K. Robert Clarke

Comparisons of dominance curves

In studies of community structure, a widely used technique for representing patterns of species abundance (or biomass) in a sample is the dominance curve, in which species are ranked by abundance and the percentage of the total number of individuals belonging to each species is plotted against (log) species rank. Alternatively, these percentages are cumulated, as in “k-dominance” curves, or separate k-dominance curves for abundance and biomass are superimposed, giving “abundance-biomass comparison” (ABC) curves. When such curves are replicated for samples from a number of sites, times or treatments, questions of statistical significance of apparent differences arise. A framework for such tests is described, and illustrated with data from the IOC/GEEP Bermuda Workshop and other studies of the effects of pollutants on benthic communities. Also discussed is an approximately linearising transformation for the y axis of a k-dominance plot, designed to improve clarity of presentation. In addition, a new descriptive tool is proposed for displaying “partial dominance” patterns in community data and it is suggested that this may mitigate a recent criticism of Warwicks ABC method, viz., its overdependence on the single most dominant species.

An analysis of fish community responses to coral mining in the Maldives

SynopsisCoral mining takes place on shallow reef flats at a number of localities in the Maldives, but not on the adjacent deeper reef slopes. A semi-quantitative census method for fish species abundance and biomass is described. Fish community structure is compared on mined and non-mined reef flats and their adjacent slopes using a variety of univariate, graphical/distributional and multivariate statistical techniques. In general, univariate and graphical distributional methods do not indicate significant differences between mined and non-mined localities with respect to the relative abundances and biomasses of species. Multivariate methods (both classification and ordination), however, indicate very clear-cut effects of mining on the reef flats, and also significant effects on reef slopes adjacent to mined flats. The effect was equally clear using non-quantitative (presence/absence) data. The fish species mainly responsible for the differences between mined and non-mined localities are identified, and the differences are explained in terms of the feeding biology of these species.

The attachment of Enteromorpha zoospores to a bacterial biofilm assemblage

This study has investigated the relationship between bacterial biofilms and the attachment of zoospores of the green macroalga Enteromorpha. Zoospore attachment to glass slides was enhanced in the presence of a bacterial biofilm assemblage, and the number attaching increased with the number of bacteria present. Zoospores also attached to control surfaces, but at lower numbers; glass surfaces conditioned in autoclaved seawater had the same number of zoospores attached as new glass surfaces. The spatial relationship between bacterial cells and attached zoospores was quantified by image analysis. The hypothesis tested was that zoospores attached preferentially to, or in the very close vicinity of, bacterial cells. Spatial microscopic analysis showed that more bacteria were covered by zoospores than would be expected if zoospore attachment was a random process and zoospores appeared to attach to bacterial clusters. The most likely explanation is that zoospores are attracted to bacterial cells growing on surfaces and the presence of a bacterial biofilm enhances their settlement. The possibility is discussed that Enteromorpha zoospores respond to a chemical signal produced by bacteria, i.e. that there may be prokaryote‐eukaryote cell signalling.

The hypoxia that developed in a microtidal estuary following an extreme storm produced dramatic changes in the benthos

Runoff from an extreme storm on 22 March 2010 led, during the next 3 months, to the formation of a pronounced halocline and underlying hypoxia in the upper reaches of the microtidal Swan–Canning Estuary. Benthic macroinvertebrates were sampled between January 2010 and October 2011 at five sites along 10 km of this region. By mid-April, the number of species, total density, Simpson’s evenness index and taxonomic distinctness had declined markedly, crustaceans had disappeared and the densities of annelids and molluscs had declined slightly. These faunal attributes (except Simpson’s index) and species composition did not recover until after the end of the hypoxia. The survival of annelids and loss of crustaceans in this period reflects different sensitivities of these taxa to severe environmental stress. The results emphasise that microtidal estuaries with long residence times are highly vulnerable to the effects of environmental perturbations, particularly during warmer periods of the year.

Within-Otolith Variability in Chemical Fingerprints: Implications for Sampling Designs and Possible Environmental Interpretation

Largely used as a natural biological tag in studies of dispersal/connectivity of fish, otolith elemental fingerprinting is usually analyzed by laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS). LA-ICP-MS produces an elemental fingerprint at a discrete time-point in the life of a fish and can generate data on within-otolith variability of that fingerprint. The presence of within-otolith variability has been previously acknowledged but not incorporated into experimental designs on the presumed, but untested, grounds of both its negligibility compared to among-otolith variability and of spatial autocorrelation among multiple ablations within an otolith. Here, using a hierarchical sampling design of spatial variation at multiple scales in otolith chemical fingerprints for two Mediterranean coastal fishes, we explore: 1) whether multiple ablations within an otolith can be used as independent replicates for significance tests among otoliths, and 2) the implications of incorporating within-otolith variability when assessing spatial variability in otolith chemistry at a hierarchy of spatial scales (different fish, from different sites, at different locations on the Apulian Adriatic coast). We find that multiple ablations along the same daily rings do not necessarily exhibit spatial dependency within the otolith and can be used to estimate residual variability in a hierarchical sampling design. Inclusion of within-otolith measurements reveals that individuals at the same site can show significant variability in elemental uptake. Within-otolith variability examined across the spatial hierarchy identifies differences between the two fish species investigated, and this finding leads to discussion of the potential for within-otolith variability to be used as a marker for fish exposure to stressful conditions. We also demonstrate that a ‘cost’-optimal allocation of sampling effort should typically include some level of within-otolith replication in the experimental design. Our findings provide novel evidence to aid the design of future sampling programs and improve our general understanding of the mechanisms regulating elemental fingerprints.

