In the early 1980s, a strategy for graphical representation of multivariate (multi-species) abundance data was introduced into marine ecology by, among others, Field, et al. (1982). A decade on, it is instructive to: (i) identify which elements of this often-quoted strategy have proved most useful in practical assessment of community change resulting from pollution impact; and (ii) ask to what extent evolution of techniques in the intervening years has added self-consistency and comprehensiveness to the approach. The pivotal concept has proved to be that of a biologically-relevant definition of similarity of two samples, and its utilization mainly in simple rank form, for example ‘sample A is more similar to sample B than it is to sample C’. Statistical assumptions about the data are thus minimized and the resulting non-parametric techniques will be of very general applicability. From such a starting point, a unified framework needs to encompass: (i) the display of community patterns through clustering and ordination of samples; (ii) identification of species principally responsible for determining sample groupings; (iii) statistical tests for differences in space and time (multivariate analogues of analysis of variance, based on rank similarities); and (iv) the linking of community differences to patterns in the physical and chemical environment (the latter also dictated by rank similarities between samples). Techniques are described that bring such a framework into place, and areas in which problems remain are identified. Accumulated practical experience with these methods is discussed, in particular applications to marine benthos, and it is concluded that they have much to offer practitioners of environmental impact studies on communities.

Non-parametric multivariate analyses of changes in community structure

Hypothesis-testing methods for multivariate data are needed to make rigorous probability statements about the effects of factors and their interactions in experiments. Analysis of variance is particularly powerful for the analysis of univariate data. The traditional multivariate analogues, however, are too stringent in their assumptions for most ecological multivariate data sets. Non-parametric methods, based on permutation tests, are preferable. This paper describes a new non-parametric method for multivariate analysis of variance, after McArdle and Anderson (in press). It is given here, with several applications in ecology, to provide an alternative and perhaps more intuitive formulation for ANOVA (based on sums of squared distances) to complement the description pro- vided by McArdle and Anderson (in press) for the analysis of any linear model. It is an improvement on previous non-parametric methods because it allows a direct additive partitioning of variation for complex models. It does this while maintaining the flexibility and lack of formal assumptions of other non-parametric methods. The test- statistic is a multivariate analogue to Fisher's F-ratio and is calculated directly from any symmetric distance or dissimilarity matrix. P-values are then obtained using permutations. Some examples of the method are given for tests involving several factors, including factorial and hierarchical (nested) designs and tests of interactions.

/pdf/a-new-method-for-non-parametric-multivariate-analysis-of-2zyb4px7ty.pdf

A new method for non-parametric multivariate analysis of variance

An essential textbook for any student or researcher in biology needing to design experiments, sample programs or analyse the resulting data The text begins with a revision of estimation and hypothesis testing methods, covering both classical and Bayesian philosophies, before advancing to the analysis of linear and generalized linear models Topics covered include linear and logistic regression, simple and complex ANOVA models (for factorial, nested, block, split-plot and repeated measures and covariance designs), and log-linear models Multivariate techniques, including classification and ordination, are then introduced Special emphasis is placed on checking assumptions, exploratory data analysis and presentation of results The main analyses are illustrated with many examples from published papers and there is an extensive reference list to both the statistical and biological literature The book is supported by a website that provides all data sets, questions for each chapter and links to software

