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17.2 Average taxonomic diversity and distinctness
Two measures, which address some of the problems identified with species richness and the other diversity indices, are defined by . They are based not just on the species abundances (denoted by $x _ i$, the number of individuals of species i in the sample) bu...
17.3 Examples: Ekofisk oil-field and Tees Bay soft-sediment macrobenthos
The earlier Fig. 14.4 demonstrated a change in the sediment macrofaunal communities around the Ekofisk oil-field {E}, out to a distance of about 3 km from the centre of drilling activity. This was only evident, however, from the multivariate (MDS and ANOSIM) ...
17.4 Other relatedness measures
The remainder of this chapter deals only with data in the form of a species list for a locality (presence/absence data). There is a substantial literature on measures incorporating, primarily, phylogenetic relationships amongst species (see references in the ...
17.5 ‘Expected distinctness’ tests
Species master list The construction of taxonomic distinctness indices from simple species lists makes it possible to address another of the ‘desirable features’ listed at the beginning of the chapter: there is a potential framework within which TD measures c...
17.6 Example: UK free-living nematodes
examined 14 species lists from a range of different habitats and impacted/undisturbed UK areas ({U}, Fig. 17.6), referring them to a 6-level classification of free-living, marine nematodes ( ), based on cladistic principles. The taxonomic groupings were: spe...
17.7 Example: N Europe groundfish surveys
An investigation of the taxonomic structure of demersal fish assemblages in the North Sea, English Channel and Irish Sea, motivated by concerns over the impacts of beam trawling, is reported by . A total of 277 ICES quarter-rectangles were sampled for 93 spec...
17.8 Variation in taxonomic distinctness, $\Lambda ^ +$
VarTD was defined in equation (17.7), as the variance of the taxonomic distances {$\omega _ {ij}$} between each pair of species i and j, about their mean distance $\Delta ^ +$. It has the potential to distinguish differences in taxonomic structure resulting, ...
17.9 Joint (AvTD, VarTD) analyses
The histogram and funnel plots of Figs. 17.7 and 17.8 are univariate analyses, concentrating on only one index at a time. Also possible is a bivariate approach in which ($\Delta ^ +$, $\Lambda ^ +$) values are considered jointly, both in respect of the observ...
17.10 Concluding remarks on taxonomic distinctness
Early applications of taxonomic distinctness ideas in marine science can be found in for demersal fish, for starfish and brittle-stars in polar regions, for starfish in the Atlantic, and for a latitudinal study of pelagic copepods. An early non-marine exam...
17.11 Taxonomic dissimilarity
A natural extension of the ideas of this chapter is from $\alpha$- or ‘spot’ diversity indices to $\beta$- or ‘turn-over’ diversity. The latter are essentially based on measures of dissimilarity between pairs of samples, the starting point for most of the meth...
17.12 Examples
Example: Island fish species lists Fish species lists extracted from FishBase for a selection of 26 world island groups {i} were slimmed down to leave only species that are ‘endemic’ to the total list, in the sense of being found at only one of these 26 locati...
18.1 Means plots
Several examples have been seen in previous chapters of the advantages of viewing ordination plots of the samples averaged over replicates within each factor level, or sometimes over the levels of other factors. This reduces the variance (technically, ‘multiva...
18.2 Example: Indonesian reef corals, S. Tikus
The point is made here in Fig 18.1 for the Shannon diversity of coral community transects (% cover data) at S. Tikus Island, Indonesia {I} first met in Fig 6.5. Normal-theory based tests are usually entirely valid for most diversity indices, often without tran...
18.3 ‘Bootstrap average’ regions
The idea of the (univariate) bootstrap () is that our best estimate of the distribution of values taken by the (n) replicates in a single group, if we are not prepared to assume a model form (e.g. normality), is just the set of observed points themselves, each...
18.4 Example: Loch Creran macrobenthos
collected a set of 256 soft-sediment macrobenthic samples along a transect in Loch Creran, Scotland {c}, data which have little or no evidence of a trend or spatial group structure and will therefore be useful here in illustrating a potential bootstrapping ar...
18.5 Example: Fal estuary macrofauna
The soft-sediment macrobenthic communities from five creeks of the Fal estuary, SW England, {f} were examined by and . For location of the creeks (Restronguet, Mylor, Pill, St Just, Percuil) see the map in Fig. 9.3, where the analysis was of the sediment meio...
Appendix 1: Index of example data
The following is a list of all (real) data sets used as examples in the text, where they are referenced by their indexing letter (A–Z, a-z). The entries give all pages on which each set is analysed or discussed and also its source reference (see also Appendix ...
Appendix 2: Principal literature sources and further reading
A list of some of the core methods papers was given in the Introduction, and the source papers for the data used in examples can be found in Appendix 1. Here we itemize, for each chapter, the source of analyses which repeat those in published literature, and w...
Appendix 3: Bibliography
Addison & Clark (1990) Addison, R.F. and Clarke, K.R. (1990) ‘Biological effects of pollutants in a subtropical environment’, J. Exp. Mar. Biol. Ecol., 138. Agard, Gobin & Warwick (1993) Agard, J.B.R., Gobin, J. and Warwick, R.M. ...
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