https://wiki.genometracker.org/index.php?action=history&feed=atom&title=Qubi%2Fbiol200Qubi/biol200 - Revision history2026-05-27T22:26:33ZRevision history for this page on the wikiMediaWiki 1.39.2https://wiki.genometracker.org/index.php?title=Qubi/biol200&diff=1710&oldid=previmported>Dphilli at 07:14, 6 August 20132013-08-06T07:14:21Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Procedures==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Procedures==</div></td></tr>
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<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">1. <big>'''Microarray Color Prediction.'''</big></del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">: Consider a microarray with only two spots, one for Gene A and one for Gene B. A researcher cultures two yeast strains in Glucose solution, extracts mRNA from the cells, creates cDNA with either red dye (for the experimental strain) or green dye (for the control strain). The dye containing cDNA is then allowed to combine with a microarray containing spots with complementary DNA for Gene A and Gene B. In each situation below, predict what color the two spots will show. The first answer is filled in for you as an example.</del></div></td><td colspan="2" class="diff-side-added"></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Access the NCBI website: http://www.ncbi.nlm.nih.gov/</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Access the NCBI website: http://www.ncbi.nlm.nih.gov/</div></td></tr>
</table>imported>Dphillihttps://wiki.genometracker.org/index.php?title=Qubi/biol200&diff=1709&oldid=previmported>Dphilli at 06:19, 6 August 20132013-08-06T06:19:10Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Procedures==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Procedures==</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"><small>'''''Materials:'''''</small> <small>Computer</small></del></div></td><td colspan="2" class="diff-side-added"></td></tr>
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<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"># Examine </del>'''<del style="font-weight: bold; text-decoration: none;">Table I</del>''', <del style="font-weight: bold; text-decoration: none;">select representative species </del>from <del style="font-weight: bold; text-decoration: none;">''Bergey’s Manual''</del>. <del style="font-weight: bold; text-decoration: none;"> Select 2 prokaryotic species from </del>each <del style="font-weight: bold; text-decoration: none;">group</del>, <del style="font-weight: bold; text-decoration: none;">giving 14 prokaryotic species total</del>. <del style="font-weight: bold; text-decoration: none;"> Also select the Eukaryotic representative, Saccharomyces cerevisiae</del>.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">1. <big></ins>'''<ins style="font-weight: bold; text-decoration: none;">Microarray Color Prediction.</ins>'''<ins style="font-weight: bold; text-decoration: none;"></big></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">: Consider a microarray with only two spots</ins>, <ins style="font-weight: bold; text-decoration: none;">one for Gene A and one for Gene B. A researcher cultures two yeast strains in Glucose solution, extracts mRNA </ins>from <ins style="font-weight: bold; text-decoration: none;">the cells, creates cDNA with either red dye (for the experimental strain) or green dye (for the control strain). The dye containing cDNA is then allowed to combine with a microarray containing spots with complementary DNA for Gene A and Gene B</ins>. <ins style="font-weight: bold; text-decoration: none;">In </ins>each <ins style="font-weight: bold; text-decoration: none;">situation below</ins>, <ins style="font-weight: bold; text-decoration: none;">predict what color the two spots will show</ins>. <ins style="font-weight: bold; text-decoration: none;">The first answer is filled in for you as an example</ins>.</div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Access the NCBI website: http://www.ncbi.nlm.nih.gov/</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Access the NCBI website: http://www.ncbi.nlm.nih.gov/</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Under the '''“Search”''' category, select '''“Nucleotide”'''.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Under the '''“Search”''' category, select '''“Nucleotide”'''.</div></td></tr>
</table>imported>Dphillihttps://wiki.genometracker.org/index.php?title=Qubi/biol200&diff=1708&oldid=previmported>Dphilli at 06:16, 6 August 20132013-08-06T06:16:27Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Materials and Methods==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Materials and Methods==</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">???</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">In this bioinformatics exercise, you will perform analysis of data from a microarray study of yeast cells by DeRisi et al (1997). At the time of the study, while many genes involved in glucose utilization had been identified, it was not clear what other genes in the yeast genome might also be involved. Furthermore, although the genome-sequencing project revealed a total of about 6,000 Open Reading Frames (ORFs, consisting of known and hypothesized genes) in the yeast genome, the functions of most of these genes were unknown. The microarray study by DeRisi et al (1997) had thus two main purposes. The first goal was to identify all genes in the yeast genome that are involved in glucose metabolism. The second goal was to characterize functions of unknown genes based on their patterns of gene expression during a physiological change.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">The approach of the DeRisi study is to use Yeast Genome Chips to take snap shots of gene expression of the yeast genome at 2hour intervals during cell growth. During the course of the experiment, the yeast cells underwent the “''diauxic shift''” from anaerobic glucose fermentation (in which alcohol is produced) to aerobic respiration (in which alcohol is used as the carbon and energy source after the glucose is exhausted). The Yeast Genome Chip is a high-density microscopic glass slide printed robotically with oligonucleotide probes, each of which is specific to one of the 6,400 ORFs found in the yeast genome.