On the distribution of plant abundance data

Effect of nitrogen and glyphosate on the plant community composition in a simulated field margin ecosystem: Model-based ordination of pin-point cover data

The effect of nitrogen and glyphosate on the plant community composition was investigated in a simulated field margin ecosystem. The plant community composition was inferred from pin-point cover data using a model-based ordination method that is suited for modelling pin-point cover data. The mean structure of the ordination model is analogous to a standard linear model, which enabled us to estimate the mean effects of nitrogen and glyphosate and their interaction in the two-dimensional ordination space. There were significant effects of both nitrogen and glyphosate on the plant community composition and overall species diversity. The effects of nitrogen and glyphosate on the plant community composition differed significantly. Furthermore, the estimated combined effects of nitrogen and glyphosate indicated that nitrogen and glyphosate enforced the effect of each other on the plant community composition by synergistic interactions. Addition of nitrogen and glyphosate was found to favor a plant community that was dominated by perennial grasses, and there was a tendency for glyphosate to select for plant communities in which annual plants were more frequent. The results suggest that using the notion of plant functional types and specific knowledge of the degree of glyphosate tolerance may be effective for predicting the effect of glyphosate on the community composition.

Devil in the details: how can we avoid potential pitfalls of CATS regression when our data do not follow a Poisson distribution?

BACKGROUND

Community assembly by trait selection (CATS) allows for the detection of environmental filtering and estimation of the relative role of local and regional (meta-community-level) effects on community composition from trait and abundance data without using environmental data. It has been shown that Poisson regression of abundances against trait data results in the same parameter estimates. Abundance data do not necessarily follow a Poisson distribution, and in these cases, other generalized linear models should be fitted to obtain unbiased parameter estimates.

AIMS

This paper discusses how the original algorithm for calculating the relative role of local and regional effects has to be modified if Poisson model is not appropriate.

RESULTS

It can be shown that the use of the logarithm of regional relative abundances as an offset is appropriate only if a log-link function is applied. Otherwise, the link function should be applied to the product of local total abundance and regional relative abundances. Since this product may be outside the domain of the link function, the use of log-link is recommended, even if it is not the canonical link. An algorithm is also suggested for calculating the offset when data are zero-inflated. The relative role of local and regional effects is measured by Kullback-Leibler R2. The formula for this measure presented by Shipley (2014) is valid only if the abundances follow a Poisson distribution. Otherwise, slightly different formulas have to be applied. Beyond theoretical considerations, the proposed refinements are illustrated by numerical examples. CATS regression could be a useful tool for community ecologists, but it has to be slightly modified when abundance data do not follow a Poisson distribution. This paper gives detailed instructions on the necessary refinement.

A Goodness-of-fit Test for Zero-Inflated Poisson Mixed Effects Models in Tree Abundance Studies

Field studies in ecology often make use of data collected in a hierarchical fashion, and may combine studies that vary in sampling design. For example, studies of tree recruitment after disturbance may use counts of individual seedlings from plots that vary in spatial arrangement and sampling density. To account for the multi-level design and the fact that more than a few plots usually yield no individuals, a mixed effects zero inflated Poisson model is often adopted. Although it is a convenient modeling strategy, various aspects of the model could be misspecified. A comprehensive test procedure, based on the cumulative sum of the residuals, is proposed. The test is proven to be consistent, and its convergence properties are established as well. The application of the proposed test is illustrated by a real data example and simulation studies.

Probability distribution of groundcover for runoff prediction in rangeland in the Burnett–Mary Region, Queensland

Considering the degree of spatial and temporal variation of groundcover in grazing land, it is desirable to use a simple and robust model to represent the spatial variation in cover in order to quantify its effect on runoff and soil loss. The purpose of the study was to test whether a two-parameter beta (β) distribution could be used to characterise cover variation in space at the sub-catchment scale. Twenty sub-catchments (area range 35.8–231km2) in the Burnett–Mary region, Queensland, were randomly selected. Thirty raster layers of groundcover at 30-m resolution were prepared for these 20 sub-catchments with the average cover for the 30 layers ranging from 24% to 91%. Three methods were used to test the appropriateness of the β distribution for characterising the cover variation in space: (i) visual goodness-of-fit assessment and Kolmogorov–Smirnov (K-S) test; (ii) the fractional area with cover ≤53%; and (iii) estimated runoff amount for a given rainfall amount for the area with cover ≤53%. The K-S test on 30×100 samples of groundcover showed that the hypothesis of β distribution for groundcover could not be rejected at P=0.05 for 97.5% of the cases. A comparison of the observed and β distributions in terms of the fractional area with cover ≤53% showed that the discrepancy was ≤8% for the 30 layers considered. A comparison in terms of the estimated runoff showed that results using the observed cover distribution and the β distribution were highly correlated (R2 range 0.91–0.98; Nash–Sutcliffe efficiency measure range 0.88–0.99). The mean absolute error of estimated runoff ranged from 0.98 to 8.10mm and the error relative to the mean was 4–16%. The results indicated that the two-parameter β distribution can be adequately used to characterise the spatial variation of cover and to evaluate the effect of cover on runoff for these predominantly grazing catchments.

