Spatial Variation in the Chemical Composition of Natal Otholiths from a Reef Fish in the Galápagos Islands

Over the past decade, researchers have used variation in the chemical composition of fish otoliths (earstones) to address a number of ecological questions, such as stock assessment and assessing rates of movement of individuals among habitats or life-history stages. However, these methods have yet to be applied successfully to the study of larval connectivity, a major unanswered question in marine ecology. Accomplishing this task requires a reference collection of pre-pelagic natal otoliths and accurate measurement of the chemical signatures of otoliths cores of recruits. We analyzed the chemical composition of natal otoliths from near-term benthic eggs of a damselfish (Stegastes beebei) from all regions of the Galápagos Archipelago. There was no consistent variation in chemical signature at the largest scale, among regions in the archipelago (separated by ~100 to 150 km). However, we found significant variation among islands within each region (10s of km), and among clutches within islands. In addition, we found that otolith cores of newly settled recruits often differed chemically from natal otoliths (which ultimately make up the otolith core as the fish grows). Variation at smaller spatial scales but not larger ones implies that otolith chemistry will only be usable if larvae disperse short distances in this system, and additional work is required to understand the relationship between the chemistry of natal otoliths and recruit cores. Otolith chemistry has the potential to address questions of connectivity, but our data suggest that these methods should be applied cautiously

MIREOT: the Minimum Information to Reference an External Ontology Term

While the Web Ontology Language (OWL) provides a mechanism to import ontologies, this mechanism is not always suitable. First, given the current state of editing tools and the issues they have working with large ontologies, direct OWL imports have sometimes proven impractical for day-to-day development. Second, ontologies chosen for integration may be under active development and not aligned with the chosen design principles. Importing heterogeneous ontologies in their entirety may lead to inconsistencies or unintended inferences. In this paper we propose a set of guidelines for importing required terms from an external resource into a target ontology. We describe the guidelines, their implementation, present some examples of application, and outline future work and extensions

Spatial and Temporal Variation in the Natal Otolith Chemistry of a Hawaiian Reef Fish: Prospects for Measuring Population Connectivity

One of the most compelling unanswered questions in marine ecology is the extent to which local populations are connected via larval exchange. Recent work has suggested that variation in the chemistry of otoliths (earstones) of fishes may function as a natural tag, potentially allowing investigators to determine sources of individual larvae and estimate larval connectivity. We analyzed the spatial and temporal variation in natal otolith chemistry of a benthic-spawning reef fish from the Hawaiian Islands. We found no consistent chemical variation at the largest scale (\u3e100 km, among islands), but found significant variation at moderate scales (sites within islands, tens of kilometres) and small scales (clutches within sites), and chemistry of otoliths was not stable between years. These results imply that we may be able to use otolith chemistry to track larval dispersal only if the scales of dispersal match those of variation in natal otolith chemistry, and that separate natal otolith collections may be needed to track different cohorts of larvae. Finally, we found that elemental composition of recruit cores often did not match that of natal otoliths, suggesting that additional methodological development is required before we can effectively apply methods in otolith chemistry to the study of larval dispersal

Patterns, Causes and Consequences of Regional Variation in the Ecology and Life History of a Reef Fish

Many species vary in their ecology across their geographic ranges in response to gradients in environmental conditions. Such variation, which can influence life history traits and subsequent demography of populations, usually occurs over large spatial scales. However, describing and understanding the causes of such variation is difficult precisely because it occurs over such large spatial scales. In this study, we document spatial variation in the ecology of a common reef fish, Stegastes beebei, in the Gala´pagos Islands and test a number of potential causal mechanisms. The pattern resembles that seen in latitudinal variation: individuals are larger, occur in higher densities, and live longer in the coldest region of the islands than those in the warmest region. However, in this system, demography varies among regional populations separated bytemperature, despite differences in the gross magnitude and timing of reproduction in different regions. A model of reproductive output suggests that fish in the warmest region are allocating a greater proportion of available energy to reproduction, resulting in apparent regional life history tradeoffs. Our data suggest that regional demographic differences in S. beebei may be driven by a combination of variation in food availability and an environmentally mediated life history tradeoff

Importance of Suspended Particulates in Riverine Delivery of Bioavailable Nitrogen to Coastal Zones

Total nitrogen (TN) loadings in riverine sediments and their coastal depocenters were compared for Il river systems worldwide to assess the potential impact of riverine particulates on coastal nitrogen budgets. Strong relationships between sediment specific surface area and TN allow these impacts to be estimated without the intense sampling normally required to achieve such budgets. About half of the systems showed higher nitrogen loadings in the riverine sediments than those from the coastal depocenter. In spite of uncertainties, these comparisons indicate that large, turbid rivers, such as the Amazon, Huanghe, and the Mississippi, deliver sediments that in turn release significant or major fractions of the total riverine nitrogen delivery. Riverine particulates must therefore be considered an essential factor in watershed nutrient loading to coastal ecosystems and may affect delivered nutrient ratios as well as total nutrient loading. The relative importance of particulate versus dissolved delivery has decreased over recent decades in the Mississippi as a result of damming and fertilizer use in the watershed

