Abundance of copepods from multinet samples during POLARSTERN cruise ANT-XX/1

Abundance and species composition of copepods were studied during the expedition ANT XXI/1 on a latitudinal transect in the eastern Atlantic from 34°49.5' N to 27°28.1' S between 2-20 November 2002. Stratified zooplankton tows were carried out at 19 stations with a multiple opening-closing net between 300 m water depth and the surface. Cyclopoid and calanoid copepods showed similar patterns of distribution and abundance. Oithona was the most abundant cyclopoid genus, followed by Oncaea. A total of 149 calanoid copepod species were identified. Clausocalanus was by far the most abundant genus, comprising on average about 45% of all calanoids, followed by Calocalanus (13%), Delibus (9%), Paracalanus (6%), and Pleuromamma (5%). All other genera comprised on average less than 5% each, with 40 genera less than 1%. The calanoid copepod communities were distinguished broadly in accordance with sea surface temperature, separating the subtropical from the tropical stations, and were largely determined by variation in species composition and species abundance. Nine Clausocalanus species were identified. The most numerous Clausocalanus species was C. furcatus, which on average comprised half of all adult of this genus. C. pergens, C. paululus, and C. jobei, contributed an average of 19%, 9%, and 9%, respectively. The Clausocalanus species differed markedly in their horizontal and vertical distributions: C. furcatus, C. jobei, and C. mastigophorus had widespread distributions and inhabited the upper water layers. Major differences between the species were found in abundance. C. paululus and C. arcuicornis were biantitropical and were absent or occurred in very low numbers in the equatorial zone. C. parapergens was found at all stations and showed a bimodal distribution pattern with maxima in the subtropics. C. pergens occurred in higher numbers only at the southern stations, where it replaced C. furcatus in dominance. In contrast to the widespread species, the bulk of the C. paululus, C. arcuicornis, C. parapergens, and C. pergens populations was concentrated in the colder, deeper water layers below the thermocline, thereby avoiding the warm surface waters. C. lividus was found only at the most northern and C. ingens only at the most southern stations. Both species were found almost exclusively in the upper 50 m. The distinct differences in abundance and horizontal and vertical distribution suggest a strong ecological differentiation among the Clausocalanus species.

Assessing the relationship between patch type and soil mites: A molecular approach

An urgent need exists for indicators of soil health and patch functionality in extensive rangelands that can be measured efficiently and at low cost. Soil mites are candidate indicators, but their identification and handling is so specialised and time-consuming that their inclusion in routine monitoring is unlikely. The aim of this study was to measure the relationship between patch type and mite assemblages using a conventional approach. An additional aim was to determine if a molecular approach traditionally used for soil microbes could be adapted for soil mites to overcome some of the bottlenecks associated with soil fauna diversity assessment. Soil mite species abundance and diversity were measured using conventional ecological methods in soil from patches with perennial grass and litter cover (PGL), and compared to soil from bare patches with annual grasses and/or litter cover (BAL). Soil mite assemblages were also assessed using a molecular method called terminal-restriction fragment length polymorphism (T-RFLP) analysis. The conventional data showed a relationship between patch type and mite assemblage. The Prostigmata and Oribatida were well represented in the PGL sites, particularly the Aphelacaridae (Oribatida). For T-RFLP analysis, the mite community was represented by a series of DNA fragment lengths that reflected mite sequence diversity. The T-RFLP data showed a distinct difference in the mite assemblage between the patch types. Where possible, T-RFLP peaks were matched to mite families using a reference 18S rDNA database, and the Aphelacaridae prevalent in the conventional samples at PGL sites were identified, as were prostigmatids and oribatids. We identified limits to the T-RFLP approach and this included an inability to distinguish some species whose DNA sequences were similar. Despite these limitations, the data still showed a clear difference between sites, and the molecular taxonomic inferences also compared well with the conventional ecological data. The results from this study indicated that the T-RFLP approach was effective in measuring mite assemblages in this system. The power of this technique lies in the fact that species diversity and abundance data can be obtained quickly because of the time taken to process hundreds of samples, from soil DNA extraction to data output on the gene analyser, can be as little as 4 days.

