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Linking multidimensional functional diversity to quantitative methods: a graphical hypothesis-evaluation framework
Get PDFFunctional trait analysis is an appealing approach to study differences among biological communities because traits determine species' responses to the environment and their impacts on ecosystem functioning. Despite a rapidly expanding quantitative literature, it remains challenging to conceptualize concurrent changes in multiple trait dimensions (“trait space”) and select quantitative functional diversity methods to test hypotheses prior to analysis. To address this need, we present a widely applicable framework for visualizing ecological phenomena in trait space to guide the selection, application, and interpretation of quantitative functional diversity methods. We describe five hypotheses that represent general patterns of responses to disturbance in functional community ecology and then apply a formal decision process to determine appropriate quantitative methods to test ecological hypotheses. As a part of this process, we devise a new statistical approach to test for functional turnover among communities. Our combination of hypotheses and metrics can be applied broadly to address ecological questions across a range of systems and study designs. We illustrate the framework with a case study of disturbance in freshwater communities. This hypothesis-driven approach will increase the rigor and transparency of applied functional trait studies.Keywords: community assembly,
trait-based ecology,
disturbance,
ordination,
functional diversity,
multivariate analysis,
multidimensional trait spaceThis is the publisher’s final pdf. The article is copyrighted by Ecological Society of America and published by John Wiley & Sons, Inc. It can be found at: http://esajournals.onlinelibrary.wiley.com/hub/journal/10.1002/%28ISSN%291939-9170
A Moving Target: Matching Graduate Education with Available Careers for Ocean Scientists
Get PDFThe objective of this paper is to look at past assessments and available data to examine the match (or mismatch) between university curricula and programs available to graduate students in the ocean sciences and the career possibilities available to those students. We conclude there is a need for fundamental change in how we educate graduate students in the ocean sciences. The change should accommodate the interests of students as well as the needs of a changing society; the change should not be constrained by the traditions or resource challenges of the graduate institutions themselves. The limited data we have been able to obtain from schools and employers are consistent with this view: desirable careers for ocean scientists are moving rapidly toward interdisciplinary, collaborative, societally relevant activities, away from traditional academic-research/professorial jobs, but the training available to the students is not keeping pace. We offer some suggestions to mitigate the mismatch. Most importantly, although anecdotes and “gut feelings” abound, the quantitative data backing our conclusions and suggestions are very sparse and barely compelling; we urge better data collection to support curricular revision, perhaps with the involvement of professional societies
The water footprint of staple crop trade under climate and policy scenarios
Get PDFTrade in staple crop commodities has become increasingly important in the global food system, with ramifications for both food security and water resources sustainability. It is thus essential to understand how the water footprint (WF) of staple crop trade may change in the future. To this end, we project international staple crop trade and its WF under climate and policy scenarios for the year 2030. We use the H08 global hydrologic model to determine the impact of climatic changes to staple crop yields and evapotranspiration. Using the yield changes projected with the H08 model, we estimate the bilateral trade of staple crops using the Global Trade Analysis Project model. We combine these projections to obtain the total and blue WF of agricultural trade and global water savings (GWS) across scenarios. This approach enables us to determine the direct impact of climate change and trade liberalization—together and in isolation—on the WF of staple crop trade. Importantly, we show that trade liberalization leads to greater WF, making it a potentially important adaptation measure to a changing climate, although future work is needed to distinguish high resolution crop water use, water stress, and commodity transfers.Keywords: agricultural trade,
climate change,
virtual water,
water footprint,
trade policy,
global water savings,
adaptatio
De Novo Reconstruction of Consensus Master Genomes of Plant RNA and DNA Viruses from siRNAs
