# Appendices



# 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 3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/appendix-3-bibliography)).  These are not always the appropriate references for the analyses which can be found in the text; the latter are generally given in [Appendix 2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/appendix-2-principal-literature-sources-and-further-reading).

A –	Amoco-Cadiz oil spill, Bay of Morlaix, France. *Macrofauna* - {{@224#bkmrk-dauvin1984a}}.  

* *pages [5.6](https://learninghub.primer-e.com/books/change-in-marine-communities/page/56-example-amoco-cadiz-oil-spill-morlaix), [5.8](https://learninghub.primer-e.com/books/change-in-marine-communities/page/58-further-nmdsmmds-developments), [7.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/73-example-amoco-cadiz-oil-spill), [10.2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/102-examples), [13.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/133-macrobenthos-and-meiobenthos), [15.2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/152-meta-analysis-of-marine-macrobenthos), [16.1](https://learninghub.primer-e.com/books/change-in-marine-communities/page/161-introduction), [16.2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/162-matching-of-ordinations), [16.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/163-example-amoco-cadiz-oil-spill), [16.5](https://learninghub.primer-e.com/books/change-in-marine-communities/page/165-second-stage-mds), [17.1](https://learninghub.primer-e.com/books/change-in-marine-communities/page/171-species-richness-disadvantages), [17.2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/172-average-taxonomic-diversity-and-distinctness)*

a –	Algal recolonisation, Calafuria, Ligurian Sea, Italy. *Macroalgae.* - {{@224#bkmrk-airoldi2000a}}.

* *page [16.8](https://learninghub.primer-e.com/books/change-in-marine-communities/page/168-example-algal-recolonisation-calafuria)*

B –	Bristol Channel, England.  *Zooplankton* - {{@224#bkmrk-collins1982a}}.

* *pages [3.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/33-example-bristol-channel-zooplankton), [3.5](https://learninghub.primer-e.com/books/change-in-marine-communities/page/35-similarity-profiles-simprof), [3.6](https://learninghub.primer-e.com/books/change-in-marine-communities/page/36-binary-divisive-clustering), [7.5](https://learninghub.primer-e.com/books/change-in-marine-communities/page/75-example-bristol-channel-zooplankton), [7.8](https://learninghub.primer-e.com/books/change-in-marine-communities/page/78-species-contributions-to-sample-dissimilarities-simper), [7.10](https://learninghub.primer-e.com/books/change-in-marine-communities/page/710-bubble-plots-plus-examples), [11.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/113-linking-biota-to-univariate-environmental-measures-and-examples)*

b –	Beam-trawl surveys, N. Europe. *Groundfish* - {{@224#bkmrk-rogers1999a}}.

* *page [17.7](https://learninghub.primer-e.com/books/change-in-marine-communities/page/177-example-n-europe-groundfish-surveys)*

C –	Celtic Sea.  *Zooplankton*.  (Collins, pers. comm.). 

* *page [5.5](https://learninghub.primer-e.com/books/change-in-marine-communities/page/55-example-celtic-sea-zooplankton)*

c –	Creran & Etive loch, Scotland. *Macrobenthos* - {{@224#bkmrk-gage1977a}}, {{@224#bkmrk-gage1972a}}.

* *pages [15.6](https://learninghub.primer-e.com/books/change-in-marine-communities/page/156-examples), [18.4](https://learninghub.primer-e.com/books/change-in-marine-communities/page/184-example-loch-creran-macrobenthos)* 

D –	Dosing experiment, Solbergstrand mesocosm, Norway (GEEP Workshop). *Nematodes* - {{@224#bkmrk-warwick1988c}}.

* *pages [4.5](https://learninghub.primer-e.com/books/change-in-marine-communities/page/45-example-dosing-experiment-solbergstrand-mesocosm), [5.4](https://learninghub.primer-e.com/books/change-in-marine-communities/page/54-example-dosing-experiment-solbergstrand), [9.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/93-multivariate-case)*

d –	Diets of W Australian fish. *Gut contents of seven nearshore species* - {{@224#bkmrk-hourston2004a}}.

* *page [7.10](https://learninghub.primer-e.com/books/change-in-marine-communities/page/710-bubble-plots-plus-examples)*  

E –	Ekofisk oil platform, N.Sea.  *Macrofauna* - {{@224#bkmrk-gray1990a}}.

* *pages [6.11](https://learninghub.primer-e.com/books/change-in-marine-communities/page/611-example-ekofisk-oil-field-macrofauna), [7.7](https://learninghub.primer-e.com/books/change-in-marine-communities/page/77-example-ekofisk-oil-field-macrofauna), [7.10](https://learninghub.primer-e.com/books/change-in-marine-communities/page/710-bubble-plots-plus-examples), [8.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/83-examples-garroch-head-and-ekofisk-macrofauna), [8.5](https://learninghub.primer-e.com/books/change-in-marine-communities/page/85-multivariate-tools-used-on-univariate-data), [10.2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/102-examples), [14.2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/142-examples-1-2-and-3), [15.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/153-increased-variability), [17.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/173-examples-ekofisk-oil-field-and-tees-bay-soft-sediment-macrobenthos)*

e –	Estuaries, W Australia. *Fish* - {{@224#bkmrk-valesini2014a}}.

* *page [11.5](https://learninghub.primer-e.com/books/change-in-marine-communities/page/115-further-best-variations)*

F –	Frierfjord, Norway (GEEP Workshop). *Macrofauna* - {{@224#bkmrk-gray1988a}}.

* *pages [1.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/13-example-frierfjord-macrofauna), [1.7](https://learninghub.primer-e.com/books/change-in-marine-communities/page/17-multivariate-techniques), [3.1](https://learninghub.primer-e.com/books/change-in-marine-communities/page/31-cluster-analysis), [3.2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/32-hierarchical-agglomerative-clustering), [6.1](https://learninghub.primer-e.com/books/change-in-marine-communities/page/61-univariate-tests-and-multivariate-tests), [6.2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/62-anosim-for-the-one-way-layout), [6.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/63-example-frierfjord-macrofauna), [8.4](https://learninghub.primer-e.com/books/change-in-marine-communities/page/84-examples-loch-linnhe-and-garroch-head-macrofauna), [9.2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/92-univariate-case), [10.1](https://learninghub.primer-e.com/books/change-in-marine-communities/page/101-species-aggregation), [13.5](https://learninghub.primer-e.com/books/change-in-marine-communities/page/135-attributes-and-recommendations), [14.2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/142-examples-1-2-and-3), [15.2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/152-meta-analysis-of-marine-macrobenthos)*

f  –	Fal estuary sediments, S.W. England.  *Meio- and macrofauna* - {{@224#bkmrk-somerfield1994a}}, {{@224#bkmrk-somerfield1994b}}.

* *pages [9.6](https://learninghub.primer-e.com/books/change-in-marine-communities/page/96-example-fal-estuary-copepods), [11.6](https://learninghub.primer-e.com/books/change-in-marine-communities/page/116-linkage-trees-and-example), [18.5](https://learninghub.primer-e.com/books/change-in-marine-communities/page/185-example-fal-estuary-macrofauna)*

G –	Garroch Head, sludge dump-ground, Scotland. *Macrofauna* - {{@224#bkmrk-pearson1984a}}.