Biological Effects Within No-Take Marine Reserves: A global Synthesis

The study and implementation of no-take marine reserves have increased rapidly over the past decade, providing ample data on the biological effects of reserve protection for a wide range of geographic locations and organisms. The plethora of new studies affords the opportunity to reevaluate previous findings and address formerly unanswered questions with extensive data syntheses. Our results show, on average, positive effects of reserve protection on the biomass, numerical density, species richness, and size of organisms within their boundaries which are remarkably similar to those of past syntheses despite a near doubling of data. New analyses indicate that (1) these results do not appear to be an artifact of reserves being sited in better locations; (2) results do not appear to be driven by displaced fishing effort outside of reserves; (3) contrary to often-made assertions, reserves have similar if not greater positive effects in temperate settings, at least for reef ecosystems; (4) even small reserves can produce significant biological responses irrespective of latitude, although more data are needed to test whether reserve effects scale with reserve size; and (5) effects of reserves vary for different taxonomic groups and for taxa with various characteristics, and not all species increase in response to reserve protection. There is considerable variation in the responses documented across all the reserves in our data set—variability which cannot be entirely explained by which species were studied. We suggest that reserve characteristics and context, particularly the intensity of fishing outside the reserve and inside the reserve before implementation, play key roles in determining the direction and magnitude of the reserve response. However, despite considerable variability, positive responses are far more common than no differences or negative responses, validating the potential for well designed and enforced reserves to serve as globally important conservation and management tools

Elevated Levels of Trace Elements in Cores of Otoliths and Their Potential for Use as Natural Tags

Variation in the chemical composition of fish otoliths has been used in recent years to address a range of ecological questions, including levels of stock mixing, variation in habitat use, and rates of larval exchange. While some of these questions have been answered with varying success, the degree to which discrete populations are connected via larval exchange remains unknown. To identify larval sources using natural variation in otolith chemistry, we must distinguish and measure the chemical composition of the otolith core, the portion of the otolith formed at the spawning site. Using laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS), we found that the core regions of otoliths from 6 different species of fishes were highly enriched in manganese (Mn), and elevated in magnesium (Mg) and barium (Ba), relative to adjacent regions of the otolith. These patterns were consistent for species drawn from different taxonomic groups, which inhabit temperate and tropical regions, are found in marine and freshwater, and utilize a variety of spawning modes. Variation among species in Mn concentration in the core also corresponds to maternal investment, measured by egg size. These data suggest that core enrichment may be a general characteristic of otoliths, and that the chemical composition of the otolith core is fundamentally different from other regions of the otolith. The localized elemental enrichment of the core underscores the importance of methods that analyze the core region in small, discrete samples if otolith chemistry is used to address questions of larval exchange among populations

OntoFox: web-based support for ontology reuse

<p>Abstract</p> <p>Background</p> <p>Ontology development is a rapidly growing area of research, especially in the life sciences domain. To promote collaboration and interoperability between different projects, the OBO Foundry principles require that these ontologies be open and non-redundant, avoiding duplication of terms through the re-use of existing resources. As current options to do so present various difficulties, a new approach, MIREOT, allows specifying import of single terms. Initial implementations allow for controlled import of selected annotations and certain classes of related terms.</p> <p>Findings</p> <p>OntoFox <url>http://ontofox.hegroup.org/</url> is a web-based system that allows users to input terms, fetch selected properties, annotations, and certain classes of related terms from the source ontologies and save the results using the RDF/XML serialization of the Web Ontology Language (OWL). Compared to an initial implementation of MIREOT, OntoFox allows additional and more easily configurable options for selecting and rewriting annotation properties, and for inclusion of all or a computed subset of terms between low and top level terms. Additional methods for including related classes include a SPARQL-based ontology term retrieval algorithm that extracts terms related to a given set of signature terms and an option to extract the hierarchy rooted at a specified ontology term. OntoFox's output can be directly imported into a developer's ontology. OntoFox currently supports term retrieval from a selection of 15 ontologies accessible via SPARQL endpoints and allows users to extend this by specifying additional endpoints. An OntoFox application in the development of the Vaccine Ontology (VO) is demonstrated.</p> <p>Conclusions</p> <p>OntoFox provides a timely publicly available service, providing different options for users to collect terms from external ontologies, making them available for reuse by import into client OWL ontologies.</p

Rates of carbonate cementation associated with sulphate reduction in DSDP/ODP sediments: implications for the formation of concretions

DSDP/ODP porewater profiles in organic carbon-bearing (<5% org. C) sediments commonly show decreases in Ca2+ concentrations and increases in alkalinity over depths where sulphate is being removed by microbial reduction. These Ca2+ depletion profiles represent the combined effect of diffusion, advection and reaction (addition by ion exchange and removal by precipitation mainly as CaCO3 and/or dolomite). A diagenetic model has been used to estimate the rate constant (k) for Ca2+ removal by precipitation during sulphate depletion over depths of 15-150 m, assuming first order kinetics. The rate constants for Ca2+ removal range from 10(-14) to 10(-11) s(-1) in 19 DSDP/ODP sediments, which span a range of bottom water temperatures (0-10 degreesC), lithologies (calcareous to clastic) and sedimentation rates (0.001-0.4 cm year(-1)). Values of k correlate with sedimentation rate (omega) such that log k=1.16 log omega-10.3, indicating that faster rates of Ca2+ removal occur at higher sedimentation rates where there are also higher degrees of saturation with respect to CaCO3 and dolomite. Depth-integrated masses of Ca2+ removed (<100 mumol cm(-2)) during sulphate depletion over these depth ranges are equivalent to a dispersed phase of approximately 1.5 wt.% CaCO3 or 3 wt.% dolomite in a compacted sediment. The complete occlusion of sediment porosity observed in concretions with isotopic signatures suggesting carbonate sourced from sulphate reduction therefore requires more time (a depositional hiatus), more rapid sulphate reduction (possibly by anaerobic methane oxidation) and/or the continued transport of isotopically light carbonate to the concretion site after sulphate reduction has ceased

VO: Vaccine Ontology

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented