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). 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.
A – Amoco-Cadiz oil spill, Bay of Morlaix, France. Macrofauna -
Dauvin (1984)
.
-
pages 5.6, 5.8, 7.3, 10.2, 13.3, 15.2, 16.1, 16.2, 16.3, 16.5, 17.1, 17.2
a – Algal recolonisation, Calafuria, Ligurian Sea, Italy. Macroalgae. -
Airoldi (2000)
.
B – Bristol Channel, England. Zooplankton -
Collins & Williams (1982)
.
b – Beam-trawl surveys, N. Europe. Groundfish -
Rogers, Clarke & Reynolds (1999)
.
C – Celtic Sea. Zooplankton. (Collins, pers. comm.).
c – Creran & Etive loch, Scotland. Macrobenthos -
Gage & Coghill (1977)
,
Gage (1972)
.
D – Dosing experiment, Solbergstrand mesocosm, Norway (GEEP Workshop). Nematodes -
Warwick, Carr, Clarke et al. (1988)
.
d – Diets of W Australian fish. Gut contents of seven nearshore species -
Hourston, Platell, Valesini et al. (2004)
.
E – Ekofisk oil platform, N.Sea. Macrofauna -
Gray, Clarke, Warwick et al. (1990)
.
e – Estuaries, W Australia. Fish -
Valesini, Tweedley, Clarke et al. (2014)
.
F – Frierfjord, Norway (GEEP Workshop). Macrofauna -
Gray, Aschan, Carr et al. (1988)
.
-
pages 1.3, 1.7, 3.1, 3.2, 6.1, 6.2, 6.3, 8.4, 9.2, 10.1, 13.5, 14.2, 15.2
f – Fal estuary sediments, S.W. England. Meio- and macrofauna -
Somerfield, Gee & Warwick (1994a)
,
Somerfield, Gee & Warwick (1994b)
.
G – Garroch Head, sludge dump-ground, Scotland. Macrofauna -
Pearson & Blackstock (1984)
.
-
pages 1.6, 1.7, 4.3, 7.3, 7.6, 8.3, 8.4, 8.7, 11.2, 11.3, 11.4, 11.7, 15.2, 16.6
g – Gullfaks A&B oilfields, Norway. Macrobenthos -
Olsgard & Gray (1995)
.
H – Hamilton Harbour, Bermuda (GEEP Workshop). Macrofauna, nematodes -
Warwick, Platt, Clarke et al. (1990)
.
I – Indonesian reef corals, S. Pari and S. Tikus Islands. Coral % cover -
Warwick, Clarke & Suharsono (1990)
.
i – Island group species lists. Fish presence/absence -
Clarke, Somerfield & Chapman (2006)
.
J – Joint NE Atlantic shelf studies (‘meta-analysis’). Macrofauna ‘production’ -
Warwick & Clarke (1993a)
.
K – Ko Phuket coral reefs, Thailand. Coral species cover - ,
Brown, Clarke & Warwick (2002)
.
k – King Wrasse diets, W Australia. Gut contents of labrid fish -
Lek, Fairclough, Platell et al. (2011)
.
L – Loch Linnhe and Loch Eil, Scotland, pulp-mill effluent. Macrofauna -
Pearson (1975)
.
l – Leschenault estuary, W Australia. Estuarine fish assemblage, over seasons -
Veale, Tweedley, Clarke et al. (2014)
.
M – Maldive Islands mining. Coral reef fish -
Dawson-Shepherd, Warwick, Clarke et al. (1992)
.
m – Messolongi lagoons, E. Central Greece. Diatoms and water-column data -
Danielidis (1991)
.
N – Nutrient-enrichment experiment, Solbergstrand mesocosm, Norway. Nematodes, copepods -
Gee, Warwick, Schaanning et al. (1985)
.
n – NE New Zealand kelp holdfasts. Macrofauna -
Anderson, Diebel, Blom et al. (2005)
.
O – Okura estuary, Long Bay, New Zealand. Inter-tidal macrofauna -
Anderson, Ford, Feary et al. (2004)
.
P – Plymouth particle-size data. Water samples with Coulter Counter. (A. Bale, pers. comm).
p – Plankton survey (Continuous Plankton Recorder), N.E. Atlantic. Zooplankton, phytoplankton -
Colebrook (1986)
.
R – Tamar estuary mud-flat, S.W. England. Nematodes, copepods -
Austen & Warwick (1989)
.
S – Scilly Isles, UK. Seaweed metazoa -
Gee & Warwick (1994a)
,
Gee & Warwick (1994b)
.
T – Tasmania, Eaglehawk Neck. Nematodes, copepods -
Warwick, Clarke & Gee (1990)
.
t - Tees Bay, N.E. England. Macrobenthos -
Warwick, Ashman, Brown et al. (2002)
.
U – UK regional studies. Nematodes -
Warwick & Clarke (1998)
.
V – Valhall oilfield, N Sea. Macrofauna -
Olsgard, Somerfield & Carr (1997)
.
W – World map. Great-circle distances among cities. (Reader’s Digest Great World Atlas, 1962)
w – Westerschelde estuary cores, Netherlands; mesocosm experiment on food supply. Nematodes -
Austen & Warwick (1995)
.
X – Exe estuary, S.W. England. Nematodes -
Warwick (1971)
.
Y – Clyde, Scotland. Nematodes -
Lambshead (1986)
.
Z – Azoic sediment recolonization experiment. Copepods -
Olafsson & Moore (1992)
.
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
Warwick (1988a)
. 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
Bayne, Clarke & Gray (1988)
,
Gray, Aschan, Carr et al. (1988)
and
Clarke & Green (1988)
, the Loch Linnhe macrofauna data (Table 1.4 and Fig. 1.3) from
Pearson (1975)
, and the ABC curves (Fig. 1.4) from
Warwick (1986)
. The species abundance distribution for Garroch Head macrofauna (Fig. 1.6) is first found in
Pearson, Gray & Johannessen (1983)
, and the multivariate linking to environmental variables (Fig. 1.11) in
Clarke & Ainsworth (1993)
. The ‘coherent species curves’ (Fig. 1.10) for the Loch Linnhe data are redrawn from
Somerfield & Clarke (2013)
. 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
Gee, Warwick, Schaanning et al. (1985)
.
Chapters 2 and 3: Similarity and clustering. These methods originated in the 1950’s and 60’s (e.g.
Florek, Lukaszewicz, Perkal et al. (1951)
;
Sneath (1957)
;
Lance & Williams (1967)
). The description here widens that of
Field, Clarke & Warwick (1982)
, with some points taken from the general texts of
Everitt (1980)
and
Cormack (1971)
. The dendrogram of Frierfjord macrofaunal samples (Fig.3.1) is redrawn from
Gray, Aschan, Carr et al. (1988)
, and the zooplankton example (Figs. 3.2 & 3.3) from
Collins & Williams (1982)
. The SIMPROF test for samples on agglomerative clusters is described in
Clarke, Somerfield & Gorley (2008)
; Fig. 3.8 mimics one in
Anderson, Gorley & Clarke (2008)
, 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
Chatfield & Collins (1980)
and
Everitt (1978)
. The MDS from a dosing experiment in the Solbergstrand mesocosms (Fig. 4.2) is from
Warwick, Carr, Clarke et al. (1988)
.
Chapter 5: Ordination by MDS. Non-metric MDS was introduced by
Shepard (1962)
and
Kruskal (1964)
; two standard texts are
Kruskal & Wish (1978)
and
Schiffman, Reynolds & Young (1981)
. Here, the exposition parallels that in
Field, Clarke & Warwick (1982)
and
Clarke (1993)
; 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
Warwick, Carr, Clarke et al. (1988)
. Metric MDS (see
Cox & Cox (2001)
), 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 (
Faith, Minchin & Belbin (1987)
,
Belbin (1991)
) 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.