* *pages [1.6](https://learninghub.primer-e.com/books/change-in-marine-communities/page/16-example-garroch-head-macrofauna), [1.7](https://learninghub.primer-e.com/books/change-in-marine-communities/page/17-multivariate-techniques), [4.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/43-example-garroch-head-macrofauna), [7.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/73-example-amoco-cadiz-oil-spill), [7.6](https://learninghub.primer-e.com/books/change-in-marine-communities/page/76-example-garroch-head-macrofauna), [8.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/83-examples-garroch-head-and-ekofisk-macrofauna), [8.4](https://learninghub.primer-e.com/books/change-in-marine-communities/page/84-examples-loch-linnhe-and-garroch-head-macrofauna), [8.7](https://learninghub.primer-e.com/books/change-in-marine-communities/page/87-multiple-diversity-indices), [11.2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/112-example-garroch-head-macrofauna), [11.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/113-linking-biota-to-univariate-environmental-measures-and-examples), [11.4](https://learninghub.primer-e.com/books/change-in-marine-communities/page/114-linking-biota-to-multivariate-environmental-patterns), [11.7](https://learninghub.primer-e.com/books/change-in-marine-communities/page/117-concluding-remarks), [15.2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/152-meta-analysis-of-marine-macrobenthos), [16.6](https://learninghub.primer-e.com/books/change-in-marine-communities/page/166-comparison-of-resemblance-measures)*

g –	Gullfaks A&B oilfields, Norway. *Macrobenthos* - {{@224#bkmrk-olsgard1995a}}. 

* *page [15.6](https://learninghub.primer-e.com/books/change-in-marine-communities/page/156-examples)*

H –	Hamilton Harbour, Bermuda (GEEP Workshop). *Macrofauna, nematodes* - {{@224#bkmrk-warwick1990c}}.

* *pages [8.1](https://learninghub.primer-e.com/books/change-in-marine-communities/page/81-univariate-measures), [8.4](https://learninghub.primer-e.com/books/change-in-marine-communities/page/84-examples-loch-linnhe-and-garroch-head-macrofauna), [13.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/133-macrobenthos-and-meiobenthos)*

I –	Indonesian reef corals, S. Pari and S. Tikus Islands.  *Coral % cover* - {{@224#bkmrk-warwick1990b}}.

* *pages [6.4](https://learninghub.primer-e.com/books/change-in-marine-communities/page/64-example-indonesian-reef-corals), [8.1](https://learninghub.primer-e.com/books/change-in-marine-communities/page/81-univariate-measures), [10.1](https://learninghub.primer-e.com/books/change-in-marine-communities/page/101-species-aggregation), [10.2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/102-examples), [13.4](https://learninghub.primer-e.com/books/change-in-marine-communities/page/134-hard-bottom-epifauna-and-hard-bottom-motile-fauna), [14.2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/142-examples-1-2-and-3), [15.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/153-increased-variability), [16.6](https://learninghub.primer-e.com/books/change-in-marine-communities/page/166-comparison-of-resemblance-measures), [18.2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/182-example-indonesian-reef-corals-s-tikus), [18.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/183-bootstrap-average-regions)*

i –	Island group species lists. *Fish presence/absence* - {{@224#bkmrk-clarke2006d}}.

* *page [17.12](https://learninghub.primer-e.com/books/change-in-marine-communities/page/1712-examples)*

J –	Joint NE Atlantic shelf studies (‘meta-analysis’). *Macrofauna ‘production’* - {{@224#bkmrk-warwick1993b}}.

* *page [15.2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/152-meta-analysis-of-marine-macrobenthos)*

K –	Ko Phuket coral reefs, Thailand.  *Coral species cover* - {{@224#bkmrk-clake1993c}}, {{@224#bkmrk-brown2002a}}.

* *pages [6.13](https://learninghub.primer-e.com/books/change-in-marine-communities/page/613-example-phuket-coral-reef-time-series), [15.4](https://learninghub.primer-e.com/books/change-in-marine-communities/page/154-breakdown-of-seriation), [16.6](https://learninghub.primer-e.com/books/change-in-marine-communities/page/166-comparison-of-resemblance-measures), [16.7](https://learninghub.primer-e.com/books/change-in-marine-communities/page/167-second-stage-interaction-plots)*

k –	King Wrasse diets, W Australia. *Gut contents of labrid fish* - {{@224#bkmrk-lek2011a}}.

* *page [6.15](https://learninghub.primer-e.com/books/change-in-marine-communities/page/615-example-king-wrasse-fish-diets-wa)*

L –	Loch Linnhe and Loch Eil, Scotland, pulp-mill effluent.  *Macrofauna* - {{@224#bkmrk-pearson1975a}}.

* *pages [1.5](https://learninghub.primer-e.com/books/change-in-marine-communities/page/15-example-loch-linnhe-macrofauna), [1.7](https://learninghub.primer-e.com/books/change-in-marine-communities/page/17-multivariate-techniques), [2.2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/22-example-loch-linnhe-macrofauna), [3.2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/32-hierarchical-agglomerative-clustering), [5.2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/52-non-metric-multidimensional-scaling-mds), [8.4](https://learninghub.primer-e.com/books/change-in-marine-communities/page/84-examples-loch-linnhe-and-garroch-head-macrofauna), [9.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/93-multivariate-case), [10.1](https://learninghub.primer-e.com/books/change-in-marine-communities/page/101-species-aggregation), [10.2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/102-examples), [15.2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/152-meta-analysis-of-marine-macrobenthos)*

l –	Leschenault estuary, W Australia. *Estuarine fish assemblage, over seasons* - {{@224#bkmrk-veale2014a}}. 

* *page [15.6](https://learninghub.primer-e.com/books/change-in-marine-communities/page/156-examples)*

M –	Maldive Islands mining.  *Coral reef fish* - {{@224#bkmrk-dawson-shepherd1992a}}.

* *pages [13.2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/132-plankton-and-fish), [14.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/143-examples-4-5-6-and-7), [15.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/153-increased-variability)*

m – Messolongi lagoons, E. Central Greece. *Diatoms and water-column data* - {{@224#bkmrk-danielidis1991a}}.

* *page [5.10](https://learninghub.primer-e.com/books/change-in-marine-communities/page/510-example-messolongi-lagoon-diatoms)*

N –	Nutrient-enrichment experiment, Solbergstrand mesocosm, Norway.  *Nematodes, copepods* - {{@224#bkmrk-gee1985a}}.

* *pages [1.8](https://learninghub.primer-e.com/books/change-in-marine-communities/page/18-example-nutrient-enrichment-experiment-solbergstrand), [10.1](https://learninghub.primer-e.com/books/change-in-marine-communities/page/101-species-aggregation), [10.2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/102-examples), [12.4](https://learninghub.primer-e.com/books/change-in-marine-communities/page/124-laboratory-experiments), [15.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/153-increased-variability)*

n –	NE New Zealand kelp holdfasts. *Macrofauna* - {{@224#bkmrk-anderson2005a}}.

* *page [6.16](https://learninghub.primer-e.com/books/change-in-marine-communities/page/616-example-nz-kelp-holdfast-macrofauna)*

O – Okura estuary, Long Bay, New Zealand. *Inter-tidal macrofauna* - {{@224#bkmrk-anderson2004a}}.

* *page [5.9](https://learninghub.primer-e.com/books/change-in-marine-communities/page/59-example-okura-estuary-macrofauna)*

P –	Plymouth particle-size data. *Water samples with Coulter Counter.* (A. Bale, pers. comm).

* *page [8.6](https://learninghub.primer-e.com/books/change-in-marine-communities/page/86-example-plymouth-particle-size-data)*

p –	Plankton survey (Continuous Plankton Recorder), N.E. Atlantic.  *Zooplankton, phytoplankton* - {{@224#bkmrk-colebrook1986a}}.

* *page [13.2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/132-plankton-and-fish)*

R –	Tamar estuary mud-flat, S.W. England.  *Nematodes, copepods* - {{@224#bkmrk-austen1989a}}.

* *page [14.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/143-examples-4-5-6-and-7)*

S –	Scilly Isles, UK.  *Seaweed metazoa* - {{@224#bkmrk-gee1994a}}, {{@224#bkmrk-gee1994b}}.

* *pages [13.4](https://learninghub.primer-e.com/books/change-in-marine-communities/page/134-hard-bottom-epifauna-and-hard-bottom-motile-fauna), [14.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/143-examples-4-5-6-and-7)*

T –	Tasmania, Eaglehawk Neck.  *Nematodes, copepods* - {{@224#bkmrk-warwick1990a}}.

