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AMOVA.html

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@@ -528,7 +529,7 @@ <h2>References</h2>
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 <div id="ref-excoffier1992analysis">
-<p>Excoffier L., Smouse PE., Quattro JM. 1992. Analysis of molecular variance inferred from metric distances among dNA haplotypes: Application to human mitochondrial dNA restriction data. <em>Genetics</em> 131:479–491. Available at: <a href="http://www.genetics.org/content/131/2/479.abstract" class="uri">http://www.genetics.org/content/131/2/479.abstract</a></p>
+<p>Excoffier L., Smouse PE., Quattro JM. 1992. Analysis of molecular variance inferred from metric distances among dna haplotypes: Application to human mitochondrial dna restriction data. <em>Genetics</em> 131:479–491. Available at: <a href="http://www.genetics.org/content/131/2/479.abstract" class="uri">http://www.genetics.org/content/131/2/479.abstract</a></p>
 </div>
 <div id="ref-grunwald2006hierarchical">
 <p>Grünwald NJ., Hoheisel G-A. 2006. Hierarchical analysis of diversity, selfing, and genetic differentiation in populations of the oomycete <em>Aphanomyces euteiches</em>. <em>Phytopathology</em> 96:1134–1141. Available at: <a href="http://apsjournals.apsnet.org/doi/abs/10.1094/PHYTO-96-1134" class="uri">http://apsjournals.apsnet.org/doi/abs/10.1094/PHYTO-96-1134</a></p>
@@ -552,6 +553,7 @@ <h2>References</h2>
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Authors.html

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@@ -276,7 +277,7 @@ <h1>
 <div class="col-md-6">
 <small> <strong>Niklaus J. Grünwald</strong> is a plant pathologist with the USDA Agricultural Research Service and a Professor in the Department of Botany and Pant Pathology and the Center for Genome Research and Biocomputing at Oregon State University. He received his PhD from UC Davis and conducted postdoctoral research at Cornell University. His research focuses on understanding the evolutionary patterns and processes of emerging pathogens using population genetic and evolutionary approaches.
 <p>
-<a href="http://grunwaldlab.cgrb.oregonstate.edu/">Grünwald lab</a> | &lt;a href=“<a href="https://scholar.google.com/citations?user=t55Dt5sAAAAJ&amp;hl=en" class="uri">https://scholar.google.com/citations?user=t55Dt5sAAAAJ&amp;hl=en</a>”&gt;Google scholar</a> | <a href="http://www.researcherid.com/rid/K-6041-2013">ResearcherID</a> | <a href="http://orcid.org/0000-0003-1656-7602">Orcid</a> | <a href="https://www.researchgate.net/profile/Niklaus_Grunwald/?ev=hdr_xprf">ResearchGate</a> | <a href="https://twitter.com/PhytophthoraLab" class="twitter-follow-button" data-show-count="false"> Follow @PhytophthoraLab </a>
+<a href="http://grunwaldlab.cgrb.oregonstate.edu/">Grünwald lab</a> | <a href="https://scholar.google.com/citations?user=t55Dt5sAAAAJ&hl=en">Google scholar</a> | <a href="http://www.researcherid.com/rid/K-6041-2013">ResearcherID</a> | <a href="http://orcid.org/0000-0003-1656-7602">Orcid</a> | <a href="https://www.researchgate.net/profile/Niklaus_Grunwald/?ev=hdr_xprf">ResearchGate</a> | <a href="https://twitter.com/PhytophthoraLab" class="twitter-follow-button" data-show-count="false"> Follow @PhytophthoraLab </a>
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 <p></small></p>
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@@ -293,7 +294,7 @@ <h1>
 <div class="col-md-6">
 <small> <strong>Zhian N. Kamvar</strong> is a graduate student in the Department of Botany and Pant Pathology at Oregon State University. His research is focused on genome sequencing and population genomics of the nursery pathogens <em>Phytophthora syringae</em> and <em>P. ramorum</em>. He is the lead developer of the <a href="http://github.com/grunwaldlab/poppr"><em>poppr</em> R package</a> and a contributor to other packages such as the <a href="http://github.com/thibautjombart/adegenet"><em>adegenet</em> R package</a> and the <a href="http://github.com/dwinter/mmod"><em>mmod</em> R package</a>. Zhian is also co-host of the award-winning radio program <a href="http://blogs.oregonstate.edu/inspiration">Inspiration</a> <a href="http://poweredbyorange.com/2013/12/17/science-through-a-microphone/">Dissemination</a>.
 <p>
-&lt;a href=“<a href="https://scholar.google.com/citations?user=UPGtLSkAAAAJ&amp;hl=en" class="uri">https://scholar.google.com/citations?user=UPGtLSkAAAAJ&amp;hl=en</a>”&gt;Google scholar</a> | <a href="https://www.researchgate.net/profile/Zhian_Kamvar">ResearchGate</a> | <a href="http://orcid.org/0000-0003-1458-7108">Orcid</a> | <a href="https://twitter.com/ZKamvar" class="twitter-follow-button" data-show-count="false"> Follow @ZKamvar </a> |
+<a href="https://scholar.google.com/citations?user=UPGtLSkAAAAJ&hl=en">Google scholar</a> | <a href="https://www.researchgate.net/profile/Zhian_Kamvar">ResearchGate</a> | <a href="http://orcid.org/0000-0003-1458-7108">Orcid</a> | <a href="https://twitter.com/ZKamvar" class="twitter-follow-button" data-show-count="false"> Follow @ZKamvar </a> |
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DAPC.html

