A new procedure to optimize the selection of groups in a classification tree

Agglomerative cluster analyses encompass many techniques, which have been widely used in various fields of science. In biology, and specifically ecology, datasets are generally highly variable and may contain outliers, which increase the difficulty to identify the number of clusters. Here we present a new criterion to determine statistically the optimal level of partition in a classification tree. The criterion robustness is tested against perturbated data (outliers) using an observation or variable with values randomly generated. The technique, called Random Simulation Test (RST), is tested on (1) the well-known Iris dataset [Fisher, R.A., 1936. The use of multiple measurements in taxonomic problems. Ann. Eugenic. 7, 179–188], (2) simulated data with predetermined numbers of clusters following Milligan and Cooper [Milligan, G.W., Cooper, M.C., 1985. An examination of procedures for determining the number of clusters in a data set. Psychometrika 50, 159–179] and finally (3) is applied on real copepod communities data previously analyzed in Beaugrand et al. [Beaugrand, G., Ibanez, F., Lindley, J.A., Reid, P.C., 2002. Diversity of calanoid copepods in the North Atlantic and adjacent seas: species associations and biogeography. Mar. Ecol. Prog. Ser. 232, 179–195]. The technique is compared to several standard techniques. RST performed generally better than existing algorithms on simulated data and proved to be especially efficient with highly variable datasets.

A synthesis of large-scale patterns in the planktonic prey of larval and juvenile cod (Gadus morhua)

Data from 40 published studies of the diet composition of larval and juvenile cod (Gadus morhua) from around the northern North Atlantic were summarized to assess generic patterns in ontogenetic and regional variability in the key prey. The results showed that larvae at the northern edge of the latitudinal range of cod depend primarily on development stages of the copepod Calanus finmarchicus, whilst those at the southern edge depend on Para- and Pseudocalanus species. Juvenile cod preyed on a wider range of taxa than larvae, but euphausiids were the main target prey. Analysis of regional variations in the relative abundances of C. finmarchicus and Para/Pseudocalanus spp. in the plankton, as estimated by the continuous plankton recorder (CPR) surveys, showed a similar geographical pattern to the larval cod stomach contents. Comparison of CPR data from the 1960s and 70s with data from the 1990s showed that the boundary between C. finmarchicus and Para/Pseudocalanus spp. dominance has shifted northwards on both sides of the Atlantic, whilst the abundance of euphausiids in the southern cod stock regions has declined. The results are discussed in relation to regional differences in the response of cod stocks to climate variability.

Spatial demography of Calanus finmarchicus in the Irminger Sea

Continuous Plankton Recorder data suggest that the Irminger Sea supports a major proportion of the surface-living population of the copepod Calanus finmarchicus in the northern North Atlantic, but there have been few studies of its population dynamics in the region. In this paper, we document the seasonal changes in the demographic structure of C finmarchicus in the Irminger Sea from a field programme during 2001/2002, and the associations between its developmental stages and various apparent bio-physical zones. Overwintering stages were found widely at depth (>500 m) across the Irminger Sea, and surviving females were widely distributed in the surface waters the following spring. However, recruitment of the subsequent generation was concentrated around the fringes of the Irminger Sea basin, along the edges of the Irminger and East Greenland Currents, and not in the central basin. In late summer animals were found descending back to overwintering depths in the Central Irminger Sea. The key factors dictating this pattern of recruitment appear to be (a) the general circulation regime, (b) predation on eggs in the spring, possibly by the surviving GO stock, and (c) mortality of first feeding naupliar stages in the central basin where food concentrations appear to be low throughout the year. We compared the demographic patterns in 2001/2002 with observations from the only previous major survey in 1963 and with data from the Continuous Plankton Recorder (CPR) surveys. In both previous data sets, the basic structure of GO ascent from the central basin and G1 recruitment around the fringes was a robust feature, suggesting that it is a recurrent phenomenon. The Irminger Sea is a complex mixing zone between polar and Atlantic water masses, and it has also been identified as a site of sporadic deep convection. The physical oceanographic characteristics of the region are therefore potentially sensitive to climate fluctuations. Despite this, the abundance of C finmarchicus in the region, as measured by the CPR surveys, appears not to have responded to climate factors linked to the North Atlantic Oscillation Index, in contrast with the stocks in eastern Atlantic areas. We speculate that this may because biological factors (production and mortality), rather than transport processes are the key factors affecting the population dynamics in the Irminger Sea. (c) 2007 Elsevier Ltd. All rights reserved.