* *pages [6.7](https://learninghub.primer-e.com/books/change-in-marine-communities/page/67-example-eaglehawk-neck-meiofauna-two-way-crossed-case), [7.9](https://learninghub.primer-e.com/books/change-in-marine-communities/page/79-example-tasmanian-meiofauna), [12.2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/122-natural-experiments), [13.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/133-macrobenthos-and-meiobenthos), [14.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/143-examples-4-5-6-and-7)*

t  -	Tees Bay, N.E. England. *Macrobenthos* - {{@224#bkmrk-warwick2002a}}.

* *pages [6.17](https://learninghub.primer-e.com/books/change-in-marine-communities/page/617-example-tees-bay-macrofauna), [15.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/153-increased-variability), [15.6](https://learninghub.primer-e.com/books/change-in-marine-communities/page/156-examples), [17.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/173-examples-ekofisk-oil-field-and-tees-bay-soft-sediment-macrobenthos)*

U –	UK regional studies. *Nematodes* - {{@224#bkmrk-warwick1998a}}. 

* *pages [17.6](https://learninghub.primer-e.com/books/change-in-marine-communities/page/176-example-uk-free-living-nematodes), [17.8](https://learninghub.primer-e.com/books/change-in-marine-communities/page/178-variation-in-taxonomic-distinctness-lambda), [17.9](https://learninghub.primer-e.com/books/change-in-marine-communities/page/179-joint-avtd-vartd-analyses)*

V –	Valhall oilfield, N Sea. *Macrofauna* - {{@224#bkmrk-olsgard1997a}}.

* *page [17.12](https://learninghub.primer-e.com/books/change-in-marine-communities/page/1712-examples)*

W – World map. *Great-circle distances among cities*. (Reader’s Digest Great World Atlas, 1962)

* *page [5.8](https://learninghub.primer-e.com/books/change-in-marine-communities/page/58-further-nmdsmmds-developments)* 

w –	Westerschelde estuary cores, Netherlands; mesocosm experiment on food supply.  *Nematodes* - {{@224#bkmrk-austen1995a}}.

* *page [6.8](https://learninghub.primer-e.com/books/change-in-marine-communities/page/68-example-mesocosm-experiment-two-way-crossed-case-with-no-replication)*

X –	Exe estuary, S.W. England.  *Nematodes* - {{@224#bkmrk-warwick1971a}}.

* *pages [5.2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/52-non-metric-multidimensional-scaling-mds), [5.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/53-diagnostics-adequacy-of-mds-representation), [6.9](https://learninghub.primer-e.com/books/change-in-marine-communities/page/69-example-exe-nematodes-no-replication-and-missing-data), [7.1](https://learninghub.primer-e.com/books/change-in-marine-communities/page/71-species-clustering), [7.2](https://learninghub.primer-e.com/books/change-in-marine-communities/page/72-type-2-and-type-3-simprof-tests), [7.4](https://learninghub.primer-e.com/books/change-in-marine-communities/page/74-shade-plots), [11.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/113-linking-biota-to-univariate-environmental-measures-and-examples), [11.4](https://learninghub.primer-e.com/books/change-in-marine-communities/page/114-linking-biota-to-multivariate-environmental-patterns), [15.6](https://learninghub.primer-e.com/books/change-in-marine-communities/page/156-examples)*

Y –	Clyde, Scotland.  *Nematodes* - {{@224#bkmrk-lambshead1986a}}.

* *page [6.6](https://learninghub.primer-e.com/books/change-in-marine-communities/page/66-example-clyde-nematodes-2-way-nested-case)*

Z –	Azoic sediment recolonization experiment.  *Copepods* - {{@224#bkmrk-olafsson1992a}}.

* *page [12.3](https://learninghub.primer-e.com/books/change-in-marine-communities/page/123-field-experiments)*

# 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 where figures have been redrawn from. Figures or analyses not mentioned can be assumed to originate with this publication. Also sometimes mentioned are historical references to earlier developments of the ideas in that chapter, or other useful background reading. 

**Chapter 1: Framework**. The categorisation here is an extension of that given by {{@224#bkmrk-warwick1988a}}.  The Frierfjord macrofauna data and analyses (Tables 1.2 & 1.6 and Figs. 1.1, 1.2 & 1.7) are extracted and re-drawn from {{@224#bkmrk-bayne1988a}}, {{@224#bkmrk-gray1988a}} and {{@224#bkmrk-clarke1988b}}, the Loch Linnhe macrofauna data (Table 1.4 and Fig. 1.3) from {{@224#bkmrk-pearson1975a}}, and the ABC curves (Fig. 1.4) from {{@224#bkmrk-warwick1986a}}.  The species abundance distribution for Garroch Head macrofauna (Fig. 1.6) is first found in {{@224#bkmrk-pearson1983a}}, and the multivariate linking to environmental variables (Fig. 1.11) in {{@224#bkmrk-clarke1993b}}.  The ‘coherent species curves’ (Fig. 1.10) for the Loch Linnhe data are redrawn from {{@224#bkmrk-somerfield2013a}}. The mescosm data from the nutrient enrichment experiment (Table 1.7) and the MDS plot for copepods and nematodes (Fig. 1.12) are extracted and redrawn from {{@224#bkmrk-gee1985a}}.

**Chapters 2 and 3: Similarity and clustering**.  These methods originated in the 1950’s and 60’s (e.g. {{@224#bkmrk-florek1951a}}; {{@224#bkmrk-sneath1957a}}; {{@224#bkmrk-lance1967a}}).  The description here widens that of {{@224#bkmrk-field1982a}}, with some points taken from the general texts of {{@224#bkmrk-everitt1980a}} and {{@224#bkmrk-cormack1971a}}.  The dendrogram of Frierfjord macrofaunal samples (Fig.3.1) is redrawn from {{@224#bkmrk-gray1988a}}, and the zooplankton example (Figs. 3.2 & 3.3) from {{@224#bkmrk-collins1982a}}. The SIMPROF test for samples on agglomerative clusters is described in {{@224#bkmrk-clarke2008a}}; Fig. 3.8 mimics one in {{@224#bkmrk-anderson2008a}}, and the other cluster methods (unconstrained divisive and k-R clustering, maximising R) are somewhat new to this publication. 

**Chapter 4: Ordination by PCA.**  This is a founding technique of multivariate statistics, see for example {{@224#bkmrk-chatfield1980a}} and {{@224#bkmrk-everitt1978a}}.  The MDS from a dosing experiment in the Solbergstrand mesocosms (Fig. 4.2) is from {{@224#bkmrk-warwick1988c}}.

**Chapter 5: Ordination by MDS.**  Non-metric MDS was introduced by {{@224#bkmrk-shepard1962a}} and {{@224#bkmrk-kruskal1964a}}; two standard texts are {{@224#bkmrk-kruskal1978a}} and {{@224#bkmrk-schiffman1981a}}.  Here, the exposition parallels that in {{@224#bkmrk-field1982a}} and {{@224#bkmrk-clarke1993a}}; the Exe nematode graphs (Figs. 5.1, 5.2, 5.4, 5.5) are redrawn from the former.  The dosing experiment (Fig. 5.6) is discussed in {{@224#bkmrk-warwick1988c}}. Metric MDS (see {{@224#bkmrk-cox2001a}}), not to be confused with the similar, but not identical, PCO ordinations (produced by PERMANOVA+ for example), was also an early introduction but is much less commonly implemented in software. The combining of nMDS and mMDS stress functions bears some relationship to hybrid and semi-strong hybrid scaling methods ({{@224#bkmrk-faith1987a}}, {{@224#bkmrk-belbin1991a}}) but with some important differences in implementation and with a different rationale here (the avoidance of collapsed sub-groups in an MDS plot, and for two nMDS stress functions, the merging of similarities of different types); see footnote on [page 5.8](https://learninghub.primer-e.com/books/change-in-marine-communities/page/58-further-nmdsmmds-developments). 