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">At each time point, an ''experimental sample'' was created by extracting cellular mRNAs and reverse transcribing the mRNAs into cDNAs in the presence of the Cy5 (a fluorescent dye, shown in red) labeled dUTPs. A reference sample was made from the cells at the start of the experiment and was labeled with another fluorescent dye Cy3 (shown in green). The experimental sample and the reference were mixed and applied to the Yeast Genome Chip. After hybridization and excessive samples washed away, the DNA chip was measured for fluorescent intensity of both the Cy3 and Cy5 dyes ('''Figure 1 & 2'''). At each probe location on the DNA chip, the relative ratio of the Cy5/Cy3 intensities reveals the level of expression of a particular gene relative to that of the reference (startingpoint) sample.</ins></div></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Procedures==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Procedures==</div></td></tr>
</table>imported>Dphillihttps://wiki.genometracker.org/index.php?title=Qubi/biol200&diff=1707&oldid=previmported>Dphilli at 06:06, 6 August 20132013-08-06T06:06:49Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Of course, when comparing DNA sequences, the question of which genes to use arises. The most widely used genes are those coding for the 16S rRNA gene in prokaryotes and the 18S rRNA gene in eukaryotes. These genes code for small subunit ribosomal RNA and are used for evolutionary analysis because they '''1)''' are found in all organisms, '''2)''' are functionally conserved, '''3)''' vary only slightly between organisms (their nucleotide sequence changed slowly throughout evolution), and '''4)''' have adequate length. In this lab, you will be performing evolutionary analysis by constructing a phylogram of 15 microbes spanning bacteria, archaea and eukarya. You will find and download rRNA sequences, align them and use that alignment to create a phylogram.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Of course, when comparing DNA sequences, the question of which genes to use arises. The most widely used genes are those coding for the 16S rRNA gene in prokaryotes and the 18S rRNA gene in eukaryotes. These genes code for small subunit ribosomal RNA and are used for evolutionary analysis because they '''1)''' are found in all organisms, '''2)''' are functionally conserved, '''3)''' vary only slightly between organisms (their nucleotide sequence changed slowly throughout evolution), and '''4)''' have adequate length. In this lab, you will be performing evolutionary analysis by constructing a phylogram of 15 microbes spanning bacteria, archaea and eukarya. You will find and download rRNA sequences, align them and use that alignment to create a phylogram.</div></td></tr>
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<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">==Materials and Methods==</ins></div></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Procedures==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Procedures==</div></td></tr>
</table>imported>Dphillihttps://wiki.genometracker.org/index.php?title=Qubi/biol200&diff=1706&oldid=previmported>Dphilli at 04:50, 30 July 20132013-07-30T04:50:50Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>==References==</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>==References <ins style="font-weight: bold; text-decoration: none;">& Resources</ins>==</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#Jungck, J. R.; Fass, M.F.; Stanley, E. D. (ed.). 2003 (2006 Revision). Microbes Count! Problem Posing, Problem Solving, and Peer Persuasion in Microbiology. BioQUEST Curriculum Consortium. (Chapter 6, pg 191)</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#Jungck, J. R.; Fass, M.F.; Stanley, E. D. (ed.). 2003 (2006 Revision). Microbes Count! Problem Posing, Problem Solving, and Peer Persuasion in Microbiology. BioQUEST Curriculum Consortium. (Chapter 6, pg 191)</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#Holt. J. G. Editor-in-Chief (1984). Bergey’s Manual of Systematic Bacteriology, Volume 1-4. Williams & Wilkins: Baltimore. http://www.cme.msu.edu/bergeys/pubinfo.html</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#Holt. J. G. Editor-in-Chief (1984). Bergey’s Manual of Systematic Bacteriology, Volume 1-4. Williams & Wilkins: Baltimore. http://www.cme.msu.edu/bergeys/pubinfo.html</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>--[[User:Dphilli|Dphilli]] ([[User talk:Dphilli|talk]]) 21:35, 29 July 2013 (EDT)</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>--[[User:Dphilli|Dphilli]] ([[User talk:Dphilli|talk]]) 21:35, 29 July 2013 (EDT)</div></td></tr>
</table>imported>Dphillihttps://wiki.genometracker.org/index.php?title=Qubi/biol200&diff=1705&oldid=previmported>Dphilli at 04:50, 30 July 20132013-07-30T04:50:10Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Introduction==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Introduction==</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>[[File:TreeLife.PNG|thumb|frameless<del style="font-weight: bold; text-decoration: none;">|left</del>|'''Figure 1'''. Tree of life based on 16S ribosomal RNA (image credit: NR Pace, Science 1997)]]</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>[[File:TreeLife.PNG|thumb|frameless|'''Figure 1'''. Tree of life based on 16S ribosomal RNA (image credit: NR Pace, Science 1997)]]</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Evolution can be defined as descent with modification. In other words, changes in the nucleotide sequence of an organsim’s genomic DNA is inherited by the next generation. According to this, all organisms are related through descent from an ancestor that lived in the distant past. Since that time, about 4 billion years ago, life has undergone an extensive process of change as new kinds of organisms arose from other kinds existing in the past.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Evolution can be defined as descent with modification. In other words, changes in the nucleotide sequence of an organsim’s genomic DNA is inherited by the next generation. According to this, all organisms are related through descent from an ancestor that lived in the distant past. Since that time, about 4 billion years ago, life has undergone an extensive process of change as new kinds of organisms arose from other kinds existing in the past.</div></td></tr>
