Creating a Phylogenetic Tree

Evolutionary or phylogenetic trees are classification tools that are generated to show how closely related different organisms are to each other. This part of the tutorial will show you how to create a phylogenetic tree. First, we need to import sequences to use in our tree.

1. You need to return to the Protein Tools homepage. In the"Show Records" window, click on the"Return" button at the bottom of the page.

2. In the Protein Tools homepage, highlight"Ndjinn ¡V Multiple Search Database" and click "Run".



3. In the input box, type"glycine trna" and select"All" in the"Hits per page" drop-down menu. (Glycine transfer RNAs (tRNAs) are informational genes that are highly conserved (changed very little over long periods of time) because they are needed for protein synthesis, hence, they are indispensable to the cell.) Select the"SWISSPROT" database and click"Search".





The next page will display the results of your search. To generate a good phylogenetic tree, we need to include sequences that represent organisms from the three Domains of life. From the search results, select the following sequences:

SWISSPROT:SYGB_ECOLI SWISSPROT:SYG_CHLTR SWISSPROT:SYG_CHLPN SWISSPROT:SYG_CHLMU SWISSPROT:SYGB_THEMA SWISSPROT:SYGB_SYNY3 SWISSPROT:SYG_HUMAN SWISSPROT:SYG_YEAST SWISSPROT:SYG_SCHPO SWISSPROT:SYG_PYRHO SWISSPROT:SYG_PYRAB SWISSPROT:SYG_METTH SWISSPROT:SYG_METJA SWISSPROT:SYG_CAEEL SWISSPROT:SYG_BOMMO SWISSPROT:SYG_ARCFU SWISSPROT:SYG_ARATH SWISSPROT:SYG_AERPE

Detailed descriptions of each sequence are provided. However, if you would like to see more information on a sequence (such as the full name of the organism, the sequence of the protein, full classification of the organism, etc.), select the sequence you would like more information about and click on the"Show Records" button.

4. Click on the"Import Sequences" button. All of the sequences that you have selected will be sent to the Protein Tools homepage.



5. Select all of the sequences that you just imported, highlight CLUSTALW in the tool menu and click on "Run"



6. On the next page, select"Rooted and Unrooted Trees" in the pull-down menu for"Guide tree display". Leave everything else as is and click on"Submit".



On the next page, a sequence alignment, a rooted tree and an unrooted tree should appear. Scroll down the page to view the different trees. Looking at the rooted tree (duplicated below), you can see that it has three prominent branches all resulting from one root (representing a common ancestor). ECOLI, CHLTR, CHLPN, CHLMU, THEMA and SYNY3 are all in one cluster which represents the Domain (EU)BACTERIA. HUMAN, YEAST, SCHPO, CAEEL, BOMMO and ARATH are in another cluster, which represents the Domain EUKARYA, and PYRHO, PYRAB, METTH, METJA, ARCFU are in yet another cluster which represents the third domain ARCHAEBACTERIA. However, more important to notice is the fact that the two lower clusters are closer to each other than to the top cluster, that is, the length of the branch connecting the two lower clusters is shorter than the branch connecting them to the top cluster. This shows that the two lower clusters, representing the Eukarya and Archaebacteria, are more closely related to each other than they are to the top cluster which represents the Eubacteria or"true" bacteria. This is even more dramatically illustrated by the unrooted tree which is also shown below. These observations support the findings of Carl Woese et al.





The exercises that you did here explored just a few of the many tools available in the Biology Workbench. There are many other things that the Workbench can do which will be explored in other tutorials. When you are finished using the Workbench, just close your window. All of the sequences that you imported and the alignments that you generated will be saved and can be accessed at any time by"resuming" your"Superkingdoms" session.