Biology subjects

Damgaard, C.

Publications and source records attributed to Damgaard, C..

16 recordsLinked to original sources

bioRxiv2024

The effect of nitrogen on the growth of Calluna vulgaris and Avenella flexuosa in a dune heath ecosystem: competition and frequency-dependence

We tested the hypothesis that both density- and frequency-dependent interactions play important roles in determining plant growth in a dune heath ecosystem at several levels of available nitrogen. Plant growth was measured using the pin-point method in a five-block experiment with four nitrogen levels. To maximize statistical power, we used only three taxonomic groups: Calluna vulgaris, Avenella flexuosa (the two most dominant species), and all other vascular plant species together. The results show that both Lotka-Volterra type interspecific competition and frequency-dependency play significant roles in determining the growth of the species in the community. Significant interspecific density-dependent competition was observed in 4 out of the 6 possible cases. Nitrogen addition increased the competitive effect of C. vulgaris on the growth of the other species. Both C. vulgaris and A. flexuosa showed frequency-dependent positive feedback dynamics on growth when they were relatively dominant at the plot scale, and this effect increased with added nitrogen. In plots with added nitrogen, there was a beneficial effect of being relatively rare on the growth of the group of other species. The study highlights the importance of the combined effects of density and frequency dependency in determining plant growth.

ecology↗

bioRxiv2024

Ecosystem dynamics in wet heathlands: spatial and temporal effects of environmental drivers on the vegetation

To understand and estimate the effects of environmental drivers on wet heathland vegetation, pin-point cover data from 42 sites sampled during a 15-year period was regressed onto environmental variables (nitrogen deposition, soil pH, soil C-N ratio, soil type, precipitation and grazing) in a spatio-temporal structural equation model using a Bayesian hierarchical model structure with latent variables to model the effect of measurement and sampling uncertainties. The results suggest that the modelled environmental variables have various regulating effects on the large-scale spatial variation as well as plant community dynamics in wet heathlands. Most noticeably, nitrogen deposition and yearly precipitation had relatively large and opposite effects on the characteristic species Erica tetralix and Molinia caerulea, where nitrogen deposition had negative effects on E. tetralix and positive effects on M. caerulea. The results of this study differed in important qualitative aspects from the findings of an earlier study where comparable data from a shorter time-series (7 years instead of 15 years) were analyzed with a similar model, which suggests that relatively long time-series are needed for studying ecosystem dynamics. Furthermore, it was concluded that the effect of nitrogen deposition on plant community dynamics mainly was through direct effects, whereas the effect of soil type on plant community dynamics was both direct and indirect mediated by the effect of soil type on soil pH. It was concluded that the modeled environmental variables are sufficient for predicting the average plant community dynamics of wet heathlands. However, caution are required if the fitted model is used for generating local ecological predictions as input to a process of generating adaptive management plans for specific wet heathland sites. Moreover, the results suggest that the ratio between the two species E. tetralix and M. caerulea may be used as an indicator for the conservation status of wet heathlands.

ecology↗

bioRxiv2022

Spatio-temporal modelling of the effect of selected environmental and land-use factors on species-rich calcareous grasslands: overgrazing, nitrogen deposition and climate change

The abundance of sensitive plant species in calcareous grasslands are threatened by agricultural intensification with nutrient addition and increased livestock densities as well as by land abandonment. In order to quantify the effect of selected environmental and land-use factors on the observed variation and changes in the vegetation of calcareous grasslands, large-scale spatial and temporal pin-point plant cover monitoring data are fitted in a structural equation model. The analyzed vegetation data come from 100 Danish sites monitored over an eight year period. The important sources of measurement- and sampling uncertainties have been included using a hierarchical model structure. Furthermore, the measurement- and sampling uncertainties are separated from the process uncertainty, which is important when generating ecological predictions that may feed into local conservation management decisions. There were significant negative effects of grazing and nitrogen deposition on the change in cover of sensitive plant species. Whereas the negative effect of nitrogen deposition on the cover of sensitive species was expected, it was surprising that the model results suggest that the class of sensitive species may be subjected to overgrazing by the grazing regimes that are currently applied at protected Danish calcareous grasslands. The standardized regression coefficients suggest that the effects of both grazing and nitrogen deposition are relatively benign compared to the effects of soil type, soil pH and precipitation. The relatively large effect of precipitation is interesting, since it is predicted that the amount of precipitation and distribution over the season will change due to climate change, and the results suggest that climate change may lead to important species compositional changes in calcareous grasslands. The fitted model may be used to quantify the uncertainties when generating ecological forecasting and local adaptive management plans.

ecology↗

bioRxiv2022

Measuring plant diversity in a two-stage sampling design by Bayesian updated relative abundances

The two-stage sampling design provides good local estimates of both the number of plant species and the relative abundances. However, it is a problem to calculate Hill diversity indices at the local scale, because some of the species found in the large plot are not present in the small plot and such species should then incorrectly be weighted with zero relative abundance. A new method for calculating local Hill diversity indices from species richness and relative abundances data is therefore needed. We suggest to replace the local relative abundances with Bayesian updated relative abundance estimates, where the prior probability distribution of the relative abundances are empirically estimated from all plots of the same habitat types. The method is applied on Danish Nardus grasslands.

ecology↗

bioRxiv2021

Limited selection towards lighter seeds in 1 Danish grasslands over an eight-year period

A time-series analysis of cover data from 236 Danish grassland sites demonstrated community selection on seed mass. Across four grassland habitat types and during an eight-year period there was a significant decline in large-seeded species. In the analysis, the continuous seed size variable was used to group plant species into functional types. This method was chosen in order to account for the sampling process of the abundance data, and is in contrast to most other analyses of trait selection, where the community weighted mean of the traits is used as the dependent variable. Generally, little is known on the causes for seed size community selection in semi-natural grasslands that are not subjected to successional processes.

ecology↗

bioRxiv2020

The need for alternative plant species interaction models

The limitations of classical Lotka-Volterra models for analyzing and interpreting competitive interactions among plant species have become increasingly clear in recent years. Three problems that have been identified are (1) the absence of frequency dependence, which is important for long-term coexistence of species, (2) the need to take unmeasured (often unmeasurable) variables influencing individual performance into account (e.g. spatial variation in soil nutrients or pathogens) and (3) the need to separate measurement error from biological variation. We modify the classical Lotka-Volterra competition models to address these limitations and we fit 8 alternative models to pin-point cover data on Festuca ovina and Agrostis capillaris over 3 years in a herbaceous plant community in Denmark, applying a Bayesian modelling framework to ascertain whether the model amendments improve the performance of the models and increase their ability to predict community dynamics and therefore to test hypotheses. Inclusion of frequency dependence and measurement error improved model performance greatly but taking possible unmeasured variables into account did not. Our results emphasize the importance of comparing alternative models in quantitative studies of plant community dynamics. Only by comparing alternative models can we identify the forces driving community assembly and change and improve our ability to predict the behavior of plant communities.

ecology↗

bioRxiv2020

Spatio-temporal structural equation modeling in a hierarchical Bayesian framework. II. What controls acid grassland vegetation?

Spatial and temporal pin-point plant cover monitoring data are fitted in a structural equation model in order to understand and quantify the effect of selected environmental and land-use drivers on the observed variation and changes in the vegetation of acid grasslands. The important sources of measurement- and sampling uncertainties have been included using a hierarchical model structure. Furthermore, the measurement- and sampling uncertainties are separated from the process uncertainty, which is important when generating ecological predictions. Generally, increasing atmospheric nitrogen deposition leads to more grass-dominated acid grassland habitats at the expense of the cover of forbs. Sandy soils are relatively more acidic, and the effect of soil type on the vegetation includes both direct effects of soil type and indirect effects mediated by the effect of soil type on soil pH. Both soil type and soil pH affected the vegetation of acid grasslands. Even though only a small part of the temporal variation in cover was explained by the model, it will still be useful to quantify the uncertainties when using the model for generating local ecological predictions and adaptive management plans.

