechanisms of climate change impacts on plants.

Integral Projection Models for host-parasite systems with an application to amphibian chytrid fungus

Host parasite models are typically constructed under either a microparasite or macroparasite paradigm. However, this has long been recognized as a false dichotomy because many infectious disease agents, including most fungal pathogens, have attributes of both microparasites and macroparasites.We illustrate how Integral Projection Models (IPM)s provide a novel, elegant modeling framework to represent both types of pathogens. We build a simple host-parasite IPM that tracks both the number of susceptible and infected hosts and the distribution of parasite burdens in infected hosts.The vital rate functions necessary to build IPMs for disease dynamics share many commonalities with classic micro and macroparasite models and we discuss how these functions can be parameterized to build a host-parasite IPM. We illustrate the utility of this IPM approach by modeling the temperature-dependent epizootic dynamics of amphibian chytrid fungus in Mountain yellow-legged frogs (Rana muscosa).The host-parasite IPM can be applied to other diseases such as facial tumor disease in Tasmanian devils and white-nose syndrome in bats. Moreover, the host-parasite IPM can be easily extended to capture more complex disease dynamics and provides an exciting new frontier in modeling wildlife disease.

COMADRE: a global data base of animal demography

The open‐data scientific philosophy is being widely adopted and proving to promote considerable progress in ecology and evolution. Open‐data global data bases now exist on animal migration, species distribution, conservation status, etc. However, a gap exists for data on population dynamics spanning the rich diversity of the animal kingdom world‐wide. This information is fundamental to our understanding of the conditions that have shaped variation in animal life histories and their relationships with the environment, as well as the determinants of invasion and extinction.

Matrix population models (MPMs) are among the most widely used demographic tools by animal ecologists. MPMs project population dynamics based on the reproduction, survival and development of individuals in a population over their life cycle. The outputs from MPMs have direct biological interpretations, facilitating comparisons among animal species as different as Caenorhabditis elegans, Loxodonta africana and Homo sapiens.

Thousands of animal demographic records exist in the form of MPMs, but they are dispersed throughout the literature, rendering comparative analyses difficult. Here, we introduce the COMADRE Animal Matrix Database, an open‐data online repository, which in its version 1.0.0 contains data on 345 species world‐wide, from 402 studies with a total of 1625 population projection matrices. COMADRE also contains ancillary information (e.g. ecoregion, taxonomy, biogeography, etc.) that facilitates interpretation of the numerous demographic metrics that can be derived from its MPMs. We provide R code to some of these examples.

Synthesis: We introduce the COMADRE Animal Matrix Database, a resource for animal demography. Its open‐data nature, together with its ancillary information, will facilitate comparative analysis, as will the growing availability of databases focusing on other aspects of the rich animal diversity, and tools to query and combine them. Through future frequent updates of COMADRE, and its integration with other online resources, we encourage animal ecologists to tackle global ecological and evolutionary questions with unprecedented sample size.

Opportunities and challenges of Integral Projection Models for modelling host-parasite dynamics

Epidemiological dynamics are shaped by and may in turn shape host demography. These feedbacks can result in hard to predict patterns of disease incidence. Mathematical models that integrate infection and demography are consequently a key tool for informing expectations for disease burden and identifying effective measures for control.

A major challenge is capturing the details of infection within individuals and quantifying their downstream impacts to understand population‐scale outcomes. For example, parasite loads and antibody titres may vary over the course of an infection and contribute to differences in transmission at the scale of the population. To date, to capture these subtleties, models have mostly relied on complex mechanistic frameworks, discrete categorization and/or agent‐based approaches.

Integral Projection Models (IPMs) allow variance in individual trajectories of quantitative traits and their population‐level outcomes to be captured in ways that directly reflect statistical models of trait–fate relationships. Given increasing data availability, and advances in modelling, there is considerable potential for extending this framework to traits of relevance for infectious disease dynamics.

Here, we provide an overview of host and parasite natural history contexts where IPMs could strengthen inference of population dynamics, with examples of host species ranging from mice to sheep to humans, and parasites ranging from viruses to worms. We discuss models of both parasite and host traits, provide two case studies and conclude by reviewing potential for both ecological and evolutionary research.

When stable-stage equilibrium is unlikely: integrating transient population dynamics improves asymptotic methods

BACKGROUND AND AIMS

Evaluation of population projection matrices (PPMs) that are focused on asymptotically based properties of populations is a commonly used approach to evaluate projected dynamics of managed populations. Recently, a set of tools for evaluating the properties of transient dynamics has been expanded to evaluate PPMs and to consider the dynamics of populations prior to attaining the stable-stage distribution, a state that may never be achieved in disturbed or otherwise ephemeral habitats or persistently small populations. This study re-evaluates data for a tropical orchid and examines the value of including such analyses in an integrative approach.

METHODS

Six small populations of Lepanthes rubripetala were used as a model system and the R software package popdemo was used to produce estimates of the indices for the asymptotic growth rate (lambda), sensitivities, reactivity, first-time step attenuation, maximum amplification, maximum attenuation, maximal inertia and maximal attenuation. The response in lambda to perturbations of demographic parameters using transfer functions and multiple perturbations on growth, stasis and fecundity were also determined. The results were compared with previously published asymptotic indices.