Macrophysiology of Calanus finmarchicus in the North Atlantic Ocean

Copepods represent the major part of the dry weight of the mesozooplankton in pelagic ecosystems and therefore have a central role in the secondary production of the North Atlantic Ocean. The calanoid copepod species Calanus finmarchicus is the main large copepod in subarctic waters of the North Atlantic, dominating the dry weight of the mesozooplankton in regions such as the northern North Sea and the Norwegian Sea. The objective of this work was to investigate the relationships between both the fundamental and realised niches of C. finmarchicus in order to better understand the future influence of global climate change on the abundance, the spatial distribution and the phenology of this key-structural species. Based on standardised Principal Component Analyses (PCAs), a macroecological approach was applied to determine factors affecting the spatial distribution of C. finmarchicus and to characterise its realised niche. Second, an ecophysiological model was used to calculate the Potential Egg Production Rate (PEPR) of C. finmarchicus and the centre of its fundamental niche. Relationships between the two niches were then investigated by correlation analysis. We found a close relationship between the fundamental and realised niches of C. finmarchicus at spatial, monthly and decadal scales. While the species is at the centre of its niche in the subarctic gyre, our joint macroecological and macrophysiological analyses show that it is at the edge of its niche in the North Sea, making the species in this region more vulnerable to temperature changes.

Transmission electron microscopy of marine crustacean eggs

Ultrastructural investigations of eggs can be important in helping to understand embryonic development. There are few transmission electron microscope studies of marine arthropod eggs, however, as they have proved difficult to fix and infiltrate with resin. Here, we describe a modification of a standard method that allows the preparation of the quite different eggs of the marine copepod, Acartia tonsa and the lobster, Homarus gammarus, for transmission electron microscopy. By using double fixation and an extended resin infiltration time we obtained good preparations for electron microscopy. We anticipate that these modifications to the standard protocol will be widely applicable and useful for the study of the eggs and early developmental stages of many marine arthropod taxa. Les recherches sur l'ultrastructure des oeufs peuvent être importantes en aidant à comprendre le développement embryonnaire. Il existe cependant peu d'études en microscopie électronique à transmission sur les oeufs d'arthropodes marins, car il est difficile de les fixer et d'y infiltrer de la résine. Dans ce travail, nous décrivons une modification de la méthode standard, qui permet la préparation pour la microscopie électronique à transmission d'oeufs aussi différents que ceux du copépode marin Acartia tonsa et du homard Homarus gammarus. En utilisant une double fixation et un temps plus long d'infiltration de la résine, nous avons obtenu de bonnes préparations pour la microscopie électronique. Nous prévoyons que ces modifications du protocole standard seront largement applicables et utiles pour l'étude des oeufs et des premiers stades de développement de nombreux taxons d'arthropodes marins.

Update on the relationship between the North Atlantic Oscillation and Calanus finmarchicus

The relationship between climate, represented by the North Atlantic Oscillation (NAO), and the calanoid copepod Calanus finmarchicus has been extensively studied. The correlation between NAO and C. finmarchicus has broken down (post-1995). In the present study, we revisit the relationship between C. finmarchicus and the NAO. Our reanalysis shows that previous treatment of this data did not take into account 2 aspects of both the C. finmarchicus and NAO index time-series: (1) the presence of significant trends and (2) significant autocorrelation. Our analysis suggests that previously reported relationships between NAO and C. finmarchicus abundance can be explained largely by the trends in both data series. Removing the trend from both time-series resulted in a decrease in the amount of C. finmarchicus abundance variability explained by the NAO. Trend removal eliminated the autocorrelation from the NAO time-series, but not from the C. finmarchicus time-series. Partial autocorrelation analysis showed that the autocorrelation present in the C. finmarchicus time-series is only found at a lag of 1 yr, suggesting strong, year-to-year connectivity in this population. We included the lagged C. finmarchicus abundance into a regression with the NAO and found that C. finmarchicus variability is explained by the previous year’s abundance and, to a much smaller extent, by NAO variability. Limiting the time-series to the most recent 22 yr period (1981 to 2002) showed that the NAO is no longer correlated to C. finmarchicus abundance, and the autocorrelation in the C. finmarchicus abundance series also appears to be weakening.

