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Citing PRIMER in publications

For referencing the software itself, it is probably best to quote the User Manual:
v6: Clarke, KR, Gorley, RN, 2006. PRIMER v6: User Manual/Tutorial. PRIMER-E, Plymouth, 192pp.
v7: Clarke, KR, Gorley, RN, 2015. PRIMER v7: User Manual/Tutorial. PRIMER-E, Plymouth, 296pp.

For the early core methods in PRIMER (Cluster, MDS, ANOSIM, SIMPER, BEST), it is suggested in the manual that you cite the (white literature) Aust J Ecol paper:
Clarke, KR (1993). Non-parametric multivariate analyses of changes in community structure. Australian Journal of Ecology 18: 117-143.

Or you could cite the (grey literature) Methods manual which comes with the software:
v6: Clarke, KR, Warwick RM (2001). Change in marine communities: an approach to statistical analysis and interpretation, 2nd edition. PRIMER-E, Plymouth, 172pp.

In connection with all the newer techniques of the last decade or so, the v7 Methods manual will point you towards the relevant publications from the list given below, or you could cite the manual itself:
v7: Clarke KR, Gorley RN, Somerfield PJ, Warwick RM (2014). Change in marine communities: an approach to statistical analysis and interpretation, 3rd edition. PRIMER-E, Plymouth, 260pp

Download a searchable list of >12000 SCI papers (title, authors and source) citing PRIMER methods, from nearly 1000 different journal titles

Papers (.doc file) - updated March 2015
Citing journals alphabetic (.doc file) - updated March 2015

Some publications with a strong component of PRIMER methodological development (and an author from Plymouth Marine Laboratory), plus number of citations [x] in (Thompson-Reuters) SCI-listed papers (updated April 2015)

FIELD JG, CLARKE KR, WARWICK RM (1982) A practical strategy for analysing multispecies distribution patterns. Mar Ecol Prog Ser 8, 37-52 [1,248]

WARWICK RM (1986) A new method for detecting pollution effects on marine macrobenthic communities. Mar Biol 92, 557-562 [373]

CLARKE KR, GREEN RH (1988) Statistical design and analysis for a 'biological effects' study. Mar Ecol Prog Ser 46, 213-226 [1,066]

CLARKE KR (1990) Comparisons of dominance curves. J exp mar Biol Ecol 138, 143-157 [167]

WARWICK RM, CLARKE KR, GEE JM (1990) The effect of disturbance by soldier crabs, Mictyris platycheles H Milne Edwards, on meiobenthic community structure. J exp mar Biol Ecol 135, 19-33 [113]

WARWICK RM, CLARKE KR (1991) A comparison of some methods for analysing changes in benthic community structure. J mar biol Ass UK 71, 225-244 [289]

CLARKE KR (1993) Non-parametric multivariate analyses of changes in community structure. Aust J Ecol 18, 117-143 [5,057]

CLARKE KR, AINSWORTH M (1993) A method of linking multivariate community structure to environmental variables. Mar Ecol Prog Ser 92, 205-219 [993]

CLARKE KR, WARWICK RM, BROWN BE (1993) An index showing breakdown of seriation, related to disturbance, in a coral-reef assemblage. Mar Ecol Prog Ser 102, 153-160 [70]

WARWICK RM (1993) Environmental impact studies on marine communities: pragmatical considerations. Aust J Ecol 18, 63-80 [318]

WARWICK RM, CLARKE KR (1993) Comparing the severity of disturbance: a meta-analysis of marine macrobenthic community data. Mar Ecol Prog Ser 92, 221-231 [204]

WARWICK RM, CLARKE KR (1993) Increased variability as a symptom of stress in marine communities. J exp mar Biol Ecol 172, 215-226 [307]

CLARKE KR, WARWICK RM (1994) Similarity-based testing for community pattern: the 2-way layout with no replication. Mar Biol 118, 167-176 [186]

SOMERFIELD PJ, GEE JM, WARWICK RM (1994) Soft sediment meiofaunal community structure in relation to a long-term heavy metal gradient in the Fal estuary system. Mar Ecol Prog Ser 105, 79-88 [97]

WARWICK RM, CLARKE KR (1994) Relearning the ABC: taxonomic changes and abundance/biomass relationships in disturbed benthic communities. Mar Biol 118, 739-744 [104]

SOMERFIELD PJ, CLARKE KR (1995) Taxonomic levels, in marine community studies, revisited. Mar Ecol Prog Ser 127, 113-119 [212]

WARWICK RM, CLARKE KR (1995) New ‘biodiversity’ measures reveal a decrease in taxonomic distinctness with increasing stress. Mar Ecol Prog Ser 129, 301-305 [405]

OLSGARD F, SOMERFIELD PJ, CARR MR (1997) Relationships between taxonomic resolution and data transformations in analyses of a macrobenthic community along an established pollution gradient. Mar Ecol Prog Ser 149, 173-181 [136]

CLARKE KR, WARWICK RM (1998) Quantifying structural redundancy in ecological communities. Oecologia 113, 278-289 [131]

CLARKE KR, WARWICK RM (1998) A taxonomic distinctness index and its statistical properties. J appl Ecol 35, 523-531 [452]

WARWICK RM, CLARKE KR (1998) Taxonomic distinctness and environmental assessment. J appl Ecol 35, 532-543 [205]

CLARKE KR (1999) Non-metric multivariate analysis in community-level ecotoxicology. Environ Toxicol Chem 18, 118-127 [77]