Effects of a harmful algal bloom on the community ecology, movements and spatial distributions of fishes in a microtidal estuary

Harmful algal blooms can adversely affect fish communities, though their impacts are highly context-dependent and typically differ between fish species. Various approaches, comprising univariate and multivariate analyses and multimetric Fish Community Indices (FCI), were employed to characterise the perceived impacts of a Karlodinium veneficum bloom on the fish communities and ecological condition of the Swan Canning Estuary, Western Australia. The combined evidence suggests that a large proportion of the more mobile fish species in the offshore waters of the bloom-affected area relocated to other regions during the bloom. This was indicated by marked declines in mean species richness, catch rates and FCI scores in the bloom region but concomitant increases in these characteristics in more distal regions, and by pronounced and atypical shifts in the pattern of inter-regional similarities in fish community composition during the bloom. The lack of any significant changes among the nearshore fish communities revealed that bloom impacts were less severe there than in deeper, offshore waters. Nearshore habitats, which generally are in better ecological condition than adjacent offshore waters in this system, may provide refuges for fish during algal blooms and other perturbations, mirroring similar observations of fish avoidance responses to such stressors in estuaries worldwide.

Aspects of Benthic Decapod Diversity and Distribution from Rocky Nearshore Habitat at Geographically Widely Dispersed Sites

Relationships of diversity, distribution and abundance of benthic decapods in intertidal and shallow subtidal waters to 10 m depth are explored based on data obtained using a standardized protocol of globally-distributed samples. Results indicate that decapod species richness overall is low within the nearshore, typically ranging from one to six taxa per site (mean = 4.5). Regionally the Gulf of Alaska decapod crustacean community structure was distinguishable by depth, multivariate analysis indicating increasing change with depth, where assemblages of the high and mid tide, low tide and 1 m, and 5 and 10 m strata formed three distinct groups. Univariate analysis showed species richness increasing from the high intertidal zone to 1 m subtidally, with distinct depth preferences among the 23 species. A similar depth trend but with peak richness at 5 m was observed when all global data were combined. Analysis of latitudinal trends, confined by data limitations, was equivocal on a global scale. While significant latitudinal differences existed in community structure among ecoregions, a semi-linear trend in changing community structure from the Arctic to lower latitudes did not hold when including tropical results. Among boreal regions the Canadian Atlantic was relatively species poor compared to the Gulf of Alaska, whereas the Caribbean and Sea of Japan appeared to be species hot spots. While species poor, samples from the Canadian Atlantic were the most diverse at the higher infraordinal level. Linking 11 environmental variables available for all sites to the best fit family-based biotic pattern showed a significant relationship, with the single best explanatory variable being the level of organic pollution and the best combination overall being organic pollution and primary productivity. While data limitations restrict conclusions in a global context, results are seen as a first-cut contribution useful in generating discussion and more in-depth work in the still poorly understood field of biodiversity distribution.

Defining Critical Habitats of Threatened and Endemic Reef Fishes with a Multivariate Approach

Understanding critical habitats of threatened and endemic animals is essential for mitigating extinction risks, developing recovery plans, and siting reserves, but assessment methods are generally lacking. We evaluated critical habitats of 8 threatened or endemic fish species on coral and rocky reefs of subtropical eastern Australia, by measuring physical and substratum-type variables of habitats at fish sightings. We used nonmetric and metric multidimensional scaling (nMDS, mMDS), Analysis of similarities (ANOSIM), similarity percentages analysis (SIMPER), permutational analysis of multivariate dispersions (PERMDISP), and other multivariate tools to distinguish critical habitats. Niche breadth was widest for 2 endemic wrasses, and reef inclination was important for several species, often found in relatively deep microhabitats. Critical habitats of mainland reef species included small caves or habitat-forming hosts such as gorgonian corals and black coral trees. Hard corals appeared important for reef fishes at Lord Howe Island, and red algae for mainland reef fishes. A wide range of habitat variables are required to assess critical habitats owing to varied affinities of species to different habitat features. We advocate assessments of critical habitats matched to the spatial scale used by the animals and a combination of multivariate methods. Our multivariate approach furnishes a general template for assessing the critical habitats of species, understanding how these vary among species, and determining differences in the degree of habitat specificity.

Long‐term Monitoring of Macroinvertebrate Communities Over 2,300 km of the Murray River Reveals Ecological Signs of Salinity Mitigation Against a Backdrop of Climate Variability

We investigated the ecological effects of salinity mitigation strategies in the Murray‐Darling Basin (MDB) using macroinvertebrate data collected over 2,300 km of the Murray River between 1980 and 2012. The MDB covers 1 × 106km2 and includes both temperate and semiarid climate zones. It was extensively developed to support irrigated agriculture in the early to mid‐1900s, and the secondary salinization that followed has become a major concern. During 1975–1985 daily salinity levels, measured as electrical conductivity above the Murray River off‐take points for South Australias major urban water supplies, were above 800 μS/cm for 40% of the time, necessitating mitigation strategies that have reduced the average salinity by about 150 μS/cm since monitoring began. The MDB has also experienced several major floods and droughts during this time, and surface temperatures in the MDB have increased by 0.8 °C since 1910, mostly in the last 50 years. We hypothesized that (1) taxa richness would increase in response to floods; (2) community structure would shift toward tolerant, opportunistic taxa in response to warming; and (3) geographical ranges of species would change in response to shifting stream isotherms and reducing salinity. Our hypotheses were supported, although increases in water temperature appeared to be due principally to the 1997–2009 Millennium drought. Importantly, against a backdrop of significant climate variability, we believe we have distinguished a change in community structure along a salinity gradient and that changes over the 33 years can in part be attributed to mitigation strategies.