Basin scale distribution of zooplankton in the Ligurian Sea (north-western Mediterranean) in late autumn

Mesozooplankton biomass and abundance were evaluated in epipelagic waters at 59 stations covering the Italian sector of the Ligurian Sea (north-western Mediterranean) in December 1990. This region is characterised by a cyclonic circulation which encloses a central divergence zone and is associated with a main thermohaline front offshore the western Ligurian coast. At the end of autumn, mesozooplankton biomass (range: 0.80–4.24 mg DW m−3) and the abundance (range: 83.8–932 ind. m−3) were lower in the divergence zone. On the contrary, in the Ligurian frontal zone at the periphery of the divergence and on the eastern continental shelf the greatest values of biomass and abundance were recorded. Copepods and appendicularians dominated the mesozooplankton community, the main taxa being the copepods Clausocalanus spp. (46% of total zooplankton) and Oithona spp. (15%) and the appendicularian Fritillaria spp. (12%). Three hydrological sub-regions, i.e. the divergence, the eastern continental shelf and the periphery of the divergence, were characterised by different zooplankton communities and characteristic species. Environmental differences between the three zones were mainly related to changes in bottom topography, sea surface temperatures and quantity of particulate organic matter. Vertical mesozooplankton abundance and taxa distribution from the surface to 1,900 m depth were also examined in one station. The results showed that the bulk of the community was concentrated in the upper 200 m, small copepods being dominant particularly in the upper 50 m. The copepod community was more diversified in sub-superficial waters, with a maximum observed in the 200–400 m layer. The distributions of main zooplankton taxa described in epipelagic waters in the eastern Ligurian Sea in autumn were compared with their distribution at surface in the north-western Mediterranean obtained by sampling performed with the Continuous Plankton Recorder in 1997–1999. The analysis of the zooplankton community in CPR samples confirms the dominance of small copepods (Paracalanus spp., Clausocalanus spp., Oithona spp.) and appendicularians in the north-western Mediterranean in late autumn-winter and shows that their distribution is mainly related to the main mesoscale hydrographic features characterising this basin.

The mid-eighties regime shift and appendicularian abundance

There is accumulating evidence suggesting that a regime shift occurred in the North Atlantic during the mid-eighties. This shift has been reported primarily from Continuous Plankton Recorder (CPR) data as a stepwise change in plankton abundance and copepod community structure. Here we analyse the CPR data for appendicularian abundance to show that a similar stepwise increase occurred in the abundance of appendicularians during the mid-eighties. Furthermore, we compare these results to data recorded by other zooplankton time series programmes to show that a similar abrupt increase in appendicularian abundance during the mid-early eighties has also been recorded in other areas. The fact that such a change occurred at locations so distant apart as Helgoland Roads in the North Sea or the White Sea in the Arctic suggests that these changes have a global origin. The strong dependence of appendicularian phenology with temperature points out to direct links to global climate change.

Effects on zooplankton of a warmer ocean: Recent evidence from the Northeast Pacific