Chapter 6: Testing. The basic permutation test and simulation of significance levels can be traced to
Mantel (1967)
and
Hope (1968)
, respectively. In this context (e.g. Figs. 6.2 & 6.3 and eqt. 6.1) it is described by
Clarke & Green (1988)
. A fuller discussion of the extension to 2-way nested and crossed ANOSIM tests (including Figs. 6.4 & 6.6) is in
Clarke (1993)
(with some asymptotic results in
Clarke (1988)
); the coral analysis (Fig. 6.5) is in
Warwick, Clarke & Suharsono (1990)
, and the Tasmanian meiofaunal MDS (Fig. 6.7) in
Warwick, Clarke & Gee (1990)
. The 2-way design without replication (Figs. 6.8-6.12) is tackled in
Clarke & Warwick (1994)
; see also
Austen & Warwick (1995)
. The ordered ANOSIM test is new to this publication, as are the extensions to 3-way crossed/nested designs.
Lek, Fairclough, Platell et al. (2011)
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 (
Anderson, Gorley & Clarke (2008)
). Fig. 6.17 is partly extracted from
Warwick, Ashman, Brown et al. (2002)
.
Chapter 7: Species analyses. Clustering on species similarities is given in
Field, Clarke & Warwick (1982)
for the Exe nematode data; see also
Clifford & Stephenson (1975)
. SIMPROF test for species (‘coherent curves’) follows
Somerfield & Clarke (2013)
; Figs. 7.1-7.6 are redrawn from there. Shade plots are described in
Clarke, Tweedley & Valesini (2014)
but have a very long history (see
Wilkinson & Friendly (2008)
), 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
Clarke (1993)
, and the 2-way crossed SIMPER first used in
Platell, Potter & Clarke (1998)
. Simple bubble plots are a staple routine for graphical output but PRIMER 7’s segmented bubble plots were first used in
Stoffels, Clarke, Rehwinkel et al. (2014)
and in
Purcell, Rushworth, Clarke et al. (2014)
.
Chapter 8: Univariate/graphical analyses.
Pielou (1975)
,
Heip, Herman & Soetaert (1988)
and
Magurran (1991)
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
Warwick, Platt, Clarke et al. (1990)
and
Warwick, Clarke & Suharsono (1990)
respectively, and the Caswell V computations (Table 8.1) are from
Warwick, Platt, Clarke et al. (1990)
. The Garroch Head species abundance distributions (Fig. 8.4) are first found in
Pearson, Gray & Johannessen (1983)
; Fig. 8.3 is redrawn from
Pearson & Blackstock (1984)
.
Warwick (1986)
introduced Abundance–Biomass Comparison curves, and the Loch Linnhe and Garroch Head illustrations (Figs. 8.7 & 8.8) are redrawn from
Warwick (1986)
and
Warwick, Pearson & Ruswahyuni (1987)
. The transformed scale and partial dominance curves of Figs. 8.9-8.11 were suggested by
Clarke (1990)
, 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
Clarke & Green (1988)
; Fig. 9.1 is recomputed from
Warwick, Carr, Clarke et al. (1988)
. Detailed description of dispersion weighting (DW) is in
Clarke, Chapman, Somerfield et al. (2006)
; Figs. 9.2, 9.4 of the Fal nematode data (
Somerfield, Gee & Warwick (1994a)
and
Somerfield, Gee & Warwick (1994b)
) are redrawn from
Clarke, Chapman, Somerfield et al. (2006)
. The use of shade plots to aid transformation or DW choices is the topic of
Clarke, Tweedley & Valesini (2014)
. A different form of weighting of variables (by their standard deviation) is described in
Hallett, Valesini & Clarke (2012)
.
Chapter 10: Aggregation. This description of the effects of changing taxonomic level is based on
Warwick (1988b)
, from which Figs. 10.2-10.4 and 10.7 are redrawn. Fig. 10.1 is discussed in
Gray, Aschan, Carr et al. (1988)
, Fig. 10.5 and 10.8 in
Warwick, Clarke & Suharsono (1990)
and Fig. 10.6 in
Gray, Clarke, Warwick et al. (1990)
(or
Warwick & Clarke (1993a)
, in this categorisation). A methodology for examining the comparative effects on an analysis of choice of taxonomic level (and transform) can be found in
Olsgard, Somerfield & Carr (1997)
,
Olsgard, Somerfield & Carr (1998)
, and
Olsgard & Somerfield (2000)
.
Chapter 11: Linking to environment. For wider reading on this type of ‘canonical’ problem, see Chapter 5 of
Jongman, ter Braak & Tongeren (1987)
, including
ter Braak (1986)
's method of canonical correspondence analysis. The approach here of performing environmental and biotic analyses separately, and then comparing them, combines that advocated by
Field, Clarke & Warwick (1982)
: superimposing variables on the biotic MDS, and by
Clarke & Ainsworth (1993)
: the BIO-ENV program. The data in Table 11.1 is from
Pearson & Blackstock (1984)
. Fig 11.3 is redrawn from
Collins & Williams (1982)
and Fig. 11.6 from
Field, Clarke & Warwick (1982)
; Figs. 11.7, 11.8, 11.10 and Table 11.2 are from
Clarke & Ainsworth (1993)
. The global BEST test is given in
Clarke, Somerfield & Gorley (2008)
, as is the description of linkage trees, the general idea of which (as ‘multivariate regression trees’) can be found in
De'Ath (2002)
. 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
Connell (1974)
,
Hurlbert (1984)
,
Green (1979)
and many papers by A J Underwood, M G Chapman and collaborators, in particular the
Underwood (1997)
book.
Underwood & Peterson (1988)
give some thoughts specifically on mesocosm experiments. Lab-based microcosm experiments on community structure, using this analysis approach, are typified by
Austen & Somerfield (1997)
and
Schratzberger & Warwick (1998a)
. Figs. 12.2 and 12.3 are redrawn from
Warwick, Clarke & Gee (1990)
and Figs. 12.5, 12.6 from
Gee, Warwick, Schaanning et al. (1985)
.
Chapter 13: Data requirements. The exposition parallels that in
Warwick (1993)
but with additional examples. Figs. 13.1-13.3 and 13.8 are redrawn from
Warwick (1993)
, and earlier found in
Colebrook (1986)
,
Dawson-Shepherd, Warwick, Clarke et al. (1992)
,
Warwick (1988b)
and
Gray, Aschan, Carr et al. (1988)
respectively. Fig. 13.4 is redrawn from
Warwick, Clarke & Gee (1990)
, Fig. 13.5 from
Warwick, Platt, Clarke et al. (1990)
, Fig. 13.6 from
Warwick, Clarke & Suharsono (1990)
and Fig. 13.7 from
Warwick & Clarke (1991)
.
Chapter 14: Relative sensitivities. This parallels the earlier sections of
Warwick & Clarke (1991)
, 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,
Gray, Aschan, Carr et al. (1988)
; Figs. 14.5-14.7,
Warwick, Clarke & Suharsono (1990)
; Figs 14.9-14.10,
Dawson-Shepherd, Warwick, Clarke et al. (1992)
); Figs. 14.11-14.12,
Gee & Warwick (1994a)
and
Gee & Warwick (1994b)
; Figs. 14.14-14.16,
Austen & Warwick (1989)
.