Early recovery signs of an Australian grassland following the management of Parthenium hysterophorus L

Parthenium weed (Parthenium hysterophorus L.) is believed to reduce the above- and below-ground plant species diversity and the above-ground productivity in several ecosystems. We quantified the impact of this invasive weed upon species diversity in an Australian grassland and assessed the resulting shifts in plant community composition following management using two traditional approaches. A baseline plant community survey, prior to management, showed that the above-ground community was dominated by P. hysterophorus, stoloniferous grasses, with a further high frequency of species from Malvaceae, Chenopodiaceae and Amaranthaceae. In heavily invaded areas, P. hysterophorus abundance and biomass was found to negatively correlate with species diversity and native species abundance. Digitaria didactyla Willd. was present in high abundance when P. hysterophorus was not, with these two species, contributing most to the dissimilarity seen between areas. The application of selective broad leaf weed herbicides significantly reduced P. hysterophorus biomass under ungrazed conditions, but this management did not yet result in an increase in species diversity. In the above-ground community, P. hysterophorus was partly replaced by the introduced grass species Cynodon dactylon L. (Pers.) 1 year after management began, increasing the above-ground forage biomass production, while D. didactyla replaced P. hysterophorus in the below-ground community. This improvement in forage availability continued to strengthen over the time of the study resulting in a total increase of 80% after 2 years in the ungrazed treatment, demonstrating the stress that grazing was imposing upon this grassland-based agro-ecosystem and showing that it is necessary to remove grazing to obtain the best results from the chemical management approach.

Bayesian analysis of community dynamics

Elucidating the mechanisms responsible for the patterns of species abundance, diversity, and distribution within and across ecological systems is a fundamental research focus in ecology. Species abundance patterns are shaped in a convoluted way by interplays between inter-/intra-specific interactions, environmental forcing, demographic stochasticity, and dispersal. Comprehensive models and suitable inferential and computational tools for teasing out these different factors are quite limited, even though such tools are critically needed to guide the implementation of management and conservation strategies, the efficacy of which rests on a realistic evaluation of the underlying mechanisms. This is even more so in the prevailing context of concerns over climate change progress and its potential impacts on ecosystems. This thesis utilized the flexible hierarchical Bayesian modelling framework in combination with the computer intensive methods known as Markov chain Monte Carlo, to develop methodologies for identifying and evaluating the factors that control the structure and dynamics of ecological communities. These methodologies were used to analyze data from a range of taxa: macro-moths (Lepidoptera), fish, crustaceans, birds, and rodents. Environmental stochasticity emerged as the most important driver of community dynamics, followed by density dependent regulation; the influence of inter-specific interactions on community-level variances was broadly minor. This thesis contributes to the understanding of the mechanisms underlying the structure and dynamics of ecological communities, by showing directly that environmental fluctuations rather than inter-specific competition dominate the dynamics of several systems. This finding emphasizes the need to better understand how species are affected by the environment and acknowledge species differences in their responses to environmental heterogeneity, if we are to effectively model and predict their dynamics (e.g. for management and conservation purposes). The thesis also proposes a model-based approach to integrating the niche and neutral perspectives on community structure and dynamics, making it possible for the relative importance of each category of factors to be evaluated in light of field data.

Integration of technologies for understanding the functional relationship between reef habitat and fish growth and production

Functional linkage between reef habitat quality and fish growth and production has remained elusive. Most current research is focused on correlative relationships between a general habitat type and presence/absence of a species, an index of species abundance, or species diversity. Such descriptive information largely ignores how reef attributes regulate reef fish abundance (density-dependent habitat selection), trophic interactions, and physiological performance (growth and condition). To determine the functional relationship between habitat quality, fish abundance, trophic interactions, and physiological performance, we are using an experimental reef system in the northeastern Gulf of Mexico where we apply advanced sensor and biochemical technologies. Our study site controls for reef attributes (size, cavity space, and reef mosaics) and focuses on the processes that regulate gag grouper (Mycteroperca microlepis) abundance, behavior and performance (growth and condition), and the availability of their pelagic prey. We combine mobile and fixed-active (fisheries) acoustics, passive acoustics, video cameras, and advanced biochemical techniques. Fisheries acoustics quantifies the abundance of pelagic prey fishes associated with the reefs and their behavior. Passive acoustics and video allow direct observation of gag and prey fish behavior and the acoustic environment, and provide a direct visual for the interpretation of fixed fisheries acoustics measurements. New application of biochemical techniques, such as Electron Transport System (ETS) assay, allow the in situ measurement of metabolic expenditure of gag and relates this back to reef attributes, gag behavior, and prey fish availability. Here, we provide an overview of our integrated technological approach for understanding and quantifying the functional relationship between reef habitat quality and one element of production – gag grouper growth on shallow coastal reefs.

