Similarity measure bias in river benthic Aufwuchs community analysis

Abstract

An extensive assessment was made of nine common similarity measures on the basis of their discriminative ability and bias in weighting of different types of variation in species abundance between samples, by using sets of river macroinvertebrate samples. Seven agglomerative hierarchical clustering methods were applied to these measures. Successful site discrimination is defined as grouping of all replicate samples from a particular site. Major differences existed in the discriminative ability between the similarity measures. The measures overweight some types of variation and underweight the others to varying extents, which is closely related to their discriminative ability. A new dissimilarity-similarity measure was devised to respond to all types of variation with minimum bias. This measure yielded a higher percentage of correct site discrimination than the others tested. Use of an extra data set confirmed the superior performance of the new measure and also indicated that it could discriminate between sites of different water quality. Water Environ. Res., 69, 95 (1997).

High habitat-specificity in fungal communities in oligo-mesotrophic, temperate Lake Stechlin (North-East Germany)

“…NMDS plots based on the fungal OTU matrix (1027 OTUs). Ordination is based on Cao distances (Cao et al 1997), which are insensitive to differences in sampling effort. Ellipses are based on standard deviations around habitat centroids (based on a confidence level of 0.95) and are coloured according to their POM type: FPOM (blue), MIX (magenta), CPOM (brown).…”

“…Differences among habitats within the fungal sub-community were examined with a non-metric multidimensional scaling (NMDS) ordination plot based on the Cao distance (Cao et al 1997), which accounts for variable sampling intensity. Ellipses correspond to the standard deviation around the habitat group centroids.…”

Long-Term Deer Exclusion Has Complex Effects On A Suburban Forest Understory

“…Cao index or CYd index (Cao et al 1997) was suggested as a minimally biased index for high beta diversity and variable sampling intensity. Cao index does not have a fixed upper limit, but can vary among sites with no shared species.…”

“…Cao index does not have a fixed upper limit, but can vary among sites with no shared species. The index is intended for count (integer) data, and it is undefined for zero abundances; these are replaced with arbitrary value 0.1 following Cao et al (1997). Cao et al (1997) used log 10 , but the current function uses natural logarithms so that the values are approximately 2.30 times higher than with 10-based logarithms.…”

“…The index is intended for count (integer) data, and it is undefined for zero abundances; these are replaced with arbitrary value 0.1 following Cao et al (1997). Cao et al (1997) used log 10 , but the current function uses natural logarithms so that the values are approximately 2.30 times higher than with 10-based logarithms. Anderson & Thompson (2004) give an alternative formulation of Cao index to highlight its relationship with Binomial index (above).…”