Chapter 15: Multivariate measures of disturbance and relating to models. The first part on multivariate measures of stress follows the format of
Warwick & Clarke (1995a)
and
Warwick & Clarke (1995b)
, and is an amalgamation of ideas from three primary papers:
Warwick & Clarke (1993a)
on ‘meta-analysis’ of NE Atlantic macrobenthic studies,
Warwick & Clarke (1993b)
on the increase in multivariate dispersion under disturbance, and
Clarke, Warwick & Brown (1993)
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
Warwick, Ashman, Brown et al. (2002)
. In the second part, the principle of matrix correlations using a Pearson coefficient dates to
Mantel (1967)
; RELATE tests are a non-parametric form. The seriation test with replication is discussed in detail by
Somerfield, Clarke & Olsgard (2002)
, the Tees data is analysed in
Warwick, Ashman, Brown et al. (2002)
, the sea-loch data in
Somerfield & Gage (2000)
, the Gullfaks Fig. 15.10 is extracted from
Somerfield, Clarke & Olsgard (2002)
and the Leschenault Fig. 15.12 redrawn from
Veale, Tweedley, Clarke et al. (2014)
.
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
Clarke & Warwick (1998a)
. 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
Somerfield & Clarke (1995)
and early examples of its use can be found in
Olsgard, Somerfield & Carr (1997)
and
Olsgard, Somerfield & Carr (1998)
. Figs. 16.1 to 16.3, and Tables 16.1 and 16.2, are extracted from
Clarke & Warwick (1998a)
, and Fig. 16.5 from
Somerfield & Clarke (1995)
. The definition and behaviour of zero-adjusted Bray-Curtis is given by
Clarke, Somerfield & Chapman (2006)
, 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 . Figs. 16.12 to 16.13 and 16.15 to 16.17 are redrawn from there.
Chapter 17: Taxonomic distinctness measures.
Warwick & Clarke (1995b)
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.
Faith (1992)
,
Faith (1994)
,
Vane-Wright, Humphries & Williams (1991)
and
Williams, Humphries & Vane-Wright (1991)
. The superior sampling properties of average taxonomic distinctness ($\Delta ^ +$), and its testing structure in the case of simple species lists, are given in
Clarke & Warwick (1998b)
, and applied to UK nematodes by
Warwick & Clarke (1998)
and
Clarke & Warwick (1999)
. Variation in taxonomic distinctness ($\Lambda ^ +$) was introduced, and its sampling properties examined, in
Clarke & Warwick (2001)
, and a review of the area can be found in
Warwick & Clarke (2001)
, from which Figs. 17.1, 17.2, 17.5, 17.11, 17.12 are redrawn. Fig. 17.3 is discussed in
Warwick & Clarke (1995b)
, Fig. 17.4 in
Warwick, Ashman, Brown et al. (2002)
, Figs. 17.6, 17.8, 17.9, 17.14, 17.17 in
Clarke & Warwick (2001)
, Fig. 17.7 in
Clarke & Warwick (1998b)
and Figs. 17.10, 17.13 in
Rogers, Clarke & Reynolds (1999)
. Taxonomic dissimilarities are discussed in
Clarke, Somerfield & Chapman (2006)
, from which the two examples, Fig. 17.19, 17.20 are taken. The measures were first defined in
Clarke & Warwick (1998a)
and
Izsak & Price (2001)
.
Chapter 18: Bootstrap average regions. Bootstrapping univariate data was introduced by
Efron (1979)
, see also
Efron & Tibshirani (1993)
. 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
Addison, R.F. and Clarke, K.R. (1990) ‘Biological effects of pollutants in a subtropical environment’, J. Exp. Mar. Biol. Ecol., 138.
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)’, Mar. Ecol. Prog. Ser., 92, pp. 233–243.
Airoldi, L. (2000) ‘Responses of algae with different life histories to temporal and spatial variability of disturbance in subtidal reefs’, Mar. Ecol. Prog. Ser., 195, pp. 81–92.
Anderson, M.J. (2001a) ‘Permutation tests for univariate or multivariate analysis of variance and regression’, Can. J. Fish. Aquat. Sci., 58, pp. 626–639.
Anderson, M.J. (2001b) ‘A new method for non-parametric multivariate analysis of variance’, Austral Ecology, 26, pp. 32–46.
Anderson, M.J. (2006) ‘Distance-based tests for homogeneity of multivariate dispersions’, Biometrics, 62, pp. 245–253.
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’, J. Exp. Mar. Biol. Ecol., 320, pp. 35–56.
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’, Mar. Ecol. Prog. Ser., 272, pp. 33–48.
Anderson, M.J., Gorley, R.N. and Clarke, K.R. (2008) PERMANOVA+ for PRIMER: Guide to software and statistical methods. Plymouth: PRIMER-E.
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’, Oecologia, 109, pp. 442–453.
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?’, Ecol. Monog, 83, pp. 557–574.
Austen, M.C. and McEvoy, A.J. (1997) ‘The use of offshore meiobenthic communities in laboratory microcosm experiments: response to heavy metal contamination’, J. Exp. Mar. Biol. Ecol., 211, pp. 247–261.
Austen, M.C. and Somerfield, P.J. (1997) ‘A community level sediment bioassay applied to an estuarine heavy metal gradient’, Mar. Envir. Res., 43, pp. 315–328.
Austen, M.C. and Thrush, S.F. (2001) ‘Experimental evidence suggesting slow or weak response of nematode community structure to a large suspension-feeder’, J. Sea Res, 46, pp. 69–84.
Austen, M.C. and Warwick, R.M. (1989) ‘Comparison of univariate and multivariate aspects of estuarine meiobenthic community structure’, Est. Cstl. Shelf Sci, 29, pp. 23–42.
Austen, M.C. and Warwick, R.M. (1995) ‘Effects of manipulation of food supply on estuarine meiobenthos’, Hydrobiologia, 311, pp. 175–184.
Austen, M.C., Widdicombe, S. and Villano-Pitacco, N. (1998) ‘Effects of biological disturbance on diversity and structure of meiobenthic nematode communities’, Mar. Ecol. Prog. Ser., 174, pp. 233–246.
Bayne, B.L., Clarke, K.R. and Gray, J.S. (eds) (1988) ‘Biological effects of pollutants: results of a practical workshop’, Mar. Ecol. Prog. Ser., 46.
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’, Aquatic toxicology , 1, pp. 159–174.
Belbin, L. (1991) ‘Semi-strong hybrid scaling, a new ordination algorithm’, J. Vegetat. Sci., 2, pp. 491–496.
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’, Mar. Biol, 99, pp. 425–433.
Box, G.E.P. and Cox, D.R. (1964) ‘An analysis of transformations’, J. R. Statist. Soc. Ser. B, 26, pp. 211–243.
Bray, J.R. and Curtis, J.T. (1957) ‘An ordination of the upland forest communities of Southern Wisconsin’, Ecol. Monogr., 27, pp. 325–349.
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’, Mar. Biol., 141, pp. 21–29.
Buchanan, J.B. (1993) ‘Evidence of benthic pelagic coupling at a station off the Northumberland coast’, J. Exp. Mar. Biol. Ecol., 172, pp. 1–10.
Caswell, H. (1976) ‘Community structure: a neutral model analysis’, Ecol. Monogr, 46, pp. 327–354.
Chapman, M.G. and Underwood, A.J. (1999) ‘Ecological patterns in multivariate assemblages: information and interpretation of negative values in ANOSIM tests’, Mar. Ecol. Prog. Ser., 180, pp. 257–265.
Chatfield, C. and Collins, A.J. (1980) Introduction to multivariate analysis. London: Chapman and Hall.