The distribution and size composition of finfish, American lobster, and long-finned squid in Long Island Sound based on the Connecticut Fisheries Division Bottom Trawl Survey, 1984–1994

The distribution, abundance, and length composition of marine finfish, lobster, and squid in Long Island Sound were examined relative to season and physical features of the Sound, using Connecticut Department of Environmental Protection trawl survey data collected from 1984 to 1994. The following are presented: seasonal distribution maps for 59 species, abundance indices for 41 species, and length frequencies for 26 species. In addition, a broader view of habitat utilization in the Sound was examined by mapping aggregated catches (total catch per tow, demersal catch per tow, and pelagic catch per tow) and by comparing species richness and mean aggregate catch/tow by analysis of variance (ANOVA) among eight habitat types defined by depth interval and bottom type. For many individual species, seasonal migration patterns and preference for particular areas within Long Island Sound were evident. The aggregate distribution maps show that overall abundance was lower in the eastern Sound than the central and western portions. Demersal and pelagic temporal abundance show opposite trends—demersals were abundant in spring and declined through summer and fall, whereas pelagic abundance was low in spring and increased into fall. The analysis of habitat types revealed significant differences for both species richness and mean catch per tow. Generally, species richness was highest in habitats within the central area of the Sound and lowest in eastern habitats. The aggregate mean catch was highest in the western and central habitats, and declined eastward. (PDF file contains 199 pages.)

Development of a sampling expert system:"FISHMAP"

This research program consisted of three major component areas: (I) development of experimental design, (II) calibration of the trawl design, and (III) development of the foundation for stock assessment analysis. The products which have I. EXPERIMENTAL DESIGN resulted from - the program are indicated below: The study was successful in identifying spatial and temporal distribution characteristics of the several key species, and the relationships between given species catches and environmental and physical factors which are thought to influence species abundance by areas within the mainstem of the Chesapeake Bay and tributaries

Importance of shoreface sand ridges as habitat for fishes off the northeast coast of the United States

To determine if shoreface sand ridges provide unique habitats for fish on the inner continental shelf, two cross-shelf trawl surveys (23 km in length) were conducted in southern New Jersey (July and September 1991−95 with a beam trawl and July and September 1997−06 with an otter trawl) to assess whether species abundance, richness, and assemblages differed on and away from the ridge. The dominant species collected with both gears were from the families Paralichthyidae, Triglidae, Gobiidae, Serranidae, Engraulidae, Stromateidae, and Sciaenidae. Overall abundance (n=41,451 individuals) and species richness (n=61 species) were distributed bimodally across the nearshore to offshore transect, and the highest values were found on either side of the sand ridge regardless of gear type. Canonical correspondence analysis revealed three species assemblages: inshore (<5 meters depth), near-ridge (9−14 meters depth), and offshore (>14 meters depth), and variation in species composition between gear types. Environmental factors that corresponded with the assemblage changes included depth, temperature, distance from the top of the ridge, and habitat complexity. The most abundant near-ridge assemblages were distinct and included economically important species. Sand ridges of the inner continental shelf appear to be important habitat for a number of fish species and therefore may not be a suitable area for sand and gravel mining.

