The use of species abundance estimates in marine benthic studies

The application of species abundance estimates, commonly used in terrestrial plant ecology, to marine benthic dredge data is advocated. Two possible scales were tested for their ability to measure adequately the structure of an assemblage by computing measures of evenness diversity McNaughton's dominance index, and Morisita's index of dispersion using both real counts obtained from grab samples and these counts transformed into the two respective abundance estimates. It is concluded that species abundance estimators, when applied to grab or dredge data result in significant savings in sample processing time with only a minimal loss of information about assemblage structure.     

Appearance and evolution of marine benthic communities in the Early Palaeozoic

The development of marine benthic communities in the Early Palaeozoic occurred mainly in the shallow water epicontinental seas. It included those stages of the Cambrian and Ordovician evolutionary radiations that were dominated by a high rate of morphogenesis, when new food and territory resources were not limited. This provided many opportunities for coadaptation of emerging organisms. At the time of the Cambrian radiation, the body plans of all animals were formed, while in the Ordovician, the maximum rank of emerging taxa did not exceed the level of class. The beginning of each radiation was explosive. Vendian benthic communities developed in cold seas and in the shallowest areas of warm seas, where organic matter from the surface layers was available at the bottom because of the absence of a thermocline. The Cambrian radiation began with the appearance of pelagic suspension feeders, because of which much of the primary production could penetrate the thermocline and settle at the bottom. This allowed the occupation of warmer seas and greater depths. At the same time, the productivity of the pelagic region sharply increased because of the emergence of positive feedback between the producers and consumers in the water, leading to increased water transparency and elongation of trophic chains. Arthropods, the first suspension feeders, were the launch group of the Cambrian radiation. Cambrian benthic suspension feeders could seize only the smallest particles, mostly bacteria, and dissolved organic matter. This food resource was contained in the thin bottom water layer. Therefore, the food grasping structures of all the Cambrian suspension feeders were near the bottom, without forming tiers. The Ordovician evolutionary radiation began with the launch of the Pelmatozoan echinoderms, which were the first benthic suspension feeders to begin feeding on plankton. The exploitation of this resource led to the creation of a 1-m tier above the bottom and an increase in their calcite productivity. Positive feedback emerged between the grounds and the community of its inhabitants and considerably changed the composition and diversity of grounds, which sharply increased the diversity of benthos. The appearance of positive feedback between different components of ecosystems resulted in explosive evolution in both the Cambrian and Ordovician.     

Relative contribution of abundant and rare species to species-energy relationships

A major goal of ecology is to understand spatial variation in species richness. The latter is markedly influenced by energy availability and appears to be influenced more by common species than rare ones; species-energy relationships should thus be stronger for common species. Species-energy relationships may arise because high-energy areas support more individuals, and these larger populations may buffer species from extinction. As extinction risk is a negative decelerating function of population size, this more-individuals hypothesis (MIH) predicts that rare species should respond more strongly to energy. We investigate these opposing predictions using British breeding bird data and find that, contrary to the MIH, common species contribute more to species-energy relationships than rare ones.     

Organic sedimentation and macrofauna as forcing factors in marine benthic nanofagellate communities

We investigated how benthic nanoflagellate communities in marine sediments respond to sedimentation of organic material and to the presence of macrofaunal organisms in controlled boxcosms. An input of 24 g C m^–2 resulted in a sharp increase in densities, from 93 to 477 × 10³ flagellates cm^–3 within 11 days. At the onset, this increase was paralleled by enhanced bacterial production and bacterial numbers. When bacterial production collapsed, flagellate ingestion rates, varying from 17 to 67 bact flag^–1 h^–1, were sufficient to control bacterial abundance. The presence of macrofauna accelerated the burst in flagellate densities. With macrofauna the same maximum densities were reached, but later densities dropped to relatively low levels. Macrofaunal bioturbation resulted in higher flagellate densities deeper in the sediment (up to 1200% at 3 cm and up to 460% at 6 cm deep). Correspondence to: R.P.M. Bak.     

Effect of domestic wastes on the benthic marine communities of southern California

A total of 3,785 million 1 of domestic wastes is emptied into the marine waters of southern California each day. Over 85% of these wastes receive primary treatment before discharge into offshore waters. Most of these wastes are discharged at four localities: El Segundo (Los Angeles City), White's Point (Los Angeles County), Newport Beach (Orange County), and Pt. Loma (San Diego City). While some studies were conducted at these localities prior to 1970, all of these sanitation districts have been monitoring the benthic environment since 1971–1973. Some predictions on the effect of domestic discharges on benthic life were made based on the amount of primary effluent discharged per day. If the amount discharged into open oceanic waters is less than 18 million 1/day, then a biological enhancement is noted with an increase in biomass, number of species and specimens, and diversity. If the amount of discharge exceeds 40–180 millions 1/day, then the biomass, number of specimens, and area affected is increased, but the number of species, diversity, and richness is decreased. A faunal index was devised by the personnel at Southern California Coastal Water Research Project to represent these generalities graphically.     

