Data and code from: Ecosystem functional response across precipitation extremes in a sagebrush steppe

<div><b>usses_water: Experimental Test of Climate Change Impacts on Grassland ANPP</b></div><div><br></div><div>Research project data and code for an analysis of drought and irrigation experiment at US Sheep Experiment State (USSES) near Dubois, ID.</div><div>Goal is to quantify the impact of a 50% increase/decrease of precipitation on:</div><div><br></div><div>* ANPP through time</div><div>* Relationship of ANPP to soil moisture</div><div>* Species composition</div><div><br></div><div><b>Running the code</b><br></div><div><br></div><div>To fully run this code you will need R and a number of R packages.</div><div>Running `00_source_usses_water_scripts` in the `code/` directory will run all necessary scripts to complete the analysis.</div><div>The code will also stop and send errors letting you know what R packages need to be installed.</div><div>Once all packages are installed, the code should run all the way through.</div><div><br></div><div>You must source the script from RStudio, rather than from command line, because we use some Rstudio-specific commands to set working directories.</div><div><br></div><div><b>Citation information</b></div><div><br></div><div>This work has been accepted for publication in PeerJ (https://peerj.com/).</div><div>It is currently in press, so for now please cite as</div><div><br></div><div>Tredennick, A.T., A.R. Kleinhesselink, J.B. Taylor, and P.B. Adler. (In press). Ecosystem functional response across precipitation extremes in a sagebrush steppe. <i>PeerJ</i>.</div><div><br></div><div>The preprint can be found at: https://www.biorxiv.org/content/early/2018/01/24/195594.</div><div><br></div><div>Additionally, please cite the Figshare fileset if reusing data or code as:</div><div><br></div><div><div>Tredennick, A.T., A.R. Kleinhesselink, J.B. Taylor, and P.B. Adler. Data and code from: Ecosystem functional response across precipitation extremes in a sagebrush steppe. Figshare. <a rel="noreferrer noopener" target="_blank">10.6084/m9.figshare.5909998</a> </div></div><div><br></div

Data and R code

The zip archive contains the data and R code used to conduct the analyses reported in the publication. Readme files in the subdirectories contain metadata and instructions for running the code. Note that changing the directory structure will cause the R scripts to fail

Domestic sheep show average <i>Coxiella burnetii</i> seropositivity generations after a sheep-associated human Q fever outbreak and lack detectable shedding by placental, vaginal, and fecal routes

<div><p><i>Coxiella burnetii</i> is a globally distributed zoonotic bacterial pathogen that causes abortions in ruminant livestock. In humans, an influenza-like illness results with the potential for hospitalization, chronic infection, abortion, and fatal endocarditis. Ruminant livestock, particularly small ruminants, are hypothesized to be the primary transmission source to humans. A recent Netherlands outbreak from 2007–2010 traced to dairy goats resulted in over 4,100 human cases with estimated costs of more than 300 million euros. Smaller human Q fever outbreaks of small ruminant origin have occurred in the United States, and characterizing shedding is important to understand the risk of future outbreaks. In this study, we assessed bacterial shedding and seroprevalence in 100 sheep from an Idaho location associated with a 1984 human Q fever outbreak. We observed 5% seropositivity, which was not significantly different from the national average of 2.7% for the U.S. (P>0.05). Furthermore, <i>C</i>. <i>burnetii</i> was not detected by quantitative PCR from placentas, vaginal swabs, or fecal samples. Specifically, a three-target quantitative PCR of placenta identified 0.0% shedding (exact 95% confidence interval: 0.0%-2.9%). While presence of seropositive individuals demonstrates some historical <i>C</i>. <i>burnetii</i> exposure, the placental sample confidence interval suggests 2016 shedding events were rare or absent. The location maintained the flock with little or no depopulation in 1984 and without <i>C</i>. <i>burnetii</i> vaccination during or since 1984. It is not clear how a zero-shedding rate was achieved in these sheep beyond natural immunity, and more work is required to discover and assess possible factors that may contribute towards achieving zero-shedding status. We provide the first U.S. sheep placental <i>C</i>. <i>burnetii</i> shedding update in over 60 years and demonstrate potential for <i>C</i>. <i>burnetii</i> shedding to reach undetectable levels after an outbreak event even in the absence of targeted interventions, such as vaccination.</p></div

Analyses of coordinated samples from 100 ewes by <i>C</i>. <i>burnetii</i> ELISA and qPCR.

<p>Analyses of coordinated samples from 100 ewes by <i>C</i>. <i>burnetii</i> ELISA and qPCR.</p

DataSheet1_Using whole genome sequence to compare variant callers and breed differences of US sheep.docx

As whole genome sequence (WGS) data sets have become abundant and widely available, so has the need for variant detection and scoring. The aim of this study was to compare the accuracy of commonly used variant calling programs, Freebayes and GATK HaplotypeCaller (GATK-HC), and to use U.S. sheep WGS data sets to identify novel breed-associated SNPs. Sequence data from 145 sheep consisting of 14 U.S. breeds were filtered and biallelic single nucleotide polymorphisms (SNPs) were retained for genotyping analyses. Genotypes from both programs were compared to each other and to genotypes from bead arrays. The SNPs from WGS were compared to the bead array data with breed heterozygosity, principal component analysis and identifying breed associated SNPs to analyze genetic diversity. The average sequence read depth was 2.78 reads greater with 6.11% more SNPs being identified in Freebayes compared to GATK-HC. The genotype concordance of the variant callers to bead array data was 96.0% and 95.5% for Freebayes and GATK-HC, respectively. Genotyping with WGS identified 10.5 million SNPs from all 145 sheep. This resulted in an 8% increase in measured heterozygosity and greater breed separation in the principal component analysis compared to the bead array analysis. There were 1,849 SNPs identified in only the Romanov sheep where all 10 rams were homozygous for one allele and the remaining 135 sheep from 13 breeds were homozygous for the opposite allele. Both variant calling programs had greater than 95% concordance of SNPs with bead array data, and either was suitably accurate for ovine WGS data sets. The use of WGS SNPs improved the resolution of PCA analysis and was critical for identifying Romanov breed-associated SNPs. Subsets of such SNPs could be used to estimate germplasm composition in animals without pedigree information.</p