Effect of towing speed on retention of zooplankton in bongo nets

Long-term time series of zooplankton data provide invaluable information about the fluctuations of species abundance and the stability of marine community structure. These data have demonstrated that environmental variability have a profound effect on zooplankton communities across the Atlantic basin (Beaugrand et al., 2002; Frank et al., 2005; Pershing et al., 2005). The value of these time series increases as they lengthen, but so does the likelihood of changes in sampling or processing methods. Sam-pling zooplankton with nylon nets is highly selective and biased because of mesh selectivity, net avoidance, and damage to fragile organisms. One sampling parameter that must be standardized and closely monitored is the speed of the net through the water column. Tow speed should be as fast as possible to minimize net avoid-ance by the organisms, but not so fast as to damage soft bodied zooplankters or extrude them through the mesh (Tranter et al., 1968; Anderson and Warren, 1991).

A comparative survey of the fish populations of 10 West-Midlands meres of SSSI status

This is a comparative survey of the Fish Populations of 10 West-Midlands Mere of Site of Special Scientific Interest Status. The meres of the Shropshire-Cheshire plain (West Midlands) comprise over 60 water bodies. Water quality in the meres ranges from naturally eutrophic to nutrient limited and some of them have received Site of Special Scientific Interest status (SSSIs). This survey was commissioned in order to obtain quantitative information on the fish fauna of selected SSSIs and evaluate the likely impact of fish on other species within the community. The current survey was concerned with 10 of the West Midlands’ meres, a cross section of sites was selected. Sites were widely distributed from Marton Pool in the south-western part of Shropshire to Tabley moat in Chesire. Meres varied in size, depth and nutrient status. All were to be sampled using the methods outlined. The report is divided into different sections for clarity and ease of reference. The materials and methods section provides an outline of the location and status of each mere and information on known fish species present. The results were considered individually and comparatively, relative abundance of fish, species present, their diet, sex, age, parasite burdens and growth. Inter-site comparisons were made using information derived from echo-soundings, growth rate, diet, and species abundance for each site. The final section will be in the form of a general discussion, comparative information from longer term studies, conclusions and recommendations.

Biological survey: River Teign and tributaries with references to the discharge of ball clay wastes

This is the Biological survey of River Teign and tributaries with references to the discharge of ball clay wastes, document produced by South West Water Authority in 1973. This report focuses on on-site assessment of the benthic macro-invertebrates of the lower River Teign, River Bovey, Ugbrooke Stream and Blatchford Brook was undertaken on 19th and 22nd August 1977 to assess the effects of discharges from ball clay mining premises. Inspection of aquatic fauna in the field is of necessity, less extensive than laboratory identification of sorted samples, so that the resulting data underestimates the water quality. This is more pronounced in the Chandler Score than in the Trent Biotic Index which does not take account of species abundance. Chandler should thus be interpreted by the trends described rather than by absolute values calculated.

Coral reef ecosystems of St. John, U.S. Virgin Islands: spatial and temporal patterns in fish and benthic communities (2001-2009)

Scientific and anecdotal observations during recent decades have suggested that the structure and function of the coral reef ecosystems around St. John, U.S. Virgin Islands have been impacted adversely by a wide range of environmental stressors. Major stressors included the mass die-off of the long-spined sea urchin (Diadema antillarum) in the early 1980s, a series of hurricanes (David and Frederick in 1979, and Hugo in 1989), overfishing, mass mortality of Acropora species and other reef-building corals due to disease and several coral bleaching events. In response to these adverse impacts, the National Centers for Coastal Ocean Science (NCCOS), Center for Coastal Monitoring and Assessment, Biogeography Branch (CCMA-BB) collaborated with federal and territorial partners to characterize, monitor, and assess the status of the marine environment around the island from 2001 to 2012. This 13-year monitoring effort, known as the Caribbean Coral Reef Ecosystem Monitoring Project (CREM), was supported by the NOAA Coral Reef Conservation Program as part of their National Coral Reef Ecosystem Monitoring Program. This technical memorandum contains analysis of nine years of data (2001-2009) from in situ fish belt transect and benthic habitat quadrat surveys conducted in and around the Virgin Islands National Park (VIIS) and the Virgin Islands Coral Reef National Monument (VICR). The purpose of this document is to: 1) Quantify spatial patterns and temporal trends in (i) benthic habitat composition and (ii) fish species abundance, size structure, biomass, and diversity; 2) Provide maps showing the locations of biological surveys and broad-scale distributions of key fish and benthic species and assemblages; and 3) Compare benthic habitat composition and reef fish assemblages in areas under NPS jurisdiction with those in similar areas not managed by NPS (i.e., outside of the VIIS and VICR boundaries). This report provides key information to help the St. John management community and others understand the impacts of natural and man-made perturbations on coral reef and near-shore ecosystems. It also supports ecosystem-based management efforts to conserve the region’s coral reef and related fauna while maintaining the many goods and ecological services that they offer to society.

