P.F.M. Verdonschot

Canonical correspondence analysis and related multivariate methods in aquatic ecology

Canonical correspondence analysis (CCA) is a multivariate method to elucidate the relationships between biological assemblages of species and their environment. The method is designed to extract synthetic environmental gradients from ecological data-sets. The gradients are the basis for succinctly describing and visualizing the differential habitat preferences (niches) of taxavia an ordination diagram. Linear multivariate methods for relating two set of variables, such as two-block Partial Least Squares (PLS2), canonical correlation analysis and redundancy analysis, are less suited for this purpose because habitat preferences are often unimodal functions of habitat variables. After pointing out the key assumptions underlying CCA, the paper focuses on the interpretation of CCA ordination diagrams. Subsequently, some advanced uses, such as ranking environmental variables in importance and the statistical testing of effects are illustrated on a typical macroinvertebrate data-set. The paper closes with comparisons with correspondence analysis, discriminant analysis, PLS2 and co-inertia analysis. In an appendix a new method, named CCA-PLS, is proposed that combines the strong features of CCA and PLS2.

From Natural to Degraded Rivers and Back Again: A Test of Restoration Ecology Theory and Practice

Extensive degradation of ecosystems, combined with the increasing demands placed on the goods and services they provide, is a major driver of biodiversity loss on a global scale. In particular, the severe degradation of large rivers, their catchments, floodplains and lower estuarine reaches has been ongoing for many centuries, and the consequences are evident across Europe. River restoration is a relatively recent tool that has been brought to bear in attempts to reverse the effects of habitat simplification and ecosystem degradation, with a surge of projects undertaken in the 1990s in Europe and elsewhere, mainly North America. Here, we focus on restoration of the physical properties (e.g. substrate composition, bank and bed structure) of river ecosystems to ascertain what has, and what has not, been learned over the last 20 years. First, we focus on three common types of restoration measures—riparian buffer management, instream mesohabitat enhancement and the removal of weirs and small dams—to provide a structured overview of the literature. We distinguish between abiotic effects of restoration (e.g. increasing habitat diversity) and biological recovery (e.g. responses of algae, macrophytes, macroinvertebrates and fishes). We then addressed four major questions: (i) Which organisms show clear recovery after restoration? (ii) Is there evidence for qualitative linkages between restoration and recovery? (iii) What is the timescale of recovery? and (iv) What are the reasons, if restoration fails? Overall, riparian buffer zones reduced fine sediment entry, and nutrient and pesticide inflows, and positive effects on stream organisms were evident. Buffer width and length were key: 5–30 m width and > 1 km length were most effective. The introduction of large woody debris, boulders and gravel were the most commonly used restoration measures, but the potential positive effects of such local habitat enhancement schemes were often likely to be swamped by larger-scale geomorphological and physico-chemical effects. Studies demonstrating long-term biological recovery due to habitat enhancement were notable by their absence. In contrast, weir removal can have clear beneficial effects, although biological recovery might lag behind for several years, as huge amounts of fine sediment may have accumulated upstream of the former barrier. Three Danish restoration schemes are provided as focal case studies to supplement the literature review and largely supported our findings. While the large-scale re-meandering and re-establishment of water levels at River Skjern resulted in significant recovery of riverine biota, habitat enhancement schemes at smaller-scales in other rivers were largely ineffective and failed to show long-term recovery. The general lack of knowledge derived from integrated, well-designed and long-term restoration schemes is striking, and we present a conceptual framework to help address this problem. The framework was applied to the three restoration types included in our study and highlights recurrent cause–effect chains, that is, commonly observed relationships of restoration measures (cause) and their effects on abiotic and biotic conditions (effect). Such conceptual models can provide useful new tools for devising more effective river restoration, and for identifying avenues for future research in restoration ecology in general.

