scholarly journals Integrating Environmental DNA Results With Diverse Data Sets to Improve Biosurveillance of River Health

2021 ◽  
Vol 9 ◽  
Author(s):  
Adam J. Sepulveda ◽  
Andrew Hoegh ◽  
Joshua A. Gage ◽  
Sara L. Caldwell Eldridge ◽  
James M. Birch ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Salmonid Fish ◽  
Weather Data ◽  
Parameter Estimates ◽  
Fish Parasite ◽  
Occupancy Models ◽  
Sample Collection ◽  
Bayesian Hierarchical ◽  
Daily Weather Data ◽  
Rare Fish

Autonomous, robotic environmental (e)DNA samplers now make it possible for biological observations to match the scale and quality of abiotic measurements collected by automated sensor networks. Merging these automated data streams may allow for improved insight into biotic responses to environmental change and stressors. Here, we merged eDNA data collected by robotic samplers installed at three U.S. Geological Survey (USGS) streamgages with gridded daily weather data, and daily water quality and quantity data into a cloud-hosted database. The eDNA targets were a rare fish parasite and a more common salmonid fish. We then used computationally expedient Bayesian hierarchical occupancy models to evaluate associations between abiotic conditions and eDNA detections and to simulate how uncertainty in result interpretation changes with the frequency of autonomous robotic eDNA sample collection. We developed scripts to automate data merging, cleaning and analysis steps into a chained-step, workflow. We found that inclusion of abiotic covariates only provided improved insight for the more common salmonid fish since its DNA was more frequently detected. Rare fish parasite DNA was infrequently detected, which caused occupancy parameter estimates and covariate associations to have high uncertainty. Our simulations found that collecting samples at least once per day resulted in more detections and less parameter uncertainty than less frequent sampling. Our occupancy and simulation results together demonstrate the advantages of robotic eDNA samplers and how these samples can be combined with easy to acquire, publicly available data to foster real-time biosurveillance and forecasting.

scholarly journals Optimising sampling and analysis protocols in environmental DNA studies

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Andrew Buxton ◽  
Eleni Matechou ◽  
Jim Griffin ◽  
Alex Diana ◽  
Richard A. Griffiths
Keyword(s):  
False Positive ◽  
False Negative ◽  
Environmental Dna ◽  
Laboratory Analysis ◽  
Parameter Estimates ◽  
Target Species ◽  
Sample Collection ◽  
Positive Error ◽  
False Positive Error ◽  
Data Set

AbstractEcological surveys risk incurring false negative and false positive detections of the target species. With indirect survey methods, such as environmental DNA, such error can occur at two stages: sample collection and laboratory analysis. Here we analyse a large qPCR based eDNA data set using two occupancy models, one of which accounts for false positive error by Griffin et al. (J R Stat Soc Ser C Appl Stat 69: 377–392, 2020), and a second that assumes no false positive error by Stratton et al. (Methods Ecol Evol 11: 1113–1120, 2020). Additionally, we apply the Griffin et al. (2020) model to simulated data to determine optimal levels of replication at both sampling stages. The Stratton et al. (2020) model, which assumes no false positive results, consistently overestimated both overall and individual site occupancy compared to both the Griffin et al. (2020) model and to previous estimates of pond occupancy for the target species. The inclusion of replication at both stages of eDNA analysis (sample collection and in the laboratory) reduces both bias and credible interval width in estimates of both occupancy and detectability. Even the collection of > 1 sample from a site can improve parameter estimates more than having a high number of replicates only within the laboratory analysis.

scholarly journals Distribution and incidence of viruses in Irish seed potato crops

2015 ◽  
Vol 54 (2) ◽  
pp. 98-106 ◽  
Author(s):  
F. Hutton ◽  
J.H. Spink ◽  
D. Griffin ◽  
S. Kildea ◽  
D. Bonner ◽  
...  
Keyword(s):  
Potato Virus ◽  
Significant Proportion ◽  
Potato Production ◽  
Weather Data ◽  
Management Approach ◽  
Potato Seed ◽  
Virus Diseases ◽  
Aphid Control ◽  
Daily Weather Data ◽  
Potato Crops

Abstract Virus diseases are of key importance in potato production and in particular for the production of disease-free potato seed. However, there is little known about the frequency and distribution of potato virus diseases in Ireland. Despite a large number of samples being tested each year, the data has never been collated either within or across years. Information from all known potato virus testing carried out in the years 2006–2012 by the Department of Agriculture Food and Marine was collated to give an indication of the distribution and incidence of potato virus in Ireland. It was found that there was significant variation between regions, varieties, years and seed classes. A definition of daily weather data suitable for aphid flight was developed, which accounted for a significant proportion of the variation in virus incidence between years. This use of weather data to predict virus risk could be developed to form the basis of an integrated pest management approach for aphid control in Irish potato crops.

scholarly journals A method for simulating risk profiles of wheat yield in data-sparse conditions