Clarke, K.R. (1988) ‘Detecting change in benthic community structure’, in Proceedings XIVth international biometric conference. Namur: Invited Papers. Societe Adolphe Quetelet, Gembloux, Belgium.
Clarke, K.R. (1990) ‘Comparisons of dominance curves’, J. Exp. Mar. Biol. Ecol., 138, pp. 143–157.
Clarke, K.R. (1993) ‘Non-parametric multivariate analyses of changes in community structure’, Aust. J. Ecol., 18, pp. 117–143.
Clarke, K.R. (1999) ‘Non-metric multivariate analysis in community-level ecotoxicology’, Environ. Toxicol. Chem., 18, pp. 118–127.
Clarke, K.R. and Ainsworth, M. (1993) ‘A method of linking multivariate community structure to environmental variables’, Mar. Ecol. Prog. Ser., 92, pp. 205–219.
Clarke, K.R., Chapman, M.G., Somerfield, P.J. and Needham, H.R. (2006) ‘Dispersion-based weighting of species counts in assemblage analyses’, Mar. Ecol. Prog. Ser, 320, pp. 11–27.
Clarke, K.R. and Gorley, R.N. (2006 or 2015) PRIMER v6 (or v7): User Manual/Tutorial. Plymouth: PRIMER-E.
Clarke, K.R. and Green, R.H. (1988) ‘Statistical design and analysis for a “biological effects” study’, Mar. Ecol. Prog. Ser, 46, pp. 213–226.
Clarke, K.R., Somerfield, P.J., Airoldi, L. and Warwick, R.M. (2006) ‘Exploring interactions by second-stage community analyses’, J. Exp. Mar. Biol. Ecol, 338, pp. 179–192.
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’, J. Exp. Mar. Biol. Ecol, 330, pp. 55–80.
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’, J. Exp. Mar. Biol. Ecol, 366, pp. 56–69.
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’, J. Mar. Biol. Ass. UK, 94, pp. 1–16.
Clarke, K.R. and Warwick, R.M. (1994) ‘Similarity-based testing for community pattern: the 2-way layout with no replication’, Mar. Biol, 118, pp. 167–176.
Clarke, K.R. and Warwick, R.M. (1998a) ‘Quantifying structural redundancy in ecological communities’, Oecologia, 113, pp. 278–289.
Clarke, K.R. and Warwick, R.M. (1998b) ‘A taxonomic distinctness index and its statistical properties’, J. Appl. Ecol, 35, pp. 523–531.
Clarke, K.R. and Warwick, R.M. (1999) ‘The taxonomic distinctness measure of biodiversity: weighting of step lengths between hierarchical levels’, Mar. Ecol. Prog. Ser., 184, pp. 21–29.
Clarke, K.R. and Warwick, R.M. (2001) ‘A further biodiversity index applicable to species lists: variation in taxonomic distinctness’, Mar. Ecol. Prog. Ser., 216, pp. 265–278.
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’, Mar. Ecol. Prog. Ser., 102, pp. 153–160.
Clifford, D.H.T. and Stephenson, W. (1975) An introduction to numerical classification. New York: Academic Press.
Colebrook, J.M. (1986) ‘Environmental influences on long-term variability in marine plankton’, Hydrobiologia, 142, pp. 309–325.
Collins, N.R. and Williams, R. (1982) ‘Zooplankton communities in the Bristol Channel and Severn Estuary’, Mar. Ecol. Prog. Ser., 9, pp. 1–11.
Colwell, R.K. and Coddington, J.A. (1994) ‘Estimating terrestrial biodiversity through extrapolation’, Phil. Trans. Roy. Soc. B, 345, pp. 101–118.
Connell, J.H. (1974) ‘Field experiments in marine ecology’, in Mariscal, R. (ed.) Experimental marine biology. New York: Academic Press.
Connell, J.H. (1978) ‘Diversity in tropical rain forests and coral reefs’, Science N.Y, 199, pp. 1302–1310.
Cormack, R.M. (1971) ‘A review of classification’, J. R. Statist. Soc. Ser. A, 134, pp. 321–367.
Cox, T.F. and Cox, M.A.A. (2001) Multidimensional scaling. Chapman and Hall.
Danielidis, D.B. (1991) A systematic and ecological study of diatoms of the lagoons of Messolongi, Aitoliko and Kleissova (Greece). Ph.D. thesis,. University of Athens.
Dauvin, J.-C. (1984) Dynamique d’ecosystemes macrobenthiques des fonds sedimentaires de la Baie de Morlaix et leur perturbation par les hydrocarbures de l’Amoco-Cadiz. Doctoral thesis,. Univ. Pierre et Marie-Curie.
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’, Environ. Biol. Fish, 33, pp. 367–380.
De’Ath, G. (2002) ‘Multivariate regression trees: a new technique for modeling species–environment relationships’, Ecology, 83(4), pp. 1105–1117.
Efron, B. (1979) ‘Bootstrap methods: Another look at the jack-knife’, Ann. Statist., 7, pp. 1–26.
Efron, B. and Tibshirani, R.J. (1993) An introduction to the bootstrap. Chapman and Hall.
Everitt, B. (1978) Graphical techniques for multivariate data. London: Heinemann.
Everitt, B. (1980) Cluster analysis. 2nd edn. London: Heinemann.
Faith, D.P. (1992) ‘Conservation evaluation and phylogenetic diversity’, Biol. Conserv., 61, pp. 1–10.
Faith, D.P. (1994) ‘Phylogenetic pattern and the quantification of organismal biodiversity’, Philos. Trans. R. Soc. Lond. Ser. B Biol. Sci., 345, pp. 45–58.
Faith, D.P., Minchin, P.R. and Belbin, L. (1987) ‘Compositional dissimilarity as a robust measure of ecological distance’, Vegetatio, 69, pp. 57–68.
Field, J.G., Clarke, K.R. and Warwick, R.M. (1982) ‘A practical strategy for analysing multispecies distribution patterns’, Mar. Ecol. Prog. Ser., 8, pp. 37–52.
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’, J. anim. Ecol., 12, pp. 42–58.
Florek, K., Lukaszewicz, J., Perkal, J., Steinhaus, H. and Zubrzycki, S. (1951) ‘Sur la liason et la division des points d’un ensemble fini’, Colloquium Math, 2, pp. 282–285.
Gage, J.D. (1972) ‘Community structure of the benthos in Scottish sea-lochs. I. Introduction and species diversity’, Mar. Biol., 14, pp. 281–297.
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.) Ecology of marine benthos. Columbia: University of South Carolina Press.
Gee, J.M. and Somerfield, P.J. (1997) ‘Do mangrove diversity and leaf litter decay promote meiofaunal diversity?’, J. Exp. Mar. Ecol. Biol., 218, pp. 13–33.
Gee, J.M. and Warwick, R.M. (1994a) ‘Metazoan community structure in relation to the fractal dimensions of marine microalgae’, Mar. Ecol. Prog. Ser., 103, pp. 141–150.
Gee, J.M. and Warwick, R.M. (1994b) ‘Body-size distribution in a marine metazoan community and the fractal dimensions of macroalgae’, J. Exp. Mar. Ecol. Biol., 178, pp. 247–259.
Gee, J.M., Warwick, R., Schaanning, M., Berge, J.A. and Ambrose Jr, W.G. (1985) ‘Effects of organic enrichment on meiofaunal abundance and community structure in sublittoral soft sediments’, J. Exp. Mar. Biol. Ecol., 91, pp. 247–262.