An experimental manipulation of oligochaete communities in mesocosms treated with chlorpyrifos or nutrient additions: multivariate analyses with Monte Carlo permutation tests

Oligochaete communities were monitored under semi-natural conditions in experimental ditch mesocosms. Twelve ditches were used in a Before-Control-After-Impact (BACI) experiment to study the effect of the insecticide chlorpyrifos. Another eight ditches were used in a randomized experiment to study the effect of eutrophication. Oligochaete communities were sampled by deploying trays of substratum for colonization over a 20-week period. The experiments were analyzed by multivariate analysis using redundancy analysis and Monte Carlo permutation to assess statistical significance. These novel methods have the advantage over classical multivariate analysis of variance (MANOVA) of being distribution-free and of having no restrictive upper limit on the number of species that can be analyzed simultaneously. In the BACI-experiment no significant effect of chlorpyrifos on oligochaete communities was detected. Eutrophication effects were observed at the higher eutrophication levels in clay ditches. Oligochaete abundances decreased in those ditches. Considerable variation was attributed to stochastic factors given that the ditches were in an early developmental stage when the experiments were initiated.Large-scale experiments such as the ones that we describe require time to develop and stabilize before parameters of community structure like population abundance, can be employed to detect changes associated with water quality manipulations.

A comparative review of recovery processes in rivers, lakes, estuarine and coastal waters

The European Water Framework Directive aims to improve ecological status within river basins. This requires knowledge of responses of aquatic assemblages to recovery processes that occur after measures have been taken to reduce major stressors. A systematic literature review comparatively assesses recovery measures across the four major water categories. The main drivers of degradation stem primarily from human population growth and increases in land use and water use changes. These drivers and pressures are the same in all four water categories: rivers, lakes, transitional and coastal waters. Few studies provide evidence of how ecological knowledge might enhance restoration success. Other major bottlenecks are the lack of data, effects mostly occur only in short-term and at local scale, the organism group(s) selected to assess recovery does not always provide the most appropriate response, the time lags of recovery are highly variable, and most restoration projects incorporate restoration of abiotic conditions and do not include abiotic extremes and biological processes. Restoration ecology is just emerging as a field in aquatic ecology and is a site, time and organism group-specific activity. It is therefore difficult to generalise. Despite the many studies only few provide evidence of how ecological knowledge might enhance restoration success.

The relative influence of catchment, riparian corridor, and reach-scale anthropogenic pressures on fish and macroinvertebrate assemblages in French rivers

This study compares the relative influences of physiography and anthropogenic pressures on river biota at catchment, riparian corridor, and reach scales. Environmental data, catchment and riparian corridor land use, anthropogenic modifications and biological data were compiled for 301 French sites sampled from 2005 to 2008. First, relationships between anthropogenic pressures and fish and macroinvertebrate assemblages were analysed using redundancy analysis. Second, the influences of physiography and the three scales of human pressures on biological assemblages were measured using variance partitioning. Distributions of fish and macroinvertebrate taxa along the pressure gradients agreed with bio-ecological knowledge. At the reach scale, assemblage variability among the 301 French sites was related to the presence of an impoundment and to poor water quality, while at larger scales it was linked to a gradient from forest to agricultural covers. In addition, a large proportion of the explained variability in assemblage composition was related to complex interactions among factors (~40%) and to physiographic variables (~30%). Furthermore, our results highlight that catchment land use better reflects local water quality impairments than hydromorphological degradations. Finally, this study supports the idea that human pressure effects on river communities are linked at several spatial scales and must be considered jointly.

