Accelerating loss of seagrasses across the globe threatens coastal ecosystems

Coastal ecosystems and the services they provide are adversely affected by a wide variety of human activities. In particular, seagrass meadows are negatively affected by impacts accruing from the billion or more people who live within 50 km of them. Seagrass meadows provide important ecosystem services, including an estimated $1.9 trillion per year in the form of nutrient cycling; an order of magnitude enhancement of coral reef fish productivity; a habitat for thousands of fish, bird, and invertebrate species; and a major food source for endangered dugong, manatee, and green turtle. Although individual impacts from coastal development, degraded water quality, and climate change have been documented, there has been no quantitative global assessment of seagrass loss until now. Our comprehensive global assessment of 215 studies found that seagrasses have been disappearing at a rate of 110 square kilometers per year since 1980 and that 29% of the known areal extent has disappeared since seagrass areas were initially recorded in 1879. Furthermore, rates of decline have accelerated from a median of 0.9% per year before 1940 to 7% per year since 1990. Seagrass loss rates are comparable to those reported for mangroves, coral reefs, and tropical rainforests and place seagrass meadows among the most threatened ecosystems on earth.

Project report: Journal Research Data Policy Registry

This document is a report from Spotlight Data to Jisc. It describes the project findings and steps required to build a prototype journal research data policy system.

EcoGIS – GIS tools for ecosystem approaches to fisheries management

Executive Summary: The EcoGIS project was launched in September 2004 to investigate how Geographic Information Systems (GIS), marine data, and custom analysis tools can better enable fisheries scientists and managers to adopt Ecosystem Approaches to Fisheries Management (EAFM). EcoGIS is a collaborative effort between NOAA’s National Ocean Service (NOS) and National Marine Fisheries Service (NMFS), and four regional Fishery Management Councils. The project has focused on four priority areas: Fishing Catch and Effort Analysis, Area Characterization, Bycatch Analysis, and Habitat Interactions. Of these four functional areas, the project team first focused on developing a working prototype for catch and effort analysis: the Fishery Mapper Tool. This ArcGIS extension creates time-and-area summarized maps of fishing catch and effort from logbook, observer, or fishery-independent survey data sets. Source data may come from Oracle, Microsoft Access, or other file formats. Feedback from beta-testers of the Fishery Mapper was used to debug the prototype, enhance performance, and add features. This report describes the four priority functional areas, the development of the Fishery Mapper tool, and several themes that emerged through the parallel evolution of the EcoGIS project, the concept and implementation of the broader field of Ecosystem Approaches to Management (EAM), data management practices, and other EAM toolsets. In addition, a set of six succinct recommendations are proposed on page 29. One major conclusion from this work is that there is no single “super-tool” to enable Ecosystem Approaches to Management; as such, tools should be developed for specific purposes with attention given to interoperability and automation. Future work should be coordinated with other GIS development projects in order to provide “value added” and minimize duplication of efforts. In addition to custom tools, the development of cross-cutting Regional Ecosystem Spatial Databases will enable access to quality data to support the analyses required by EAM. GIS tools will be useful in developing Integrated Ecosystem Assessments (IEAs) and providing pre- and post-processing capabilities for spatially-explicit ecosystem models. Continued funding will enable the EcoGIS project to develop GIS tools that are immediately applicable to today’s needs. These tools will enable simplified and efficient data query, the ability to visualize data over time, and ways to synthesize multidimensional data from diverse sources. These capabilities will provide new information for analyzing issues from an ecosystem perspective, which will ultimately result in better understanding of fisheries and better support for decision-making. (PDF file contains 45 pages.)

JRDPR Research Data Policy Survey

Spreadsheet list of discovered journal research data policies, gathered in 2015 as a part of the JRPDR project. Research conducted for Jisc by Research Consulting and Spotlight Data. Underpins project final report [http://repository.jisc.ac.uk/6264/ ]

Data for research data policy registry final report

Underpins final report at: http://repository.jisc.ac.uk/6264/ Spreadsheet of discovered research data journal policies, collected late 2015.

Coastal & Marine Issues Survey

Florida Sea Grant management and extension specialists developed a questionnaire to solicit information regarding the recipient’s county of residence, occupation, and primary coastal activities. Survey recipients were also asked to select from a list the top five marine-related topics that defined prior strategic plan themes (i.e., marine bio-technology, fisheries, aquaculture, seafood safety, coastal communities, ecosystem health, coastal hazards, and marine education). In addition, questionnaire recipients were asked to evaluate (on a scale of one to five) the importance of a series of listed outcomes that characterize priority planning themes. Last, survey recipients identified up to three priority themes and outcomes that they felt were particularly important and in need of resolution. (PDF contains 36 pages.)