Goldman, N. and Lambshead, P.J.D. (1989) ‘Optimization of the Ewens/Caswell neutral model program for community diversity analysis’, Mar. Ecol. Prog. Ser., 50, pp. 255–261.
Gower, J.C. (1966) ‘Some distance properties of latent root and vector methods used in multivariate analysis’, Biometrika, 53, pp. 325–328.
Gower, J.C. (1971) ‘Statistical methods of comparing different multivariate analyses of the same data’, in Hodson, F.R., Kendall, D.G., and Tautu, P. (eds) Mathematics in the archaeological and historical sciences. Edinburgh: Edinburgh University Press, pp. 138–149.
Gower, J.C. and Ross, G.J.S. (1969) ‘Minimum spanning trees and single linkage cluster analysis’, Appl. Statist., 18, pp. 54–64.
Gray, J.S., Aschan, M., Carr, M.R., Clarke, K.R., Green, R.H., Pearson, T.H., Rosenberg, R. and Warwick, R.M.(1988) ‘Analysis of community attributes of the benthic macrofauna of Frierfjord/Langesundfjord and in a mesocosm experiment’, Mar. Ecol. Prog. Ser., 46, pp. 151–165.
Gray, J.S., Clarke, K.R., Warwick, R.M. and Hobbs, G. (1990) ‘Detection of initial effects of pollution on marine benthos: an example from the Ekofisk and Eldfisk oilfields, North Sea’, Mar. Ecol. Prog. Ser., 66, pp. 285–299.
Gray, J.S. and Pearson, T.H. (1982) ‘Objective selection of sensitive species indicative of pollution-induced change in benthic communities. I. Comparative methodology'. Mar. Ecol. Prog. Ser., 9, pp. 111–119.
Green, R.H. (1979) Sampling design and statistical methods for environmental biologists. New York: Wiley.
Greenacre, M.J. (1984) Theory and applications of correspondence analysis. London: Academic Press.
Hall, S.J. and Greenstreet, S.P. (1998) ‘Taxonomic distinctness and diversity measures: responses in marine fish communities’, Mar. Ecol. Prog. Ser., 166, pp. 227–229.
Hallett, C.S., Valesini, F.J. and Clarke, K.R. (2012) ‘A method for selecting health index metrics in the absence of independent measures of ecological condition’, Ecol. Indicat., 19, pp. 240–252.
Harper, J.L. and Hawksworth, D.L. (1994) ‘Biodiversity: measurement and estimation (preface)’, Phil. Trans. Roy. Soc. Lond. Ser. B, 345, pp. 5–12.
Heip, C., Herman, P.M.J. and Soetaert, K. (1988) ‘Data processing, evaluation, and analysis’, in Higgins, R.P. and Thiel, H. (eds) Introduction to the study of meiofauna. Washington DC: Smithsonian Institution, pp. 197–231.
Hill, M.O. (1973a) ‘Reciprocal averaging: an eigenvector method of ordination’, J. Ecol, 61, pp. 237–249.
Hill, M.O. (1973b) ‘Diversity and evenness: a unifying notation and its consequences’, Ecology, 54, pp. 427–432.
Hill, M.O. (1979a) DECORANA – A FORTRAN program for detrended correspondence analysis and reciprocal averaging. Ithaca, New York: Cornell University.
Hill, M.O. (1979b) TWINSPAN – A FORTRAN program for arranging multivariate data in an ordered two-way table by classification of individuals and attributes. Ithaca, New York: Cornell University.
Hill, M.O. and Gauch, H.G. (1980) ‘Detrended correspondence analysis, an improved ordination technique’, Vegetatio, 42, pp. 47–48.
Hope, A.C.A. (1968) ‘A simplified Monte Carlo significance test procedure’, J. R. Statist. Soc. Ser. B, 30, pp. 582–598.
Hourston, M., Platell, M.E., Valesini, F.J. and Potter, I.C. (2004) ‘Factors influencing the diets of four morphologically divergent fish species in nearshore marine waters’, J. Mar. Biol. Assoc. UK, 84, pp. 805–817.
Howson, C.M. (ed.) (1987) Directory of the British marine fauna and flora. Ross-on-Wye, Hertfordshire: Marine Conservation Society.
Humphries, C.J., Williams, P.H. and Vane-Wright, R.I. (1995) ‘Measuring biodiversity value for conservation’, Ann. Rev. Ecol. Syst., 26, pp. 93–111.
Hurlbert, S.H. (1971) ‘The nonconcept of species diversity: a critique and alternative parameters’, Ecology, 52, pp. 577–586.
Hurlbert, S.H. (1984) ‘Pseudoreplication and the design of ecological field experiments’, Ecol. Monogr., 54, pp. 187–211.
Huston, M. (1979) ‘A general hypothesis of species diversity’, Am. Nat., 113, pp. 81–101.
Ibanez, F. and Dauvin, J.-C. (1988) ‘Long-term changes (1977–1987) in a muddy fine sand Abra alba – Melinna palmata community from the Western English Channel: multivariate time-series analysis’, Mar. Ecol. Prog. Ser., 49, pp. 65–81.
Izsak, C. and Price, A.R.G. (2001) ‘Measuring β-diversity using a taxonomic similarity index, and its relation to spatial scale’, Mar. Ecol. Prog. Ser., 215, pp. 69–77.
Jayasree, K. (1976) Systematics and ecology of free-living marine nematodes from polluted intertidal sand in Scotland. Ph.D. thesis,. University of Aberdeen.
Jongman, R.H.G., ter Braak, C.F.J. and Tongeren, O.F.R. (1987) Data analysis in community and landscape ecology. Wageningen: Pudoc.
Kendall, M.A. and Widdicombe, S. (1999) ‘Small scale patterns in the structure of macrofaunal assemblages of shallow soft sediments’, J. Exp. Mar. Biol. Ecol., 237, pp. 127–140.
Kendall, M.G. (1970) Rank correlation methods. London: Griffin.
Kenkel, N.C. and Orloci, L. (1986) ‘Applying metric and nonmetric multidimensional scaling to some ecological studies: some new results’, Ecology, 67, pp. 919–928.
Kruskal, J.B. (1964) ‘Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis’, Psychometrika, 29, pp. 1–27.
Kruskal, J.B. and Wish, M. (1978) Multidimensional scaling. Beverley Hills, California: Sage Publications.
Krzanowski, W.J. (2002) ‘Multifactorial analysis of distance in studies of ecological community structure’, J. Agric. Biol. Environ. Stat., 7, pp. 222–232.
Kulczynski, S. (1928) ‘Die Pflanzenassoziationen der Pieninen’, Bull. Int. Acad. Pol. Sci. Lett. Cl. Sci. Math. Nat. Ser. B, Suppl II, pp. 57–203.
Lambshead, P.J.D. (1986) ‘Sub-catastrophic sewage and industrial waste contamination as revealed by marine nematode faunal analysis’, Mar. Ecol. Prog. Ser., 29, pp. 247–260.
Lambshead, P.J.D., Platt, H.M. and Shaw, K.M. (1983) ‘The detection of differences among assemblages of marine benthic species based on an assessment of dominance and diversity’, J. Nat. Hist., 17, pp. 859–874.
Lance, G.N. and Williams, W.T. (1967) ‘A general theory of classificatory sorting strategies: 1 Hierarchical Systems’, Comp. J., 9, pp. 373–380.
Legendre, P. and Anderson, M.J. (1999) ‘Distance-based redundancy analysis: testing multispecies responses in multifactorial ecological experiments’, Ecol. Monogr., 69, pp. 1–24.
Legendre, P. and Legendre, L. (2012) Numerical Ecology, 3rd English edition. Amsterdam: Elsevier.
Lek, E., Fairclough, D.V., Platell, M.E., Clarke, K.R., Tweedley, J.R. and Potter, I.C. (2011) ‘To what extent are the dietary compositions of three abundant, co-occurring labrid species different and related to latitude, habitat, body size and season?’, J. Fish Biol., 78, pp. 1913–1943.
Lorenzen, S. (1994) The phylogenetic systematics of free-living nematodes. London: Ray Society.
Magurran, A.E. (1991) Ecological diversity and its measurement. London: Chapman and Hall.
Mantel, N. (1967) ‘The detection of disease clustering and a generalized regression approach’, Cancer Res., 27, pp. 209–220.
Mardia, K.V., Kent, J.T. and Bibby, J.M. (1979) Multivariate analysis. London: Academic Press.
May, R.M. (1990) ‘Taxonomy as destiny’, Nature, 347, pp. 129–130.
McArdle, B.H. and Anderson, M.J. (2001) ‘Fitting multivariate models to community data: a comment on distance-based redundancy analysis’, Ecology, 82, pp. 290–297.
McEachran, J.D. and Miyake, T. (1990) ‘Phylogenetic interrelationships of skates: a working hypothesis (Chondrichthyes, Rajoidea). In: Elasmobranchs as living resources: advances in the biology, ecology, systematics, and the status of the fisheries’, in Pratt, H.L. et al. (eds.) NOAA technical report NMFS, pp. 285–304.
Morrisey, D.J., Underwood, A.J. and Howitt, L. (1996) ‘Effects of copper on the faunas of marine soft-sediments: an experimental field study’, Mar. Biol., 125, pp. 199–213.
Mumby, P.J., Clarke, K.R., and Harborne, A.R. (1996) ‘Weighting species abundance estimates for marine resource assessment’, Aquat. Conserv.: Mar. Freshw. Ecosyst., 6(3), pp. 115–120.
Nei, M. (1996) ‘Phylogenetic analysis in molecular evolutionary genetics’, Ann. Rev. Genet., 30, pp. 371–403.
Nelson, J.S. (1994) Fishes of the world, 3rd edn. New York: Wiley.
Ochiai, A. (1957) ‘Zoogeographic studies on the soleoid fishes found in Japan and its neighbouring regions’, Bull. Jpn. Soc. Sci. Fish, 22, pp. 526–530.
Olafsson, E. and Moore, C.G. (1992) ‘Effects of macroepifauna on developing nematode and harpacticoid assemblages in a subtidal muddy habitat’, Mar. Ecol. Prog. Ser., 84, pp. 161–171.
Olsgard, F. and Gray, J.S. (1995) ‘A comprehensive analysis of the effects of offshore oil and gas exploration and production on the benthic communities of the Norwegian continental shelf’, Mar. Ecol. Prog. Ser., 122, pp. 277–306.
Olsgard, F. and Somerfield, P.J. (2000) ‘Surrogates in marine benthic investigations – which taxonomic unit to target?’, J. Aquat. Ecosyst. Stress Recov., 7, pp. 25–42.
Olsgard, F., Somerfield, P.J. and Carr, M.R. (1997) ‘Relationships between taxonomic resolution and data transformations in analyses of a macrobenthic community along an established pollution gradient’, Mar. Ecol. Prog. Ser., 149, pp. 173–181.
Olsgard, F., Somerfield, P.J. and Carr, M.R. (1998) ‘Relationships between taxonomic resolution, macrobenthic community patterns and disturbance’, Mar. Ecol. Prog. Ser., 172, pp. 25–36.
Paul, W.L. and Anderson, M.J. (2013) ‘Causal modelling with multi-variate species data’, J. Exp. Mar. Biol. Ecol., 448, pp. 72–84.
Pearson, T.H. (1975) ‘The benthic ecology of Loch Linnhe and Loch Eil, a sea-loch system on the west coast of Scotland. IV. Changes in the benthic fauna attributable to organic enrichment’, J. Exp. Mar. Biol. Ecol., 20, pp. 1–41.
Pearson, T.H. and Blackstock, J. (1984) ‘Garroch Head sludge dumping ground survey’, final report, Dunstaffnage Marine Research Laboratory (unpublished}.
Pearson, T.H., Gray, J.S. and Johannessen, P.J. (1983) ‘Objective selection of sensitive species indicative of pollution-induced change in benthic communities. 2. Data analyses. Mar. Ecol. Prog. Ser., 12, pp. 237–255.
Pielou, E.C. (1975) Ecological diversity. New York: Wiley.
Pielou, E.C. (1984) The interpretation of ecological data. A primer on classification and ordination. New York: Wiley.
Piepenburg, D., Voss, J. and Gutt, J. (1997) ‘Assemblages of sea stars (Echinodermata: Asteroidea) and brittle stars (Echinodermata: Ophiuroidea) in the Weddell Sea (Antarctica) and off Northeast Greenland (Arctic): a comparison of diversity and abundance’, Polar Biology, 17, pp. 305–322.
Platell, M.E., Potter, I.C. and Clarke, K.R. (1998) ‘Resource partitioning by four species of elasmobranchs (Batoidea: Urolophidae) in coastal waters of temperate Australia’, Mar. Biol., 131, pp. 719–734.
Platt, H.M. and Warwick, R.M. (1983) Freeliving marine nematodes. Part I. British enoplids. Synopses of the british fauna no 28. Cambridge: Cambridge University Press.
Platt, H.M. and Warwick, R.M. (1988) Freeliving marine nematodes. Part II. British chromadorids. Leiden: E.J. Brill.
Potter, I.C., Bird, D.J., Claridge, P.N., Clarke, K.R., Hyndes, G.A. and Newton, L.C. (2001) ‘Fish fauna of the Severn Estuary. Are there long-term changes in abundance and species composition and are the recruitment patterns of the main marine species correlated?’, Mar. Ecol. Prog. Ser., 258, pp. 15–37.
Potter, I.C., Claridge, P.N., Hyndes, G.A. and Clarke, K.R. (1997) ‘Seasonal, annual and regional variations in ichthyofaunal compos¬ition in the inner Severn Estuary and inner Bristol Channel’, J. Mar. Biol. Assoc. U.K., 77, pp. 507–525.
Price, A.R.G., Keeling, M.J. and O’Callaghan, C.J. (1999) ‘Ocean-scale patterns of “biodiversity” of Atlantic asteroids determined from taxonomic distinctness and other measures’, Biol. J. Linn. Soc., 66, pp. 187–203.
Purcell, S.W., Rushworth, K., Clarke, K.R. and Dalton, S.J. (2014) ‘Defining critical habitats of threatened and endemic reef fishes using a multivariate approach’, Conserv. Biol. [Preprint].
Raffaelli, D. and Mason, C.F. (1981) ‘Pollution monitoring with meiofauna using the ratio of nematodes to copepods’, Mar. Poll. Bull., 12, pp. 158–163.
Reid, P.C., Barges, M.D.F. and Svendsen, E. (2001) ‘A regime shift in the North Sea circa 1988 linked to changes in the North Sea horse mackerel fishery’, Fish. Res., 50, pp. 163–171.
Rogers, S.I., Clarke, K.R. and Reynolds, J.D. (1999) ‘The taxonomic distinctness of coastal bottom-dwelling fish communities of the North-east Atlantic’, J. Anim. Ecol., 68, pp. 769–782.
Sanders, H.L. (1968) ‘Marine benthic diversity: a comparative study’, Am. Nat., 102, pp. 243–282.