2021 ◽  
pp. 1-12
Author(s):  
G. Bracho-Mujica ◽  
P.T. Hayman ◽  
V.O. Sadras ◽  
B. Ostendorf
Keyword(s):  
Reference Site ◽  
Climate Impacts ◽  
Weather Data ◽  
Climate Data ◽  
High Quality ◽  
Risk Profiles ◽  
Record Length ◽  
Daily Weather Data ◽  
Study Sites

Abstract Process-based crop models are a robust approach to assess climate impacts on crop productivity and long-term viability of cropping systems. However, these models require high-quality climate data that cannot always be met. To overcome this issue, the current research tested a simple method for scaling daily data and extrapolating long-term risk profiles of modelled crop yields. An extreme situation was tested, in which high-quality weather data was only available at one single location (reference site: Snowtown, South Australia, 33.78°S, 138.21°E), and limited weather data was available for 49 study sites within the Australian grain belt (spanning from 26.67 to 38.02°S of latitude, and 115.44 to 151.85°E of longitude). Daily weather data were perturbed with a delta factor calculated as the difference between averaged climate data from the reference site and the study sites. Risk profiles were built using a step-wise combination of adjustments from the most simple (adjusted series of precipitation only) to the most detailed (adjusted series of precipitation, temperatures and solar radiation), and a variable record length (from 10 to 100 years). The simplest adjustment and shortest record length produced bias of modelled yield grain risk profiles between −10 and 10% in 41% of the sites, which increased to 86% of the study sites with the most detailed adjustment and longest record (100 years). Results indicate that the quality of the extrapolation of risk profiles was more sensitive to the number of adjustments applied rather than the record length per se.

scholarly journals Impact of Extreme Weather on Healthcare Utilization by People with HIV in Metropolitan Miami

2021 ◽  
Vol 18 (5) ◽  
pp. 2442
Author(s):  
Daniel Samano ◽  
Shubhayu Saha ◽  
Taylor Corbin Kot ◽  
JoNell E. Potter ◽  
Lunthita M. Duthely
Keyword(s):  
Relative Risk ◽  
The United States ◽  
Extreme Weather ◽  
South Florida ◽  
Heat Index ◽  
Extreme Weather Events ◽  
Weather Data ◽  
Steady Increase ◽  
Daily Weather Data ◽  
The Impact

Extreme weather events (EWE) are expected to increase as climate change intensifies, leaving coastal regions exposed to higher risks. South Florida has the highest HIV infection rate in the United States, and disruptions in clinic utilization due to extreme weather conditions could affect adherence to treatment and increase community transmission. The objective of this study was to identify the association between EWE and HIV-clinic attendance rates at a large academic medical system serving the Miami-Dade communities. The following methods were utilized: (1) Extreme heat index (EHI) and extreme precipitation (EP) were identified using daily observations from 1990–2019 that were collected at the Miami International Airport weather station located 3.6 miles from the studied HIV clinics. Data on hurricanes, coastal storms and flooding were collected from the National Oceanic and Atmospheric Administration Storms Database (NOAA) for Miami-Dade County. (2) An all-HIV clinic registry identified scheduled daily visits during the study period (hurricane seasons from 2017–2019). (3) Daily weather data were linked to the all-HIV clinic registry, where patients’ ‘no-show’ status was the variable of interest. (4) A time-stratified, case crossover model was used to estimate the relative risk of no-show on days with a high heat index, precipitation, and/or an extreme natural event. A total of 26,444 scheduled visits were analyzed during the 383-day study period. A steady increase in the relative risk of ‘no-show’ was observed in successive categories, with a 14% increase observed on days when the heat index was extreme compared to days with a relatively low EHI, 13% on days with EP compared to days with no EP, and 10% higher on days with a reported extreme weather event compared to days without such incident. This study represents a novel approach to improving local understanding of the impacts of EWE on the HIV-population’s utilization of healthcare, particularly when the frequency and intensity of EWE is expected to increase and disproportionately affect vulnerable populations. More studies are needed to understand the impact of EWE on routine outpatient settings.

scholarly journals A dataset of future daily weather data for crop modelling over Europe derived from climate change scenarios

2015 ◽  
Vol 127 (3-4) ◽  
pp. 573-585 ◽  
Author(s):  
G. Duveiller ◽  
M. Donatelli ◽  
D. Fumagalli ◽  
A. Zucchini ◽  
R. Nelson ◽  
...  
Keyword(s):  
Climate Change ◽  
Weather Data ◽  
Climate Change Scenarios ◽  
Crop Modelling ◽  
Daily Weather ◽  
Daily Weather Data

scholarly journals Integrated assessment of impact of water resources of important river basins in Eastern India under projected climate conditions

2015 ◽  
Vol 17 (3) ◽  
pp. 594-606 ◽  
Keyword(s):  
Climate Change ◽  
Water Resources ◽  
Catchment Area ◽  
River Basins ◽  
Weather Data ◽  
Distributed Hydrological Model ◽  
Eastern India ◽  
Impact Of Climate Change ◽  
Daily Weather Data ◽  
The Impact