**Chapter 6: Testing.**  The basic permutation test and simulation of significance levels can be traced to {{@224#bkmrk-mantel1967a}} and {{@224#bkmrk-hope1968a}}, respectively.  In this context (e.g. Figs. 6.2 & 6.3 and eqt. 6.1) it is described by {{@224#bkmrk-clarke1988b}}.  A fuller discussion of the  extension to 2-way nested and crossed ANOSIM tests (including Figs. 6.4 & 6.6) is in {{@224#bkmrk-clarke1993a}} (with some asymptotic results in {{@224#bkmrk-clarke1988a}});  the coral analysis (Fig. 6.5) is in {{@224#bkmrk-warwick1990b}}, and the Tasmanian meiofaunal MDS (Fig. 6.7) in {{@224#bkmrk-warwick1990a}}.  The 2-way design without replication (Figs. 6.8-6.12) is tackled in {{@224#bkmrk-clarke1994a}}; see also {{@224#bkmrk-austen1995a}}. The ordered ANOSIM test is new to this publication, as are the extensions to 3-way crossed/nested designs. {{@224#bkmrk-lek2011a}} give the ‘flattened’ 2-way ANOSIM tests for the 3-way crossed example of labrid diets; Fig. 6.15 is redrawn from there. The NZ kelp holdfast data is provided with the PERMANOVA+ software ({{@224#bkmrk-anderson2008a}}). Fig. 6.17 is partly extracted from {{@224#bkmrk-warwick2002a}}. 

**Chapter 7: Species analyses.**  Clustering on species similarities is given in {{@224#bkmrk-field1982a}} for the Exe nematode data; see also {{@224#bkmrk-clifford1975a}}. SIMPROF test for species (‘coherent curves’) follows {{@224#bkmrk-somerfield2013a}}; Figs. 7.1-7.6 are redrawn from there. Shade plots are described in {{@224#bkmrk-clarke2014a}} but have a very long history (see {{@224#bkmrk-wilkinson2008a}}), though there are some novelties in the options outlined here, in terms of combinations of input data,  axis ordering, cluster analysis choices, and so on. The SIMPER (similarity percentages) procedure is given in {{@224#bkmrk-clarke1993a}}, and the 2-way crossed SIMPER first used in {{@224#bkmrk-platell1998a}}. Simple bubble plots are a staple routine for graphical output but PRIMER 7’s segmented bubble plots were first used in {{@224#bkmrk-stoffels2014a}} and in {{@224#bkmrk-purcell2014a}}. 

**Chapter 8: Univariate/graphical analyses.**  {{@224#bkmrk-pielou1975a}}, {{@224#bkmrk-heip1988a}} and {{@224#bkmrk-magurran1991a}} are useful texts, summarising a large literature on a variety of diversity indices and ranked species abundance plots.  The diversity examples here (Figs. 8.1 & 8.2) are discussed by {{@224#bkmrk-warwick1990c}} and {{@224#bkmrk-warwick1990b}} respectively, and the Caswell *V* computations (Table 8.1) are from {{@224#bkmrk-warwick1990c}}.  The Garroch Head species abundance distributions (Fig. 8.4) are first found in {{@224#bkmrk-pearson1983a}}; Fig. 8.3 is redrawn from {{@224#bkmrk-pearson1984a}}. {{@224#bkmrk-warwick1986a}} introduced Abundance–Biomass Comparison curves, and the Loch Linnhe and Garroch Head illustrations (Figs. 8.7 & 8.8) are redrawn from {{@224#bkmrk-warwick1986a}} and {{@224#bkmrk-warwick1987a}}.  The transformed scale and partial dominance curves of Figs. 8.9-8.11 were suggested by {{@224#bkmrk-clarke1990a}}, which paper also tackles issues of summary statistics (Fig. 8.12, equation 8.7, and as employed in Fig. 8.13) and significance tests for dominance curves (the DOMDIS routine in PRIMER). Use of ANOSIM on distances among curves (growth curves, particle size distributions etc) has been advocated at PRIMER courses for some years and there are now a few examples in the literature. Similarly, the treatment of multiple diversity indices by multivariate methods, to ascertain the true (and limited) dimensionality of information captured, and the consistent (mechanistic) relationships between indices seen in ordination patterns (such as Fig. 8.16), has long been a staple of PRIMER courses, though never specifically published. 

**Chapter 9:  Transformations**. The chapter start is an expansion of the discussion in {{@224#bkmrk-clarke1988b}}; Fig. 9.1 is recomputed from {{@224#bkmrk-warwick1988c}}. Detailed description of dispersion weighting (DW) is in {{@224#bkmrk-clarke2006a}}; Figs. 9.2, 9.4 of the Fal nematode data ({{@224#bkmrk-somerfield1994a}} and {{@224#bkmrk-somerfield1994b}}) are redrawn from {{@224#bkmrk-clarke2006a}}. The use of shade plots to aid transformation or DW choices is the topic of {{@224#bkmrk-clarke2014a}}. A different form of weighting of variables (by their standard deviation) is described in {{@224#bkmrk-hallett2012a}}. 

**Chapter 10:  Aggregation**.  This description of the effects of changing taxonomic level is based on {{@224#bkmrk-warwick1988b}}, from which Figs. 10.2-10.4 and 10.7 are redrawn.  Fig. 10.1 is discussed in {{@224#bkmrk-gray1988a}}, Fig. 10.5 and 10.8 in {{@224#bkmrk-warwick1990b}} and Fig. 10.6 in {{@224#bkmrk-gray1990a}} (or {{@224#bkmrk-warwick1993b}}, in this categorisation). A methodology for examining the comparative effects on an analysis of choice of taxonomic level (and transform) can be found in {{@224#bkmrk-olsgard1997a}}, {{@224#bkmrk-olsgard1998a}}, and {{@224#bkmrk-olsgard2000a}}.

**Chapter 11:  Linking to environment**.  For wider reading on this type of ‘canonical’ problem, see Chapter 5 of {{@224#bkmrk-jongman1987a}}, including {{@224#bkmrk-terbraak1986a}}'s method of canonical correspondence analysis.  The approach here of performing environmental and biotic analyses separately, and then comparing them, combines that advocated by {{@224#bkmrk-field1982a}}: superimposing variables on the biotic MDS, and by {{@224#bkmrk-clarke1993b}}: the BIO-ENV program.  The data in Table 11.1 is from {{@224#bkmrk-pearson1984a}}.  Fig 11.3 is redrawn from {{@224#bkmrk-collins1982a}} and Fig. 11.6 from {{@224#bkmrk-field1982a}}; Figs. 11.7, 11.8, 11.10 and Table 11.2 are from {{@224#bkmrk-clarke1993b}}. The global BEST test is given in {{@224#bkmrk-clarke2008a}}, as is the description of linkage trees, the general idea of which (as ‘multivariate regression trees’) can be found in {{@224#bkmrk-death2002a}}. The modification to a constrained (2-way) BEST is new to this publication.

**Chapter 12:  Community experiments**.  Influential papers and books on field experiments, and causal interpretation from observational studies in general, include {{@224#bkmrk-connell1974a}}, {{@224#bkmrk-hurlbert1984a}}, {{@224#bkmrk-green1979a}} and many papers by A J Underwood, M G Chapman and collaborators, in particular the {{@224#bkmrk-underwood1997a}} book. {{@224#bkmrk-underwood1988a}} give some thoughts specifically on mesocosm experiments. Lab-based microcosm experiments on community structure, using this analysis approach, are typified by {{@224#bkmrk-austen1997b}} and {{@224#bkmrk-schratzberger1998a}}.  Figs. 12.2 and 12.3 are redrawn from {{@224#bkmrk-warwick1990a}} and Figs. 12.5, 12.6 from {{@224#bkmrk-gee1985a}}.