</table>imported>Dphillihttps://wiki.genometracker.org/index.php?title=Qubi/biol200&diff=1704&oldid=previmported>Dphilli at 04:49, 30 July 20132013-07-30T04:49:33Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Introduction==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Introduction==</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>[[File:TreeLife.PNG|thumb|frameless|'''Figure 1'''. Tree of life based on 16S ribosomal RNA (image credit: NR Pace, Science 1997)]]</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>[[File:TreeLife.PNG|thumb|frameless<ins style="font-weight: bold; text-decoration: none;">|left</ins>|'''Figure 1'''. Tree of life based on 16S ribosomal RNA (image credit: NR Pace, Science 1997)]]</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Evolution can be defined as descent with modification. In other words, changes in the nucleotide sequence of an organsim’s genomic DNA is inherited by the next generation. According to this, all organisms are related through descent from an ancestor that lived in the distant past. Since that time, about 4 billion years ago, life has undergone an extensive process of change as new kinds of organisms arose from other kinds existing in the past.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Evolution can be defined as descent with modification. In other words, changes in the nucleotide sequence of an organsim’s genomic DNA is inherited by the next generation. According to this, all organisms are related through descent from an ancestor that lived in the distant past. Since that time, about 4 billion years ago, life has undergone an extensive process of change as new kinds of organisms arose from other kinds existing in the past.</div></td></tr>
</table>imported>Dphillihttps://wiki.genometracker.org/index.php?title=Qubi/biol200&diff=1703&oldid=previmported>Dphilli at 04:49, 30 July 20132013-07-30T04:49:13Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Introduction==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Introduction==</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Evolution can be defined as descent with modification. In other words, changes in the nucleotide sequence of an organsim’s genomic DNA is inherited by the next generation. According to this, all organisms are related through descent from an ancestor that lived in the distant past. Since that time, about 4 billion years ago, life has undergone an extensive process of change as new kinds of organisms arose from other kinds existing in the past.</del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[File:TreeLife.PNG|thumb|frameless|'''Figure 1'''. Tree of life based on 16S ribosomal RNA (image credit: NR Pace, Science 1997)]]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[File:TreeLife.PNG|thumb|frameless|'''Figure 1'''. Tree of life based on 16S ribosomal RNA (image credit: NR Pace, Science 1997)]]</div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Evolution can be defined as descent with modification. In other words, changes in the nucleotide sequence of an organsim’s genomic DNA is inherited by the next generation. According to this, all organisms are related through descent from an ancestor that lived in the distant past. Since that time, about 4 billion years ago, life has undergone an extensive process of change as new kinds of organisms arose from other kinds existing in the past.</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The evolutionary history of a group is called a phylogeny, and can be represented by a phylogram ['''''Figure 1''''']. A major goal of evolutionary analysis is to understand this history. We do not have direct knowledge of the path of evolution, as by definition, extinct organisms no longer exist. Therefore, phylogeny must be inferred indirectly. Originally, evolutionary analysis was based upon the organisms’ morphology and metabolism. This is the basis for the Linnaean classification scheme (the “Five Kingdoms” scheme). However, this method can lead to mistaken relationships. Different species living in the same environment may have similar morphologies in order to deal with specific environmental factors. Thus these similarities have nothing to do with how related the organisms are, but are a direct result of shared surroundings. However, with the advent of genomics, organisms can be grouped based upon their sequence relatedness. Since evolution is a process of inherited nucleotide change, analyzing DNA sequence differences allows for the reconstruction of a better phylogenetic history.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The evolutionary history of a group is called a phylogeny, and can be represented by a phylogram ['''''Figure 1''''']. A major goal of evolutionary analysis is to understand this history. We do not have direct knowledge of the path of evolution, as by definition, extinct organisms no longer exist. Therefore, phylogeny must be inferred indirectly. Originally, evolutionary analysis was based upon the organisms’ morphology and metabolism. This is the basis for the Linnaean classification scheme (the “Five Kingdoms” scheme). However, this method can lead to mistaken relationships. Different species living in the same environment may have similar morphologies in order to deal with specific environmental factors. Thus these similarities have nothing to do with how related the organisms are, but are a direct result of shared surroundings. However, with the advent of genomics, organisms can be grouped based upon their sequence relatedness. Since evolution is a process of inherited nucleotide change, analyzing DNA sequence differences allows for the reconstruction of a better phylogenetic history.</div></td></tr>