Schafer, L.N., Platell, M.E., Valesini, F.J. and Potter, I.C. (2002) ‘Comparisons between the influence of habitat type, season and body size on the dietary compositions of fish species in nearshore marine waters’, J. Exp. Mar. Biol. Ecol., 278, pp. 67–92.
Scheffe, H. (1959) The analysis of variance. New York: Wiley.
Schiffman, S.S., Reynolds, M.L. and Young, F.W. (1981) Introduction to multi-dimensional scaling. Theory, methods and applications. London: Academic Press.
Schratzberger, M. and Warwick, R.M. (1998a) ‘Effects of physical disturbance on nematode communities in sand and mud: a microcosm experiment’, Mar. Biol., 130, pp. 643–650.
Schratzberger, M. and Warwick, R.M. (1998b) ‘Effects of the intensity and frequency of organic enrichment on two estuarine nematode communities’, Mar. Ecol. Prog. Ser., 164, pp. 83–94.
Schratzberger, M. and Warwick, R.M. (1999) ‘Differential effects of various types of disturbances on the structure of nematode assemblages: an experimental approach’, Mar. Ecol. Prog. Ser., 181, pp. 227–236.
Schwinghamer, P. (1981) ‘Characteristic size distributions of integral benthic communities’, Can. J. Fish. Aquat. Sci., 38, pp. 1255–1263.
Seber, G.A.F. (1984) Multivariate observations. New York: Wiley.
Shepard, R.N. (1962) ‘The analysis of proximities: multidimensional scaling with an unknown distance function’, Psychometrika, 27, pp. 125–140.
Shimatani, K. (2001) ‘On the measurement of species diversity incorporating species differences’, Oikos, 93, pp. 135–147.
Simpson, E.H. (1949) ‘Measurement of diversity’, Nature, 163, p. 688.
Smith, W.H. and Rissler, L.J. (2010) ‘Quantifying disturbance in terrestrial communities: Abundance-Biomass Comparisons of herpetofauna closely track forest succession’, Restor. Ecol., 18, pp. 195–204.
Sneath, P.H.A. (1957) ‘The application of computers to taxonomy’, J. Gen. Microbiol., 17, pp. 201–226.
Sneath, P.H.A. and Sokal, R.R. (1973) Numerical taxonomy. San Francisco: Freeman.
Sokal, R.R. and Rohlf, F.J. (1981) Biometry. San Francisco: Freeman.
Somerfield, P.J., Atkins, M., Bolam, S.G., Clarke, K.R., Garnacho, E., Rees, H.L. and Warwick, R.M. (2006) ‘Relative impacts at sites of dredged-material relocation in the coastal environment: a phylum-level meta-analysis approach’, Marine Biology, 148, pp. 1231–1240.
Somerfield, P.J., Clarke, K.R., Warwick, R.M. and Dulvy, N.K. (2008) ‘Average functional distinctness as a measure of the composition of assemblages’, ICES J. Mar. Sci., 65, pp. 1462–1468.
Somerfield, P.J. and Clarke, K.R. (1995) ‘Taxonomic levels, in marine community studies, revisited’, Mar. Ecol. Prog. Ser., 127, pp. 113–119.
Somerfield, P.J. and Clarke, K.R. (1997) ‘A comparison of some methods commonly used for the collection of sublittoral sediments and their associated fauna’, Mar. Environ. Res., 43, pp. 143–156.
Somerfield, P.J. and Clarke, K.R. (2013) ‘Inverse analysis in non-parametric multivariate analyses: distinguishing groups of associated species which covary coherently across samples’, J. Exp. Mar. Biol. Ecol., 449, pp. 261–273.
Somerfield, P.J., Clarke, K.R. and Olsgard, F. (2002) ‘A comparison of the power of categorical and correlational tests applied to community ecology data from gradient studies’, J. Anim. Ecol., 71, pp. 581–593.
Somerfield, P.J. and Gage, J.D. (2000) ‘Community structure of the benthos in Scottish sea-lochs. IV. Multivariate spatial pattern’, Mar. Biol., 136, pp. 1133–1145.
Somerfield, P.J., Gee, J.M. and Warwick, R.M. (1994a) ‘Benthic community structure in relation to an instantaneous discharge of waste water from a tin mine’, Mar. Pollut. Bull., 28, pp. 363–369.
Somerfield, P.J., Gee, J.M. and Warwick, R.M. (1994b) ‘Soft sediment meiofaunal community structure in relation to a long-term heavy metal gradient in the Fal estuary system’, Mar. Ecol. Prog. Ser., 105, pp. 79–88.
Somerfield, P.J., Gee, J.M. and Widdicombe, S. (1993) The use of meiobenthos in marine pollution monitoring programmes. Plymouth: Plymouth Marine Laboratory Miscellaneous Publication LIB-33A,B.
Somerfield, P.J., Olsgard, F. and Carr, M.R. (1997) ‘A further examination of two new taxonomic distinctness measures’, Mar. Ecol. Prog. Ser., 154, pp. 303–306.
Somerfield, P.J., Rees, H.L. and Warwick, R.M. (1995) ‘Interrelationships in community structure between shallow-water marine meiofauna and macrofauna in relation to dredgings disposal’, Mar. Ecol. Prog. Ser., 127, pp. 103–112.
Stephenson, W., Williams, W.T. and Cook, S.D. (1972) ‘Computer analysis of Petersen’s original data on bottom communities’, Ecol. Monogr., 42, pp. 387–415.
Stoffels, R.J., Clarke, K.R., Rehwinkel, R.A. and McCarthy, B.J. (2014) ‘Response of a floodplain fish community to river-floodplain connectivity: natural versus managed reconnection’, Can. J. Fish. Aquat. Sci., 71, pp. 236–245.
ter Braak, C.F.J. (1986) ‘Canonical correspondence analysis: a new eigenvector technique for multivariate direct gradient analysis’, Ecology, 67, pp. 1167–1179.
ter Braak, C.F.J. and Smilauer, P. (2002) ‘CANOCO reference manual and CanoDraw for Windows user’s guide: software for canonical community ordination (v4.5)’. Microcomputer Power, Itaca.
Tweedley, J.R., Hallett, C.S., Warwick, R.M., Clarke, K.R. and Potter, I.C. (2015) ‘The hypoxia that developed in a microtidal estuary following an extreme storm produced dramatic changes in the benthos’, Mar. Freshw. Res., 67, pp. 327-341.
Underwood, A.J. (1981) ‘Techniques of analysis of variance in experimental marine biology and ecology’, Oceanogr. Mar. Biol. Ann. Rev., 19, pp. 513–605.
Underwood, A.J. (1992) ‘Beyond BACI: the detection of environ-mental impact on populations in the real, but variable, world’, J. Exp. Mar. Biol. Ecol., 161, pp. 145–178.
Underwood, A.J. (1997) Experiments in ecology: their logical design and interpretation using analysis of variance. Cambridge: Cambridge University Press.
Underwood, A.J. and Chapman, M.G. (1998) ‘A method for analysing spatial scales of variation in composition of assemblages’, Oecologia, 117, pp. 570–578.
Underwood, A.J. and Peterson, C.H. (1988) ‘Towards an ecological framework for investigating pollution’, Mar. Ecol. Prog. Ser., 46, pp. 227–234.
Valesini, F.J., Clarke, K.R., Eliot, I. and Potter, I.C. (2003) ‘A user-friendly quantitative approach to classifying nearshore marine habitats along a heterogeneous coast’, Est. Coast. Shelf Sci., 57, pp. 163–177.
Valesini, F.J., Tweedley, J.R., Clarke, K.R. and Potter, I.C. (2014) ‘The importance of regional, system-wide and local spatial scales in structuring temperate estuarine fish communities’, Estuar. Coasts, 37, pp. 525–547.