ecology↗

bioRxiv2020

Adaptive management plans rooted in quantitative ecological predictions of ecosystem processes: putting monitoring data to practical use

It is demonstrated how a hierarchical structural equation model that is fitted to temporal ecological monitoring data from a number of sites may be used to generate local ecological predictions and how these local ecological predictions may form the basis of adaptive management plans. Local ecological predictions will be made for the cover of cross-leaved heath on Danish wet heathlands, which is one of the indicators that determine the conservation status of wet heathlands under different management scenarios. Based on a realistic example, the model predictions concludes that grazing by domestic herbivores on wet heathlands with a relatively low cover cross-leaved heath cannot be recommended as the only management practice. Generally, it is recommended to use ecological monitoring data to generate quantitative and credible local adaptive management plans where the uncertainty is taken into account.

ecology↗

bioRxiv2020

Identity and provenance of neighbors, genotype-specific traits and abiotic stress affect intraspecific interactions in the annual legume Medicago truncatula

O_LIAccounting for intraspecific variation may improve our understanding of species coexistence. However, our knowledge of what factors maintain intraspecific variation is limited. We predicted that 1) a plant grows larger when with non-kin (i.e. different genotypes) than kin (i.e. same genotype) neighbors, 2) abiotic stress alters the outcome of kin vs. non-kin interactions, 3) genetic identity of plants affects composition of soil microbiome. C_LIO_LIWe set up mini-communities of Medicago truncatula, where focal genotypes were grown together with two kin or two non-kin neighbors from different origins. We analyzed how origin, identity of interacting genotypes and abiotic stress affected growth and fruit production. We also analyzed the composition of soil microbial communities. C_LIO_LIFocal plants grew larger in non-kin than in kin mini-communities. This pattern was stronger in low level of abiotic stress and when interacting genotypes were from similar origins. However, genotypic variation in growth and response to competition had a stronger effect on growth than mini-community type. Plant genotype identity did not affect soil microbiome. C_LIO_LIWe find that intraspecific variation is affected by genotype-specific traits and abiotic stress. Geographic, rather than genetic, distance among interacting genotypes affects the outcome of intraspecific interactions. C_LI

plant biology↗

bioRxiv2020

Estimating plant abundance in irregular polygons: plot-based sampling with a conditional spatial configuration

When estimating plant species abundance using plot-based methods in irregular polygons, there are some constraints to the spatial configuration of the sampling plots: i) the sample plots must be positioned within the polygon, ii) the sample plots may not overlap, iii) due to the spatial variation in abundance often found in natural plant communities, the spatial coverage must be relatively large in order to decrease the sampling variance, iv) due to a possible mosaic structure of the vegetation, systematic designs should be avoided due to the possibility of biased estimates. Here, we suggest a protocol using simulations of the possible random spatial configurations to select a conditional spatial configuration that meets these constraints.

ecology↗

bioRxiv2020

Changes in the abundance of Danish orchids over the past 30 years

Orchid abundance data collected over the past 30 years (1987-2016) from 440 sites within the National Orchid Monitoring Program were analysed to quantify the population trends of orchids in Denmark, and the underlying reasons for the observed population trends were analysed and discussed. Twenty of the 45 monitored Danish orchids showed a significant decrease in abundance over the past 30 years (16, if only orchids with at least 50 observations each were selected), thus corroborating the previous observations of declining orchid abundances at European scale. Generally, there was a significant negative effect of overgrowing with tall-growing herbs and shrubs on the abundance of Danish orchids mainly caused by change of farming practises, as extensive management, such as grazing or mowing of light-open grassland areas, has decreased.

plant biology↗

bioRxiv2020

On the problems of not accounting for measurement- and sampling uncertainty in ecological and environmental models

In many applied cases of ecological and environmental modelling, there is a sizeable variation among the measured variables due to measurement- and sampling error. Such measurement- and sampling error among the independent variables may lead to regression dilution and biased prediction intervals in traditional empirical modelling. It is possible to avoid these shortcomings by subsampling and hierarchical modelling, but this is still not a common practice. Here, it is recommended to model the measurement- and sampling errors by integrating the stochastic modelling of the errors into hierarchical ecological and environmental models.

ecology↗

bioRxiv2020

Model-based ordination of pin-point cover data: effect of management on dry heathland

Recently, there has been an increasing interest in model-based approaches for the statistical modelling of the joint distribution of multi-species abundances. The Dirichlet-multinomial distribution has been proposed as a suitable candidate distribution for the joint species distribution of pin-point plant cover data and is here applied in a model-based ordination framework. Unlike most model-based ordination methods, both fixed and random effects are in our proposed model structured as p-dimensional vectors and added to the latent variables before the inner product with the species-specific coefficients. This changes the interpretation of the parameters, so that the fixed and random effects now measure the relative displacement of the vegetation by the fixed and random factors in the p-dimensional latent variable space. This parameterization allows statistical inference of the effect of fixed and random factors in vector space, and makes it easier for practitioners to perform inferences on species composition in a multivariate setting. The method was applied on plant pin-point cover data from dry heathlands that had received different management treatments (burned, grazed, harvested, unmanaged), and it was found that treatment have a significant effect on heathland vegetation both when considering plant functional groups or when the taxonomic resolution was at the species level.

ecology↗

bioRxiv2019

Limited selection on leaf traits in Danish grasslands

Across four grassland habitat types, the cover of thin-leaved plants was found to decrease significantly, but generally only limited trait selection was observed on leaf traits (SLA and LDMC) in a study of an extensive Danish grassland vegetation dataset from an eight-year period. The mostly negative result of this study may partly be due to the relatively conservative analysis, where the continuous plant trait variables are used for grouping plant species into functional types, which are then treated as dependent variables. This procedure is in contrast to most other analyses of trait selection, where it is the community weighted mean of the traits that is used as the dependent variable. However, it is not the traits, but rather individual plants that are sampled and, consequently, it is important to consider the sampling of species abundance in the statistical modelling of plant traits. This misapprehension has not received sufficient proper attention in the plant trait literature.

ecology↗

bioRxiv2018

Integrating hierarchical statistical models and machine learning algorithms for ground-truthing drone images of the vegetation: taxonomy, abundance and population ecological models

In order to fit population ecological models, e.g. plant competition models, to new drone-aided image data, we need to develop statistical models that may take the new type of measurement uncertainty when applying machine-learning algorithms into account and quantify its importance for statistical inferences and ecological predictions. Here, it is proposed to quantify the uncertainty and bias of image predicted plant taxonomy and abundance in a hierarchical statistical model that is linked to ground-truth data obtained by the pin-point method. It is critical that the error rate in the species identification process is minimized when the image data are fitted to the population ecological models, and several avenues for reaching this objective are discussed. The outlined method to statistically model known sources of uncertainty when applying machine-learning algorithms may be relevant for other applied scientific disciplines.

ecology↗

bioRxiv2018

The effect of spatial variation for predicting aphid epidemics

In order to improve forecasting of aphid epidemics, it is important to know the spatial scale at which specific forecasts are reliable. To investigate the spatial scale of aphid epidemics, we have developed a spatio-temporal stochastic aphid population growth model, and fitted the model to empirical spatial time-series aphid population data using a Bayesian hierarchical fitting procedure. Furthermore, detailed spatial data of the initial phases of epidemic development was investigated in a semivariogram. Our results suggest that there is limited spatial variation in the initial occurrence probability at a spatial scale of 10 km. Consequently, the results support the hypothesis that initial aphid population sizes and epidemics may be predicted in fields within a 10 km radius. For farmers, this may imply that they can rely their decision of whether to spray against aphids on observations made by other nearby farmers or by the consultancy service.

ecology↗