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@@ -507,7 +508,7 @@ <h1>Conclusions</h1>
 <h1>References</h1>
 <div id="refs" class="references">
 <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" class="uri">http://dx.doi.org/10.1371/journal.ppat.1000583</a></p>
+<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" class="uri">http://dx.doi.org/10.1371/journal.ppat.1000583</a></p>
 </div>
 <div id="ref-grunwald2011evolution">
 <p>Grünwald NJ., Goss EM. 2011. Evolution and population genetics of exotic and re-emerging pathogens: Novel tools and approaches. <em>Annual Review of Phytopathology</em> 49:249–267. Available at: <a href="http://www.annualreviews.org/doi/abs/10.1146/annurev-phyto-072910-095246?journalCode=phyto" class="uri">http://www.annualreviews.org/doi/abs/10.1146/annurev-phyto-072910-095246?journalCode=phyto</a></p>
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Data_Preparation.html

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Data_sets.html

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@@ -299,7 +300,7 @@ <h2>References</h2>
 <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.</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" class="uri">http://dx.doi.org/10.1371/journal.ppat.1000583</a></p>
+<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" class="uri">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" class="uri">http://www.pnas.org/content/early/2014/05/29/1401884111.abstract</a></p>
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First_Steps.html

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@@ -426,58 +427,58 @@ <h2>Calculating genotypic diversity</h2>
 </colgroup>
 <thead>
 <tr class="header">
-<th align="left">Abbreviation</th>
-<th align="left">Statistic</th>
+<th>Abbreviation</th>
+<th>Statistic</th>
 </tr>
 </thead>
 <tbody>
 <tr class="odd">
-<td align="left"><code>Pop</code></td>
-<td align="left">Population name.</td>
+<td><code>Pop</code></td>
+<td>Population name.</td>
 </tr>
 <tr class="even">
-<td align="left"><code>N</code></td>
-<td align="left">Number of individuals observed.</td>
+<td><code>N</code></td>
+<td>Number of individuals observed.</td>
 </tr>
 <tr class="odd">
-<td align="left"><code>MLG</code></td>
-<td align="left">Number of multilocus genotypes (MLG) observed.</td>
+<td><code>MLG</code></td>
+<td>Number of multilocus genotypes (MLG) observed.</td>
 </tr>
 <tr class="even">
-<td align="left"><code>eMLG</code></td>
-<td align="left">The number of expected MLG at the smallest sample size ≥ 10 based on rarefaction</td>
+<td><code>eMLG</code></td>
+<td>The number of expected MLG at the smallest sample size ≥ 10 based on rarefaction</td>
 </tr>
 <tr class="odd">
-<td align="left"><code>SE</code></td>
-<td align="left">Standard error based on eMLG.</td>
+<td><code>SE</code></td>
+<td>Standard error based on eMLG.</td>
 </tr>
 <tr class="even">
-<td align="left"><code>H</code></td>
-<td align="left">Shannon-Wiener Index of MLG diversity <span class="citation">(Shannon, 2001)</span>.</td>
+<td><code>H</code></td>
+<td>Shannon-Wiener Index of MLG diversity <span class="citation">(Shannon, 2001)</span>.</td>
 </tr>
 <tr class="odd">
-<td align="left"><code>G</code></td>