Description and growth of larval and pelagic juvenile pygmy rockfish (Sebastes wilsoni) (family Sebastidae)

A developmental series of larval and pelagic juvenile pygmy rockfish (Sebastes wilsoni) from central California is illustrated and described. Sebastes wilsoni is a non- commercially, but ecologically, important rockfish, and the ability to differentiate its young stages will aid researchers in population abundance studies. Pigment patterns, meristic characters, morphometric measurements, and head spination were recorded from specimens that ranged from 8.1 to 34.4 mm in standard length. Larvae were identified initially by meristic characters and the absence of ventral and lateral midline pigment. Pelagic juveniles developed a prominent pigment pattern of three body bars that did not extend to the ventral surface. Species identification was confirmed subsequently by using mitochondrial sequence data of four representative specimens of various sizes. As determined from the examination of otoliths, the growth rate of larval and pelagic juvenile pygmy rockfish was 0.28 mm/day, which is relatively slow in comparison to the growth rate of other species of Sebastes. These data will aid researchers in determining species abundance.

意大利威尼托（Veneto）的刺叶栎林-植物社会学生物多样性研究

刺叶栎( Quercus ilex L．)是地中海的常绿树种，属于古老的第三纪植物区系成份。本文根据苏黎世——蒙特利尔学派的植被学基本原理，全面地研究了分布在整个威尼托(Veneto)大区的剌叶栎林，详细研究刺叶栎林的群落组成、结构及类型划分。同时，对威尼托的刺叶栎林同北京山区的栎林进行了比较研究。最后，着重研究了威尼托刺叶栎林的生物多样性。 威尼托的刺叶栎林主要分布在亚得里亚海沿岸（包括Foci del Tagtiamento和Bosco Nordio e Rosolina Mare两地）、Lago di Garda和Colli Euganei。 在气候上，亚得里亚海沿岸属于半地中海气候。加尔达湖区域(Laqo di Garda)则是接近欧洲中部的大陆性气候，且维持半地中海的气候特点。Co t l i Euganei是这两地气候的过渡类型，且更接近亚得里亚海沿岸的类型。 在亚得里亚海沿岸的刺叶栎林可以分为三类，第一类(I)是一些矮树丛，这是Fraxinus ornus和Quercus ilex混交林的前身，较干旱。第二类群落(II)缺少乔木层，灌木层是由一些盖度不大的刺叶栎代替，更干旱。第三类群落(Ⅲ)是一群在外貌上相同的成熟群落．Fraxinus ornus和Quercus ilex得到充分发展，较中生。 在加尔达湖区的刺叶栎林可划分为三类。第一类群落(I)代表一组耐旱、开敞的矮树丛，含有Sesterio Variae-Ostryelum群丛的特征种，这一类可划分为SesLerio Variae-Ostryetum群 丛，土壤贫脊和干旱。