Vane-Wright, R.I., Humphries, C.J. and Williams, P.H. (1991) ‘What to protect? Systematics and the agony of choice’, Biol. Conserv., 55, pp. 235–254.
Veale, L., Tweedley, J.R., Clarke, K.R., Hallett, C.S. and Potter, I.C. (2014) ‘Characteristics of the ichthyofauna of a temperate microtidal estuary with a reverse salinity gradient, including inter-decadal comparisons’, J. Fish Biol., 85, pp. 1320–1354.
Warton, D.I., Wright, S.T. and Wang, Y. (2012) ‘Distance-based multivariate analyses confound location and dispersion effects’, Methods Ecol. Evol., 3, pp. 89–101.
Warwick, R.M. (1971) ‘Nematode associations in the Exe estuary’, J. Mar. Biol. Assoc. U.K, 51, pp. 439–454.
Warwick, R.M. (1984) ‘Species size distributions in marine benthic communities’, Oecologia (Berlin), 61, pp. 32–41.
Warwick, R.M. (1986) ‘A new method for detecting pollution effects on marine macrobenthic communities’, Mar. Biol., 92, pp. 557–562.
Warwick, R.M. (1988a) ‘Effects on community structure of a pollutant gradient – summary’, Mar. Ecol. Prog. Ser., 46, pp. 207–211.
Warwick, R.M. (1988b) ‘The level of taxonomic discrimination required to detect pollution effects on marine benthic communities’, Mar. Pollut. Bull., 19, pp. 259–268.
Warwick, R.M. (1993) ‘Environmental impact studies on marine communities: pragmatical considerations’, Aust. J. Ecol., 18, pp. 63–80.
Warwick, R.M., Ashman, C.M., Brown, A.R., Clarke, K.R., Dowell, B., Hart, B., Lewis, R.E., Shillabeer, N., Somerfield, P.J. and Tapp, J.F. (2002) ‘Inter-annual changes in the biodiversity and community stucture of the macrobenthos in Tees Bay and the Tees estuary, UK, associated with local and regional environ-mental events’, Mar. Ecol. Prog. Ser., 234, pp. 1–13.
Warwick, R.M. and Buchanan, J.B. (1970) ‘The meiofauna off the coast of Northumberland. I: The structure of the nematode population’, J. Mar. Biol. Assoc. U.K., 50, pp. 129–146.
Warwick, R.M., Carr, M.R., Clarke, K.R., Gee, J.M. and Green, R.H.(1988) ‘A mesocosm experiment on the effects of hydrocarbon and copper pollution on a sublittoral soft-sediment meiobenthic community’, Mar. Ecol. Prog. Ser., 46, pp. 181–191.
Warwick, R.M. and Clarke, K.R. (1991) ‘A comparison of methods for analysing changes in benthic community structure’, J. Mar. Biol. Assoc. U.K, 71, pp. 225–244.
Warwick, R.M. and Clarke, K.R. (1993a) ‘Comparing the severity of disturbance: a meta-analysis of marine macrobenthic community data’, Mar. Ecol. Prog. Ser., 92, pp. 221–231.
Warwick, R.M. and Clarke, K.R. (1993b) ‘Increased variability as a symptom of stress in marine communities’, J. Exp. Mar. Biol. Ecol., 172, pp. 215–226.
Warwick, R.M. and Clarke, K.R. (1994) ‘Relearning the ABC: taxonomic changes and abundance/biomass relationships in disturbed benthic communities’, Mar. Biol., 118, pp. 739–744.
Warwick, R.M. and Clarke, K.R. (1995a) ‘Multivariate measures of community stress and their application to marine pollution studies in the East Asian region’, Phuket Mar. Biol. Cent. Res. Bull., 60, pp. 99–113.
Warwick, R.M. and Clarke, K.R. (1995b) ‘New “biodiversity” measures reveal a decrease in taxonomic distinctness with increasing stress’, Mar. Ecol. Prog. Ser., 129, pp. 301–305.
Warwick, R.M. and Clarke, K.R. (1998) ‘Taxonomic distinctness and environmental assessment’, J. Appl. Ecol., 35, pp. 532–543.
Warwick, R.M. and Clarke, K.R. (2001) ‘Practical measures of marine biodiversity based on relatedness of species’, Oceanogr. Mar. Biol. Ann. Rev., 39, pp. 207–231.
Warwick, R.M., Clarke, K.R. and Gee, J.M. (1990) ‘The effects of disturbance by soldier crabs, Mictyris platycheles H. Milne Edwards, on meiobenthic community structure’. J. Exp. Mar. Biol. Ecol., 135, pp. 19–33.
Warwick, R.M., Clarke, K.R., and Suharsono (1990) ‘A statistical analysis of coral community responses to the 1982–3 El Nino in the Thousand Islands, Indonesia’, Coral reefs, 8, pp. 171–179.
Warwick, R.M. and Coles, J.W. (1977) ‘The marine flora and fauna of the Isles of Scilly. Free-living Nematoda’, J. Nat. Hist., 11, pp. 393–407.
Warwick, R.M. and Light, J. (2002) ‘Death assemblages of molluscs on st martin’s flats, isles of scilly: a surrogate for regional biodiversity?, Biodivers. Conserv., 11, pp. 99–112.
Warwick, R.M., Pearson, T.H., and Ruswahyuni (1987) ‘Detection of pollution effects on marine macrobenthos: further evaluation of the species abundance/biomass method’, Mar. Biol., 95, pp. 193–200.
Warwick, R.M., Platt, H.M., Clarke, K.R., Agard, J. and Gobin, J. (1990) ‘Analysis of macrobenthic and meiobenthic community structure in relation to pollution and disturbance in Hamilton Harbour, Bermuda’, J. Exp. Mar. Biol. Ecol., 138, pp. 119–142.
Warwick, R.M., Platt, H.M. and Somerfield, P.J. (1998) Freeliving marine nematodes. Part III. British Monhysterida. Synopses of the British Fauna No 38. EJ Brill, Dr. W. Backhuys for the Linnean Society of London and the Estuarine and Brackish-water Sciences Associatio.
Warwick, R.M. and Somerfield, P.J. (2008) ‘All animals are equal but some animals are more equal than others’, J. Exp. Mar. Biol. Ecol., 366, pp. 184–186.
Whittaker, R.H. (1952) ‘A study of summer foliage insect communities in the Great Smoky Mountains’, Ecol. Monogr., 22, pp. 1–44.
Widdicombe, S. and Austen, M.C. (1998) ‘Experimental evidence for the role of Brissopsis lyrifera (Forbes, 1841) as a critical species in the maintenance of benthic diversity and the modification of sediment chemistry’, J. Exp. Mar. Biol. Ecol., 228, pp. 241–255.
Widdicombe, S. and Austen, M.C. (2001) ‘The interaction between physical disturbance and organic enrichment: an important element in structuring benthic communities’, Limnol. Oceanog., 46, pp. 1720–1733.
Wilkinson, D.M. (1999) ‘The disturbing history of intermediate disturbance’, Oikos, 84, pp. 145–147.
Wilkinson, L. and Friendly, M. (2008) ‘The history of the cluster heat map’, Amer. Statist., 63, pp. 179–184.
Williams, P.H., Humphries, C.J. and Vane-Wright, R.I. (1991) ‘Measuring biodiversity: taxonomic relatedness for conservation priorities’, Aust. Syst. Bot., 4, pp. 665–679.
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’, Mar. Ecol. Prog. Ser., 236, pp. 189–203.