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<h1 class="title toc-ignore">Data sets used in this primer</h1>
</div>
<div id="aflp-diploid-clonal-aeut" class="section level2">
<h2>AFLP (diploid, clonal): <code>Aeut</code></h2>
<p>This data is for a population of the diploid plant pathogen <em>Aphanomyces euteiches</em> using AFLP as a marker system <span class="citation">(Grünwald & Hoheisel, 2006)</span>. A total of 187 pathogen isolates were sampled hierarchically in two regions in Oregon (N = 97) and Washington (N = 90). The alleles observed were treated as dominant markers with presence or absence. Analysis included clone-correction, genotypic diversity, linkage disequilibrium using the index of association, dendrograms based on Nei’s genetic distance, and AMOVA.</p>
</div>
<div id="microsatellite-haploid-clonal-monpop" class="section level2">
<h2>Microsatellite (haploid, clonal): <code>monpop</code></h2>
<p>This is microsatellite data for a population of the haploid plant pathogen <em>Monilinia fructicola</em> that causes disease within peach tree canopies <span class="citation">(Everhart & Scherm, 2015)</span>. Entire populations within trees were sampled across 3 years (2009, 2010, and 2011) in a total of four trees, where one tree was sampled in all three years, for a total of 6 within-tree populations. Within each year, samples in the spring were taken from affected blossoms (termed “BB” for blossom blight) and in late summer from affected fruits (termed “FR” for fruit rot). There are a total of 694 isolates with 65 to 173 isolates within each canopy population that were characterized using a set of 13 microsatellite markers.</p>
</div>
<div id="microsatellite-diploid-sexual-microbov" class="section level2">
<h2>Microsatellite (diploid, sexual): <code>microbov</code></h2>
<p>This data set contains 704 bovine samples over 30 microsatellite loci for 15 breeds, 2 species and 2 countries. From <span class="citation">(Laloe et al., 2007)</span>.</p>
</div>
<div id="microsatellite-diploid-sexual-nancycats" class="section level2">
<h2>Microsatellite (diploid, sexual): <code>nancycats</code></h2>
<p>This is a data set of 217 cats <em>Felis catus</em> L. from Nancy, France genotyped over 9 microsatellite loci. They have been divided into 17 populations with spatial coordinates in the <code>@other</code> slot. It comes from the <em>adegenet</em> package without a published reference. Likely, the source paper is <a href="http://dx.doi.org/10.1016/j.mambio.2008.01.001">here</a>.</p>
</div>
<div id="microsatellite-triploid-sexualclonal-pinf" class="section level2">
<h2>Microsatellite (triploid, sexual/clonal): <code>Pinf</code></h2>
<p>This microsatellite data comes from a larger data set of populations of <em>Phytophthora infestans</em> <span class="citation">(Goss et al., 2014)</span>. It contains 86 individuals representing 72 multilocus genotypes that have been genotyped over 11 loci. They are grouped by continent and country. This data set is used to demonstrate clone correction and linkage disequilibrium.</p>
</div>
<div id="microsatellite-diploid-clonal-pram" class="section level2">
<h2>Microsatellite (diploid, clonal): <code>Pram</code></h2>
<p>This data set contains populations of <em>Phytophthora ramorum</em> from Nurseries in California and Oregon <span class="citation">(Goss et al., 2009)</span> and Forests in Curry County, Oregon from 2001 to 2014 <span class="citation">(Kamvar et al., 2015)</span>. There are 729 samples representing 98 multilocus genotypes genotyped over 5 microsatellite loci.</p>
</div>
<div id="snp-haploid-clonal-h3n2" class="section level2">
<h2>SNP (haploid, clonal): <code>H3N2</code></h2>
<p>This is a SNP data set from the hemaglutinin segment of the H3N2 strain of seasonal influenza contained within the <em>adegenet</em> package. It contains 1902 samples genotyped over 125 SNP markers. It contains a wealth of information in the <code>@other</code> slot including year isolated, month isolated, country of origin, and more. This data set is utilized to demonstrate the DAPC function in <em>adegenet</em>.</p>
</div>
<div id="gbs-diploid-prubi_gbs" class="section level2">
<h2>GBS (diploid): <code>Prubi_gbs</code></h2>
<p>We will use a data set of 94 samples of the red raspberry pathogen <em>Phytophthora rubi</em> <span class="citation">(Tabima et al., 2018)</span>. This pathogen is diploid and a fungal like Oomycete. Populations were obtained by sampling individual pathogen strains from roots of infected red raspberry in the states of California (CA), Oregon (OR), and Washington (WA). A total of 94 samples of <em>P. rubi</em> were sequenced using the Illumina HiSeq 3000 technology with 150 bp paired end reads and a target insert size of 500 bp. Currently, there is little information about the population structure of <em>P. rubi</em> in the western USA. We are interested in studying the population structure of <em>P. rubi</em> populations in the western US. The VCF data for this population can be downloaded from: <a href="prubi_gbs.vcf.gz">prubi_gbs.vcf.gz</a>.</p>
</div>
<div id="genomic-diploid-pinfsc50" class="section level2">
<h2>Genomic (diploid): <code>pinfsc50</code></h2>
<p>For genomics examples we’ll use the pinfsc50 dataset. The <a href="https://CRAN.R-project.org/package=pinfsc50">pinfsc50</a> dataset is from a number of published <em>P. infestans</em> genomics projects where the data has been subset here to supercontig_1.50. This dataset is available as a stand alone R package <span class="citation">(Knaus & Grünwald, 2017)</span>. By subsetting the data to one supercontig it creates a dataset of a size that can be conveniently used for examples. This dataset illustrates some important strengths and weaknesses of these studies. A strength is the amount of data we have for each individual. Among the weaknesses are that the samples are ‘opportunistic’ in that we have no control over the design of the experiment. Also, because of the large investment in data per sample, there is a relatively small number of samples.</p>
</div>
<div id="references" class="section level2 unnumbered">
<h2>References</h2>
<div id="refs" class="references">
<div id="ref-everhart2014finescale">
<p>Everhart S., Scherm H. 2015. Fine-scale genetic structure of <em>Monilinia fructicola</em> during brown rot epidemics within individual peach tree canopies. <em>Phytopathology</em> 105:542–549. Available at: <a href="https://doi.org/10.1094/PHYTO-03-14-0088-R">https://doi.org/10.1094/PHYTO-03-14-0088-R</a></p>
</div>
<div id="ref-goss2009population">
<p>Goss EM., Larsen M., Chastagner GA., Givens DR., Grünwald NJ. 2009. Population genetic analysis infers migration pathways of phytophthora ramorum in us nurseries. <em>PLoS Pathog</em> 5:e1000583. Available at: <a href="http://dx.doi.org/10.1371/journal.ppat.1000583">http://dx.doi.org/10.1371/journal.ppat.1000583</a></p>
</div>
<div id="ref-goss2014irish">
<p>Goss EM., Tabima JF., Cooke DEL., Restrepo S., Fry WE., Forbes GA., Fieland VJ., Cardenas M., Grünwald NJ. 2014. The Irish potato famine pathogen <em>phytophthora infestans</em> originated in central mexico rather than the andes. <em>Proceedings of the National Academy of Sciences</em> 111:8791–8796. Available at: <a href="http://www.pnas.org/content/early/2014/05/29/1401884111.abstract">http://www.pnas.org/content/early/2014/05/29/1401884111.abstract</a></p>
</div>
<div id="ref-grunwald2006hierarchical">
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