A new procedure to optimize the selection of groups in a classification tree: Applications for ecological data

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.     

Changes in pH as a measure of photosynthesis by marine macroalgae

An automatically operated method for high precision measurements of steady-state photosynthesis by macroalgae was developed. Changes in pH and oxygen content of seawater passing the algae in a flowthrough system, could be measured with extremely high accuracy over very long periods of time. The method is especially suitable for measurements on flowthrough systems with high rates of water exchanges (i.e. short retention time), and can be used to study exchange processes for marine plants, animals and small ecosystems. Since the same measuring unit is used for several flowthrough chambers, the method is very suitable for comparisons between different species, or between differently pretreated specimens of the same species (e.g. in toxicological studies). The method was used to study the ratio: [oxygen production] to [CO₂+H⁺ uptake] at different light intensities for several macroalgae belonging to different systematic groups and from different habitats. At lower photosynthetic rates this ratio was similar for all of the algae studied (1.17±0.02). For brown algae of the fucacean family, the ratio increased by 0.08 units at higher photosynthetic rates. This increase was thought to be related to the crassulacean acid metabolism (CAM)-like strategies connected to these algae. For all other algae studied, the ratio remained constant or decreased slightly (at most by 0.04 units) at higher photosynthetic rates. The relations between the abovementioned ratio and the photosynthetic quotient are discussed on a theoretical basis.     

Interactions between nutritional status and long-term responses to ultraviolet-B radiation stress in a marine diatom

Influences of nutritional status on the photoinhibitory effects of ultraviolet-B radiation (UVBR: 290 to 320 nm) on the specific growth rates (_obs) and biomass of Phaeodactylum tricornutum were determined using nutrient-replete batch cultures and nutrient-limited continuous cultures. P. tricornutum cultures were exposed to UVBR doses representative of current mid-latitude and ozone-depletion intensities. Specific growth rates and biomass were inhibited from 2 to 16% by UVBR during nutrient-replete growth. However, no effect of UVBR on _obs or biomass was detectable when nutrient limitation exceeded the potential for limitation by UVBR. Thus, a competitive interaction appears to occur between macronutrient stress and UVBR stress, such that _obs and biomass will be determined by the most limiting factor. Our results suggest that measurable decreases in phytoplankton _obs and biomass from UVBR are most likely in nutrient-rich areas of the ocean, while these parameters may not be appropriate for measuring UVBR stress in regions of nutrient limitation.     

A flow-through system for field measurements of production by marine macroalgae

A continuous flow-through chamber for the in situ measurement of primary production in macrophytic algae (as exemplified by Ulva lactuca) is described. Rapid mixing occurred within the chamber independent of flow rate or amount of algal tissue, so that the complete-mix reactor model of sanitary engineering was closely approximated. Field experiments with the apparatus revealed a rapid response to short-term variations in production rate as well as a close correlation between production and changing light levels. The flowthrough apparatus was compared to a closed system (the traditional bell jar approach); when the water in the latter was mixed, the two methods gave similar results for incubations not longer than several hours. However, during longer incubations, the productivity in the static system was sometimes depressed, possibly due to nutrient depletion or to abnormally high levels of oxygen. Thus, the flow-through system permits reliable measurements of macroalgal production for periods of 12 h or longer.     

A new context-based approach to assess marine mammal behavioral responses to anthropogenic sounds

Acute effects of anthropogenic sounds on marine mammals, such as from military sonars, energy development, and offshore construction, have received considerable international attention from scientists, regulators, and industry. Moreover, there has been increasing recognition and concern about the potential chronic effects of human activities (e.g., shipping). It has been demonstrated that increases in human activity and background noise can alter habitats of marine animals and potentially mask communications for species that rely on sound to mate, feed, avoid predators, and navigate. Without exception, regulatory agencies required to assess and manage the effects of noise on marine mammals have addressed only the acute effects of noise on hearing and behavior. Furthermore, they have relied on a single exposure metric to assess acute effects: the absolute sound level received by the animal. There is compelling evidence that factors other than received sound level, including the activity state of animals exposed to different sounds, the nature and novelty of a sound, and spatial relations between sound source and receiving animals (i.e., the exposure context) strongly affect the probability of a behavioral response. A more comprehensive assessment method is needed that accounts for the fact that multiple contextual factors can affect how animals respond to both acute and chronic noise. We propose a three-part approach. The first includes measurement and evaluation of context-based behavioral responses of marine mammals exposed to various sounds. The second includes new assessment metrics that emphasize relative sound levels (i.e., ratio of signal to background noise and level above hearing threshold). The third considers the effects of chronic and acute noise exposure. All three aspects of sound exposure (context, relative sound level, and chronic noise) mediate behavioral response, and we suggest they be integrated into ecosystem-level management and the spatial planning of human offshore activities.     