Effect of density-dependent individual movement on emerging spatial population distribution: Brownian motion vs Levy flights

Individual animal movement has been a focus of intense research and considerable controversy over the last two decades, however the understanding of wider ecological implications of various movement behaviours is lacking. In this paper, we consider this issue in the context of pattern formation. Using an individual-based modelling approach and computer simulations, we first show that density dependence ("auto-taxis") of the individual movement in a population of random walkers typically results in the formation of a strongly heterogeneous population distribution consisting of clearly defined animal clusters or patches. We then show that, when the movement takes place in a large spatial domain, the properties of the clusters are significantly different in the populations of Brownian and non-Brownian walkers. Whilst clusters tend to be stable in the case of Brownian motion, in the population of Levy walkers clusters are dynamical so that the number of clusters fluctuates in the course of time. We also show that the population dynamics of non-Brownian walkers exhibits two different time scales: a short time scale of the relaxation of the initial condition and a long time scale when one type of dynamics is replaced by another. Finally, we show that the distribution of sample values in the populations of Brownian and non-Brownian walkers is significantly different.

Catching ghosts with a coarse net: use and abuse of spatial sampling data in detecting synchronization

Synchronization of population dynamics in different habitats is a frequently observed phenomenon. A common mathematical tool to reveal synchronization is the (cross)correlation coefficient between time courses of values of the population size of a given species where the population size is evaluated from spatial sampling data. The corresponding sampling net or grid is often coarse, i.e. it does not resolve all details of the spatial configuration, and the evaluation error-i.e. the difference between the true value of the population size and its estimated value-can be considerable. We show that this estimation error can make the value of the correlation coefficient very inaccurate or even irrelevant. We consider several population models to show that the value of the correlation coefficient calculated on a coarse sampling grid rarely exceeds 0.5, even if the true value is close to 1, so that the synchronization is effectively lost. We also observe 'ghost synchronization' when the correlation coefficient calculated on a coarse sampling grid is close to 1 but in reality the dynamics are not correlated. Finally, we suggest a simple test to check the sampling grid coarseness and hence to distinguish between the true and artifactual values of the correlation coefficient.

Estimating plant abundance using inflated beta distributions: Applied learnings from a lichen-caribou ecosystem

Quantifying abundance and distribution of plant species can be difficult because data are often inflated with zero values due to rarity or absence from many ecosystems. Terrestrial fruticose lichens (Cladonia and Cetraria spp.) occupy a narrow ecological niche and have been linked to the diets of declining caribou and reindeer populations (Rangifer tarandus) across their global distribution, and conditions related to their abundance and distribution are not well understood. We attempted to measure effects related to the occupancy and abundance of terrestrial fruticose lichens by sampling and simultaneously modeling two discrete conditions: absence and abundance. We sampled the proportion cover of terrestrial lichens at 438 vegetation plots, including 98 plots having zero lichens. A zero‐inflated beta regression model was employed to simultaneously estimate both the absence and the proportion cover of terrestrial fruticose lichens using fine resolution satellite imagery and light detection and ranging (LiDAR) derived covariates. The probability of lichen absence significantly increased with shallower groundwater, taller vegetation, and increased Sphagnum moss cover. Vegetation productivity, Sphagnum moss cover, and seasonal changes in photosynthetic capacity were negatively related to the abundances of terrestrial lichens. Inflated beta regression reliably estimated the abundance of terrestrial lichens (R² = .74) which was interpolated on a map at fine resolution across a caribou range to support ecological conservation and reclamation. Results demonstrate that sampling for and simultaneously estimating both occupancy and abundance offer a powerful approach to improve statistical estimation and expand ecological inference in an applied setting. Learnings are broadly applicable to studying species that are rare, occupy narrow niches, or where the response variable is a proportion value containing zero or one, which is typical of vegetation cover data.