/pdf/experimental-design-and-data-analysis-for-biologists-8ybva8d53x.pdf

Experimental Design and Data Analysis for Biologists

Pseudoreplication is defined. as the use of inferential statistics to test for treatment effects with data from experiments where either treatments are not replicated (though samples may be) or replicates are not statistically independent. In ANOVA terminology, it is the testing for treatment effects with an error term inappropriate to the hypothesis being considered. Scrutiny of 176 experi- mental studies published between 1960 and the present revealed that pseudoreplication occurred in 27% of them, or 48% of all such studies that applied inferential statistics. The incidence of pseudo- replication is especially high in studies of marine benthos and small mammals. The critical features of controlled experimentation are reviewed. Nondemonic intrusion is defined as the impingement of chance events on an experiment in progress. As a safeguard against both it and preexisting gradients, interspersion of treatments is argued to be an obligatory feature of good design. Especially in small experiments, adequate interspersion can sometimes be assured only by dispensing with strict random- ization procedures. Comprehension of this conflict between interspersion and randomization is aided by distinguishing pre-layout (or conventional) and layout-specifit alpha (probability of type I error). Suggestions are offered to statisticians and editors of ecological j oumals as to how ecologists' under- standing of experimental design and statistics might be improved.

/pdf/pseudoreplication-and-the-design-of-ecological-field-44o8kzdaoi.pdf

Pseudoreplication and the Design of Ecological Field Experiments

Plastics have outgrown most man-made materials and have long been under environmental scrutiny. However, robust global information, particularly about their end-of-life fate, is lacking. By identifying and synthesizing dispersed data on production, use, and end-of-life management of polymer resins, synthetic fibers, and additives, we present the first global analysis of all mass-produced plastics ever manufactured. We estimate that 8300 million metric tons (Mt) as of virgin plastics have been produced to date. As of 2015, approximately 6300 Mt of plastic waste had been generated, around 9% of which had been recycled, 12% was incinerated, and 79% was accumulated in landfills or the natural environment. If current production and waste management trends continue, roughly 12,000 Mt of plastic waste will be in landfills or in the natural environment by 2050.

Production, use, and fate of all plastics ever made

The grey mangrove tree, Avicennia marina, forms a hard substratum in an area otherwise dominated by soft-sediment. Various intertidal organisms attach to and move about on the trees. The abundant barnacles Elminius covenus, Hexaminius popeiana and Hexaminius foliorum live on a variety of substrata in mangrove forests. Their patterns of distribution and abundance were recorded and models proposed to explain these patterns. Densities of barnacles on bark, leaves and twigs of A. marina were estimated in a locality near Sydney. Elminius covenus were more abundant on bark than on leaves or twigs of A. marina. Hexaminius popeiana, although less abundant on bark than E. covenus, were not found on twigs or leaves. In contrast, H. foliorum were more abundant on twigs than leaves and were not found on the bark of A. marina. Densities of barnacles were greater in the seaward than in landward parts of the forest. Elminius covenus were the most abundant barnacles, H. foliorum were less abundant and H. popeiana were virtually absent in the landward zone. Barnacles in the seaward zone were most abundant at mid-tidal levels, less at high and low tidal levels of trunks and more abundant on lower than upper surfaces of trunks and leaves. The densities of barnacles differed according to the orientation of the bark or leaf.



Models are proposed to explain the patterns of distribution and abundance of these barnacles. Each involves larval supply, settlement and post-settlement mortality. It is concluded that similar processes determining patterns of distribution and abundance for sessile organisms living on rock platforms may be applicable to sessile organisms living in the very different habitats of mangrove forests.

The distribution and abundance of barnacles in a mangrove forest

Experiments on topographic influences on density and dispersion of Littorina unifasciata in New South Wales

Artificial structures are becoming common features of the landscape in shallow waters of urban areas, but very little is known about their ecology. In Sydney Harbour (NSW, Australia), intertidal seawalls replace considerable portions of natural habitats, including rocky shores. Previous studies have shown that seawalls and rocky shores generally support similar assemblages of plants and animals, with important differences in relative abundances of some species. The behaviour of key consumers can have a fundamental role in structuring benthic assemblages, and it is, therefore, necessary to assess whether it is changed by the replacement of natural habitats with artificial structures. This study compares patterns of movement of the common patellid limpet Cellana tramoserica between seawalls and vertical rocky shores. The distances displaced, the orientation of movement and the homing behaviour of marked individuals were recorded from day to day, over a period of several tidal cycles (14 d) and for a longer period (ca. 3 mo), on several seawalls and rocky shores. Short-term patterns of movement (1 to 14 d) did not differ between structures. In contrast, after 3 mo, although the orientation of the movement remained random on both kinds of structures, limpets on seawalls had dispersed longer distances and tended not to retain their original positions. These results suggest that long-term dispersal of C. tramoserica, rather than foraging bouts, could be altered by the replacement of rocky shores with artificial structures. Differences in use of habitat by key consumers should be incorporated in models aimed at identifying the mechanisms responsible for the occurrence of different assemblages on natural and artificial structures.