Get PDFVirus-infected plants accumulate abundant, 21–24 nucleotide viral siRNAs which are generated by the evolutionary conserved RNA interference (RNAi) machinery that regulates gene expression and defends against invasive nucleic acids. Here we show that, similar to RNA viruses, the entire genome sequences of DNA viruses are densely covered with siRNAs in both sense and antisense orientations. This implies pervasive transcription of both coding and non-coding viral DNA in the nucleus, which generates double-stranded RNA precursors of viral siRNAs. Consistent with our finding and hypothesis, we demonstrate that the complete genomes of DNA viruses from Caulimoviridae and Geminiviridae families can be reconstructed by deep sequencing and de novo assembly of viral siRNAs using bioinformatics tools. Furthermore, we prove that this ‘siRNA omics’ approach can be used for reliable identification of the consensus master genome and its microvariants in viral quasispecies. Finally, we utilized this approach to reconstruct an emerging DNA virus and two viroids associated with economically-important red blotch disease of grapevine, and to rapidly generate a biologically-active clone representing the wild type master genome of Oilseed rape mosaic virus. Our findings show that deep siRNA sequencing allows for de novo reconstruction of any DNA or RNA virus genome and its microvariants, making it suitable for universal characterization of evolving viral quasispecies as well as for studying the mechanisms of siRNA biogenesis and RNAi-based antiviral defense
HoweDanaZoologyUsingMitogenomicNuclear_SupportingInformation.zip
No full textNematodes within the Xiphinema americanum species complex are economically important because they vector
nepoviruses which cause considerable damage to a variety of agricultural crops. The taxonomy of X. americanum species
complex is controversial, with the number of putative species being the subject of debate. Accurate phylogenetic
knowledge of this group is highly desirable as it may ultimately reveal genetic differences between species. For this study,
nematodes belonging to the X. americanum species complex, including potentially mixed species populations, were
collected from 12 geographically disparate locations across the U.S. from different crops and in varying association with
nepoviruses. At least four individuals from each population were analyzed. A portion of the 18S nuclear ribosomal DNA
(rDNA) gene was sequenced for all individuals while the internal transcribed spacer region 1 (ITS1) of rDNA was cloned and
2 to 6 clones per individual were sequenced. Mitochondrial genomes for numerous individuals were sequenced in parallel
using high-throughput DNA sequencing (HTS) technology. Phylogenetic analysis of the 18S rDNA revealed virtually identical
sequences across all populations. Analysis of ITS1 rDNA sequences revealed several well-supported clades, with some
degree of congruence with geographic location and viral transmission, but also numerous presumably paralogous
sequences that failed to form clades with other sequences from the same population. Analysis of mitochondrial DNA
(mtDNA) indicated the presence of three distinct monophyletic clades of X. americanum species complex nematodes. Two
clades contained nematodes found in association with nepovirus and the third contained divergent mtDNA sequences from
three nematode populations from the western U.S. where nepovirus was absent. The inherent heterogeneity in ITS1 rDNA
sequence data and lack of informative sites in 18S rDNA analysis suggests that mtDNA may be more useful in sorting out
the taxonomic confusion of the X. americanum species complex
Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations
Get PDFNitrosomonas sp. Is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to the family Nitrosomonadaceae within the phylum Proteobacteria. Ammonia oxidation is the first step of nitrification, an important process in the global nitrogen cycle ultimately resulting in the production of nitrate. Nitrosomonas sp. Is79 is an ammonia oxidizer of high interest because it is adapted to low ammonium and can be found in freshwater environments around the world. The 3,783,444-bp chromosome with a total of 3,553 protein coding genes and 44 RNA genes was sequenced by the DOE-Joint Genome Institute Program CSP 2006.Keywords: nitrification,
Ammonia-oxidizing bacteria,
Ammonia oxidation,
Nitrosomonas,
nitrogen cycle,
oligotrophic,
freshwate
Does temperature affect the accuracy of vented pressure transducer in fine-scale water level measurement?
Get PDFSubmersible pressure transducers have been utilized
for collecting water level data since the early 1960s.
Together with a digital data logger, it is a convenient way
to record water level fluctuations for long-term monitoring.
Despite the wide use of pressure transducers for water level
monitoring, little has been reported regarding their accuracy
and performance under field conditions. The effects of temperature
fluctuations on the output of vented pressure transducers
were considered in this study. The pressure transducers
were tested under both laboratory and field conditions.
