Importance of timely metadata curation to the global surveillance of genetic diversity

Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies produce large amounts of genome-scale genetic diversity data for wild populations, but most (87%) do not include the associated spatial and temporal metadata necessary for them to be reused in monitoring programs or for acknowledging the sovereignty of nations or Indigenous peoples. We undertook a distributed datathon to quantify the availability of these missing metadata and to test the hypothesis that their availability decays with time. We also worked to remediate missing metadata by extracting them from associated published papers, online repositories, and direct communication with authors. Starting with 848 candidate genomic data sets (reduced representation and whole genome) from the International Nucleotide Sequence Database Collaboration, we determined that 561 contained mostly samples from wild populations. We successfully restored spatiotemporal metadata for 78% of these 561 data sets (n = 440 data sets with data on 45,105 individuals from 762 species in 17 phyla). Examining papers and online repositories was much more fruitful than contacting 351 authors, who replied to our email requests 45% of the time. Overall, 23% of our email queries to authors unearthed useful metadata. The probability of retrieving spatiotemporal metadata declined significantly as age of the data set increased. There was a 13.5% yearly decrease in metadata associated with published papers or online repositories and up to a 22% yearly decrease in metadata that were only available from authors. This rapid decay in metadata availability, mirrored in studies of other types of biological data, should motivate swift updates to data-sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost to conservation science forever.     

Abusive supervision and feedback avoidance: The mediating role of emotional exhaustion

The occurrence of abusive supervision is steadily rising. Extant literature continues to expand the number of destructive consequences linked to such improper workplace behavior. This study tested a model linking abusive supervision to feedback avoidance through emotional exhaustion. We invoked conservation of resources theory in our examination of the role that the loss of valued resources plays in instances where abuse is perceived. Results from three rounds of matched data from 460 nurses and 220 working adults demonstrated support for our model, suggesting a mediating effect for exhaustion on the relationship between abuse and feedback avoidance. Findings also revealed that feedback avoidance was associated with subsequent exhaustion, representing a loss spiral. These findings are important as they reveal the link between a subordinate's reactions (exhaustion) and coping behavior (feedback avoidance) when supervisory abuse is perceived. Theoretical and practical implications, limitations, and directions for future research are offered. Copyright © 2012 John Wiley & Sons, Ltd.     

Conservation and social outcomes of private protected areas

Government administered protected areas (PAs) have dominated conservation strategies, discourse, and research, yet private actors are increasingly managing land for conservation. Little is known about the social and environmental outcomes of these privately protected areas (PPAs). We searched the global literature in English on PPAs and their environmental and social outcomes and identified 412 articles suitable for inclusion. Research on PPAs was geographically skewed; more studies occurred in the United States. Environmental outcomes of PPAs were mostly positive (89%), but social outcomes of PPAs were reported less (12% of all studies), and these outcomes were more mixed (65% positive). Private protected areas increased the number or extent of ecosystems, ecoregions, or species covered by PAs (representativeness) and PA network connectivity and effectively reduced deforestation and restored degraded lands. Few PPA owners reported negative social outcomes, experienced improved social capital, increased property value, or a reduction in taxes. Local communities benefited from increased employment, training, and community-wide development (e.g., building of schools), but they reported reduced social capital and no significant difference to household income. The causal mechanisms through which PPAs influence social and environmental outcomes remain unclear, as does how political, economic, and social contexts shape these mechanisms. Future research should widen the geographical scope and diversify the types of PPAs studied and focus on determining the casual mechanisms through which PPA outcomes occur in different contexts. We propose an assessment framework that could be adopted to facilitate this process.     

Marine diatoms grown in chemostats under silicate or ammonium limitation. III. Cellular chemical composition and morphology of Chaetoceros debilis,Skeletonema costatum,and Thalassiosira gravida