第二类群落(Ⅱ)代表一类较郁闭的矮树丛，含有较多的Prunetalia群落目的成份，土壤较贫脊。第三类群(Ⅲ)代表一类郁闭的群落，乔木具有很大的密度因而林下灌木不能充分发展。SesLerio Variae-Ostryetum群丛和Prunetalia群落目的成份均不多。 在Colli Euganei的刺叶栎林可划分为二类。第一类群落(I)是一些不郁闲的矮树林组成。大体上分为地中海旱生栎林和地中海假灌丛。第二类群落(II)代表了较中生状态的植被，刺叶标种群绝对郁闭。 北京地处华北大平原的西北部。北京山地的气候为温带陆地性季风气候，其地带性的落叶阔叶林是以栎林为典型。虽然这些栎林同意大利威尼托刺叶栎林是两种不同的森林类型，但两者之间是存在着一定的联系。其共有的科有20个，共有属有11个。他们在植物组成中，以禾本科，蔷薇科和豆科的植物种类为最多。在乔木层中，他们都是以壳斗科的栎属(Quercus)为优势，其中木犀科的白蜡属(Fraxinus)和槭树属(Acer)较多。 本文对威尼托大区刺叶栎林的物种多度分布格局进行了全面探讨，计算出刺叶栎林的几何分布模型、Broken-stick分布模型、Log分布模型、Log-normat分布模型等四种物种多度分布的理论模型，并将这些理论分布模型用“序列／多度”图解和“多度／频度”图解表示出来。其中，几何分布模型．Broken-stick1分布模型用“序列／多度”图解表示。Broken-stick2分布模型、Log分布模型、Log-normal分布模型用“多度／频度”图解表示。 对上述四个物种多度的理论分布同实际现察的物种多度分布进行X2分析，在5％的显著性水平上，对整个威托大区的刺叶 栎林，几何分布模型最能代表其物种多度分布，显著性最大;Log-normal分布模型也可以用来代表威尼托刺叶标妹的物种多度分布，其显著性次于几何分布模型的显著性。这表明威尼托的刺叶栎林尚处于演替的早期阶段，这些刺叶栎林曾受到严重破坏，现正在恢复。 通过比较Foci del Tagtiamento和Bosco Nordio加尔达湖区、Colli Euganei四个地方刺叶栎林的物种多度的几何分布模型和Log-normal分布模型，显示出Lago di Garda（加尔达湖区）的刺叶栎林生物多样性最好、Foci del Tagtiamento刺叶栎林生物多样性较好．Bosco Nordio的剌叶栎林生物多样性较差．Colli Euganei的刺叶栎林生物多样性最差。 再利用多样性指数计算全部威尼托大区剌叶栎林的生物多样性。计算的多样性指数有丰富度指数（包括Margalef指数、Men-hinick指数、Monk指数）、多样性指数(Shannon信息指数、Bri llouin个息指数、Gini指数、PIE指数、Mcintosh指数)、优势度指数(Berger-Parker指数、Simpson指数)、均一度指数(Pielou均一度指数、Brillouin均一度指数，PIE的V’均一度指数．PIE的V均一度指数，N2的V’均一度指数，N2的V均一度指数，Mclntosh均一度指数，Hill的F10均一度指数，Hill的E21均一度指数，Hill的F21的一度指数）。通过比较丰富度指数，多样性指数、均一度指数与优势度之间的关系，结果，Simpson优势度指数同Men-hinick物种丰富度指数、Shannon信息指数、Bril-louin信息指数、Pielou均一度指数，Brillouin均一度指数，Mcintosh均一度指数、PIE的V’均一度指数呈负相关关系，因此，上述生物多样性指数可以较好地反映威尼托大区刺叶栎林的生物多样性。反映出的结果是：加尔达湖区刺叶栎林生物多样性最好，Foci del Tagtiamento刺叶栎林生物多样性较好，Bosco Nordio的剌叶栎林生物多样性较差．Colli Euganei的刺叶栎林生物多样性最差。 生物多样性的研究显示出生物多样性同生境状况的密切联系。往往受人为干扰严重的群落生物多样性低、如Coli Euganei和亚得里亚海岸刺叶栋林;而受人为破坏较轻的群落其生物多样性高，如加尔达湖区刺叶栎。 生物多样性的研究还显示出生物多样性同群落演替的发展阶段密切相关，在群落演替初期，由于缺乏优势种，而又有大量物种侵入，物多样性相对较高。在群落演替中期，由于形成了一个或几个优势种，优势度的增加导致了生物多样性相对减低。如Foci del Tagtiamento刺叶栎林生物多样性高于Bosco Nordio刺叶栎林的生物多样性。到演替后期，随着更多物种的侵入，群落结构的复杂化、生物多样性又将逐步提高。