Testing the field of dreams hypothesis: functional responses to urbanization and restoration in stream ecosystems

As catchments become increasingly urban, the streams that drain them become increasingly degraded. Urban streams are typically characterized by high-magnitude storm flows, homogeneous habitats, disconnected riparian zones, and elevated nitrogen concentrations. To reverse the degradation of urban water quality, watershed managers and regulators are increasingly turning to stream restoration approaches. By reshaping the channel and reconnecting the surface waters with their riparian zone, practitioners intend to enhance the natural nutrient retention capacity of the restored stream ecosystem. Despite the exponential growth in stream restoration projects and expenditures, there has been no evaluation to date of the efficacy of urban stream restoration projects in enhancing nitrogen retention or in altering the underlying ecosystem metabolism that controls instream nitrogen consumption. In this study, we compared ecosystem metabolism and nitrate uptake kinetics in four stream restoration projects within urban watersheds to ecosystem functions measured in four unrestored urban stream segments and four streams draining minimally impacted forested watersheds in central North Carolina, U.S.A. All 12 sites were surveyed in June through August of 2006 and again in January through March of 2007. We anticipated that urban streams would have enhanced rates of ecosystem metabolism and nitrate uptake relative to forested streams due to the increases in nutrient loads and temperature associated with urbanization, and we predicted that restored streams would have further enhanced rates for these ecosystem functions by virtue of their increased habitat heterogeneity and water residence times. Contrary to our predictions we found that stream metabolism did not differ between stream types in either season and that nitrate uptake kinetics were not different between stream types in the winter. During the summer, restored stream reaches had substantially higher rates of nitrate uptake than unrestored or forested stream reaches; however, we found that variation in stream temperature and canopy cover explained 80% of the variation across streams in nitrate uptake. Because the riparian trees are removed during the first stage of natural channel design projects, the restored streams in this study had significantly less canopy cover and higher summer temperatures than the urban and forested streams with which they were compared.     

Fatty acid composition of marine macroalgae from the Black Sea and Dardanelles

The fatty acid (FA) composition was determined in 14 species of marine macroalgae belonging to the Chlorophyta, Phaeophyta and Rhodophyta, which were collected from ?ile in the Black Sea and Kepez in the Dardanelles. Generally, polyunsaturated FAs and monounsaturated FAs were major components (50–77%). Total saturated FAs ranged from 22% to 50%, with 16?:?0 as the most abundant saturate (32–38%). Two samples of Cystoseira barbata collected from a different station had some differences from each other in their contents of 18?:?2n-6 and 18?:?3n-3 and in the 18?:?2n-6/20?:?4n-6 ratios. Green algal species had a significantly higher proportion of unsaturated FAs and a significantly lower proportion of saturated FAs than the red and brown algae. The amount of n-3 FAs was significantly higher in Ulva rigita, Chaetomorpha linum, Enteromorpha linza and Gracilaria verrucosa (8.88, 6.44, 5.31 and 5.24, respectively).     

Emerson enhancement effect and quantum yield of photosynthesis for marine macroalgae in simulated underwater light fields

The contribution of enhancement to the total photosynthesis of marine macroalgae in their natural habitats was estimated by comparing the photosynthesis measured by O₂-electrode in five broad-band light fields with that predicted (on the assumption that no enhancement was occurring) from the photosynthetic action spectrum of each plant and the spectral distribution of the light fields. The excess of measured values divided by calculated values provided a measure of enhancement. Although 37% enhancement was observed for red algae in unfiltered quartz-iodine light, and 18% for green and brown algae, substantially lower values were obtained for all species in more natural light fields. In those typical of shallow coastal waters, phycoerythrin-rich red algae exhibited 15 to 20% enhancement, but little enhancement (<5%) was detected in other algae. In a green light field, representing deep coastal water, there was no significant enhancement in any species, and only green and brown algae showed any enhancement (ca 8%) in broad-band blue light, similar to that in deep oceanic waters. Quantum yields of 0.09 to 0.10 O₂ molecules per absorbed photon were recorded in most light fields for green and brown algae with thin thalli, but yields decreased in the blue light field and in species with thicker thalli. All red algae had quantum yields of about 0.08 O₂ molecules per absorbed photon, except in the blue light field, in which quantum yields were reduced by 70%.     