The role of benthic microhabitats in determining the effects of hydromorphological river restoration on macroinvertebrates

Despite the large number of river restoration projects carried out worldwide, evidence for strong and long-term positive ecological effects of hydromorphological restoration on macroinvertebrates is scarce. To improve the understanding of the success and failure of restoration measures, a standardized field study was carried out in nineteen paired restored and degraded river sections in mid-sized lowland and mountain rivers throughout Europe. We investigated if there were effects of restoration on macroinvertebrate biodiversity, and if these effects could be related to changes in microhabitat composition, diversity and patchiness. Effects were quantified for all taxa combined, as well as Ephemeroptera, Plecoptera and Trichoptera separately. Additionally, species trait classifications of microhabitat preference types were used as a functional indicator. Restoration had no overall positive effects on the selected macroinvertebrate metrics. Rather, we did find positive relationships between the macroinvertebrate responses and the effect of restoration on the diversity and patchiness of microhabitats. Furthermore, the effects on macroinvertebrates could be related to changes in the cover of specific substrate types in the restored sections. We conclude that the limited effect of restoration on macroinvertebrate diversity overall reflected, at least in part, the limited effect of most restoration measures on microhabitat composition and diversity.

Bayesian model-based cluster analysis for predicting macrofaunal communities

Abstract To predict macrofaunal community composition from environmental data a two-step approach is often followed: (1) the water samples are clustered into groups on the basis of the macrofauna data and (2) the groups are related to the environmental data, e.g. by discriminant analysis. For the cluster analysis in step 1 many hard, seemingly arbitrary choices have to be made that nevertheless influence the solution (similarity measure, clustering strategy, number of clusters). The stability of the solution is often of concern, e.g. in clustering by the twinspan program. In the discriminant analysis of step 2 it can occur that a water sample is misclassified on the basis of the environmental data but on further inspection happens to be a borderline case in the cluster analysis. One would then rather reclassify such a sample and iterate the two steps. Bayesian latent class analysis is a flexible, extendable model-based cluster analysis approach that recently has gained popularity in the statistical literature and that has the potential to address these problems. It allows the macrofauna and environmental data to be modelled and analyzed in a single integrated analysis. An exciting extension is to incorporate in the analysis prior information on the habitat preferences of the macrofauna taxa such as is available in lists of indicator values. The output of the analysis is not a hard assignment of water samples to clusters but a probabilistic (fuzzy) assignment. The number of clusters is determined on the basis of the Bayes factor. A standard feature of the Bayesian method is to make predictions and to assess their uncertainty. We applied this approach to a data set consisting of 70 water samples, 484 macrofauna taxa and four environmental variables for which previously a five cluster solution had been proposed. The standard for Bayesian estimation, the Gibbs sampler, worked fine on a subset with only 12 selected taxa but did not converge on the full set with 484 taxa. This is due to many configurations in which the assignment probabilities are all very close to either 0 or 1. This convergence problem is comparable with the local optima problem in classical cluster optimization algorithms, including the EM algorithm used in Latent Gold, a Windows program for latent class analysis. The convergence problem needs to be solved before the benefits of Bayesian latent class analysis can come to fruition in this application. We discuss possible solutions.

From Natural to Degraded Rivers and Back Again

Extensive degradation of ecosystems, combined with the increasing demands placed on the goods and services they provide, is a major driver of biodiversity loss on a global scale. In particular, the severe degradation of large rivers, their catchments, floodplains and lower estuarine reaches has been ongoing for many centuries, and the consequences are evident across Europe. River restoration is a relatively recent tool that has been brought to bear in attempts to reverse the effects of habitat simplification and ecosystem degradation, with a surge of projects undertaken in the 1990s in Europe and elsewhere, mainly North America. Here, we focus on restoration of the physical properties (e.g. substrate composition, bank and bed structure) of river ecosystems to ascertain what has, and what has not, been learned over the last 20 years. First, we focus on three common types of restoration measures—riparian buffer management, instream mesohabitat enhancement and the removal of weirs and small dams—to provide a structured overview of the literature. We distinguish between abiotic effects of restoration (e.g. increasing habitat diversity) and biological recovery (e.g. responses of algae, macrophytes, macroinvertebrates and fishes). We then addressed four major questions: (i) Which organisms show clear recovery after restoration? (ii) Is there evidence for qualitative linkages between restoration and recovery? (iii) What is the timescale of recovery? and (iv) What are the reasons, if restoration fails? Overall, riparian buffer zones reduced fine sediment entry, and nutrient and pesticide inflows, and positive effects on stream organisms were evident. Buffer width and length were key: 5–30 m width and > 1 km length were most effective. The introduction of large woody debris, boulders and gravel were the most commonly used restoration measures, but the potential positive effects of such local habitat enhancement schemes were often likely to be swamped by larger-scale geomorphological and physico-chemical effects. Studies demonstrating long-term biological recovery due to habitat enhancement were notable by their absence. In contrast, weir removal can have clear beneficial effects, although biological recovery might lag behind for several years, as huge amounts of fine sediment may have accumulated upstream of the former barrier. Three Danish restoration schemes are provided as focal case studies to supplement the literature review and largely supported our findings. While the large-scale re-meandering and re-establishment of water levels at River Skjern resulted in significant recovery of riverine biota, habitat enhancement schemes at smaller-scales in other rivers were largely ineffective and failed to show long-term recovery. The general lack of knowledge derived from integrated, well-designed and long-term restoration schemes is striking, and we present a conceptual framework to help address this problem. The framework was applied to the three restoration types included in our study and highlights recurrent cause–effect chains, that is, commonly observed relationships of restoration measures (cause) and their effects on abiotic and biotic conditions (effect). Such conceptual models can provide useful new tools for devising more effective river restoration, and for identifying avenues for future research in restoration ecology in general.

Using discharge dynamics characteristics to predict the effects of climate change on macroinvertebrates in lowland streams

Abstract Despite the uncertainties in the rate of climate change, the Atlantic zone of northwestern Europe is expected to experience warmer, wetter winters and wetter summers than at present. Summer precipitation probably will depend on short, heavy rain showers between dry periods. Changes in the amount, frequency, and intensity of precipitation are expected to change stream discharge patterns, especially in rainwater-fed lowland streams, which will shift toward more dynamic flow regimes. Indices of discharge dynamics were used to assess the effect of changes in climate through changes in hydrology and land and water use on natural lowland stream macroinvertebrate communities. Discharge dynamics were significantly correlated with macroinvertebrate community structure, current velocity, and organic material preference. Our results demonstrate important influences of dynamic discharge regimes and extreme flows on macroinvertebrate community structure. Predictions of the ecological effects of climate change and of changes in land and water use indicate impaired ecological conditions in lowland streams of the Atlantic zone of northwestern Europe. Scenario tests involving different climate and landuse options suggest that current restoration practices and planned restoration activities can positively interact to reduce negative effects of climate change on lowland stream ecosystems.

The significance of climate change in streams utilised by humans.

To better understand the role of climate change in catchments that are already under pressure of human activities one needs to study past, current and future conditions. Therefore, the catchment of the river Vecht (The Netherlands), representative for many human utilised, medium-sized lowland river catchments in this ecoregion, was chosen as case example. Canalisation of the river Vecht went along with changes in land-use and took place during three major time-intervals: ±1895-1905, 1925-1935, and 1955-1965. As elsewhere in Europe, the agricultural, urban and other human uses increased and the morphological features of the streams showed degradation over the last 100 years. Most streams were straightened, total stream length was shortened (20 %), many connected side-arms got lost (40 %), and the number of oxbows decreased (38 %). There was a positive trend in temperature and precipitation observed over the last hundred years. But land-use and hydromorphology changes were independent from climate change. Six climate scenarios (two current and four for the years 2070-2100; SIMGRO model) showed that discharge will become somewhat more dynamic. The future low flow conditions predicted (MLR-EKOO model) macroinvertebrate assemblages that are more often found in temporary, -mesosaprobic, natural upper courses and polysaprobic, natural and canalised upper- and middle courses. This indicates slight quality deterioration. But comparing the major changes in land-use in the past that dramatically affected the stream ecosystems with these predicted small climate change induced changes justifies the conclusion that future land-use change will be of much greater importance than the effect of climate change