The consequences for pelagic communities of warming trends in mid and high latitude ocean regions could be substantial, but their magnitude and trajectory are not yet known. Environmental changes predicted by climate models (and beginning to be confirmed by observations) include warming and freshening of the upper ocean and reduction in the extent and duration of ice cover. One way to evaluate response scenarios is by comparing how "similar" zooplankton communities have differed among years and/or locations with differing temperature. The subarctic Pacific is a strong candidate for such comparisons, because the same mix of zooplankton species dominates over a wide range of temperature climatologies, and observations have spanned substantial temperature variability at interannual-to-decadal time scales. In this paper, we review and extend copepod abundance and phenology time series from net tow and Continuous Plankton Recorder surveys in the subarctic Northeast Pacific. The two strongest responses we have observed are latitudinal shifts in centers of abundance of many species (poleward under warm conditions), and changes in the life cycle timing of Neocalanus plumchrus in both oceanic and coastal regions (earlier by several weeks in warm years and at warmer locations). These zooplankton data, plus indices of higher trophic level responses such as reproduction, growth and survival of pelagic fish and seabirds, are all moderately-to-strongly intercorrelated (vertical bar r vertical bar = 0.25-0.8) with indices of local and basin-scale temperature anomalies. A principal components analysis of the normalized anomaly time series from 1979 to 2004 shows that a single "warm-and-low-productivity" vs. "cool-and-high-productivity" component axis accounts for over half of the variance/covariance. Prior to 1990, the scores for this component were negative ("cool" and "productive") or near zero except positive in the El Nino years 1983 and 1987. The scores were strongly and increasingly positive ("warm" and "low productivity") from 1992 to 1998; negative from 1999 to 2002; and again increasingly positive from 2003-present. We suggest that, in strongly seasonal environments, anomalously high temperature may provide misleading environmental cues that contribute to timing mismatch between life history events and the more-nearly-fixed seasonality of insolation, stratification, and food supply. Crown Copyright (c) 2007 Published by Elsevier Ltd. All rights reserved.

Zooplankton response to a warmer northern Wadden Sea

Weekly measurements of mesozooplankton (>76 mu m) and hydrographic parameters have been carried out since 1984 in the List Tidal Basin (northern Wadden Sea). Monthly water temperature significantly increased by 0.04 degrees C year. The largest increase by 3 degrees C in 22 years occurred in September, implying, an extension of the warm summer period. Mean annual copepod abundance and length of copepod season correlated significantly with mean temperature from January to May. Except for an increasing Acartia sp. abundance during spring (April-May), no longterm trends in copepod abundance were observed. The percentage of carnivorous zooplankton increased significantly since 1984 mainly due to a sudden increase in the cyclopoid copepod Oithona similis in 1997. We expect that global warming will lead to a longer copepod season and higher copepod abundances in the northern Wadden Sea.

Variation among northeast Atlantic regions in the responses of zooplankton to climate change: Not all areas follow the same path

Broad scale climate forcing can interact with local environmental processes to affect the observed ecological phenomena. This causes potential problems of over-extrapolation for results from a limited number of sites or the averaging out of region-specific responses if data from too wide an area are combined. In this study, an area similar in extent to the Celtic Biscay Large Marine Ecosystem, but including off-shelf areas, was partitioned using clustering of satellite chlorophyll (chl-a) measurements. The resulting clusters were used to define areas over which to combine copepod data from the Continuous Plankton Recorder. Following filtering due to data limitations, nine regions were defined with sufficient records for analysis. These regions were consistent with known oceanographic structure in the study area. Off-shelf regions showed a progressively later timing in the seasonal peak of chl-a measurements moving northwards. Generalised additive models were used to estimate seasonal and multiannual signals in the adult and juvenile stages of Calanus finmarchicus, C. helgolandicus and the Paracalanus–Pseudocalanus group. Associations between variables (sea surface temperature (SST), phenology and annual abundance) differed among taxonomic groups, but even within taxonomic groups, relationships were not consistent across regions. For example, in the deep waters off Spain and Portugal the annual abundance of Calanus finmarchicus has a weak positive association with SST, in contrast to the pattern in most other regions. The regions defined in this study provide an objective basis for investigations into the long term dynamics of plankton populations and suggest suitable sub regions for deriving pelagic system indicators.

Mediterranean marine copepods: basin-scale trends of the calanoid Centropages typicus

The Mediterranean Sea is located in a crossroad of mid-latitude and subtropical climatic modes that enhance contrasting environmental conditions over both latitudinal and longitudinal ranges. Here, we show that the large-scale environmental forcing is reflected in the basin scale trends of the adult population of the calanoid copepod Centropages typicus. The species is distributed over the whole Mediterranean basin, and maximal abundances were found in the north-western basin associated to oceanic fronts, and in the Adriatic Sea associated to shallow and semi enclosed waters. The peak of main abundances of C. typicus correlates with the latitudinal temperature gradient and the highest seasonal abundances occurred in spring within the 14–18°C temperature window. Such thermal cline may define the latitudinal geographic region where C. typicus seasonally dominates the >200 μm-sized spring copepod community in the Mediterranean Sea. The approach used here is generally applicable to investigate the large-scale spatial patterns of other planktonic organisms and to identify favourable environmental windows for population development.

