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Change in Marine Communities

An Approach to Statistical Analysis and Interpretation, 3rd edition

by
K R Clarke, R N Gorley, P J Somerfield & R M Warwick
(2014)

Introduction and acknowledgements

Chapter 1: A framework for studying changes in community structure

Chapter 2: Simple measures of similarity of species ‘abundance’ between samples

Chapter 3: Clustering methods

Chapter 4: Ordination of samples by principal components analysis (PCA)

Chapter 5: Ordination of samples by multi-dimensional scaling (MDS)

5.1 Other ordination methods

Principal Co-ordinates Analysis The two main weaknesses of PCA, identified at the end of Chapter ...

5.2 Non-metric multidimensional scaling (MDS)

The method of non-metric MDS was introduced by and , for application to problems in psychology; ...

5.3 Diagnostics: Adequacy of MDS representation

Is the stress value small? By definition, stress reduces with increasing dimensionality of the ...

5.4 EXAMPLE: Dosing experiment, Solbergstrand

The nematode abundance data from the dosing experiment {D} at the GEEP Oslo Workshop was previous...

5.5 Example: Celtic Sea zooplankton

In situations where the samples are strongly grouped, as in Figs. 5.4 and 5.5, both clustering an...

5.6 Example: Amoco-Cadiz oil spill, Morlaix

Benthic macrofaunal abundances of 251 species were sampled by at 21 times between April 1977 and ...

5.7 MDS strengths and weaknesses

MDS strengths MDS is simple in concept. The numerical algorithm is undeniably complex, but it ...

5.8 Further nMDS/mMDS developments

Higher dimensional solutions MDS solutions can be sought in higher dimensions and we noted previo...

5.9 Example: Okura estuary macrofauna

describe macrofauna samples from the Okura estuary {O}, on the northern fringes of urban Aucklan...

5.10 Example: Messolongi lagoon diatoms

sampled 17 lagoons in E Central Greece for diatom communities (193 species), and also recorded a...

5.11 Recommendations

Non-metric MDS can be recommended as the best general ordination technique available (e.g. ). Im...

Chapter 6: Testing for differences between groups of samples

6.1 Univariate tests and multivariate tests

Many community data sets possess some a priori defined structure within the set of samples, for e...

6.2 ANOSIM for the one-way layout

Fig.6.3 displays the MDS based only on the 12 samples (4 replicates per site) from the B, C and D...

6.3 Example: Frierfjord macrofauna

The rank similarities underlying Fig. 6.3 are shown in Table 6.2 (note that these are the similar...

6.4 Example: Indonesian reef-corals

examined data from 10 replicate transects across a single coral-reef site in S. Tikus Island, Th...

6.5 ANOSIM for two-way layouts

Three types of field and laboratory designs are considered here: a) the 2-way nested case can ari...

6.6 Example: Clyde nematodes (2-way nested case)

analysed meiobenthic communities from three putatively polluted (P) areas of the Firth of Clyde ...

6.7 Example: Eaglehawk Neck meiofauna (two-way crossed case)

An example of a two-way crossed design is given in and is introduced more fully here in Chapter ...

6.8 Example: Mesocosm experiment (two-way crossed case with no replication)

Although the above test may still function if a few random cells in the 2-way layout have only a ...

6.9 Example: Exe nematodes (no replication and missing data)

A final example demonstrates a positive outcome to such a test, in a common case of a 2-way layou...

6.10 ANOSIM for ordered factors

Generalised ANOSIM statistic for the 1-way case Now return to the simple one-way case of page 6.2...

6.11 Example: Ekofisk oil-field macrofauna

studied the soft-sediment macrobenthos at 39 sites at different distances (100m to 8km) and diff...

6.12 Two-way ordered ANOSIM designs

Under the non-parametric framework adopted in this manual (and in the PRIMER package) three forms...

6.13 Example: Phuket coral-reef time series

These data are discussed more fully in Chapters 15 and 16; sampling of coral assemblages took pla...

6.14 Three-way ANOSIM designs

Table 6.4 details all viable combinations of 3 factors, A, B, C, in crossed/nested form, ordered/...

6.15 Example: King Wrasse fish diets, WA

We begin the 3-factor examples with a fully crossed design A$\times$B$\times$C of the composition...

6.16 Example: NZ kelp holdfast macrofauna

We now consider the fully nested design, C(B(A)). In north-eastern New Zealand, examined assembl...

6.17 Example: Tees Bay macrofauna

The final example in this chapter is of a mixed nested and crossed design B$\times$C(A), for a to...

6.18 Recommendations

For typical species abundance matrices, it is much preferable to use a non-parametric ANOSIM-ty...

Chapter 7: Species analyses

Chapter 8: Diversity measures, dominance curves and other graphical analyses

Chapter 9: Transformations and dispersion weighting

Chapter 10: Species aggregation to higher taxa

Chapter 11: Linking community analyses to environmental variables

Chapter 12: Causality - community experiments in the field and laboratory

Chapter 13: Data requirements for biological effects studies - which components and attributes of the marine biota to examine?

Chapter 14: Relative sensitivities and merits of univariate, graphical/distributional and multivariate techniques

Chapter 15: Multivariate measures of community stress and relating to models

Chapter 16: Further multivariate comparisons and resemblance measures

Chapter 17: Biodiversity and dissimilarity measures based on relatedness of species

17.1 Species richness disadvantages

Chapter 8 discussed a range of diversity indices based on species richness and the species abunda...

17.2 Average taxonomic diversity and distinctness

Two measures, which address some of the problems identified with species richness and the other d...

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 Ek...

17.4 Other relatedness measures

The remainder of this chapter deals only with data in the form of a species list for a locality (...

17.5 ‘Expected distinctness’ tests

Species master list The construction of taxonomic distinctness indices from simple species lists ...

17.6 Example: UK free-living nematodes

examined 14 species lists from a range of different habitats and impacted/undisturbed UK areas (...

17.7 Example: N Europe groundfish surveys

An investigation of the taxonomic structure of demersal fish assemblages in the North Sea, Englis...

17.8 Variation in taxonomic distinctness, $\Lambda ^ +$

VarTD was defined in equation (17.7), as the variance of the taxonomic distances {$\omega _ {ij}$...

17.9 Joint (AvTD, VarTD) analyses

The histogram and funnel plots of Figs. 17.7 and 17.8 are univariate analyses, concentrating on o...

17.10 Concluding remarks on taxonomic distinctness

Early applications of taxonomic distinctness ideas in marine science can be found in for demersa...

17.11 Taxonomic dissimilarity

A natural extension of the ideas of this chapter is from $\alpha$- or ‘spot’ diversity indices to...

17.12 Examples

Example: Island fish species lists Fish species lists extracted from FishBase (www. fishbase.org)...

Chapter 18: Bootstrapped averages for region estimates in multivariate means plots

Appendices