Three marine diatoms, Skeletonema costatum, Chaetoceros debilis, and Thalassiosira gravida were grown under no limitation and ammonium or silicate limitation or starvation. Changes in cell morphology were documented with photomicrographs of ammonium and silicate-limited and non-limited cells, and correlated with observed changes in chemical composition. Cultures grown under silicate starvation or limitation showed an increase in particulate carbon, nitrogen and phosporus and chlorophyll a per unit cell volume compared to non-limited cells; particulate silica per cell volume decreased. Si-starved cells were different from Si-limited cells in that the former contained more particulate carbon and silica per cell volume. The most sensitive indicator of silicate limitation or starvation was the ratio C:Si, being 3 to 5 times higher than the values for non-limited cells. The ratios Si:chlorophyll a and S:P were lower and N:Si was higher than non-limited cells by a factor of 2 to 3. The other ratios, C:N, C:P, C:chlorophyll a, N:chlorophyll a, P:chlorophyll a and N:P were considered not to be sensitive indicators of silicate limitation or starvation. Chlorophyll a, and particulate nitrogen per unit cell volume decreased under ammonium limitation and starvation. NH₄-starved cells contained more chlorophyll a, carbon, nitrogen, silica, and phosphorus per cell volume than NH₄-limited cells. N:Si was the most sensitive ratio to ammonium limitation or starvation, being 2 to 3 times lower than non-limited cells. Si:chlorophyll a, P:chlorophyll a and N:P were less sensitive, while the ratios C:N, C:chlorophyll a, N:chlorophyll a, C:Si, C:P and Si:P were the least sensitive. Limited cells had less of the limiting nutrient per unit cell volume than starved cells and more of the non-limiting nutrients (i.e., silica and phosphorus for NH₄-limited cells). This suggests that nutrient-limited cells rather than nutrient-starved cells should be used along with non-limited cells to measure the full range of potential change in cellular chemical composition for one species under nutrient limitation.Contribution No. 943 from the Department of Oceanography, University of Washington, Seattle, Washington 98195, USA.     

Quantification of Extinction Risk: IUCN's System for Classifying Threatened Species

Abstract: The International Union for Conservation of Nature (IUCN) Red List of Threatened Species was increasingly used during the 1980s to assess the conservation status of species for policy and planning purposes. This use stimulated the development of a new set of quantitative criteria for listing species in the categories of threat: critically endangered, endangered, and vulnerable. These criteria, which were intended to be applicable to all species except microorganisms, were part of a broader system for classifying threatened species and were fully implemented by IUCN in 2000. The system and the criteria have been widely used by conservation practitioners and scientists and now underpin one indicator being used to assess the Convention on Biological Diversity 2010 biodiversity target. We describe the process and the technical background to the IUCN Red List system. The criteria refer to fundamental biological processes underlying population decline and extinction. But given major differences between species, the threatening processes affecting them, and the paucity of knowledge relating to most species, the IUCN system had to be both broad and flexible to be applicable to the majority of described species. The system was designed to measure the symptoms of extinction risk, and uses 5 independent criteria relating to aspects of population loss and decline of range size. A species is assigned to a threat category if it meets the quantitative threshold for at least one criterion. The criteria and the accompanying rules and guidelines used by IUCN are intended to increase the consistency, transparency, and validity of its categorization system, but it necessitates some compromises that affect the applicability of the system and the species lists that result. In particular, choices were made over the assessment of uncertainty, poorly known species, depleted species, population decline, restricted ranges, and rarity; all of these affect the way red lists should be viewed and used. Processes related to priority setting and the development of national red lists need to take account of some assumptions in the formulation of the criteria.     

Genus-specific associations of marine sponges with group I crenarchaeotes

Sponges have rich and diverse associated microbial communities, which may have important functions in their metabolism. A survey of the archaeal communities of 23 poriferan species, focusing on the family Axinellidae, was conducted over the period 2002–2004 using 16S rDNA gene libraries created with archaeal-specific primers. The 28S rDNA sequences of the sponge hosts were also obtained. Of 23 species, 19 showed evidence of archaeal communities from group C1a (marine group I; Crenarchaeota), with three of these also showing evidence of Archaea from group E2 (marine group II; Euryarchaeota). Within the Crenarchaeota, two strongly supported sponge-specific clades were identified corresponding to the sponge family Axinellidae, and a novel sponge clade denoted clade C. These findings suggest that these archaea have evolved closely with their sponge hosts and are likely to play an important role in their metabolism.

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Mobilization of metals and phosphorus from intact forest soil cores by dissolved inorganic carbon

Increased dissolved inorganic carbon (DIC) enhances the mobilization of metals and nutrients in soil solutions. Our objective was to investigate the mobilization of Al, Ca, Fe, and P in forest soils due to fluctuating DIC concentrations. Intact soil cores were taken from the O and B horizons at the Bear Brook Watershed in Maine (BBWM) to conduct soil column transport experiments. Solutions with DIC concentrations (～20–600 ppm) were introduced into the columns. DIC was reversibly sorbed and its migration was retarded by a factor of 1.2 to 2.1 compared to the conservative sodium bromide tracer, corresponding to a log K _D?=???0.82 to ?0.07. Elevated DIC significantly enhanced the mobilization of all Al, Fe, Ca, and P. Particulate (>0.4 μm) Al and Fe were mobilized during chemical and flow transitions, such as increasing DIC and dissolved organic carbon (DOC), and resumption of flow after draining the columns. Calcium and P were primarily in dissolved forms. Mechanisms such as ion exchange (Al, Fe, Ca), ligand- and proton-promoted dissolution (Al and Fe), and ligand exchange (P) were the likely chemical mechanisms for the mobilization of these species. One column was packed with dried and sieved B-horizon soil. The effluent from this column had DOC, Al, and Fe concentrations considerably higher than those in the intact columns, suggesting that these species were mobilized from soil’s microporous structure that was otherwise not exposed to the advective flow. Calcium and P concentrations, however, were similar to those in the intact columns, suggesting that these elements were less occluded in soil particles.     

