Publications by authors named "Rebecca R Murphy"

10 Publications

  • Page 1 of 1

Advancing estuarine ecological forecasts: seasonal hypoxia in Chesapeake Bay.

Ecol Appl 2021 Sep 21;31(6):e02384. Epub 2021 Jul 21.

U.S. Geological Survey Chesapeake Bay Program Office, Annapolis, Maryland, 21403, USA.

Ecological forecasts are quantitative tools that can guide ecosystem management. The coemergence of extensive environmental monitoring and quantitative frameworks allows for widespread development and continued improvement of ecological forecasting systems. We use a relatively simple estuarine hypoxia model to demonstrate advances in addressing some of the most critical challenges and opportunities of contemporary ecological forecasting, including predictive accuracy, uncertainty characterization, and management relevance. We explore the impacts of different combinations of forecast metrics, drivers, and driver time windows on predictive performance. We also incorporate multiple sets of state-variable observations from different sources and separately quantify model prediction error and measurement uncertainty through a flexible Bayesian hierarchical framework. Results illustrate the benefits of (1) adopting forecast metrics and drivers that strike an optimal balance between predictability and relevance to management, (2) incorporating multiple data sources in the calibration data set to separate and propagate different sources of uncertainty, and (3) using the model in scenario mode to probabilistically evaluate the effects of alternative management decisions on future ecosystem state. In the Chesapeake Bay, the subject of this case study, we find that average summer or total annual hypoxia metrics are more predictable than monthly metrics and that measurement error represents an important source of uncertainty. Application of the model in scenario mode suggests that absent watershed management actions over the past decades, long-term average hypoxia would have increased by 7% compared to 1985. Conversely, the model projects that if management goals currently in place to restore the Bay are met, long-term average hypoxia would eventually decrease by 32% with respect to the mid-1980s.
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http://dx.doi.org/10.1002/eap.2384DOI Listing
September 2021

Nutrient limitation of phytoplankton in Chesapeake Bay: Development of an empirical approach for water-quality management.

Water Res 2021 Jan 7;188:116407. Epub 2020 Sep 7.

U.S. Geological Survey / Chesapeake Bay Program, 410 Severn Avenue, Annapolis, MD 21403, USA.

Understanding the temporal and spatial roles of nutrient limitation on phytoplankton growth is necessary for developing successful management strategies. Chesapeake Bay has well-documented seasonal and spatial variations in nutrient limitation, but it remains unknown whether these patterns of nutrient limitation have changed in response to nutrient management efforts. We analyzed historical data from nutrient bioassay experiments (1992-2002) and data from long-term, fixed-site water-quality monitoring program (1990-2017) to develop empirical approaches for predicting nutrient limitation in the surface waters of the mainstem Bay. Results from classification and regression trees (CART) matched the seasonal and spatial patterns of bioassay-based nutrient limitation in the 1992-2002 period much better than two simpler, non-statistical approaches. An ensemble approach of three selected CART models satisfactorily reproduced the bioassay-based results (classification rate = 99%). This empirical approach can be used to characterize nutrient limitation from long-term water-quality monitoring data on much broader geographic and temporal scales than would be feasible using bioassays, providing a new tool for informing water-quality management. Results from our application of the approach to 21 tidal monitoring stations for the period of 2007-2017 showed modest changes in nutrient limitation patterns, with expanded areas of nitrogen-limitation and contracted areas of nutrient saturation (i.e., not limited by nitrogen or phosphorus). These changes imply that long-term reductions in nitrogen load have led to expanded areas with nutrient-limited phytoplankton growth in the Bay, reflecting long-term water-quality improvements in the context of nutrient enrichment. However, nutrient limitation patterns remain unchanged in the majority of the mainstem, suggesting that nutrient loads should be further reduced to achieve a less nutrient-saturated ecosystem.
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http://dx.doi.org/10.1016/j.watres.2020.116407DOI Listing
January 2021

Chesapeake Bay's water quality condition has been recovering: Insights from a multimetric indicator assessment of thirty years of tidal monitoring data.

Sci Total Environ 2018 Oct 24;637-638:1617-1625. Epub 2018 May 24.