<div> <p>The impact of climate change on water resources through increased evaporation combined with regional changes in precipitation characteristics has the potential to affect mean runoff, frequency and intensity of floods and droughts, soil moisture and water supply for irrigation and hydroelectric power generation. The Ganga-Brahmaputra-Meghna (GBM) system is the largest in India with a catchment area of about 110Mha, which is more than 43% of the cumulative catchment area of all the major rivers in the country. The river Damodar is an important sub catchment of GBM basin and its three tributaries- the Bokaro, the Konar and the Barakar form one important tributary of the Bhagirathi-Hughli (a tributary of Ganga) in its lower reaches. The present study is an attempt to assess the impacts of climate change on water resources of the four important Eastern River Basins namely Damodar, Subarnarekha, Mahanadi and Ajoy, which have immense importance in industrial and agricultural scenarios in eastern India. A distributed hydrological model (HEC-HMS) has been used on the four river basins using HadRM2 daily weather data for the period from 2041 to 2060 to predict the impact of climate change on water resources of these river systems.&nbsp;</p> </div> <p>&nbsp;</p>

scholarly journals Irrigation management strategies for winter wheat using AquaCrop model

2013 ◽  
Vol 3 ◽  
pp. 106-113
Author(s):  
M.H. Ali ◽  
I. Abustan
Keyword(s):  
Winter Wheat ◽  
Irrigation Management ◽  
Weather Data ◽  
Water Model ◽  
High Yield ◽  
Management Decision ◽  
Soil Conditions ◽  
Irrigation Frequency ◽  
Aquacrop Model ◽  
Daily Weather Data

Many regions of the world face the challenge to ensure high yield with limited water supply. This calls for utilization of available water in an efficient and sustainable manner. Quantitative models can assist in management decision and planning purposes. The FAO’s newly developed crop-water model, AquaCrop, which simulates yield in response to water, has been calibrated for winter wheat and subsequently used to simulate yield under different sowing dates, irrigation frequencies, and irrigation sequences using 10 years daily weather data. The simulation results suggest that “2 irrigation frequency” is the most water-efficient schedule for wheat under the prevailing climatic and soil conditions. The results also indicate decreasing yield trend under late sowing. The normal/recommended sequence of irrigation performed better than the seven-days shifting from the normal. The results will help to formulate irrigation management plan based on the resource availability (water, and land availability from previous crop).

A Bayesian hierarchical approach to improve model parameter estimates and predictions of silage maize phenology in Germany

2021 ◽  
Author(s):  
Michelle Viswanathan ◽  
Tobias KD Weber ◽  
Andreas Scheidegger ◽  
Thilo Streck
Keyword(s):  
Environmental Conditions ◽  
Plant Phenology ◽  
Parameter Estimates ◽  
Crop Species ◽  
Bayesian Hierarchical ◽  
Crop Models ◽  
Hierarchical Framework ◽  
Silage Maize ◽  
Parameterized Model ◽  
Species Specific

&lt;p&gt;Crop models are used to evaluate the impact of climate change on food security by simulating plant phenology, yield, biomass and leaf area index. Plant phenology defines the timing of crucial growth stages and physiological processes that influence organ appearance and assimilate partitioning. It is governed by environmental factors such as solar radiation, temperature and water availability. Plant phenology is not only specific for the crop species, but also depends on the cultivar. Additionally, growth of a cultivar could vary depending on the environment. Common crop models cannot fully capture the influence of the environment on phenology, resulting in cultivar-specific parameters that are environment-dependent. These parameter estimates may be unreliable in case of limited data. Moreover, crucial species-specific information is ignored. On the other hand, in large regional-scale models covering multiple cultivars and environments, information about the cultivars grown is generally not available. In this case, a shared set of parameters for the crop species would suppress within-species differences leading to unreliable predictions.&lt;/p&gt;&lt;p&gt;A Bayesian hierarchical framework enables us to alleviate these problems by honouring the multi-level data structure. Additionally, we can reflect the uncertainty from different sources, for example, model inputs and measurements. In this study we implement a Bayesian hierarchical framework to estimate parameters of the Soil-Plant-Atmosphere System Simulation (SPASS) model for simulating phenological development of different cultivars of silage maize grown over all the contrasting climatological regions of Germany.&lt;/p&gt;&lt;p&gt;We used data from the German weather service on the phenological development stages of silage maize grown across Germany between 2009 and 2019. During this period, silage maize was grown in over 3000 unique location-year combinations. Maize crops were differentiated into early, mid-early, mid-late and late ripening groups and were further classified into cultivars within each ripening group. Within the hierarchical framework, we estimate maize species-specific parameters as well as parameters per ripening group and cultivar, through Bayesian model calibration. We analyse the influence of environmental conditions on parameter estimates, to further develop the hierarchical structure. We perform cross-validation to assess the prediction quality of the parameterized model.&lt;/p&gt;&lt;p&gt;With this approach, we show that robust parameter estimates account for differences between cultivars, ripening groups as well as different environmental conditions. The parameterized model can be used for large-scale phenology predictions of silage maize grown across Germany. These parameter estimates may perform better than independent species- or cultivar-specific estimates, in predicting phenology of future cultivars where specific cultivar characteristics are not known.&lt;/p&gt;

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