Plant colonization and survival along a hydrological gradient: demography and niche dynamics

Predicting the effect of a changing environment, e.g., caused by climate change, on realized niche dynamics, and consequently, biodiversity is a challenging scientific question that needs to be addressed. One promising approach is to use estimated demographic parameters for predicting plant abundance and occurrence probabilities. Using longitudinal pinpoint cover data sampled along a hydrological gradient in the Marais poitevin grasslands, France, the effect of the gradient on the demographic probabilities of colonization and survival was estimated. The estimated probabilities and calculated elasticities of survival and colonization covaried with the observed cover of the different species along the hydrological gradient. For example, the flooding tolerant grass A. stolonifera showed a positive response in both colonization and survival to flooding, and the hydrological gradient is clearly the most likely explanation for the occurrence pattern observed for A. stolonifera. The results suggest that knowledge on the processes of colonization and survival of the individual species along the hydrological gradient is sufficient for at least a qualitative understanding of species occurrences along the gradient. The results support the hypothesis that colonization has a predominant role for determining the ecological success along the hydrological gradient compared to survival. Importantly, the study suggests that it may be possible to predict the realized niche of different species from demographic studies. This is encouraging for the important endeavor of predicting realized niche dynamics.

Trends in sustainable landfilling in Malaysia, a developing country

In Malaysia, landfills are being filled up rapidly due to the current daily generation of approximately 30,000 tonnes of municipal solid waste. This situation creates the crucial need for improved landfilling practices, as sustainable landfilling technology is yet to be achieved here. The objective of this paper is to identify and evaluate the development and trends in landfilling practices in Malaysia. In 1970, the disposal sites in Malaysia were small and prevailing waste disposal practices was mere open-dumping. This network of relatively small dumps, typically located close to population centres, was considered acceptable for a relatively low population of 10 million in Malaysia. In the 1980s, a national programme was developed to manage municipal and industrial wastes more systematically and to reduce adverse environmental impacts. The early 1990s saw the privatization of waste management in many parts of Malaysia, and the establishment of the first sanitary landfills for MSW and an engineered landfill (called 'secure landfill' in Malaysia) for hazardous waste. A public uproar in 2007 due to contamination of a drinking water source from improper landfilling practices led to some significant changes in the government's policy regarding the country's waste management strategy. Parliament passed the Solid Waste and Public Cleansing Management (SWPCM) Act 2007 in August 2007. Even though the Act is yet to be implemented, the government has taken big steps to improve waste management system further. The future of the waste management in Malaysia seems somewhat brighter with a clear waste management policy in place. There is now a foundation upon which to build a sound and sustainble waste management and disposal system in Malaysia.

Evidence for acidification-driven ecosystem collapse of Danish Erica tetralix wet heathland

We report observations of disappearance of Erica tetralix in wet heathland, which is unlikely to be caused by competition, as E. tetralix is dying before its place is taken up by other species. To investigate the causes, we used both old and new data. Results showed that presence of Molinia caerulea and Calluna vulgaris were substantial in the former E. tetralix dominated areas. Measurements of the C/N ratio in the morlayer were between 21 and 26 under the E. tetralix stands. As the expected C/N ratio in a healthy nutrient poor ecosystem like the E. tetralix wet heathland is around 30, this indicates that the ratio is probably decreasing and, correspondingly, the probability of nitrogen leaching from the ecosystem is increasing. The morlayer pH was extremely low-between 3.03 and 3.78. This represents a pH decline since the 1960s, where pH values generally were above 4. This supports the hypothesis that the decrease in morlayer pH is the major factor explaining the disappearance of E. tetralix and that measures to increase pH should be considered as part of the recommendations for relevant future management.

A native species with invasive behaviour in coastal dunes: evidence for progressing decay and homogenization of habitat types

A new species has recently invaded coastal dune ecosystems in North West Europe. The native and expansive inland grass, Deschampsia flexuosa, progressively dominating inland heaths, has recently invaded coastal dunes in Denmark, occasionally even as a dominant species. A total of 222 coastal locations with 5,000 random sample plots have been investigated. These findings are in contrast to historical records, and D. flexuosa has never been considered belonging to coastal dune ecosystems. The occurrence of the typical inland grass in the coastal dunes is a strong indication of increase in nutrient level and that human influences may cause a native species to be invasive in new ecosystems. This could be a radical example of change in species composition due to a long lasting exceedance of critical load of nitrogen. The investigation also showed a general increase in cover of the most dominant species.