U.S. Geological Survey/U.S. Environmental Protection Agency Chesapeake Bay Program, 410 Severn Avenue, Annapolis, MD 21403, USA.

To protect the aquatic living resources of Chesapeake Bay, the Chesapeake Bay Program partnership has developed guidance for state water quality standards, which include ambient water quality criteria to protect designated uses (DUs), and associated assessment procedures for dissolved oxygen (DO), water clarity/underwater bay grasses, and chlorophyll-a. For measuring progress toward meeting the respective states' water quality standards, a multimetric attainment indicator approach was developed to estimate combined standards attainment. We applied this approach to three decades of monitoring data of DO, water clarity/underwater bay grasses, and chlorophyll-a data on annually updated moving 3-year periods to track the progress in all 92 management segments of tidal waters in Chesapeake Bay. In 2014-2016, 40% of tidal water segment-DU-criterion combinations in the Bay (n = 291) are estimated to meet thresholds for attainment of their water quality criteria. This index score marks the best 3-year status in the entire record. Since 1985-1987, the indicator has followed a nonlinear trajectory, consistent with impacts from extreme weather events and subsequent recoveries. Over the period of record (1985-2016), the indicator exhibited a positive and statistically significant trend (p < 0.05), indicating that the Bay has been recovering since 1985. Patterns of attainment of individual DUs are variable, but improvements in open water DO, deep channel DO, and water clarity/submerged aquatic vegetation have combined to drive the improvement in the Baywide indicator in 2014-2016 relative to its long-term median. Finally, the improvement in estimated Baywide attainment was statistically linked to the decline of total nitrogen, indicating responsiveness of attainment status to the reduction of nutrient load through various management actions since at least the 1980s.
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http://dx.doi.org/10.1016/j.scitotenv.2018.05.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6688177PMC
October 2018

Long-term nutrient reductions lead to the unprecedented recovery of a temperate coastal region.

Proc Natl Acad Sci U S A 2018 04 5;115(14):3658-3662. Epub 2018 Mar 5.

US Environmental Protection Agency, Annapolis, MD 21403.

Humans strongly impact the dynamics of coastal systems, yet surprisingly few studies mechanistically link management of anthropogenic stressors and successful restoration of nearshore habitats over large spatial and temporal scales. Such examples are sorely needed to ensure the success of ecosystem restoration efforts worldwide. Here, we unite 30 consecutive years of watershed modeling, biogeochemical data, and comprehensive aerial surveys of Chesapeake Bay, United States to quantify the cascading effects of anthropogenic impacts on submersed aquatic vegetation (SAV), an ecologically and economically valuable habitat. We employ structural equation models to link land use change to higher nutrient loads, which in turn reduce SAV cover through multiple, independent pathways. We also show through our models that high biodiversity of SAV consistently promotes cover, an unexpected finding that corroborates emerging evidence from other terrestrial and marine systems. Due to sustained management actions that have reduced nitrogen concentrations in Chesapeake Bay by 23% since 1984, SAV has regained 17,000 ha to achieve its highest cover in almost half a century. Our study empirically demonstrates that nutrient reductions and biodiversity conservation are effective strategies to aid the successful recovery of degraded systems at regional scales, a finding which is highly relevant to the utility of environmental management programs worldwide.
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http://dx.doi.org/10.1073/pnas.1715798115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5889635PMC
April 2018

Chesapeake Bay Dissolved Oxygen Criterion Attainment Deficit: Three Decades of Temporal and Spatial Patterns.

Front Mar Sci 2018 ;5

Chesapeake Bay Program Office, U.S. Environmental Protection Agency, Annapolis, MD, United States.