**Chapter 13:  Data requirements.**  The exposition parallels that in {{@224#bkmrk-warwick1993a}} but with additional examples.  Figs. 13.1-13.3 and 13.8 are redrawn from {{@224#bkmrk-warwick1993a}}, and earlier found in {{@224#bkmrk-colebrook1986a}}, {{@224#bkmrk-dawson-shepherd1992a}}, {{@224#bkmrk-warwick1988b}} and {{@224#bkmrk-gray1988a}} respectively.  Fig. 13.4 is redrawn from {{@224#bkmrk-warwick1990a}}, Fig. 13.5 from {{@224#bkmrk-warwick1990c}}, Fig. 13.6 from {{@224#bkmrk-warwick1990b}} and Fig. 13.7 from {{@224#bkmrk-warwick1991a}}. 

**Chapter 14: Relative sensitivities.**  This parallels the earlier sections of {{@224#bkmrk-warwick1991a}}, from which all these figures (except Figs. 14.11 & 14.14) have been redrawn.   Primary  source versions  of  the figures can be found as follows: Figs. 14.1-14.3, {{@224#bkmrk-gray1988a}}; Figs. 14.5-14.7, {{@224#bkmrk-warwick1990b}}; Figs 14.9-14.10, {{@224#bkmrk-dawson-shepherd1992a}}); Figs. 14.11-14.12, {{@224#bkmrk-gee1994a}} and {{@224#bkmrk-gee1994b}}; Figs. 14.14-14.16, {{@224#bkmrk-austen1989a}}.

**Chapter 15:  Multivariate measures of disturbance and relating to models**. The first part on multivariate measures of stress follows the format of {{@224#bkmrk-warwick1995a}} and {{@224#bkmrk-warwick1995b}}, and is an amalgamation of ideas from three primary papers:{{@224#bkmrk-warwick1993b}} on ‘meta-analysis’ of NE Atlantic macrobenthic studies, {{@224#bkmrk-warwick1993c}} on the increase in multivariate dispersion under disturbance, and {{@224#bkmrk-clarke1993c}} on the breakdown of seriation patterns.  Figs. 15.1-15.3 and Table 15.1 are redrawn and extracted from the first reference, Fig. 15.4 and Table 15.2 from the second and Figs. 15.5 & 15.6 and Table 15.5 from the third. The analysis in Table 15.4 is from {{@224#bkmrk-warwick2002a}}. In the second part, the principle of matrix correlations using a Pearson coefficient dates to {{@224#bkmrk-mantel1967a}}; RELATE tests are a non-parametric form. The seriation test with replication is discussed in detail by {{@224#bkmrk-somerfield2002a}}, the Tees data is analysed in {{@224#bkmrk-warwick2002a}}, the sea-loch data in {{@224#bkmrk-somerfield2000a}}, the Gullfaks Fig. 15.10 is extracted from {{@224#bkmrk-somerfield2002a}} and the Leschenault Fig. 15.12 redrawn from {{@224#bkmrk-veale2014a}}.

**Chapter 16:  Further multivariate comparisons and resemblance measures.**  The general extension of the Bio-Env approach of Chapter 11, to combinations other than selecting environmental variables to match biotic patterns, is described in {{@224#bkmrk-clarke1998a}}.  This details the forward/backward stepping search algorithm BVStep, and uses it to select subsets of ‘influential’ species from a biotic matrix. Second-stage MDS was defined by {{@224#bkmrk-somerfield1995a}} and early examples of its use can be found in {{@224#bkmrk-olsgard1997a}} and {{@224#bkmrk-olsgard1998a}}.  Figs. 16.1 to 16.3, and Tables 16.1 and 16.2, are extracted from {{@224#bkmrk-clarke1998a}}, and Fig. 16.5 from {{@224#bkmrk-somerfield1995a}}. The definition and behaviour of zero-adjusted Bray-Curtis is given by {{@224#bkmrk-clarke2006d}}, and that paper also discusses the relative merits of the resemblance measures covered here and introduces the use of second-stage MDS for comparing coefficients. Figs. 16.7 to 16.10 are a recalculated form of some of the figures of that paper; Fig. 16.11 expands the set of coefficients considered there. The very different use of second-stage analysis to generate ‘interaction-type’ plots is the subject of {{@224#bkmrk-clarke1906c}}. Figs. 16.12 to 16.13 and 16.15 to 16.17  are redrawn from there.

**Chapter 17:  Taxonomic distinctness measures.**  {{@224#bkmrk-warwick1995b}} first defined taxonomic diversity/distinctness.  Earlier work, from a conservation perspective, and using different species relatedness properties (such as PD), can be found in, e.g. {{@224#bkmrk-faith1992a}}, {{@224#bkmrk-faith1994a}}, {{@224#bkmrk-vane-wright1991a}} and {{@224#bkmrk-williams1991a}}.  The superior sampling properties of  average taxonomic distinctness ($\Delta ^ +$), and its testing structure in the case of simple species lists, are given in {{@224#bkmrk-clarke1998b}}, and applied to UK nematodes by {{@224#bkmrk-warwick1998a}} and {{@224#bkmrk-clarke1999b}}.  Variation in taxonomic distinctness ($\Lambda ^ +$) was introduced, and its sampling properties examined, in {{@224#bkmrk-clarke2001a}}, and a  review of the area can be found in {{@224#bkmrk-warwick2001a}}, from which Figs. 17.1, 17.2, 17.5, 17.11, 17.12 are redrawn.  Fig. 17.3 is discussed in {{@224#bkmrk-warwick1995b}}, Fig. 17.4 in {{@224#bkmrk-warwick2002a}}, Figs. 17.6, 17.8, 17.9, 17.14, 17.17 in {{@224#bkmrk-clarke2001a}}, Fig. 17.7 in {{@224#bkmrk-clarke1998b}} and Figs. 17.10, 17.13 in {{@224#bkmrk-rogers1999a}}. Taxonomic dissimilarities are discussed in {{@224#bkmrk-clarke2006d}}, from which the two examples, Fig. 17.19, 17.20 are taken. The measures were first defined in {{@224#bkmrk-clarke1998a}} and {{@224#bkmrk-izsak2001a}}.   

**Chapter 18:  Bootstrap average regions**. Bootstrapping univariate data was introduced by {{@224#bkmrk-efron1979a}}, see also {{@224#bkmrk-efron1993a}}. Its specific application to these complex multivariate contexts is new to this publication and might best be treated as experimental, for the moment. Certainly the nominal region coverage probabilities (e.g. 95%) should not be given a formal 95% confidence region interpretation, since some sources of uncertainty are, inevitably, not included in that probability statement – primarily how well the lower-dimensional region represents the higher-dimensional reality.

# Appendix 3: Bibliography

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<div id="bkmrk-addison1990a" >
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    Addison & Clark (1990)
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</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Addison, R.F. and Clarke, K.R. (1990) ‘Biological effects of pollutants in a subtropical environment’, <i>J. Exp. Mar. Biol. Ecol.</i>, 138.</div>
  
  --- 
<div id="bkmrk-agard1993a" >
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    Agard, Gobin & Warwick (1993)
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</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Agard, J.B.R., Gobin, J. and Warwick, R.M. (1993) ‘Analysis of marine macrobenthic community structure in relation to pollution, natural oil seepage and seasonal disturbance in a tropical environment (Trinidad, West Indies)’, <i>Mar. Ecol. Prog. Ser.</i>, 92, pp. 233–243.</div>
   
  --- 
<div id="bkmrk-airoldi2000a" >
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    Airoldi (2000)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Airoldi, L. (2000) ‘Responses of algae with different life histories to temporal and spatial variability of disturbance in subtidal reefs’, <i>Mar. Ecol. Prog. Ser.</i>, 195, pp. 81–92.</div>
   