https://www.int-res.com/articles/meps2004/281/m281p121.pdf

Patterns of movement of the limpet Cellana tramoserica on rocky shores and retaining seawalls

Patterns of phytoplankton in areas with seagrass (Zostera capricorni, Halophila ovalis, and Ruppia megacarpa) and areas without seagrass were quantified in an estuary near Sydney, NSW, Australia. Replicate samples (separated by metres) were collected on 20 randomly chosen occasions over almost 3 years, from two sites (separated by tens of metres) nested in both habitats, at four locations (separated by kilometres). Areas with seagrass often supported a significantly different assemblage of phytoplankton compared with areas without seagrass. Dissimilarities were due to small differences in the relative abundance of taxa, particularly the diatom Pseudonitzschia cf. pseudodelicatissima, rather than the presence or absence of specific taxa. In both habitats, abundances of phytoplankton were patchy at all of the spatial scales sampled, although most of the variation was among replicate samples. These findings emphasise the need to incorporate a hierarchy of scales in programs designed to understand processes that cause spatial and temporal patterns of phytoplankton or to detect changes in response to human activities.

Comparisons of assemblages of phytoplankton between open water and seagrass habitats in a shallow coastal lagoon

Summary Environmental managers are often confronted with unplanned or accidental disturbances that may lead to environmental impacts. Procedures for detecting or measuring the size of such impacts are complicated because of the lack of data available before the disturbance and because of the intrinsic variability of most natural measures. Here, a protocol for detecting impacts is illustrated for single-measure variables (numbers of individual species) and multivariate measures (relative abundances of invertebrates in assemblages). The present paper describes a case concerning drainage of acidified water into an estuary due to construction of a drainage channel in an area of wetland for which there had been no prior investigations (i.e. no ‘before’ data). The spatial extent of any impact was also unknowable. Sampling was, therefore, designed to allow for impacts of only a few tens of metres (using control sites 50 m from the mouth of the channel) and impacts covering much larger areas (500 m and 1 km from the mouth of the channel). Invertebrates in the mud around the channel and in control sites were sampled in replicated cores and the amount of seagrass in each core was weighed. Average abundances of invertebrate animals and weights of seagrass were compared, as was variation among samples in potentially impacted and control sites (using univariate analyses of variance). Sets of species were compared using multivariate methods to test the hypothesis that there was an impact at one of the scales examined. In fact, there was no evidence for any sort of impact on the fauna or seagrasses; the disturbance was a short-term pulse without any obvious or sustained ecological response. One consequence of the study was that the local council was able to demonstrate no impact requiring remediation and no penalties were imposed for the unapproved construction of the channel. The implications of this type of study after an environmental disturbance are discussed. The present study identifies the need for clear definition of relevant hypotheses, coupled with rigorous planning of sampling and analyses, so that reliable answers are available to regulators and managers.

A. J. Underwood

Papers

The distribution and abundance of barnacles in a mangrove forest

Experiments on topographic influences on density and dispersion of Littorina unifasciata in New South Wales

Patterns of movement of the limpet Cellana tramoserica on rocky shores and retaining seawalls

Comparisons of assemblages of phytoplankton between open water and seagrass habitats in a shallow coastal lagoon

A practical protocol to assess impacts of unplanned disturbance: a case study in Tuggerah Lakes Estuary, NSW