-<td align="left">Stoddart and Taylor’s Index of MLG diversity <span class="citation">(Stoddart &amp; Taylor, 1988)</span>.</td>
+<td><code>G</code></td>
+<td>Stoddart and Taylor’s Index of MLG diversity <span class="citation">(Stoddart &amp; Taylor, 1988)</span>.</td>
 </tr>
 <tr class="even">
-<td align="left"><code>lambda</code></td>
-<td align="left">Simpson’s Index <span class="citation">(Simpson, 1949)</span>.</td>
+<td><code>lambda</code></td>
+<td>Simpson’s Index <span class="citation">(Simpson, 1949)</span>.</td>
 </tr>
 <tr class="odd">
-<td align="left"><code>E.5</code></td>
-<td align="left">Evenness, <span class="math inline">\(E_5\)</span> <span class="citation">(Pielou, 1975; Ludwig &amp; Reynolds, 1988; Grünwald et al., 2003)</span>.</td>
+<td><code>E.5</code></td>
+<td>Evenness, <span class="math inline">\(E_5\)</span> <span class="citation">(Pielou, 1975; Ludwig &amp; Reynolds, 1988; Grünwald et al., 2003)</span>.</td>
 </tr>
 <tr class="even">
-<td align="left"><code>Hexp</code></td>
-<td align="left">Nei’s unbiased gene diversity <span class="citation">(Nei, 1978)</span>.</td>
+<td><code>Hexp</code></td>
+<td>Nei’s unbiased gene diversity <span class="citation">(Nei, 1978)</span>.</td>
 </tr>
 <tr class="odd">
-<td align="left"><code>Ia</code></td>
-<td align="left">The index of association, <span class="math inline">\(I_A\)</span> <span class="citation">(Brown, Feldman &amp; Nevo, 1980; Smith et al., 1993)</span>.</td>
+<td><code>Ia</code></td>
+<td>The index of association, <span class="math inline">\(I_A\)</span> <span class="citation">(Brown, Feldman &amp; Nevo, 1980; Smith et al., 1993)</span>.</td>
 </tr>
 <tr class="even">
-<td align="left"><code>rbarD</code></td>
-<td align="left">The standardized index of association, <span class="math inline">\(\bar{r}_d\)</span> <span class="citation">(Agapow &amp; Burt, 2001)</span>.</td>
+<td><code>rbarD</code></td>
+<td>The standardized index of association, <span class="math inline">\(\bar{r}_d\)</span> <span class="citation">(Agapow &amp; Burt, 2001)</span>.</td>
 </tr>
 </tbody>
 </table>
@@ -510,9 +511,6 @@ <h2>References</h2>
 <div id="ref-grunwald2006hierarchical">
 <p>Grünwald NJ., Hoheisel G-A. 2006. Hierarchical analysis of diversity, selfing, and genetic differentiation in populations of the oomycete <em>Aphanomyces euteiches</em>. <em>Phytopathology</em> 96:1134–1141. Available at: <a href="http://apsjournals.apsnet.org/doi/abs/10.1094/PHYTO-96-1134" class="uri">http://apsjournals.apsnet.org/doi/abs/10.1094/PHYTO-96-1134</a></p>
 </div>
-<div id="ref-hurlbert1971nonconcept">
-<p>Hurlbert SH. 1971. The nonconcept of species diversity: A critique and alternative parameters. <em>Ecology</em> 52:577–586. Available at: <a href="http://www.jstor.org/discover/10.2307/1934145?uid=3739856&amp;uid=2&amp;uid=4&amp;uid=3739256&amp;sid=21103760010461" class="uri">http://www.jstor.org/discover/10.2307/1934145?uid=3739856&amp;uid=2&amp;uid=4&amp;uid=3739256&amp;sid=21103760010461</a></p>
-</div>
 <div id="ref-ludwig1988statistical">
 <p>Ludwig JA., Reynolds JF. 1988. <em>Statistical ecology: A primer in methods and computing</em>. Wiley.com.</p>
 </div>
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