Low dissolved oxygen (DO) conditions are a recurring issue in waters of Chesapeake Bay, with detrimental effects on aquatic living resources. The Chesapeake Bay Program partnership has developed criteria guidance supporting the definition of state water quality standards and associated assessment procedures for DO and other parameters, which provides a binary classification of attainment or impairment. Evaluating time series of these two outcomes alone, however, provides limited information on water quality change over time or space. Here we introduce an extension of the existing Chesapeake Bay water quality criterion assessment framework to quantify the amount of impairment shown by space-time exceedance of DO criterion ("attainment deficit") for a specific tidal management unit (i.e., segment). We demonstrate the usefulness of this extended framework by applying it to Bay segments for each 3-year assessment period between 1985 and 2016. In general, the attainment deficit for the most recent period assessed (i.e., 2014-2016) is considerably worse for deep channel (DC; n = 10) segments than open water (OW; n = 92) and deep water (DW; n = 18) segments. Most subgroups - classified by designated uses, salinity zones, or tidal systems - show better (or similar) attainment status in 2014-2016 than their initial status (1985-1987). Some significant temporal trends (p < 0.1) were detected, presenting evidence on the recovery for portions of Chesapeake Bay with respect to DO criterion attainment. Significant, improving trends were observed in seven OW segments, four DW segments, and one DC segment over the 30 3-year assessment periods (1985-2016). Likewise, significant, improving trends were observed in 15 OW, five DW, and four DC segments over the recent 15 assessment periods (2000-2016). Subgroups showed mixed trends, with the Patuxent, Nanticoke, and Choptank Rivers experiencing significant, improving short-term (2000-2016) trends while Elizabeth experiencing a significant, degrading short-term trend. The general lack of significantly improving trends across the Bay suggests that further actions will be necessary to achieve full attainment of DO criterion. Insights revealed in this work are critical for understanding the dynamics of the Bay ecosystem and for further assessing the effectiveness of management initiatives aimed toward Bay restoration.
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http://dx.doi.org/10.3389/fmars.2018.00422DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6750769PMC
January 2018

Multiple stressors threaten the imperiled coastal foundation species eelgrass (Zostera marina) in Chesapeake Bay, USA.

Glob Chang Biol 2017 09 6;23(9):3474-3483. Epub 2017 Feb 6.

Virginia Institute of Marine Science, The College of William & Mary, Gloucester Point, VA, 23062, USA.

Interactions among global change stressors and their effects at large scales are often proposed, but seldom evaluated. This situation is primarily due to lack of comprehensive, sufficiently long-term, and spatially extensive datasets. Seagrasses, which provide nursery habitat, improve water quality, and constitute a globally important carbon sink, are among the most vulnerable habitats on the planet. Here, we unite 31 years of high-resolution aerial monitoring and water quality data to elucidate the patterns and drivers of eelgrass (Zostera marina) abundance in Chesapeake Bay, USA, one of the largest and most valuable estuaries in the world, with an unparalleled history of regulatory efforts. We show that eelgrass area has declined 29% in total since 1991, with wide-ranging and severe ecological and economic consequences. We go on to identify an interaction between decreasing water clarity and warming temperatures as the primary drivers of this trend. Declining clarity has gradually reduced eelgrass cover the past two decades, primarily in deeper beds where light is already limiting. In shallow beds, however, reduced visibility exacerbates the physiological stress of acute warming, leading to recent instances of decline approaching 80%. While degraded water quality has long been known to influence underwater grasses worldwide, we demonstrate a clear and rapidly emerging interaction with climate change. We highlight the urgent need to integrate a broader perspective into local water quality management, in the Chesapeake Bay and in the many other coastal systems facing similar stressors.
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http://dx.doi.org/10.1111/gcb.13623DOI Listing
September 2017

Numerical and qualitative contrasts of two statistical models for water quality change in tidal waters.

J Am Water Resour Assoc 2017 Jan;53(1):197-219

University of Maryland Center for Environmental Science at Chesapeake Bay Program, 410 Severn Avenue, Suite 112, Annapolis, MD 21403.