KEY RESULTS

It was found that combining asymptotic and transient dynamics expands the understanding of possible population changes. Comparison of the predicted density from reactivity and first-time step attenuation with the observed change in population size in two orchid populations showed that the observed density was within the predicted range. However, transfer function analysis suggests that the traditional approach of measuring perturbation of growth rates and persistence (inertia) may be misleading and is likely to result in erroneous management decisions.

CONCLUSIONS

Based on the results, an integrative approach is recommended using traditional PPMs (asymptotic processes) with an evaluation of the diversity of dynamics that may arise when populations are not at a stable-stage distribution (transient processes). This method is preferable for designing rapid and efficient interventions after disturbances, and for developing strategies to establish new populations.

Building integral projection models: a user's guide

In order to understand how changes in individual performance (growth, survival or reproduction) influence population dynamics and evolution, ecologists are increasingly using parameterized mathematical models. For continuously structured populations, where some continuous measure of individual state influences growth, survival or reproduction, integral projection models (IPMs) are commonly used. We provide a detailed description of the steps involved in constructing an IPM, explaining how to: (i) translate your study system into an IPM; (ii) implement your IPM; and (iii) diagnose potential problems with your IPM. We emphasize how the study organism's life cycle, and the timing of censuses, together determine the structure of the IPM kernel and important aspects of the statistical analysis used to parameterize an IPM using data on marked individuals. An IPM based on population studies of Soay sheep is used to illustrate the complete process of constructing, implementing and evaluating an IPM fitted to sample data. We then look at very general approaches to parameterizing an IPM, using a wide range of statistical techniques (e.g. maximum likelihood methods, generalized additive models, nonparametric kernel density estimators). Methods for selecting models for parameterizing IPMs are briefly discussed. We conclude with key recommendations and a brief overview of applications that extend the basic model. The online Supporting Information provides commented R code for all our analyses.

Elucidating the population dynamics of Japanese knotweed using integral projection models

Plant demographic studies coupled with population modeling are crucial components of invasive plant management because they inform managers when in a plant’s life cycle it is most susceptible to control efforts. Providing land managers with appropriate data can be especially challenging when there is limited data on potentially important transitions that occur belowground. For 2 years, we monitored 4 clonal Japanese knotweed (Polygonumcuspidatum) infestations for emergence, survival, shoot height until leaf senescence, dry shoot biomass after senescence, and rhizome connections for 424 shoots. We developed an integral projection model using both final autumn shoot height and shoot biomass as predictors of survival between years, growth from year to year, and number of rhizomes produced by a shoot (fecundity). Numbers of new shoots within an infestation (population growth rate λ) were projected to increase 13-233% in a year, with the greatest increase at the most frequently disturbed site. Elasticity analysis revealed population growth at 3 of the 4 sites was primarily due to ramet survival between years and to year-to-year growth in shoot height and shoot biomass. Population growth at the fourth site, the most disturbed, was due to the large production of new rhizomes and associated shoots. In contrast to previous studies, our excavation revealed that most of the shoots were not interconnected, suggesting rhizome production may be limited by the size or age of the plants, resource availability, disturbance frequency, or other factors. Future integration of plant population models with more data on belowground growth structures will clarify the critical stages in Japanese knotweed life cycle and support land managers in their management decisions.

Plants do not count… or do they? New perspectives on the universality of senescence

1. Senescence, the physiological decline that results in decreasing survival and/or reproduction with age, remains one of the most perplexing topics in biology. Most theories explaining the evolution of senescence (i.e. antagonistic pleiotropy, accumulation of mutations, disposable soma) were developed decades ago. Even though these theories have implicitly focused on unitary animals, they have also been used as the foundation from which the universality of senescence across the tree of life is assumed. 2. Surprisingly, little is known about the general patterns, causes and consequences of whole-individual senescence in the plant kingdom. There are important differences between plants and most animals, including modular architecture, the absence of early determination of cell lines between the soma and gametes, and cellular division that does not always shorten telomere length. These characteristics violate the basic assumptions of the classical theories of senescence and therefore call the generality of senescence theories into question. 3. This Special Feature contributes to the field of whole-individual plant senescence with five research articles addressing topics ranging from physiology to demographic modelling and comparative analyses. These articles critically examine the basic assumptions of senescence theories such as age-specific gene action, the evolution of senescence regardless of the organism's architecture and environmental filtering, and the role of abiotic agents on mortality trajectories. 4.Synthesis. Understanding the conditions under which senescence has evolved is of general importance across biology, ecology, evolution, conservation biology, medicine, gerontology, law and social sciences. The question 'why is senescence universal or why is it not?' naturally calls for an evolutionary perspective. Senescence is a puzzling phenomenon, and new insights will be gained by uniting methods, theories and observations from formal demography, animal demography and plant population ecology. Plants are more amenable than animals to experiments investigating senescence, and there is a wealth of published plant demographic data that enable interpretation of experimental results in the context of their full life cycles. It is time to make plants count in the field of senescence.