CLARKE KR, WARWICK RM (1999) The taxonomic distinctness measure of biodiversity: weighting of step lengths between hierarchical levels. Mar Ecol Prog Ser 184, 21-29 [180]

SOMERFIELD PJ, GAGE JD (2000) Community structure of the benthos in Scottish sea-lochs. IV Multivariate spatial pattern. Mar Biol 136, 1133-1145 [19]

CLARKE KR, WARWICK RM (2001) A further biodiversity index applicable to species lists: variation in taxonomic distinctness. Mar Ecol Prog Ser 216, 265-278 [373]

POTTER IC, BIRD DJ, CLARIDGE PN, CLARKE KR, HYNDES GA, NEWTON LC (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? J exp mar Biol Ecol 258, 15-37 [54]

WARWICK RM, CLARKE KR (2001) Practical measures of marine biodiversity based on relatedness of species. Oceanog Mar Biol Ann Rev 39, 207-231 [190]

SOMERFIELD PJ, CLARKE KR, 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: 581-593 [39]

WARWICK RM, ASHMAN CM, BROWN AR, CLARKE KR, DOWELL B, HART B, LEWIS RE, SHILLABEER N, SOMERFIELD PJ, TAPP JF (2002) Inter-annual changes in the biodiversity and community structure of the macrobenthos in Tees Bay and the Tees estuary, UK, associated with local and regional environmental events. Mar Ecol Prog Ser 234, 1-13 [79]

VALESINI FJ, CLARKE KR, ELIOT I, POTTER IC (2003) A user-friendly quantitative approach to classifying nearshore marine habitats along a heterogeneous coast. Estuar Coast Shelf Sci 57, 163-177 [24]

CLARKE KR, SOMERFIELD PJ, CHAPMAN MG (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, 55-80 [319]

CLARKE KR, CHAPMAN MG, SOMERFIELD PJ, NEEDHAM HR (2006) Dispersion-based weighting of species counts in assemblage analyses. Mar Ecol Progr Ser 320, 11-27 [65]

CLARKE KR, SOMERFIELD PJ, AIROLDI L, WARWICK RM (2006) Exploring interactions by second-stage community analyses. J Exp Mar Biol Ecol 338, 179-192 [43]

LEONARD DRP, CLARKE KR, SOMERFIELD PJ, WARWICK RM (2006) The application of an indicator based on taxonomic distinctness for UK marine biodiversity assessments. J Environ Manage 78, 52-62 [63]

ALLEN I, CLARKE KR (2007) Effects of demersal trawling on ecosystem functioning in the North Sea: a modelling study. Mar Ecol Progr Ser 336, 63-75 [19]

CLARKE KR, SOMERFIELD PJ, GORLEY RN (2008) Exploratory null hypothesis testing for community data: similarity profiles and biota-environment linkage. J Exp Mar Biol Ecol 366, 56-69 [183]

SOMERFIELD PJ, JAAP WC, CLARKE KR et al (2008) Changes in coral reef communities among the Florida Keys, 1996-2003. Coral Reefs 27, 951-965 [27]

SOMERFIELD PJ, CLARKE KR, WARWICK RM, DULVY NK (2008) Average functional distinctness as a measure of the composition of assemblages. ICES J Mar Sci 65, 1462-1468 [24]

ALLEN JI, SOMERFIELD PJ (2009) A multivariate approach to model skill assessment. J Mar System 76, 83-94 [18]

FRENCH B, CLARKE KR, PLATELL ME, POTTER IC (2013) An innovative approach to constructing a readily comprehensible food web for a demersal fish community. Estuar Coast Shelf Sci 125, 43-56 [2]

SOMERFIELD PJ, CLARKE KR (2013) Inverse analysis in non-parametric multivariate analyses: distinguishing groups of associated species which covary coherently across samples. J Exp Mar Biol Ecol 449, 261-273 [5]

CLARKE KR, TWEEDLEY JT, VALESINI FJ (2014) Simple shade plots aid better long-term choices of data pre-treatment in multivariate assemblage studies. J Mar Biol Assoc UK 94, 1-16 [5]

PURCELL SW, CLARKE KR, RUSHWORTH K, DALTON SJ (2014) Defining critical habitats of threatened and endemic reef fishes with a multivariate approach. Conserv Biol 28, 1688-1698 [0]

SOMERFIELD PJ, BURTON M, SANDERSON WG (2014) Analyses of sublittoral macrobenthic community change in a marine nature reserve using similarity profiles (SIMPROF). Mar Environ Res 102, 51-58 [0]

VALESINI FJ, TWEEDLEY JR, CLARKE KR, POTTER IC (2014) The importance of local, system-wide and regional spatial scales in structuring temperate estuarine fish communities. Estuar Coasts 37, 525-547 [2]

VEALE L, TWEEDLEY JR, CLARKE KR, HALLETT CS, POTTER IC (2014) Characteristics of the ichthofauna of a temperate microtidal estuary with a reverse salinity gradient, including inter-decadal comparisons. J Fish Biol 85, 1320-1354 [0]

Books/manuals

CLARKE KR, WARWICK RM (1994, 2001, 2014) Change in Marine Communities: An Approach to Statistical Analysis and Interpretation. PRIMER-E, Plymouth, UK. 1st ed 144pp; 2nd ed 172pp; 3rd ed (authors CLARKE KR, GORLEY RN, SOMERFIELD PJ, WARWICK RM) 260pp [6,542]

CLARKE KR, GORLEY RN (2001, 2006, 2015) PRIMER v5, v6 & v7: User manual/tutorial, PRIMER-E, Plymouth UK, 91pp, 192pp & 296pp [5,231]