Differences in performance among four indices used to evaluate diversity in planktonic ecosystems

The performance of four common estimators of diversity are investigated using calanoid copepod data from the Continuous Plankton Recorder (CPR) survey. The region of the North Atlantic and the North Sea was divided into squares of 400 nautical miles for each 2-month period. For each 144 possible cases, Pielou's pooled quadrat method was performed with the aims of determining asymptotic diversity and investigating the CPR sample-size dependence of diversity estimators. It is shown that the performance of diversity indices may greatly vary in space and time (at a seasonal scale). This dependence is more pronounced in higher diverse environments and when the sample size is small. Despite results showing that all estimators underestimate the `actual' diversity, comparison of sites remained reliable from a few pooled CPR samples. Using more than one CPR sample, the Gini coefficient appears to be a better diversity estimator than any other indices and spatial or temporal comparisons are highly satisfactory. In situations where comparative studies are needed but only one CPR sample is available, taxonomic richness was the preferred method of estimating diversity. Recommendations are proposed to maximise the efficiency of diversity estimations with the CPR data.

Coastal upwelling and downwelling forcing of circulation in a semi-enclosed bay: Ria de Vigo

Semi-enclosed bays in upwelling regions are exposed to forcing related to winds, currents and buoyancy over the shelf. The influence of this external forcing is moderated by factors such as connectivity to the open ocean, shelter by surrounding topography, dimensions of the bay, and freshwater outflows. Such bays, preferred locations for ports, mariculture, marine industry, recreational activities and coastal settlement, present a range of characteristics, understanding of which is necessary to their rational management. Observations in such a semi-enclosed bay, the Ria de Vigo in Spain, are used to characterize the influence of upwelling and downwelling pulses on its circulation. In this location, near the northern limit of the Iberian upwelling system, upwelling events dominate during a short summer season and downwelling events the rest of the year. The ria response to the external forcing is central to nutrient supply and resultant plankton productivity that supports its high level of cultured mussel production. Intensive field studies in September 2006 and June 2007 captured a downwelling event and an upwelling event, respectively. Data from eight current profiler moorings and boat-based MiniBat/ADCP surveys provided an unprecedented quasi-synoptic view of the distribution of water masses and circulation patterns in any ria. In the outer ria, circulation was dominated by the introduction of wind-driven alongshore flow from the external continental shelf through the ria entrances and its interaction with the topography. In the middle ria, circulation was primarily related to the upwelling/downwelling cycle, with a cool, salty and dense lower layer penetrating to the inner ria during upwelling over the shelf. A warmer, lower salinity and less dense surface layer of coastal waters flowed inward during downwelling. Without external forcing, the inner ria responded primarily to tides and buoyancy changes related to land runoff. Under both upwelling and downwelling conditions, the flushing of the ria involved shelf responses to wind pulses. Their persistence for a few days was sufficient to allow waters from the continental shelf to penetrate the innermost ria. Longer term observations supported by numerical modeling are required to confirm the generality of such flushing events in the ria and determine their typical frequency, while comparative studies should explore how these scenarios fit into the range of conditions experienced in other semi-enclosed bays.

Simple shade plots aid better long-term choices of data pre-treatment in multivariate assemblage studies

Shade plots, simple visual representations of abundance matrices from multivariate species assemblage studies, are shown to be an effective aid in choosing an overall transformation (or other pre-treatment) of quantitative data for long-term use, striking an appropriate balance between dominant and less abundant taxa in ensuing resemblance-based multivariate analyses. Though the exposition is entirely general and applicable to all community studies, detailed illustrations of the comparative power and interpretative possibilities of shade plots are given in the case of two estuarine assemblage studies in south-western Australia: (a) macrobenthos in the upper Swan Estuary over a two-year period covering a highly significant precipitation event for the Perth area; and (b) a wide-scale spatial study of the nearshore fish fauna from five divergent estuaries. The utility of transformations of intermediate severity is again demonstrated and, with greater novelty, the potential importance seen of further mild transformation of all data after differential down-weighting (dispersion weighting) of spatially clumped' or schooled' species. Among the new techniques utilized is a two-way form of the RELATE test, which demonstrates linking of assemblage structure (fish) to continuous environmental variables (water quality), having removed a categorical factor (estuary differences). Re-orderings of sample and species axes in the associated shade plots are seen to provide transparent explanations at the species level for such continuous multivariate patterns.

High-quality RNA extraction from copepods for Next Generation Sequencing: A comparative study

Despite the ecological importance of copepods, few Next Generation Sequencing studies (NGS) have been performed on small crustaceans, and a standard method for RNA extraction is lacking. In this study, we compared three commonly-used methods: TRIzol®, Aurum Total RNA Mini Kit and Qiagen RNeasy Micro Kit, in combination with preservation reagents TRIzol® or RNAlater®, to obtain high-quality and quantity of RNA from copepods for NGS. Total RNA was extracted from the copepods Calanus helgolandicus, Centropages typicus and Temora stylifera and its quantity and quality were evaluated using NanoDrop, agarose gel electrophoresis and Agilent Bioanalyzer. Our results demonstrate that preservation of copepods in RNAlater® and extraction with Qiagen RNeasy Micro Kit were the optimal isolation method for high-quality and quantity of RNA for NGS studies of C. helgolandicus. Intriguingly, C. helgolandicus 28S rRNA is formed by two subunits that separate after heat-denaturation and migrate along with 18S rRNA. This unique property of protostome RNA has never been reported in copepods. Overall, our comparative study on RNA extraction protocols will help increase gene expression studies on copepods using high-throughput applications, such as RNA-Seq and microarrays.