Two statistical approaches, weighted regression on time, discharge, and season (WRTDS) and generalized additive models (GAMs), have recently been used to evaluate water quality trends in estuaries. Both models have been used in similar contexts despite differences in statistical foundations and products. This study provided an empirical and qualitative comparison of both models using 29 years of data for two discrete time series of chlorophyll- (chl-) in the Patuxent River Estuary. Empirical descriptions of each model were based on predictive performance against the observed data, ability to reproduce flow-normalized trends with simulated data, and comparisons of performance with validation datasets. Between-model differences were apparent but minor and both models had comparable abilities to remove flow effects from simulated time series. Both models similarly predicted observations for missing data with different characteristics. Trends from each model revealed distinct mainstem influences of the Chesapeake Bay with both models predicting a roughly 65% increase in chl- over time in the lower estuary, whereas flow-normalized predictions for the upper estuary showed a more dynamic pattern, with a nearly 100% increase in chl- in the last 10 years. Qualitative comparisons highlighted important differences in the statistical structure, available products, and characteristics of the data and desired analysis.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6161536PMC
January 2017

NxRepair: error correction in de novo sequence assembly using Nextera mate pairs.

PeerJ 2015 2;3:e996. Epub 2015 Jun 2.

Illumina Cambridge, Chesterford Research Park , Essex , UK.

Scaffolding errors and incorrect repeat disambiguation during de novo assembly can result in large scale misassemblies in draft genomes. Nextera mate pair sequencing data provide additional information to resolve assembly ambiguities during scaffolding. Here, we introduce NxRepair, an open source toolkit for error correction in de novo assemblies that uses Nextera mate pair libraries to identify and correct large-scale errors. We show that NxRepair can identify and correct large scaffolding errors, without use of a reference sequence, resulting in quantitative improvements in the assembly quality. NxRepair can be downloaded from GitHub or PyPI, the Python Package Index; a tutorial and user documentation are also available.
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http://dx.doi.org/10.7717/peerj.996DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4458127PMC
June 2015

Bayesian inference of accurate population sizes and FRET efficiencies from single diffusing biomolecules.

Anal Chem 2014 Sep 18;86(17):8603-12. Epub 2014 Aug 18.

Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, United Kingdom.

It is of significant biophysical interest to obtain accurate intramolecular distance information and population sizes from single-molecule Förster resonance energy transfer (smFRET) data obtained from biomolecules in solution. Experimental methods of increasing cost and complexity are being developed to improve the accuracy and precision of data collection. However, the analysis of smFRET data sets currently relies on simplistic, and often arbitrary methods, for the selection and denoising of fluorescent bursts. Although these methods are satisfactory for the analysis of simple, low-noise systems with intermediate FRET efficiencies, they display systematic inaccuracies when applied to more complex systems. We have developed an inference method for the analysis of smFRET data from solution studies based on rigorous model-based Bayesian techniques. We implement a Monte Carlo Markov chain (MCMC) based algorithm that simultaneously estimates population sizes and intramolecular distance information directly from a raw smFRET data set, with no intermediate event selection and denoising steps. Here, we present both our parametric model of the smFRET process and the algorithm developed for data analysis. We test the algorithm using a combination of simulated data sets and data from dual-labeled DNA molecules. We demonstrate that our model-based method systematically outperforms threshold-based techniques in accurately inferring both population sizes and intramolecular distances.
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http://dx.doi.org/10.1021/ac501188rDOI Listing
September 2014

Inhalation health risk to golfers from turfgrass pesticides at three northeastern U.S. sites.

Environ Sci Technol 2007 Feb;41(3):1038-43

Biological and Environmental Engineering, Riley-Robb Hall, Cornell University, Ithaca, New York 14853, USA.

Chronic health risks from inhalation of vapors from 15 pesticides were estimated for golfers in Boston, MA, Philadelphia, PA, and Rochester, NY. Two previously tested fate and transport models were used to determine exposures from pesticide inhalation for an adult golfer, and the exposures were in turn used to evaluate health risks from chronic non-carcinogenic effects through calculation of hazard quotients. Hazard quotients for all 15 chemicals were found to be much less one, indicating little risk of non-carcinogenic effects. Carcinogenic health risks for the five pesticides considered to be likely or possible carcinogens were determined to be much less than 10(-6). Based on these results, long-term health risks to golfers from inhalation of these 15 pesticides appear to be minimal in the Northeastern U.S. Estimated hazard quotients were found to be similar to those calculated from field measurements.
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http://dx.doi.org/10.1021/es060964bDOI Listing
February 2007
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