| Summary: | 1. Ordination and clustering methods are widely applied to ecological data that are nonnegative, for example species abundances or biomasses. These methods rely on a measure of multivariate proximity that quantifies differences between the sampling units (e.g. individuals, stations, time points), leading to results such as: (i) ordinations of the units, where interpoint distances optimally display the measured differences; (ii) clustering the units into homogeneous clusters; or (iii) assessing differences between pre-specified groups of units (e.g., regions, periods, treatment-control groups). 2. These methods all conceal a fundamental question: To what extent are the differences between the sampling units, computed according to the chosen proximity function, capturing the "size" in the multivariate observations, or their "shape"? "Size" means the overall level of the measurements: for example, some samples contain higher total abundances or more biomass, others less. "Shape" means the relative levels of the measurements: for example, some samples have different relative abundances, i.e. different compositions. To answer this question, several well-known proximity measures are considered and applied to two data sets, one of which is used in a simulation exercise where "shape" differences have been eliminated by randomization. For any data set and any proximity measure, a quantification is achieved of the proportion of "size" variance and "shape" variance that the measure is capturing, as well as the proportion of variance that confounds "size" and "shape" together. 3. The results consistently show that the Bray-Curtis coefficient incorporates both "size" and "shape" differences, to varying degrees. These two components are thus always confounded by this proximity measure in the determination of ordinations, clusters, group comparisons and relations to environmental variables. 4. There are several implications of these results, the main one being that researchers should be aware of this issue when they choose a ...
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