</table>imported>Dphillihttps://wiki.genometracker.org/index.php?title=Qubi/biol200&diff=1702&oldid=previmported>Dphilli at 04:47, 30 July 20132013-07-30T04:47:13Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 04:47, 30 July 2013</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Why do we use 18S rRNA information for yeast and 16S for prokaryotes? Could we use other molecules as phylogenetic markers? What constitutes a “good” phylogenetic marker for building a tree of life?</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Why do we use 18S rRNA information for yeast and 16S for prokaryotes? Could we use other molecules as phylogenetic markers? What constitutes a “good” phylogenetic marker for building a tree of life?</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><big></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><big></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>'''Bonus Question'''</big></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>'''Bonus Question<ins style="font-weight: bold; text-decoration: none;">:</ins>'''</big></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*Define 16S “phylo-species” and “metagenomics”. Describe how PCR amplification and sequencing of 16S rRNA molecules from environmental microbial samples (e.g., sea water, soil, human gut, hot springs) can be used to define species composition of an environment.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">:</ins>*Define 16S “phylo-species” and “metagenomics”. Describe how PCR amplification and sequencing of 16S rRNA molecules from environmental microbial samples (e.g., sea water, soil, human gut, hot springs) can be used to define species composition of an environment.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----</div></td></tr>
</table>imported>Dphillihttps://wiki.genometracker.org/index.php?title=Qubi/biol200&diff=1701&oldid=previmported>Dphilli at 04:34, 30 July 20132013-07-30T04:34:57Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 04:34, 30 July 2013</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l269">Line 269:</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><big>'''Analyzing your phylogram'''</big></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><big>'''Analyzing your phylogram'''</big></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>A phyolgram is composed of nodes and branches <del style="font-weight: bold; text-decoration: none;">(</del>Figure 2<del style="font-weight: bold; text-decoration: none;">)</del>. The internal nodes represent extinct ancestors, and the tips of the branches, also called nodes, are individual strains of microorganisms that exist now, and from which the sequence data were obtained. The internal nodes are points in evolution where an extinct ancestor diverged into two new entities, each of which began to accumulate differences during its subsequent independent evolution. The branches define the order of descent and the ancestry of the nodes. The branch length represents the number of changes that have occurred along that branch. Thus, the more recently two organisms share a common ancestor, the more closely related they are. Trees can be either “unrooted” or “rooted”. Unrooted trees show the relationships among the microorganisms under study, but not the evolutionary path leading from an ancestor to a strain. A rooted tree shows the unique path from an ancestor (internal node) to each strain. Trees are rooted by inclusion of an outgroup in the analysis. An outgroup is an organism that is less closely related to the other organisms under study than the organisms are to each other.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">[[File:Phylogram.png|thumb|frameless|'''Figure 2'''. Phylogram with internal nodes (a, b, c, d) and tips (1, 2, 3, 4, 5). Nodes at the tips are species that exist today, and internal nodes are extinct ancestors.]]</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>A phyolgram is composed of nodes and branches <ins style="font-weight: bold; text-decoration: none;">['''''</ins>Figure 2<ins style="font-weight: bold; text-decoration: none;">''''']</ins>. The internal nodes represent extinct ancestors, and the tips of the branches, also called nodes, are individual strains of microorganisms that exist now, and from which the sequence data were obtained. The internal nodes are points in evolution where an extinct ancestor diverged into two new entities, each of which began to accumulate differences during its subsequent independent evolution. The branches define the order of descent and the ancestry of the nodes. The branch length represents the number of changes that have occurred along that branch. Thus, the more recently two organisms share a common ancestor, the more closely related they are. Trees can be either “unrooted” or “rooted”. Unrooted trees show the relationships among the microorganisms under study, but not the evolutionary path leading from an ancestor to a strain. A rooted tree shows the unique path from an ancestor (internal node) to each strain. Trees are rooted by inclusion of an outgroup in the analysis. An outgroup is an organism that is less closely related to the other organisms under study than the organisms are to each other.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">[[File:Phylo.PNG|thumbnail]]</del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Figure_2._Phylogram_interal_nodes.png </del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----</div></td></tr>
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</table>imported>Dphilli