The results of this study indicate that temperature fluctuation
has a strong effect on the transducer output. Rapid changes
in temperature introduce noise and fluctuations in the water
level readings under a constant hydraulic head while the absolute
temperature is also related to sensor errors. The former
is attributed to venting and the latter is attributed to
temperature compensation effects in the strain gauges. Individual
pressure transducers responded differently to the thermal
fluctuations in the same testing environment. In the field
of surface hydrology, especially when monitoring fine-scale
water level fluctuations, ignoring or failing to compensate for
the temperature effect can introduce considerable error into
pressure transducer readings. It is recommended that a performance
test for the pressure transducer is conducted before
field deployment.This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by Copernicus Publications on behalf of the European Geosciences Union. The published article can be found at: http://www.geoscientific-instrumentation-methods-and-data-systems.net/. For a previous discussion paper please see: http://hdl.handle.net/1957/5652
Carbon budget estimation of a subarctic catchment using a dynamic ecosystem model at high spatial resolution
Get PDFLarge amount of organic carbon is stored in high latitude soils. A substantial proportion of this carbon stock is vulnerable and may decompose rapidly due to temperature increases that are already greater than the global average. It is therefore crucial to quantify and understand carbon exchange between the atmosphere and subarctic/arctic ecosystems. In this paper, we combine an arctic-enabled version of the process-based dynamic ecosystem model, LPJ-GUESS (version LPJG-WHyMe-TFM) with comprehensive observations of terrestrial and aquatic carbon fluxes to simulate long-term carbon exchange in a subarctic catchment comprising both mineral and peatland soils. The model is applied at 50 m resolution and is shown to be able to capture the seasonality and magnitudes of observed fluxes at this fine scale. The modelled magnitudes of CO₂ uptake generally follow the descending sequence: birch forest, non-permafrost Eriophorum, Sphagnum and then tundra heath during the observation periods. The catchment-level carbon fluxes from aquatic systems are dominated by CO₂ emissions from streams. Integrated across the whole catchment, we estimate that the area is a carbon sink at present, and will become an even stronger carbon sink by 2080, which is mainly a result of a projected densification of birch forest and its encroachment into tundra heath. However, the magnitudes of the modelled sinks are very dependent on future atmospheric CO₂ concentrations. Furthermore, comparisons of global warming potentials between two simulations with and without CO₂ increase since 1960 reveal that the increased methane emission from the peatland could double the warming effects of the whole catchment by 2080 in the absence of CO₂ fertilization of the vegetation. This is the first process-based model study of the temporal evolution of a catchment-level carbon budget at high spatial resolution, integrating comprehensive and diverse fluxes including both terrestrial and aquatic carbon. Though this study also highlights some limitations in modelling subarctic ecosystem responses to climate change including aquatic system flux dynamics, nutrient limitation, herbivory and other disturbances and peatland expansion, our application provides a mechanism to resolve the complexity of carbon cycling in subarctic ecosystems while simultaneously pointing out the key model developments for capturing complex subarctic processes.This discussion paper has been under review for the journal Biogeosciences (BG). Please refer to the corresponding final paper in BG. The published article is copyrighted by the author(s) and published by Copernicus Publications on behalf of the European Geosciences Union. The final revised paper is available at: http://hdl.handle.net/1957/5694
GRACE storage-streamflow hystereses reveal the dynamics of regional watersheds
Get PDFWe characterize how regional watersheds function as simple, dynamic systems through a series of hysteresis loops. These loops illustrate the temporal relationship between runoff and terrestrial water storage using measurements from NASA's Gravity Recovery and Climate Experiment (GRACE) satellites in three regional-scale watersheds (>150 000 km² ) of the Columbia River Basin, USA and Canada. The direction of the hystereses for the GRACE signal move in opposite directions from the isolated groundwater hystereses, suggesting that regional scale watersheds require soil water storage to reach a certain threshold before groundwater recharge and peak runoff occur. While the physical processes underlying these hystereses are inherently complex, the vertical integration of terrestrial water in the GRACE signal encapsulates the processes that govern the non-linear function of regional-scale watersheds. We use this process-based understanding to test how GRACE data can be applied prognostically to predict seasonal runoff (mean R² of 0.91) and monthly runoff (mean R² of 0.77) in all three watersheds. The global nature of GRACE data allows this same methodology to be applied in other regional-scale studies, and could be particularly useful in regions with minimal data and in trans-boundary watersheds.This discussion paper has been under review for the journal Hydrology and Earth System Sciences (HESS). Please refer to the corresponding final paper in HESS. The published article is copyrighted by the author(s) and published by Copernicus Publications on behalf of the European Geosciences Union. The published article can be found at: http://hdl.handle.net/1957/5716
McKayCEOASInter-DecadalChangesIntensitySupplement.pdf
No full textWe reconstructed oxygenation changes in the Oxygen Minimum Zone of the upwelling ecosystem off Concepción (36° S), Chile, using inorganic and organic proxies in a sediment core covering the last ca. 110 years of sedimentation in this area. Authigenic enrichments of Mo, U and Cd were observed between ca. 1935–1971 CE indicating a prolonged period of more reduced conditions in bottom waters and surface sediments. Significant positive correlations (p < 0.05; Spearman) between redox sensitive metals, algal sterols, biomarkers of anaerobic microorganisms, and archaeal glycerol dialkyl glycerol tetraether indicated a coupling among bottom water oxygen depletion, and increased primary and export production, suggesting that the period with low O₂ of ca. 35 years, follows low frequency inter-decadal variation of the Pacific Decadal Oscillation, which may have resulted in O₂ depletion over the entire continental shelf off Concepción. Taken together with the concurrent increase in sedimentary molecular indicators of anaerobic microbes allow us to suggest that the prokaryote community has been influenced by changes in oxygenation of the water column