Adsorption of trace metals to plastic resin pellets in the marine environment

Plastic production pellets collected from beaches of south west England contain variable concentrations of trace metals (Cr, Co, Ni, Cu, Zn, Cd and Pb) that, in some cases, exceed concentrations reported for local estuarine sediments. The rates and mechanisms by which metals associate with virgin and beached polyethylene pellets were studied by adding a cocktail of 5 μg L(-1) of trace metals to 10 g L(-1) pellet suspensions in filtered seawater. Kinetic profiles were modelled using a pseudo-first-order equation and yielded response times of less than about 100 h and equilibrium partition coefficients of up to about 225 ml g(-1) that were consistently higher for beached pellets than virgin pellets. Adsorption isotherms conformed to both the Langmuir and Freundlich equations and adsorption capacities were greater for beached pellets than for virgin pellets. Results suggest that plastics may represent an important vehicle for the transport of metals in the marine environment.     

Measurements of Cd, Cu, Pb and Zn in the lower reaches of major Eurasian arctic rivers using trace metal clean techniques

Concentrations of dissolved and particulate Cd, Cu, Pb and Zn were determined in samples collected in summer 1998 from the lower reaches of six major Eurasian arctic rivers: the Onega, Severnaya Dvina, Mezen, Pechora, Ob and Yenisey. These data comprise some of the earliest measurements of trace metals in Eurasian arctic rivers above the estuaries using recognized clean techniques. Significant (α = 0.05) differences were observed among mean concentrations of particulate metals in the individual rivers (F ≤ 0.006), with highest levels overall observed in the Severnaya Dvina and Yenisey. No significant differences were observed among mean concentrations of dissolved metals in the individual rivers (F = 0.10-0.84). Contributions from anthropogenic sources are suggested by comparison of trace metal ratios in the samples to crustal abundances. These results establish a baseline for assessing future responses of Eurasian arctic river systems to climate-related environmental changes and shifting patterns of pollutant discharge.     

Investigation of time-resolved atmospheric conditions and indoor/outdoor particulate matter concentrations in homes with gas and biomass cook stoves in Nogales,Sonora, Mexico

This paper reports findings from a case study designed to investigate indoor and outdoor air quality in homes near the United States–Mexico border. During the field study, size-resolved continuous particulate matter (PM) concentrations were measured in six homes, while outdoor PM was simultaneously monitored at the same location in Nogales, Sonora, Mexico, during March 14–30, 2009. The purpose of the experiment was to compare PM in homes using different fuels for cooking, gas versus biomass, and to obtain a spatial distribution of outdoor PM in a region where local sources vary significantly (e.g., highway, border crossing, unpaved roads, industry). Continuous PM data were collected every 6 seconds using a valve switching system to sample indoor and outdoor air at each home location. This paper presents the indoor PM data from each home, including the relationship between indoor and outdoor PM. The meteorological conditions associated with elevated ambient PM events in the region are also discussed. Results indicate that indoor air pollution has a strong dependence on cooking fuel, with gas stoves having hourly averaged median PM₃ concentrations in the range of 134 to 157 μg m^?3 and biomass stoves 163 to 504 μg m^?3. Outdoor PM also indicates a large spatial heterogeneity due to the presence of microscale sources and meteorological influences (median PM₃: 130 to 770 μg m^?3). The former is evident in the median and range of daytime PM values (median PM₃: 250 μg m^?3, maximum: 9411 μg m^?3), while the meteorological influences appear to be dominant during nighttime periods (median PM₃: 251 μg m^?3, maximum: 10,846 μg m^?3). The atmospheric stability is quantified for three nighttime temperature inversion episodes, which were associated with an order of magnitude increase in PM10 at the regulatory monitor in Nogales, AZ (maximum increase: 12 to 474 μg m^?3).

Implications:Regulatory air quality standards are based on outdoor ambient air measurements. However, a large fraction of time is typically spent indoors where a variety of activities including cooking, heating, tobacco smoking, and cleaning can lead to elevated PM concentrations. This study investigates the influence of meteorology, outdoor PM, and indoor activities on indoor air pollution (IAP) levels in the United States–Mexico border region. Results indicate that cooking fuel type and meteorology greatly influence the IAP in homes, with biomass fuel use causing the largest increase in PM concentration.