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 (Polygonum cuspidatum) 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 yearto- 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

Forest hoverfly community collapse: Abundance and species richness drop over four decades

To study insect decline, an important threat to biodiversity, long-term datasets are needed. Here we present a study of hoverfly (Diptera: Syrphidae) abundance and diversity in a Dutch forest, surrounded by other forests, and analyse the variation in insect numbers over four decades. Between 1982 and 2021, abundance decreased by 80%. Until 1990, abundance showed a strong decrease of 10.9% per year, mainly in nationally rare species with carnivorous larvae exposed to air. From 1990, abundance stabilised, whereas from 2000, a second period of strong decline of 9.0% per year occurred, mainly in very common species. Species richness also declined strongly between 1979 and 2021: the total number of species observed in five monitoring days dropped by 44% over those 43 years. The characteristic set of dry-forest hoverfly species disappeared over four decades. The number of nationally rare species observed at the study site declined from 19 to 9 early on, in a period (1979–1984) that coincided with intense nitrogen input and acidification caused by agriculture in the same region. The more recent decline is likely also caused by factors from outside the forest, as forest management and conditions remained constant. Continued influx of nutrients and pesticides at a regional level, as well as climate change are possible causes of the decline. Research is needed to quantify their relative effects

Speeding up ecological and evolutionary computations in R; essentials of high performance computing for biologists

Computation has become a critical component of research in biology. A risk has emerged that computational and programming challenges may limit research scope, depth, and quality. We review various solutions to common computational efficiency problems in ecological and evolutionary research. Our review pulls together material that is currently scattered across many sources and emphasizes those techniques that are especially effective for typical ecological and environmental problems. We demonstrate how straightforward it can be to write efficient code and implement techniques such as profiling or parallel computing. We supply a newly developed R package (aprof) that helps to identify computational bottlenecks in R code and determine whether optimization can be effective. Our review is complemented by a practical set of examples and detailed Supporting Information material (S1–S3 Texts) that demonstrate large improvements in computational speed (ranging from 10.5 times to 14,000 times faster). By improving computational efficiency, biologists can feasibly solve more complex tasks, ask more ambitious questions, and include more sophisticated analyses in their research

The hidden cost of disturbance: Eurasian Oystercatchers (Haematopus ostralegus) avoid a disturbed roost site during the tourist season

Disturbance may impact individual birds and ultimately bird populations. If animals avoid disturbed sites this may prevent them from being disturbed directly but may also negatively impact their movement patterns and energy budgets. Avoidance is, however, challenging to study, because it requires following individuals over large spatial scales in order to compare their movement rates between sites in relation to spatiotemporal variation in disturbance intensity. We studied how 48 GPS-tracked non-breeding Eurasian Oystercatchers Haematopus ostralegus used two neighbouring roost sites in the Wadden Sea. One roost site is highly influenced by seasonal recreational disturbance whereas the other is an undisturbed sandbar. We analysed roost choice and the probability of moving away from the disturbed roost site with regard to a seasonal recreation activity index, weekends and night-time. Oystercatchers often chose to roost on the undisturbed site, even if they were foraging closer to the disturbed roost. The probability that Oystercatchers chose to roost on the disturbed site was negatively correlated with the recreation activity index and was lowest in the tourist season (summer and early autumn), indicating that birds used the site less often when recreation levels were high. Furthermore, the probability that birds moved away from the disturbed site during high tide was positively correlated with the recreation activity index. The choice to roost on the undisturbed site implies that birds must fly an additional 8 km during one high-tide period, which equates to 3.4% of daily energy expenditure of an average Oystercatcher. Our study tentatively suggests that the costs of avoidance may outweigh the energetic cost of direct flight responses and hence that avoidance of disturbed sites requires more attention in future disturbance impact studies. Nature managers should evaluate whether high-quality undisturbed roosting sites are available near foraging sites, and in our case closing of a section of the disturbed site during high tides in the tourist season may mitigate much disturbance impact

A Host–parasite Model Explains Variation in Liana Infestation Among Co‐occurring Tree Species

Lianas are structural parasites of trees that reduce the growth, survival and reproduction of their hosts. Given that co‐occurring tree species differ strongly in the proportion of individuals that are infested by lianas (liana prevalence), lianas could differentially impact tree species and thereby influence tree community composition. Surprisingly, little is known about what governs variation in liana prevalence. Here, we apply an approach inspired by disease ecology to investigate the dynamics of liana prevalence over 11 years on Barro Colorado Island, Panama. We followed the fate of 1,938 individual trees from 21 tree species, recording deaths and change in liana infestation status. With these data, we fit species‐specific Markov chain models to estimate four rates: colonization by lianas (analogous to disease transmission), shedding or loss of lianas (analogous to host recovery), baseline mortality of uninfested trees (baseline mortality) and additional mortality of infested trees (parasite lethality). Models explained 58% of variation in liana prevalence among tree species, and revealed that host shedding of lianas and parasite lethality were the most important contributors to interspecific variation in liana prevalence at our site. These rates were also strongly related to shade tolerance, with light‐demanding species having greater rates of shedding and lethality, and lower rates of liana prevalence. An indirect path analysis with a structural equation model revealed that both greater rates of liana shedding and liana‐induced lethality contribute to the observed lower rates of liana prevalence for light‐demanding tree species. Synthesis. Our approach revealed that the prevalence of liana infestation among tree species is driven via indirect pathways operating on the rates of shedding and lethality, which relate to the ability (or inability) of trees to shed and/or tolerate lianas. Shade‐tolerant trees have greater proportions of trees infested by lianas because they are both less able to shed lianas and more able to tolerate infestation

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

Roadsides are an important habitat for invasive common ragweed, Ambrosia artemisiifolia 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

State-dependent environmental sensitivity of reproductive success and survival in a shorebird

To understand the consequences of anthropogenic and environmental changes for wildlife populations, it is important to study how individuals differ in their sensitivity to environmental change, and whether this depends on individual characteristics. An individual’s reproductive performance may provide an integrative, unidimensional proxy of an individual’s characteristics. In this study, we define an individual’s characteristics by three such reproductive states, namely successful-, failed-, and non-breeders in the previous year. We used a 16-year dataset of individually marked breeding Eurasian Oystercatchers Haematopus ostralegus to examine the inter-annual fluctuations in reproductive success and survival among breeding states, and their state-dependent sensitivity to environmental conditions. Environmental conditions included available biomass of the main prey species of breeding Oystercatchers (Ragworm, Baltic Tellin and Lugworm), tidal height which reflects one of the main causes of nest loss (flooding) and conditions that may impact the energetic requirements during incubation, such as temperature. We also included environmental variables measured in winter, including available biomass of the main winter prey species (Blue Mussel and Common Cockle) along with factors that may affect food availability and energetic requirements for homeostasis, namely bivalve weight loss, windchill, winter severity, and precipitation. Breeding birds that were successful the previous year had higher survival, and were more likely to remain successful, than failed- and non-breeders. The effects of environmental conditions acted in the same direction on reproductive success but had opposite effects on survival among the three breeding states, especially for windchill and Blue Mussel biomass. The contrasting state-dependent effects of the environment on survival thus averaged out when examining consequences for lifetime reproductive nest success (LRnS); instead LRnS was largely influenced by environmental conditions acting upon reproduction. Our study indicates that an individual’s previous breeding state provides an integrative measure of heterogeneity in individuals’ sensitivity of reproduction and survival to environmental change. Incorporating previous breeding state as a source of individual heterogeneity in population modelling may improve predictions of future population dynamics in a rapidly changing world

Host–parasite dynamics shaped by temperature and genotype : quantifying the role of underlying vital rates

Global warming challenges the persistence of local populations, not only through heat-induced stress, but also through indirect biotic changes. We study the interactive effects of temperature, competition and parasitism in the water flea Daphnia magna. We carried out a common garden experiment monitoring the dynamics of Daphnia populations along a temperature gradient. Halfway through the experiment, all populations became infected with the ectoparasite Amoebidium parasiticum, enabling us to study the interactive effects of temperature and parasite dynamics. We combined Integral Projection Models with epidemiological models, parameterized using the experimental data on the performance of individuals within dynamic populations. This enabled us to quantify the contribution of different vital rates and epidemiological parameters to population fitness across temperatures and Daphnia clones originating from two latitudes. Interactions between temperature and parasitism shaped competition, where Belgian clones performed better under infection than Norwegian clones. Infected Daphnia populations performed better at higher than at lower temperatures, mainly due to an increased host capability of reducing parasite loads. Temperature strongly affected individual vital rates, but effects largely cancelled out on a population-level. In contrast, parasitism strongly reduced fitness through consistent negative effects on all vital rates. As a result, temperature-mediated parasitism was more important than the direct effects of temperature in shaping population dynamics. Both the outcome of the competition treatments and the observed extinction patterns support our modelling results. Our study highlights that shifts in biotic interactions can be equally or more important for responses to warming than direct physiological effects of warming, emphasizing that we need to include such interactions in our studies to predict the competitive ability of natural populations experiencing global warming.publishedVersio

Host–parasite dynamics shaped by temperature and genotype: Quantifying the role of underlying vital rates

1. Global warming challenges the persistence of local populations, not only through heat-induced stress, but also through indirect biotic changes. We study the interactive effects of temperature, competition and parasitism in the water flea Daphnia magna. 2. We carried out a common garden experiment monitoring the dynamics of Daphnia populations along a temperature gradient. Halfway through the experiment, all populations became infected with the ectoparasite Amoebidium parasiticum, enabling us to study the interactive effects of temperature and parasite dynamics. We combined Integral Projection Models with epidemiological models, parameterized using the experimental data on the performance of individuals within dynamic populations. This enabled us to quantify the contribution of different vital rates and epidemiological parameters to population fitness across temperatures and Daphnia clones originating from two latitudes. 3. Interactions between temperature and parasitism shaped competition, where Belgian clones performed better under infection than Norwegian clones. Infected Daphnia populations performed better at higher than at lower temperatures, mainly due to an increased host capability of reducing parasite loads. Temperature strongly affected individual vital rates, but effects largely cancelled out on a population-level. In contrast, parasitism strongly reduced fitness through consistent negative effects on all vital rates. As a result, temperature-mediated parasitism was more important than the direct effects of temperature in shaping population dynamics. Both the outcome of the competition treatments and the observed extinction patterns support our modelling results. 4. Our study highlights that shifts in biotic interactions can be equally or more important for responses to warming than direct physiological effects of warming, emphasizing that we need to include such interactions in our studies to predict the competitive ability of natural populations experiencing global warming

Conceptualizing and quantifying body condition using structural equation modelling:A user guide

Body condition is an important concept in behaviour, evolution and conservation, commonly used as a proxy of an individual's performance, for example in the assessment of environmental impacts. Although body condition potentially encompasses a wide range of health state dimensions (nutritional, immune or hormonal status), in practice most studies operationalize body condition using a single (univariate) measure, such as fat storage. One reason for excluding additional axes of variation may be that multivariate descriptors of body condition impose statistical and analytical challenges. Structural equation modelling (SEM) is used in many fields to study questions relating multidimensional concepts, and we here explain how SEM is a useful analytical tool to describe the multivariate nature of body condition. In this ‘Research Methods Guide’ paper, we show how SEM can be used to resolve different challenges in analysing the multivariate nature of body condition, such as (a) variable reduction and conceptualization, (b) specifying the relationship of condition to performance metrics, (c) comparing competing causal hypothesis and (d) including many pathways in a single model to avoid stepwise modelling approaches. We illustrated the use of SEM on a real-world case study and provided R-code of worked examples as a learning tool. We compared the predictive power of SEM with conventional statistical approaches that integrate multiple variables into one condition variable: multiple regression and principal component analyses. We show that model performance on our dataset is higher when using SEM and led to more accurate and precise estimates compared to conventional approaches. We encourage researchers to consider SEM as a flexible framework to describe the multivariate nature of body condition and thus understand how it affects biological processes, thereby improving the value of body condition proxies for predicting organismal performance. Finally, we highlight that it can be useful for other multidimensional ecological concepts as well, such as immunocompetence, oxidative stress and environmental conditions