   --- 
<div id="bkmrk-anderson2001a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-anderson2001a">
    Anderson (2001a)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Anderson, M.J. (2001a) ‘Permutation tests for univariate or multivariate analysis of variance and regression’, <i>Can. J. Fish. Aquat. Sci.</i>, 58, pp. 626–639.</div>
  
  --- 
<div id="bkmrk-anderson2001b" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-anderson2001b">
    Anderson (2001b)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Anderson, M.J. (2001b) ‘A new method for non-parametric multivariate analysis of variance’, <i>Austral Ecology</i>, 26, pp. 32–46.</div>
 
   ---
<div id="bkmrk-anderson2006a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-anderson2006a">
    Anderson (2006)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Anderson, M.J. (2006) ‘Distance-based tests for homogeneity of multivariate dispersions’, <i>Biometrics</i>, 62, pp. 245–253.</div>
  
   --- 
<div id="bkmrk-anderson2005a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-anderson2005a">
    Anderson, Diebel, Blom <i>et al.</i>  (2005) 
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Anderson, M.J., Diebel, C.E., Blom, W.M. and Landers, T.J. (2005) ‘Consistency and variation in kelp holdfast assemblages: spatial patterns of biodiversity for the major phyla at different taxonomic resolutions’, <i>J. Exp. Mar. Biol. Ecol.</i>, 320, pp. 35–56.</div>
  
  --- 
<div id="bkmrk-anderson2004a" >
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    Anderson, Ford, Feary <i>et al.</i> (2004)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Anderson, M.J., Ford, R.B., Feary, D.A. and Honeywill, C. (2004) ‘Quantitative measures of sedimentation in an estuarine system and its relationship with intertidal soft-sediment infauna’, <i>Mar. Ecol. Prog. Ser.</i>, 272, pp. 33–48.</div>
 
  ---
<div id="bkmrk-anderson2008a" >
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    Anderson, Gorley & Clarke (2008)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Anderson, M.J., Gorley, R.N. and Clarke, K.R. (2008) <i>PERMANOVA+ for PRIMER: Guide to software and statistical methods</i>. Plymouth: PRIMER-E.</div>
  
  ---
<div id="bkmrk-anderson1997a" >
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    Anderson & Underwood (1997)
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</div> 
  <div class="csl-entry" style="margin-bottom: 1em;">Anderson, M.J. and Underwood, A.J. (1997) ‘Effects of gastropod grazers on recruitment and succession of an estuarine assemblage: a multivariate and univariate approach’, <i>Oecologia</i>, 109, pp. 442–453.</div>
   
  --- 
<div id="bkmrk-anderson2013a" >
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   Anderson & Walsh (2013)
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</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Anderson, M.J. and Walsh, D.C.I. (2013) ‘PERMANOVA, ANOSIM and the Mantel test in the face of heterogeneous dispersions: what null hypothesis are you testing?’, <i>Ecol. Monog</i>, 83, pp. 557–574.</div>
   
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<div id="bkmrk-austen1997a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-austen1997a">
    Austen & McEvoy (1997)
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</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Austen, M.C. and McEvoy, A.J. (1997) ‘The use of offshore meiobenthic communities in laboratory microcosm experiments: response to heavy metal contamination’, <i>J. Exp. Mar. Biol. Ecol.</i>,  211, pp. 247–261.</div>  
  
  ---
<div id="bkmrk-austen1997b" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-austen1997b">
    Austen & Somerfield (1997)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Austen, M.C. and Somerfield, P.J. (1997) ‘A community level sediment bioassay applied to an estuarine heavy metal gradient’, <i>Mar. Envir. Res.<i/>, 43, pp. 315–328.</div>
   
  --- 
<div id="bkmrk-austen2001a" >
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    Austen & Thrush (2001)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Austen, M.C. and Thrush, S.F. (2001) ‘Experimental evidence suggesting slow or weak response of nematode community structure to a large suspension-feeder’, <i>J. Sea Res</i>, 46, pp. 69–84.</div>
   
  --- 
<div id="bkmrk-austen1989a" >
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    Austen & Warwick (1989)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Austen, M.C. and Warwick, R.M. (1989) ‘Comparison of univariate and multivariate aspects of estuarine meiobenthic community structure’, <i>Est. Cstl. Shelf Sci</i>, 29, pp. 23–42.</div>
   
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<div id="bkmrk-austen1995a" >
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    Austen & Warwick (1995)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Austen, M.C. and Warwick, R.M. (1995) ‘Effects of manipulation of food supply on estuarine meiobenthos’, <i>Hydrobiologia</i>, 311, pp. 175–184.</div>
   
  --- 
<div id="bkmrk-austen1998a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-austen1998a">
    Austen, Widdicombe & Villano-Pitacco (1998)
  </a>
</div>
  <div class="csl-entry">Austen, M.C., Widdicombe, S. and Villano-Pitacco, N. (1998) ‘Effects of biological disturbance on diversity and structure of meiobenthic nematode communities’, <i>Mar. Ecol. Prog. Ser.</i>, 174, pp. 233–246.</div>
   
  --- 
<div id="bkmrk-bayne1988a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-bayne1988a">
    Bayne, Clarke & Gray (1988)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Bayne, B.L., Clarke, K.R. and Gray, J.S. (eds) (1988) ‘Biological effects of pollutants: results of a practical workshop’, <i>Mar. Ecol. Prog. Ser.</i>, 46.</div>
   
  --- 
<div id="bkmrk-bayne1981a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-bayne1981a">
    Bayne, Clarke & Moore (1981) 
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Bayne, B.L., Clarke, K.R. and Moore, M.N. (1981) ‘Some practical considerations in the measurement of pollution effects on bivalve molluscs, and some possible ecological consequences’, <i>Aquatic toxicology </i>, 1, pp. 159–174.</div>
   
  --- 
<div id="bkmrk-belbin1991a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-belbin1991a">
    Belbin (1991)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Belbin, L. (1991) ‘Semi-strong hybrid scaling, a new ordination algorithm’, <i>J. Vegetat. Sci.</i>, 2, pp. 491–496.</div>
   
  --- 
<div id="bkmrk-beukema1988a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-beukema1988a">
    Beukema (1988)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Beukema, J.J. (1988) ‘An evaluation of the ABC–method (abundance /biomass comparison) as applied to macrozoobenthic communities living on tidal flats in the Dutch Wadden Sea’, <i>Mar. Biol</i>, 99, pp. 425–433.</div>
   
  --- 
<div id="bkmrk-box1964a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-box1964a">
    Box & Cox (1964)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Box, G.E.P. and Cox, D.R. (1964) ‘An analysis of transformations’, <i>J. R. Statist. Soc. Ser. B</i>, 26, pp. 211–243.</div>
   
 
  --- 
<div id="bkmrk-bray1957a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-bray1957a">
    Bray & Curtis (1957)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Bray, J.R. and Curtis, J.T. (1957) ‘An ordination of the upland forest communities of Southern Wisconsin’, <i>Ecol. Monogr.</i>, 27, pp. 325–349.</div>
   
  --- 
<div id="bkmrk-brown2002a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-brown2002a">
    Brown, Clarke & Warwick (2002)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Brown, B.E., Clarke, K.R. and Warwick, R.M. (2002) ‘Serial patterns of biodiversity change in corals across shallow reef flats in Ko Phuket, Thailand, due to the effects of local (sedimentation) and regional (climatic) perturbations’, <i>Mar. Biol.</i>, 141, pp. 21–29.</div>
   
  --- 
<div id="bkmrk-buchanan1993a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-buchanan1993a">
    Buchanan (1993)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Buchanan, J.B. (1993) ‘Evidence of benthic pelagic coupling at a station off the Northumberland coast’, <i>J. Exp. Mar. Biol. Ecol.</i>, 172, pp. 1–10.</div>
   
  --- 
<div id="bkmrk-caswell1976a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-caswell1976a">
    Caswell (1976)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Caswell, H. (1976) ‘Community structure: a neutral model analysis’, <i>Ecol. Monogr</i>, 46, pp. 327–354.</div>
   