Spatio-Temporal Variability of the North Sea Cod Recruitment in Relation to Temperature and Zooplankton

The North Sea cod (Gadus morhua, L.) stock has continuously declined over the past four decades linked with overfishing and climate change. Changes in stock structure due to overfishing have made the stock largely dependent on its recruitment success, which greatly relies on environmental conditions. Here we focus on the spatio-temporal variability of cod recruitment in an effort to detect changes during the critical early life stages. Using International Bottom Trawl Survey (IBTS) data from 1974 to 2011, a major spatio-temporal change in the distribution of cod recruits was identified in the late 1990s, characterized by a pronounced decrease in the central and southeastern North Sea stock. Other minor spatial changes were also recorded in the mid-1980s and early 1990s. We tested whether the observed changes in recruits distribution could be related with direct (i.e. temperature) and/or indirect (i.e. changes in the quantity and quality of zooplankton prey) effects of climate variability. The analyses were based on spatially-resolved time series, i.e. sea surface temperature (SST) from the Hadley Center and zooplankton records from the Continuous Plankton Recorder Survey. We showed that spring SST increase was the main driver for the most recent decrease in cod recruitment. The late 1990s were also characterized by relatively low total zooplankton biomass, particularly of energy-rich zooplankton such as the copepod Calanus finmarchicus, which have further contributed to the decline of North Sea cod recruitment. Long-term spatially-resolved observations were used to produce regional distribution models that could further be used to predict the abundance of North Sea cod recruits based on temperature and zooplankton food availability.

Pattern and scale of variability among Northwest Atlantic Shelf plankton communities

Continuous plankton recorders (CPRs) have been used in the Northwest Atlantic for almost 50 years. While data collected by these surveys have provided valuable information on long-term variability in plankton populations, all previous analyses have been limited to only a portion of the geographic range of the available data. Here we present an analysis of the CPR data from the Mid Atlantic Bight to the Labrador Sea. Across this wide geographic range, we found many common associations among the taxa. In particular, the changes in most regions were strongly size structured, with small and medium copepods varying together and often positively related to indicators of phytoplankton abundance. The time series from nearby regions were strongly correlated; however, after 1990, the spatial pattern became more complex. During this period, several of the copepod taxa, noticeably Calanus finmarchicus and Centropages typicus, experienced a series of anomalies that appeared to propagate from northeast to southwest. Although the direction of propagation was consistent with the shelf circulation, the anomalies propagated at a rate much slower than typical current speeds. The timing of the copepod anomalies and their phase speed were similar in character to observed changes in salinity and the position of the Shelf Slope Front. The correspondence between the changes in the plankton community and changes in the physical environmental suggests that physical conditions are a strong driver of interannual variability in Northwest Atlantic Shelf ecosystems.

Comparison of Zooplankton Sampling Performance of Longhurst-Hardy Plankton Recorder and Bongo Nets

Data on the abundance and biomass of zooplankton off the northwestern Portuguese coast, separately estimated with a Longhurst-Hardy Plankton Recorder (LHPR) and a Bongo net, were analysed to assess the comparative performance of the samplers. Zooplankton was collected along four transects perpendicular to the coast, deployments alternating between samplers. Total zooplankton biomass measured using the LHPR was significantly higher than that using the Bongo net. Apart from Appendicularia and Cladocera, abundances of other taxa (Copepoda, Mysidacea, Euphausiacea, Decapoda larvae, Amphipoda, Siphonophora, Hydromedusae, Chaetognatha and Fish eggs) were also consistently higher in the LHPR. Some of these differences were probably due to avoidance by the zooplankton of the Bongo net. This was supported by a comparative analysis of prosome length of the copepod Calanus helgolandicus sampled by the two nets that showed that Calanus in the LHPR samples were on average significantly larger, particularly in day samples. A ratio estimator was used to produce a factor to convert Bongo net biomass and abundance estimates to equate them with those taken with the LHPR. This method demonstrates how results from complementary zooplankton sampling strategies can be made more equivalent.