The contrasting invertebrate fauna of freshwater habitats in the Swavesey fens of East Anglia

During July and August 1988, 21 ponds and 33 ditch sites were sampled at Swavesey fens in East Anglia. Water from each site was collected and analysed at monthly intervals in the year preceding faunal sampling. Temperature and oxygen were measured on site. The "quality" of the faunal community was assessed by three approaches: a modification of the BMWP scoring system (Biological Monitoring Working Party); faunal richness was calculated as the number of faunal "groups" at each site; and by using Simpson's index of diversity. Statistical analysis was carried out to explore the relationships between sites, environmental variables and faunal diversity. The survey clearly showed the detrimental effects of elevated nitrate and phosphate from agricultural sources and the localised impacts of treated sewage effluent on invertebrates in ditches.

Computationally Guided Monomerization of Red Fluorescent Proteins of the Class Anthozoa

Red fluorescent proteins (RFPs) have attracted significant engineering focus because of the promise of near infrared fluorescent proteins, whose light penetrates biological tissue, and which would allow imaging inside of vertebrate animals. The RFP landscape, which numbers ~200 members, is mostly populated by engineered variants of four native RFPs, leaving the vast majority of native RFP biodiversity untouched. This is largely due to the fact that native RFPs are obligate tetramers, limiting their usefulness as fusion proteins. Monomerization has imposed critical costs on these evolved tetramers, however, as it has invariably led to loss of brightness, and often to many other adverse effects on the fluorescent properties of the derived monomeric variants. Here we have attempted to understand why monomerization has taken such a large toll on Anthozoa class RFPs, and to outline a clear strategy for their monomerization. We begin with a structural study of the far-red fluorescence of AQ143, one of the furthest red emitting RFPs. We then try to separate the problem of stable and bright fluorescence from the design of a soluble monomeric β-barrel surface by engineering a hybrid protein (DsRmCh) with an oligomeric parent that had been previously monomerized, DsRed, and a pre-stabilized monomeric core from mCherry. This allows us to use computational design to successfully design a stable, soluble, fluorescent monomer. Next we took HcRed, which is a previously unmonomerized RFP that has far-red fluorescence (λemission = 633 nm) and attempted to monomerize it making use of lessons learned from DsRmCh. We engineered two monomeric proteins by pre-stabilizing HcRed’s core, then monomerizing in stages, making use of computational design and directed evolution techniques such as error-prone mutagenesis and DNA shuffling. We call these proteins mGinger0.1 (λem = 637 nm / Φ = 0.02) and mGinger0.2 (λem = 631 nm Φ = 0.04). They are the furthest red first generation monomeric RFPs ever developed, are significantly thermostabilized, and add diversity to a small field of far-red monomeric FPs. We anticipate that the techniques we describe will be facilitate future RFP monomerization, and that further core optimization of the mGingers may allow significant improvements in brightness.

Solid-state NMR study of bioactive binary borosilicate glasses

A series of binary borosilicate glasses prepared by the sol-gel method are shown to be bioactive. Tetraethyl orthosilicate (TEOS) and trimethylborate (TMB) in acidic medium are used to prepare xB(2)O(3)center dot(1-x)SiO2 glass systems for x = 0.045-0.167. The formation of a layer of apatite-like mineral on the glass surface becomes apparent after soaking in simulated body fluid for 48 h. We have measured the B-11-B-11 homonuclear second moments of the borosilicate glasses and inferred that no macroscopic phase separation occurred in our glasses. The B-11 chemical shift data also show that the formation of clustered boroxol rings is negligible in our glass system. Although the bioactivity of our borosilicate glasses is less than that of CaO-SiO2 sol-gel glasses, these simple binary systems could be taken as reference glass systems for the search of new bioactive borosilicate glasses. (C) 2008 Elsevier Ltd. All rights reserved.