  --- 
<div id="bkmrk-chapman1999a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-chapman1999a">
    Chapman & Underwood (1999) 
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Chapman, M.G. and Underwood, A.J. (1999) ‘Ecological patterns in multivariate assemblages: information and interpretation of negative values in ANOSIM tests’, <i>Mar. Ecol. Prog. Ser.</i>, 180, pp. 257–265.</div>
   
  --- 
<div id="bkmrk-chatfield1980a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-chatfield1980a">
    Chatfield & Collins (1980)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Chatfield, C. and Collins, A.J. (1980) <i>Introduction to multivariate analysis</i>. London: Chapman and Hall.</div>
   
  --- 
<div id="bkmrk-clarke1988a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-clarke1988a">
   Clarke (1988)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Clarke, K.R. (1988) ‘Detecting change in benthic community structure’, in <i>Proceedings XIVth international biometric conference</i>. Namur: Invited Papers. Societe Adolphe Quetelet, Gembloux, Belgium.</div>
   
  --- 
<div id="bkmrk-clarke1990a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-clarke1990a">
    Clarke (1990)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Clarke, K.R. (1990) ‘Comparisons of dominance curves’, <i>J. Exp. Mar. Biol. Ecol.</i>,  138, pp. 143–157.</div>
  
   --- 
<div id="bkmrk-clarke1993a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-clarke1993a">
    Clarke (1993)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Clarke, K.R. (1993) ‘Non-parametric multivariate analyses of changes in community structure’, <i>Aust. J. Ecol.</i>, 18, pp. 117–143.</div>
   
  --- 
<div id="bkmrk-clarke1999a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-clarke1999a">
    Clarke (1999)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Clarke, K.R. (1999) ‘Non-metric multivariate analysis in community-level ecotoxicology’, <i>Environ. Toxicol. Chem.</i>, 18, pp. 118–127.</div>

   --- 
<div id="bkmrk-clarke1993b" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-clarke1993b">
   Clarke & Ainsworth (1993)
  </a>
</div>
  <div class="csl-entry">Clarke, K.R. and Ainsworth, M. (1993) ‘A method of linking multivariate community structure to environmental variables’, <i>Mar. Ecol. Prog. Ser.</i>, 92, pp. 205–219.</div>

  
  --- 
<div id="bkmrk-clarke2006a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-clarke2006a">
    Clarke, Chapman, Somerfield <i>et al.</i> (2006)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Clarke, K.R., Chapman, M.G., Somerfield, P.J. and Needham, H.R. (2006) ‘Dispersion-based weighting of species counts in assemblage analyses’, <i>Mar. Ecol. Prog. Ser</i>, 320, pp. 11–27.</div>
   
   --- 
<div id="bkmrk-clarke2006b" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-clarke2006b">
    Clarke & Gorley (2006 or 2015)
  </a>
</div> 
  <div class="csl-bib-body" style="line-height: 1.35; ">
  <div class="csl-entry">Clarke, K.R. and Gorley, R.N. (2006 or 2015) <i>PRIMER v6 (or v7): User Manual/Tutorial</i>. Plymouth: PRIMER-E.</div>
</div>
  
   --- 
<div id="bkmrk-clarke1988b" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-clarke1988b">
    Clarke & Green (1988)
  </a>
</div> 
  <div class="csl-bib-body" style="line-height: 1.35; ">
  <div class="csl-entry">Clarke, K.R. and Green, R.H. (1988) ‘Statistical design and analysis for a “biological effects” study’, <i>Mar. Ecol. Prog. Ser</i>, 46, pp. 213–226.</div>
</div>
  
  
  --- 
<div id="bkmrk-clarke2006c" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-clarke2006c">
    Clarke, Somerfield, Airoldi <i>et al.</i> (2006)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Clarke, K.R., Somerfield, P.J., Airoldi, L. and Warwick, R.M. (2006) ‘Exploring interactions by second-stage community analyses’, <i>J. Exp. Mar. Biol. Ecol</i>, 338, pp. 179–192.</div>
   

  --- 
<div id="bkmrk-clarke2006d" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-clarke2006d">
    Clarke, Somerfield & Chapman (2006)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Clarke, K.R., Somerfield, P.J. and Chapman, M.G. (2006) ‘On resemblance measures for ecological studies, including taxonomic dissimilarities and a zero-adjusted Bray-Curtis coefficient for denuded assemblages’, <i>J. Exp. Mar. Biol. Ecol</i>, 330, pp. 55–80.</div>
   
  --- 
<div id="bkmrk-clarke2008a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-clarke2008a">
    Clarke, Somerfield & Gorley (2008)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Clarke, K.R., Somerfield, P.J. and Gorley, R.N. (2008) ‘Testing of null hypotheses in exploratory community analyses: similarity profiles and biota-environment linkage’, <i>J. Exp. Mar. Biol. Ecol</i>, 366, pp. 56–69.</div>
   
  --- 
<div id="bkmrk-clarke2014a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-clarke2014a">
    Clarke, Tweedley & Valesini (2014)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Clarke, K.R., Tweedley, J.R. and Valesini, F.J. (2014) ‘Simple shade plots aid better long-term choices of data pre-treatment in multivariate assemblage studies’, <i>J. Mar. Biol. Ass. UK</i>, 94, pp. 1–16.</div>
   
  --- 
<div id="bkmrk-clarke1994a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-clarke1994a">
    Clarke & Warwick (1994)
  </a>
  </div>
  <div class="csl-entry" style="margin-bottom: 1em;">Clarke, K.R. and Warwick, R.M. (1994) ‘Similarity-based testing for community pattern: the 2-way layout with no replication’, <i>Mar. Biol</i>, 118, pp. 167–176.</div>
   
  --- 
<div id="bkmrk-clarke1998a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-clarke1998a">
    Clarke & Warwick (1998a)
  </a>
</div>
    <div class="csl-entry" style="margin-bottom: 1em;">Clarke, K.R. and Warwick, R.M. (1998a) ‘Quantifying structural redundancy in ecological communities’, <i>Oecologia</i>, 113, pp. 278–289.</div>

  --- 
<div id="bkmrk-clarke1998b" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-clarke1998b">
    Clarke & Warwick (1998b)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Clarke, K.R. and Warwick, R.M. (1998b) ‘A taxonomic distinctness index and its statistical properties’, <i>J. Appl. Ecol</i>, 35, pp. 523–531.</div>
   
   
  --- 
<div id="bkmrk-clarke1999b" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-clarke1999b">
    Clarke & Warwick (1999)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Clarke, K.R. and Warwick, R.M. (1999) ‘The taxonomic distinctness measure of biodiversity: weighting of step lengths between hierarchical levels’, <i>Mar. Ecol. Prog. Ser.</i>, 184, pp. 21–29.</div>
   
  --- 
<div id="bkmrk-clarke2001a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-clarke2001a">
    Clarke & Warwick (2001)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Clarke, K.R. and Warwick, R.M. (2001) ‘A further biodiversity index applicable to species lists: variation in taxonomic distinctness’, <i>Mar. Ecol. Prog. Ser.</i>, 216, pp. 265–278.</div>
   
  --- 
<div id="bkmrk-clarke1993c" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-clarke1993c">
    Clarke, Warwick & Brown (1993)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Clarke, K.R., Warwick, R.M. and Brown, B.E. (1993) ‘An index showing breakdown of seriation, related to disturbance, in a coral-reef assemblage’, <i>Mar. Ecol. Prog. Ser.</i>, 102, pp. 153–160.</div>
   
  --- 
<div id="bkmrk-clifford1975a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-clifford1975a">
    Clifford & Stephenson (1975)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Clifford, D.H.T. and Stephenson, W. (1975) <i>An introduction to numerical classification</i>. New York: Academic Press.</div>
   
  --- 
<div id="bkmrk-colebrook1986a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-colebrook1986a">
    Colebrook (1986)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Colebrook, J.M. (1986) ‘Environmental influences on long-term variability in marine plankton’, <i>Hydrobiologia</i>, 142, pp. 309–325.</div>
   
  --- 
<div id="bkmrk-collins1982a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-collins1982a">
    Collins & Williams (1982)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Collins, N.R. and Williams, R. (1982) ‘Zooplankton communities in the Bristol Channel and Severn Estuary’, <i>Mar. Ecol. Prog. Ser.</i>, 9, pp. 1–11.</div>
   
  --- 
<div id="bkmrk-colwell1994a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-colwell1994a">
    Colwell & Coddington (1994)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Colwell, R.K. and Coddington, J.A. (1994) ‘Estimating terrestrial biodiversity through extrapolation’, <i>Phil. Trans. Roy. Soc. B</i>, 345, pp. 101–118.</div>
   
  --- 
<div id="bkmrk-connell1974a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-connell1974a">
    Connell (1974)
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</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Connell, J.H. (1974) ‘Field experiments in marine ecology’, in Mariscal, R. (ed.) <i>Experimental marine biology</i>. New York: Academic Press.</div>
   
  --- 
<div id="bkmrk-connell1978a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-connell1978a">
    Connell (1978)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Connell, J.H. (1978) ‘Diversity in tropical rain forests and coral reefs’, <i>Science N.Y</i>, 199, pp. 1302–1310.</div>
   
  --- 
<div id="bkmrk-cormack1971a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-cormack1971a">
    Cormack (1971)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Cormack, R.M. (1971) ‘A review of classification’, <i>J. R. Statist. Soc. Ser. A</i>, 134, pp. 321–367.</div>
   
  --- 
<div id="bkmrk-cox2001a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-cox2001a">
    Cox & Cox (2001)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Cox, T.F. and Cox, M.A.A. (2001) <i>Multidimensional scaling</i>. Chapman and Hall.</div>
   
  --- 
<div id="bkmrk-danielidis1991a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-danielidis1991a">
    Danielidis (1991)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Danielidis, D.B. (1991) <i>A systematic and ecological study of diatoms of the lagoons of Messolongi, Aitoliko and Kleissova (Greece)</i>. Ph.D. thesis,. University of Athens.</div>
  
   --- 
<div id="bkmrk-dauvin1984a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-dauvin1984a">
    Dauvin (1984)
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</div> 
  <div class="csl-entry" style="margin-bottom: 1em;">Dauvin, J.-C. (1984) <i>Dynamique d’ecosystemes macrobenthiques des fonds sedimentaires de la Baie de Morlaix et leur perturbation par les hydrocarbures de l’Amoco-Cadiz</i>. Doctoral thesis,. Univ. Pierre et Marie-Curie.</div>
   
  --- 
<div id="bkmrk-dawson-shepherd1992a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-dawson-shepherd1992a">
    Dawson-Shepherd, Warwick, Clarke <i>et al.</i> (1992)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Dawson-Shepherd, A., Warwick, R.M., Clarke, K.R. and Brown, B.E. (1992) ‘An analysis of fish community responses to coral mining in the Maldives’, <i>Environ. Biol. Fish</i>, 33, pp. 367–380.</div>
   
   --- 
<div id="bkmrk-death2002a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-death2002a">
    De'Ath (2002)
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</div>  
  <div class="csl-bib-body" style="line-height: 1.35; ">
  <div class="csl-entry">De’Ath, G. (2002) ‘Multivariate regression trees: a new technique for modeling species–environment relationships’, <i>Ecology</i>, 83(4), pp. 1105–1117.</div>

  --- 
<div id="bkmrk-efron1979a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-efron1979a">
    Efron (1979)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Efron, B. (1979) ‘Bootstrap methods: Another look at the jack-knife’, <i>Ann. Statist.</i>, 7, pp. 1–26.</div>
   
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<div id="bkmrk-efron1993a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-efron1993a">
    Efron & Tibshirani (1993)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Efron, B. and Tibshirani, R.J. (1993) <i>An introduction to the bootstrap</i>. Chapman and Hall.</div>
   
  --- 
<div id="bkmrk-everitt1978a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-everitt1978a">
    Everitt (1978)
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</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Everitt, B. (1978) <i>Graphical techniques for multivariate data</i>. London: Heinemann.</div>
   
  --- 
<div id="bkmrk-everitt1980a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-everitt1980a">
   Everitt (1980)
  </a>
</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Everitt, B. (1980) <i>Cluster analysis</i>. 2nd edn. London: Heinemann.</div>
   
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<div id="bkmrk-faith1992a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-faith1992a">
    Faith (1992)
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</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Faith, D.P. (1992) ‘Conservation evaluation and phylogenetic diversity’, <i>Biol. Conserv.</i>, 61, pp. 1–10.</div>
   
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<div id="bkmrk-faith1994a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-faith1994a">
    Faith (1994)
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</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Faith, D.P. (1994) ‘Phylogenetic pattern and the quantification of organismal biodiversity’, <i>Philos. Trans. R. Soc. Lond. Ser. B Biol. Sci.</i>, 345, pp. 45–58.</div>
   
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<div id="bkmrk-faith1987a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-faith1987a">
    Faith, Minchin & Belbin (1987)
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</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Faith, D.P., Minchin, P.R. and Belbin, L. (1987) ‘Compositional dissimilarity as a robust measure of ecological distance’, <i>Vegetatio</i>, 69, pp. 57–68.</div>
   
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<div id="bkmrk-field1982a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-field1982a">
   Field, Clarke & Warwick (1982)
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</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Field, J.G., Clarke, K.R. and Warwick, R.M. (1982) ‘A practical strategy for analysing multispecies distribution patterns’, <i>Mar. Ecol. Prog. Ser.</i>, 8, pp. 37–52.</div>
   
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<div id="bkmrk-fisher1943a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-fisher1943a">
    Fisher, Corbet & Williams (1943)
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</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Fisher, R.A., Corbet, A.S. and Williams, C.B. (1943) ‘The relation between the number of species and the number of individuals in a random sample of an animal population’, <i>J. anim. Ecol.</i>, 12, pp. 42–58.</div>
   
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<div id="bkmrk-florek1951a" >
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    Florek, Lukaszewicz, Perkal <i>et al.</i> (1951)
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  <div class="csl-entry">Florek, K., Lukaszewicz, J., Perkal, J., Steinhaus, H. and Zubrzycki, S. (1951) ‘Sur la liason et la division des points d’un ensemble fini’, <i>Colloquium Math</i>, 2, pp. 282–285.</div>
   
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<div id="bkmrk-gage1972a" >
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    Gage (1972)
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  <div class="csl-entry" style="margin-bottom: 1em;">Gage, J.D. (1972) ‘Community structure of the benthos in Scottish sea-lochs. I. Introduction and species diversity’, <i>Mar. Biol.</i>, 14, pp. 281–297.</div>
  
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<div id="bkmrk-gage1977a" >
  <a href="https://learninghub.primer-e.com/link/224#bkmrk-gage1977a">
    Gage & Coghill (1977)
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</div>
  <div class="csl-entry" style="margin-bottom: 1em;">Gage, J.D. and Coghill, G.G. (1977) ‘Studies on the dispersion patterns of Scottish sea-loch benthos from contiguous core transects’, in Coull, B. (ed.) <i>Ecology of marine benthos</i>. Columbia: University of South Carolina Press.</div>
    
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<div id="bkmrk-gee1997a" >
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    Gee & Somerfield (1997)
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  <div class="csl-entry" style="margin-bottom: 1em;">Woodd-Walker, R.S., Ward, P. and Clarke, A. (2002) ‘Large-scale patterns in diversity and community structure of surface water copepods from the Atlantic Ocean’, <i>Mar. Ecol. Prog. Ser.</i>, 236, pp. 189–203.</div>
     
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