Leaf-trait responses to environmental gradients in moorland communities: contribution of intraspecific variation,species replacement and functional group replacement

The values of many important traits of plants in a community change along environmental gradients. Such changes may involve intraspecific variation and replacement by species that have different trait values. We hypothesized that they also involve the variation within and among functional groups (FGs) to the environmental dependence of trait values at the community level. We studied environmental dependence of trait values in 27 moorlands at various scales and analyzed to what extent intraspecific variation, species replacement within FGs and FG replacement contribute to the gradient of community trait values. The community structure in moorlands was influenced mainly by two environmental factors: temperature and water condition. Plants inhabiting sites with low temperature and low-pH generally tended to have lower maximum leaf height, greater leaf mass per area, and smaller leaf size. At the community level, site-mean of maximum leaf height and leaf size generally increased with increasing temperature and water pH. Our analysis demonstrated that the relative contributions of intraspecific variation, species replacement within FGs and FG replacement differed depending on combinations of the traits and environments. The contribution of FG replacement varied considerably among cases (0.6–34.5 %). Species replacement within FGs, which has received little attention in previous studies, was most responsible for the community-level changes (31.6–65.3 %) and intraspecific variation also made a large contribution (22.9–57.9 %). Understanding such various mechanisms involving intraspecific variation and species replacement should help us better predict how the structure and functioning of moorland plant communities will respond to climate change.     

A device to measure in situ lotic benthic metabolism

A method is described to measure in situ lotic benthic community metabolism partitioned into autotrophic, heterotrophic, bacterial and inorganic components of oxidation.     

Host ontogeny and the temporal decay of similarity in parasite communities of marine fish

Geographical distances between host populations are key determinants of how many parasite species they share. In principle, decay in similarity should also occur with increasing distance along any other dimension that characterizes some form of separation between communities. Here, we apply the biogeographical concept of distance decay in similarity to ontogenetic changes in the metazoan parasite communities of three species of marine fish from the Atlantic coast of South America. Using differences in body length between all possible pairs of size classes as measures of ontogenetic distances, we find that, using an index of similarity (Bray-Curtis) that takes into account the abundance of each parasite species, the similarity in parasite communities showed a very clear decay pattern; using an index (Jaccard) based on presence/absence of species only, we obtained slightly weaker but nevertheless similar patterns. As we predicted, the slope of the decay relationship was significantly steeper in the fish Cynoscion guatucupa, which goes through clear ontogenetic changes in diet and therefore in exposure to parasites, than in the other species, Engraulis anchoita and Micropogonias furnieri, which maintain a roughly similar diet throughout their lives. In addition, we found that for any given ontogenetic distance, i.e. for a given length difference between two size classes, the similarity in parasite communities was almost always higher if they were adult size classes, and almost always lower if they were juvenile size classes. This, combined with comparisons among individual fish within size classes, shows that parasite communities in juvenile fish are variable and subject to stochastic effects. We propose the distance decay approach as a rigorous and quantitative method to measure rates of community change as a function of host age, and for comparisons across host species to elucidate the role of host ecology in the development of parasite assemblages.     

On the direct impact of ice on marine benthic communities, a review

Ice has a significant impact on the polar and sub-polar benthos, but relationships between corresponding physical and biological processes are not yet sufficiently understood. Sea ice contributes to a vertical zonation in shallow waters, which also experience other important disturbances. Due to the length of the non-glaciated coastline, sea ice is of greater relevance in the north than in the south. Scouring by icebergs and ridged sea ice causes an increased diversity when different recolonisation stages coexist. Frequently scoured areas do not recover, especially in the Antarctic, due to slow growth rates of the fauna. Iceberg grounding in the Arctic is mainly restricted to the western Eurasian and northeastern American shelf, including Greenland. Around Antarctica, scouring is more evenly distributed. Glacier termini prevent sessile animals from settling in their proximity where only few motile species occur.     

Measuring the structural similarity of two communities composed of the same species

Summary The primary purpose of this paper is to propose empirical measures of the structural differences between two communities of plants or animals composed of the same species. Structure is defined to consist of; 1) the species in the community, 2) the pattern of interactions as represented by the covariance or correlation matrix of successive observations on each species, and 3) the mean abundances of each species in each of the two communities. Statistical tests are proposed for testing whether the covariance matrices and the vectors of mean densities for each community are equal and empirical measures of the differences between the covariance matrices and mean vectors are proposed. Given unequal covariance or correlation matrices the factor analysis model is used to derive empirical measures of the degree to which each variable of the ecosystem is responsible for the observed defferences in the pattern of interactions in each community. These tests and measures were applied to data gathered byHunter (1966) on the abundances of six species ofDrosophila censused monthly over a period of approximately two and a half years in two adjacent, but different habitats near Bogota, colombia. The two covariance matrices were significantly different indicating different patterns of interactions in the twoDrosophila communities.     

Variability in the settlement of non-indigenous species in benthic communities from an oceanic island

The introduction of non-indigenous species (NIS) in new environments represents a major threat for coastal ecosystems. A good understanding of the mechanisms and magnitude of the impact of NIS colonisation on native ecosystems is becoming increasingly crucial to develop mitigation measures and prevent new invasions. In this present study, we asked if distinct coastal benthic communities from an oceanic island can have different vulnerability to NIS colonisation process. First, PVC settlement plates were deployed for 1 year on the rocky shore of two different locations of Madeira Island (North versus South coast). Then, we implemented a mesocosm experiment where recruited plate communities were maintained under different levels of NIS propagule pressure in order to assess their vulnerability to NIS colonisation process. Results showed that NIS colonisation success was not influenced by the level of propagule pressure, but however, final colonisation patterns varied depending on the origin of the communities. This variability can be attributed to major structural differences between the preponderant species of each community and therefore to the biotic substrate they offer to colonisers. This study highlights how biotic features can alter the NIS colonisation process and importantly, shows that in an urbanisation context, the nature of the resident communities facing invasions risks needs to be closely assessed.     

Implications of 2D versus 3D surveys to measure the abundance and composition of benthic coral reef communities

Coral Reefs - A paramount challenge in coral reef ecology is to estimate the abundance and composition of the communities residing in such complex ecosystems. Traditional 2D projected surface cover...     

Geographical variation in species diversity: A comparison of marine polychaetes and nematodes

The aim of this study was to determine if marine species diversity was influenced by geographical location and whether it was higher at lower latitudes. Artificial collectors (made of nylon pan scourers) were employed as a standard substratum for the colonisation of marine invertebrates inhabiting subtidal (12 to 15 m) hard, rocky bottom substrata. These artificial substrate units (ASUs) were deployed at different latitudes including northern and southern temperate (South West England, UK and New Zealand), tropical (Trinidad and Tobago, West Indies) and polar (Signy Island, Antarctica) areas. The polychaetes, representative of the macrofauna and the nematodes, representative of the meiofauna fractions of the total invertebrate fauna collected were analysed.Neither polychaete nor nematode species diversity showed a trend based on latitude and each taxon showed a different pattern of diversity variation in relation to location. Polychaete diversity varied from area to area with highest species diversity occurring in the southern temperate (New Zealand). Nematode species diversity however was similar for the northern and southern temperate (UK and New Zealand) and the tropical area (Trinidad and Tobago). Thus, although the number of locations studied was limited, these data do not conform to a gradient in species diversity with latitude as has been previously supposed. The success of ASUs to compare species diversities in standardised habitat units augurs well for their future use in other ecological areas such as biogeographical or pollution studies.     

一种新的基因注释语义相似度计算方法

基因本体(GO)数据库为基因提供了统一的注释,有效地解决了不同数据库描述相同基因的不一致问题。但是,根据基因注释如何比较基因的功能相似性,这个问题仍然没有得到有效解决。本文提出一种新的基因注释语义相似度计算方法,这种方法在本质上是基于基因的生物学特性,其特点在于结点的语义相似度与结点所在集合无关,只与结点在GO图的位置有关,语义相似度可被重复利用。它既考虑了基因所映射的GO结点深度,又考虑了两GO结点之间所有路径对结点语义相似度的影响。文中以酵母菌的异亮氨酸降解代谢通路和谷氨酸合成代谢通路为实验,实验结果表明这种算法能准确地计算基因注释语义相似度。     

Structure and similarity of helminth communities of six species of Australian turtles

Patterns of infracommunity structure and infra- and component community similarity were examined for helminths of 6 species of turtles, each collected from a single locality in Australia in 1993 and 1994. Elseya latisternum (N = 11) and Emydura kreffti (N = 16) were collected from northern Queensland, Emydura macquarii macquarii (N = 11) from southern Queensland, Emydura macquarii dhara (N = 11) and Chelodina longicollis (N = 11) from northern New South Wales, and Chelodina oblonga (N = 5) from Western Australia. Local parasite species richness was not correlated with host geographical range. Differences in parasite diversity among host species were related primarily to differences in evenness, a pattern attributed to local habitat characteristics, rather than species-specific differences in colonization potential. Ordination and analysis of similarity demonstrated the patterns of infracommunity structure of Chelodina spp. to be distinct from those of the other host species sampled, which showed considerable overlap among patterns of infracommunity structure. Despite overlap with the component communities of Em. kreffti and El. latisternum, the component communities of Em. m. dhara and Em. m. macquarii were more distinct from one another than either was to the component communities of Em. kreffti or El. latisternum.     

Partitioning the effects of algal species identity and richness on benthic marine primary production

Influential research in terrestrial habitats indicates that several ecosystem processes are related to plant biodiversity, yet these links remain poorly studied in marine ecosystems. We conducted one field and one mesocosm experiment to quantify the relative effects of macroalgal species identity and richness on primary production in coral reef macroalgal communities off the north coast of Jamaica. We measured production as the net accumulation of algal biomass in the absence of consumers and as photosynthetic rate using oxygen probes in sealed aquaria. We used two recently developed techniques to attribute deviations in expected relative yield to components associated with species identity or diversity and then to further partition diversity effects into mechanistic components based on dominance, trait-dependent complementarity, and trait-independent complementarity. Our results indicate that algal identity had far greater effects on absolute net growth and photosynthesis than richness. The most diverse mixture of macroalgae did not outperform the most productive monoculture or the average monoculture in either measure of primary production (i.e. we did not find evidence of either transgressive or non-transgressive overyielding). Trait-independent complementarity effects were positive but dominance and trait-dependent complementarity were both negative and became stronger when richness was increased. Thus the potentially positive influence of species interactions and niche partitioning on production were negated by dominance and other negative selection effects. These results demonstrate that the counteracting influence of component effects can diminish the net richness effects on production. This could explain frequently observed weak net richness effects in other aquatic and terrestrial systems and suggests that life history tradeoffs greatly reduce the potential for ecologically relevant plant biodiversity effects on ecosystem properties.     

Colonization,variability, and the use of substratum-filled trays for biomonitoring benthic communities

Sampling variability and colonization rate of introduced substrates (plastic trays filled with pebble and cobble) in two southwestern Virginia streams are described. Substrates were rapidly colonized by aquatic macroinvertebrates, but colonization rates differed between years, possibly due to annual variability in macroinvertebrate abundance. To examine the applicability of using these substrates for biomonitoring benthic communities, trays were placed at several locations in a river receiving power plant discharges. Only six samples were necessary to detect a 15%reduction in macroinvertebrate density and a 12% reduction in number of taxa at effluent sites. Benthic communities established on rock-filled trays and multiplate samplers collected from the same stations during the same period were compared. Although multiplate samplers were more variable than rock trays and were selective for different taxa, both substrate types showed significant differences in community parameters among locations. Rock trays at all sites were dominated by Cheumatopsyche sp., whereas chironomids were more abundant on multiplate samplers. The relative abundance of mayflies was reduced at the effluent site on both substrate types.     

Stochastic population dynamics and life-history variation in marine fish species

Abstract We examined whether differences in life-history characteristics can explain interspecific variation in stochastic population dynamics in nine marine fish species living in the Barents Sea system. After observation errors in population estimates were accounted for, temporal variability in natural mortality rate, annual recruitment, and population growth rate was negatively related to generation time. Mean natural mortality rate, annual recruitment, and population growth rate were lower in long-lived species than in short-lived species. Thus, important species-specific characteristics of the population dynamics were related to the species position along the slow-fast continuum of life-history variation. These relationships were further associated with interspecific differences in ecology: species at the fast end were mainly pelagic, with short generation times and high natural mortality, annual recruitment, and population growth rates, and also showed high temporal variability in those demographic traits. In contrast, species at the slow end were long-lived, deepwater species with low rates and reduced temporal variability in the same demographic traits. These interspecific relationships show that the life-history characteristics of a species can predict basic features of interspecific variation in population dynamical characteristics of marine fish, which should have implications for the choice of harvest strategy to facilitate sustainable yields.