Population connectivity among Dry Tortugas, Florida, and Caribbean populations of mutton snapper (Lutjanus analis), inferred from multiple microsatellite loci

Determining patterns of population connectivity is critical to the evaluation of marine reserves as recruitment sources for harvested populations. Mutton snapper (Lutjanus analis) is a good test case because the last known major spawning aggregation in U.S. waters was granted no-take status in the Tortugas South Ecological Reserve (TSER) in 2001. To evaluate the TSER population as a recruitment source, we genotyped mutton snapper from the Dry Tortugas, southeast Florida, and from three locations across the Caribbean at eight microsatellite loci. Both Fstatistics and individual-based Bayesian analyses indicated that genetic substructure was absent across the five populations. Genetic homogeneity of mutton snapper populations is consistent with its pelagic larval duration of 27 to 37 days and adult behavior of annual migrations to large spawning aggregations. Statistical power of future genetic assessments of mutton snapper population connectivity may benefit from more comprehensive geographic sampling, and perhaps from the development of less polymorphic DNA microsatellite loci. Research where alternative methods are used, such as the transgenerational marking of embryonic otoliths with barium stable isotopes, is also needed on this and other species with diverse life history characteristics to further evaluate the TSER as a recruitment source and to define corridors of population connectivity across the Caribbean and Florida.

Prevalence of the commensal barnacle Xenobalanus globicipitis on cetacean species in the eastern tropical Pacific Ocean, and a review of global occurrence

Distribution and prevalence of the phoretic barnacle Xenobalanus on cetacean species are reported for 22 cetaceans in the eastern tropical Pacific Ocean (21 million km2). Four cetacean species are newly reported hosts for Xenobalanus: Bryde’s whale (Balaenoptera edeni), long-beaked common dolphin (Delphinus capensis), humpback whale (Megaptera novaeangliae), and spinner dolphin (Stenella longirostris). Sightings of Xenobalanus in pelagic waters are reported for the first time, and concentrations were located within three productive zones: near the Baja California peninsula, the Costa Rica Dome and waters extending west along the 10°N Thermocline Ridge, and near Peru and the Galapagos Archipelago. Greatest prevalence was observed on blue whales (Balaenoptera musculus) indicating that slow swim speeds are not necessary for effective barnacle settlement. Overall, prevalence and prevalence per sighting were generally lower than previously reported. The number of barnacles present on an individual whale was greatest for killer whales, indicating that Xenobalanus larvae may be patchily distributed. The broad geographic distribution and large number of cetacean hosts, indicate an extremely cosmopolitan distribution. A better understanding of the biology of Xenobalanus is needed before this species can be used as a biological tag.

Modification of the biological intercept model to account for ontogenetic effects in laboratory-reared delta smelt (Hypomesus transpacificus)*

We investigated age, growth, and ontogenetic effects on the proportionality of otolith size to fish size in laboratory-reared delta smelt (Hypomesus transpacificus) from the San Francisco Bay estuary. Delta smelt larvae were reared from hatching in laboratory mesocosms for 100 days. Otolith increments from known-age fish were enumerated to validate that growth increments were deposited daily and to validate the age of fish at first ring formation. Delta smelt were found to lay down daily ring increments; however, the first increment did not form until six days after hatching. The relationship between otolith size and fish size was not biased by age or growth-rate effects but did exhibit an interruption in linear growth owing to an ontogenetic shift at the postflexon stage. To back-calculate the size-at-age of individual fish, we modified the biological intercept (BI) model to account for ontogenetic changes in the otolith-size−fish-size relationship and compared the results to the time-varying growth model, as well as the modified Fry model. We found the modified BI model estimated more accurately the size-at-age from hatching to 100 days after hatching. Before back-calculating size-at-age with existing models, we recommend a critical evaluation of the effects that age, growth, and ontogeny can have on the otolith-size−fish-size relations

NMFS / Interagency Working Group Evaluation of CITES Criteria and Guidelines.

EXECUTIVE SUMMARY: At present, the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) criteria used to assess whether a population qualifies for inclusion in the CITES Appendices relate to (A) size of the population, (B) area of distribution of the population, and (C) declines in the size of the population. Numeric guidelines are provided as indicators of a small population (less than 5,000 individuals), a small subpopulation (less than 500 individuals), a restricted area of distribution for a population (less than 10,000 km2), a restricted area of distribution for a subpopula-tion (less than 500 km2), a high rate of decline (a decrease of 50% or more in total within 5 years or two generations whichever is longer or, for a small wild population, a decline of 20% or more in total within ten years or three generations whichever is longer), large fluctuations (population size or area of distribution varies widely, rapidly and frequently, with a variation greater than one order of magnitude), and a short-term fluctuation (one of two years or less). The Working Group discussed several broad issues of relevance to the CITES criteria and guidelines. These included the importance of the historical extent of decline versus the recent rate of decline; the utility and validity of incorporating relative population productivity into decline criteria; the utility of absolute numbers for defining small populations or small areas; the appropriateness of generation times as time frames for examining declines; the importance of the magnitude and frequency of fluctuations as factors affecting risk of extinction; and the overall utility of numeric thresh-olds or guidelines.