Development of a new antifouling method for a marine cooling water system

Variations in meristic characters occur within and between samples of milkfish Chanos chanos (Forsskal) collected on June 1977 from five localities in Philippine waters. The unbranched anal and ventral fin rays are the most plastic, and vertebral number is the most stable of nine meristic characters examined. The number of ventral fin rays is the only meristic feature which differed consistently enough to suggest distinct population groups: South China Sea, comprising samples from Ilocos and Panay Island; Pacific Ocean from Bicol; and Celebes Sea, from Zamboanga and Davao. A discriminant analysis which incorporated generalized distance (Mahanalobis D²) and percent overlap of a reduced set of characters indicated several morphometric subgroups of milkfish in Philippine waters, although geographic subgroups were not clearly demonstrated.SEAFDEC Contribution No. 218     

Comments on optimizing the selection of the number of groups in a classification tree

In a recent issue of this journal Guidi et al. (2009) proposed a Random Simulation Test (RST) to assist with the determination of the optimal number of clusters to be extracted from a hierarchical classification tree. This short note illustrates the potential influence that the richness of a simulated new site has on the determination of the optimal level to cut the dendrogram. This is discussed in the context of the need for clear objectives and criteria against which a classification tree can be evaluated. A simple modification of the RST is proposed that the simulated new site of the matrix has an appropriate number of positive entries that lies within the range of the observed matrix. The impact of this modification is then evaluated using an ecological community site-by-species matrix.     

Physiological responses of Nodularia harveyana to osmotic stress

The effects of salinity stress on biomass yield, photosynthetic O₂ evolution and nitrogenase activity were investigated using axenic cultures of Nodularia harveyana (Thwaites) Thuret originally isolated from a salt marsh at Gibraltar Point, Lincolnshire, UK in 1971 and studied in this laboratory in 1983. Biomass yields, as chlorophyll a per culture, were highest in the 0 to 100% seawater (0 to 35 sea salt) range with negligible growth in 200% seawater; growth on NH ₄ ⁺ was greater than on N₂ and NO ₃ ^- , which did not differ significantly from each other. In short-term experiments, photosynthetic O₂ evolution remained high at salinities up to 150% seawater (52.5 sea salt); nitrogenase activity remained high at salinities up to 100% seawater (35 sea salt). The major internal low molecular weight carbohydrate which accumulated in response to increased salinity was sucrose, the levels of which fluctuated markedly and rapidly in response to salinity change.     

Collaborative assessment of California spiny lobster population and fishery responses to a marine reserve network

Assessments of the conservation and fisheries effects of marine reserves typically focus on single reserves where sampling occurs over narrow spatiotemporal scales. A strategy for broadening the collection and interpretation of data is collaborative fisheries research (CFR). Here we report results of a CFR program formed in part to test whether reserves at the Santa Barbara Channel Islands, USA, influenced lobster size and trap yield, and whether abundance changes in reserves led to spillover that influenced trap yield and effort distribution near reserve borders. Industry training of scientists allowed us to sample reserves with fishery relevant metrics that we compared with pre-reserve fishing records, a concurrent port sampling program, fishery effort patterns, the local ecological knowledge (LEK) of fishermen, and fishery-independent visual surveys of lobster abundance. After six years of reserve protection, there was a four- to eightfold increase in trap yield, a 5-10% increase in the mean size (carapace length) of legal sized lobsters, and larger size structure of lobsters trapped inside vs. outside of three replicate reserves. Patterns in trap data were corroborated by visual scuba surveys that indicated a four- to sixfold increase in lobster density inside reserves. Population increases within reserves did not lead to increased trap yields or effort concentrations (fishing the line) immediately outside reserve borders. The absence of these catch and effort trends, which are indicative of spillover, may be due to moderate total mortality (Z = 0.59 for legal sized lobsters outside reserves), which was estimated from analysis of growth and length frequency data collected as part of our CFR program. Spillover at the Channel Islands reserves may be occurring but at levels that are insufficient to influence the fishery dynamics that we measured. Future increases in fishing effort (outside reserves) and lobster biomass (inside reserves) are likely and may lead to increased spillover, and CFR provides an ideal platform for continued assessment of fishery-reserve interactions.     

Physiological responses of Cladophora glomerata to cyanotoxins: a potential new phytoremediation species for the Green Liver Systems

Due to increased pollution of potable water sources as a consequence of eutrophication and anthropogenic xenobiotics, sustainable water purification is an essential concern. Therefore, the Green Liver System, a natural, economic and sustainable water purification system employing the biotransformation capabilities of aquatic plants, was developed. To expand the capacities and applications of this system, new aquatic plants are continually evaluated for their potential to remediate various aquatic pollutants. In this study, the potential of Cladophora glomerata to internalize cyanotoxins, microcystins (MCs) and anatoxin-a, and consequently its ability to cope with the subsequent oxidative stress associated with toxin-uptake were investigated. C. glomerata was able to take up all three of the tested MC congeners as well as anatoxin-a, similarly to previous toxin internalizations reported for aquatic plants such as Ceratophyllum demersum, Myriophyllum spicatum and Hydrilla versiculata. The antioxidative stress defense of C. glomerata proved to efficiently endure the toxin-uptake with no adverse effects. Subsequently, the uptake potential of C. glomerata was investigated at lab-scale by exposure to the three MC congeners and anatoxin-a collectively. After a period of seven days, 95–97% of the MCs and 100% of anatoxin-a were removed from the exposure media. C. glomerata therefore, is a suitable candidate to be incorporated in future Green Liver Systems.     

Variability in grazer-mediated defensive responses of green and red macroalgae on the south coast of South Africa

Variabilities in the responses of several South African red and green macroalgae to direct grazing and the responses of one green alga to cues from grazers were tested. We used two feeding experiments: (1) testing the induced responses of three red and one green algae to direct grazing by mesograzers and (2) a multi-treatment experiment, in which the direct and indirect effects of one macrograzer species on the green alga Codium platylobium were assessed. Consumption rates were assessed in feeding assays with intact algal pieces and with agar pellets containing non-polar extracts of the test algae. Defensive responses were induced for intact pieces of Galaxaura diessingiana, but were not induced in pellets, suggesting either morphological defence or chemical defence using polar compounds other than polyphenols. In contrast, exposure to grazing stimulated consumption of Gracilaria capensis and Hypnea spicifera by another grazing species. In the multi-treatment experiment, waterborne cues from both grazing and non-grazing snails induced defensive algal traits in C. platylobium. We suggest that inducible defences among macroalgae are not restricted to brown algae, but that both the responses of algae to grazers and of grazers to the defences of macroalgae are intrinsically variable and complex.     

Behavioural responses of the marine bivalve Macomona liliana exposed to copper- and chlordane-dosed sediments

Sublethal behavioural responses including avoidance and burial rate were compared with 10 d acute morbidity and mortality in bioassays using juvenile Macomona liliana 1 to 3 mm long. The bivalves showed significant movement away from all copper-dosed sediments, with maximal movement after 96 h at 25 mg Cu kg (dry wt)^-1. Increasing copper concentrations slowed the rate of burial, and above 15 mg Cu kg (dry wt)^-1, most shellfish failed to bury after 90 min. After 10 d exposure, morbidity (defined as inability to rebury) occurred at 15 mg Cu kg (dry wt)^-1 and mortality at 30 mg Cu kg (dry wt)^-1. In avoidance trials, chlordane had a significant effect on overall movement from 20 g kg (dry wt)^-1, but increasing concentrations reduced movement away from dosed sediment. Chlordance appeared to have no effect on burial rate. Survival was affected by 10 d exposure to 400 g chlordane kg (dry wt)^-1, with increased morbidity and death. The relative sensitivities of the responses shown by M. liliana to copper were avoidance > burial/morbidity > mortality, with a 6-fold difference in the response threshold between avoidance and mortality. With chlordance, an avoidance response was detected at a concentration 20-fold lower than that causing morbidity. Behavioural responses of M. liliana have the potential to provide a sensitive bioassay.     

Testing the presence of marine protected areas against their ability to reduce pressures on biodiversity

Marine protected areas (MPAs) are the preferred tool for preventing marine biodiversity loss, as reflected in international protected area targets. Although the area covered by MPAs is expanding, there is a concern that opposition from resource users is driving them into already low-use locations, whereas high-pressure areas remain unprotected, which has serious implications for biodiversity conservation. We tested the spatial relationships between different human-induced pressures on marine biodiversity and global MPAs. We used global, modeled pressure data and the World Database on Protected Areas to calculate the levels of 15 different human-induced pressures inside and outside the world's MPAs. We fitted binomial generalized linear models to the data to determine whether each pressure had a positive or negative effect on the likelihood of an area being protected and whether this effect changed with different categories of protection. Pelagic and artisanal fishing, shipping, and introductions of invasive species by ships had a negative relationship with protection, and this relationship persisted under even the least restrictive categories of protection (e.g., protected areas classified as category VI under the International Union for Conservation of Nature, a category that permits sustainable use). In contrast, pressures from dispersed, diffusive sources (e.g., pollution and ocean acidification) had positive relationships with protection. Our results showed that MPAs are systematically established in areas where there is low political opposition, limiting the capacity of existing MPAs to manage key drivers of biodiversity loss. We suggest that conservation efforts focus on biodiversity outcomes and effective reduction of pressures rather than prescribing area-based targets, and that alternative approaches to conservation are needed in areas where protection is not feasible.     

Standing crops and vertical distribution of four groups of marine planktonic ciliates in relation to phytoplankton chlorophyll a

Standing crops and the vertical distribution of four groups of ciliates, autotrophic naked ciliates (ANC), heterotrophic naked ciliates (HNC ), mixotrophic naked ciliates (MNC) and loricated ciliates (LC ), were analysed in relation to phytoplankton chlorophyll a in the western Pacific. Data were gathered from the upper 60 to 200 m of water in the subarctic North Pacific in spring, in the subtropical North Pacific in spring, in Toyama Bay in summer, off eastern Australia in spring and off Sanriku in spring and fall. Of the four groups, the standing crop of HNC (cells l⁻¹) showed the highest correlation to phytoplankton chloro- phyll a [CHL, μg l⁻¹; r=0.66, n=365 (HNC=490 ×CHL ^0.653)]. Depths of the maximum layers of HNC and MNC were usually shallower than that of chlorophyll a, while those of ANC and LC occurred frequently beneath the chlorophyll maximum layer. This indicates that these four ciliate groups are substantially different from each other, and that each group holds a different ecological position in the marine microbial food web. Received: 27 October 1997 / Accepted: 27 June 1998     

Chlorophyll a fluorescence in marine centric diatoms: Responses of chloroplasts to light and nutrient stress

Observations at sea of large variations in the cellular fluorescence of phytoplankton prompted a study of the fluorescence responses in marine diatoms to light and nutrient stress. When older cultures of Lauderia borealis were exposed to intense light, the in vivo fluorescence of chlorophyll a declined within the first 2 min of exposure. This initial response to light stress appeared to be correlated with a contraction of the chloroplasts. Continued exposure led to a second decline in fluorescence, which required 30 to 60 min for completion. A movement of chloroplasts to the valvar ends of the cell caused this secondary response. Both the contraction and intracellular movement of chloroplasts appeared to be related to both photoinhibition of photosynthesis and diel fluctuations in cellular fluorescence. An investigation of continuous cultures of Cyclotella nana showed that in vivo chlorophyll a fluoresced more strongly in nitrogen-starved cells than in enriched ones. Photoinhibition of cellular fluorescence also increased with the cell's state of nitrogen deficiency.     

Method for determination of turgor pressure in macroalgae,with particular reference to the Phaeophyta

A procedure is described for the determination of the internal osmotic pressure and turgor pressure of marine macroalgae, for use in the laboratory and on the shore. A volume-related parameter (either thallus fresh weight, or area) is measured before and after transfer of plant material to a range of hyperosmotic solutions. Plotting the final fresh weight/area as a percentage of the initial value gives a biphasic curve, with an initial component of negative slope due to the change in thallus volume in less extreme hyperosmotic solutions, where the non-rigid thallus contracts in response to decreasing cell turgor pressure. The second component has a shallower slope and represents plasmolysis in more extreme hyperosmotic solutions, i.e., where turgor pressure is reduced to zero and the protoplast shrinks away from the cell wall; the extraprotoplast space created by plasmolysis will be filled with the external solution and thus no further changes in weight occur. These two components intersect at the lowest osmotic pressure at which cell turgor is zero. By correcting for any effects of the cell wall on thallus volume, the relationship can be used to calculate internal osmotic pressure and hence turgor pressure, assuming that the remaining change in thallus volume of the initial component is due entirely to variation in the intraprotoplast volume (approximately equivalent to the intraprotoplast water content, determined by subtraction of the extraprotoplast water and dry weight from the thallus fresh weight). Using this procedure, the turgor pressures of Fucus spiralis L., Ectocarpus siliculosus, (Dillw.) Lyngb. and Laminaria digitata (Huds.) Lamour. (from Fife Ness, Scotland, May–August 1987) in a seawater-based medium were 0.82, 0.58 and 1.34 Osmol kg^–1, respectively. The turgor pressure of F. spiralis on the shore at Fife Ness (June 1987) was 0.74 Osmol kg^–1.