The demonstration that proteins are frequently similar in many species begs for an explanation.  The DRAWTREE and DRAWGRAM algorithms use the sequence differences calculated by CLUSTAL W to generate graphics which illustrate phylogenetic trees and genetic distance ( see below for an explanation of these terms), and provide insight into the evolutionary divergence of the species. The biological interpretation of the similarities and differences in the amino acid sequences between species is that these changes represent evolutionary differences.  Two proteins which are very similar to each other (such as human and chimpanzee myoglobins) will have the same amino acids at most positions - these are said to be conserved.  When the amino acid sequences are "highly conserved" the two species are considered to be evolutionarily close to each other.  The extent of conservation is therefore a measure of genetic distance and allows us to retrace the course of evolution which can then be depicted as a phylogenetic tree.

The above  is a personal statement by Dr. William Barnes to promote individual thought about these topics.

An Unrooted Phylogenetic Tree The "RETURN" button in BOXSHADE should have returned you to the Biology Workbench Alignment Tools page which shows the CLUSTAL W alignment (below).
Click to see thumbnail full-size!	As before, click on the check box to select the CLUSTAL W alignment.  This time however, instead of selecting BOXSHADE in the scroll box, click on DRAWTREE.  Click on the "Run" button.
Click to see thumbnail full-size!	A new page will appear which is entitled: "DRAWTREE - Draw Unrooted Phylogenetic Tree from Alignment".  Leave all the selection boxes at their default values.  Click on the "Submit" button.
Click to see thumbnail full-size!	A page entitled "DRAWTREE - Draw Unrooted Phylogenetic Tree from Alignment" will appear with the output from DRAWTREE.  This includes a list of the sequences analyzed and a graphic showing their similarity, and by implication, the evolutionary relationships of the species.  It should appear as shown below.
Download the graphic by placing the cursor over it, holding down the right mouse button and selecting "save image as".  In the dialog box, enter a title and select a destination for the file.  Click on "Save" to download as a gif file. Click on the "RETURN" button to go back to the Biology Workbench Alignment Tools page.

A Rooted Phylogenetic Tree The "RETURN" button in DRAWTREE should have returned you to the Biology Workbench Alignment Tools page which shows the CLUSTAL W alignment (below).
Click to see thumbnail full-size!	As before, click on the check box to select the CLUSTAL W alignment.  This time however, instead of selecting DRAWTREE in the scroll box, click on DRAWGRAM.  Click on the "Run" button.
Click to see thumbnail full-size!	A new page will appear which is entitled: "DRAWGRAM - Draw Rooted Phylogenetic Tree from Alignment".  Leave all the selection boxes at their default values.  Click on the "Submit" button.
Click to see thumbnail full-size!	A page entitled "DRAWGRAM - Draw Rooted Phylogenetic Tree from Alignment" will appear with the output from DRAWTREE.  This includes a list of the sequences analyzed and a graphic showing their similarity, and by implication, the evolutionary relationships of the species.  It should appear as shown below.
Download the graphic by placing the cursor over it, holding down the right mouse button and selecting "save image as".  In the dialog box, enter a title and select a destination for the file.  Click on "Save" to download as a gif file. Click on the "RETURN" button to go back to the Biology Workbench Alignment Tools page.

A closer look at the output from DRAWTREE and DRAWGRAM:
 

click on the images to see them full size!

An unrooted phylogenetic tree drawn to emphasize genetic distance with DRAWTREE. Note:   Humans These trees actually show the evolutionary divergence of the myoglobin gene - not necessarily the divergence of individual species. For example the myoglobin family of genes may have undergone a rapid diversification among mammals 40 million years ago (50 mya), while another family of genes underwent a rapid diversification only 15 mya. Also the same genes may diverge at different rates in different taxa. It would be expected that these differences in evolutionary tempo would produce different rooted and unrooted trees. Thus the inference of species evolution must be based on many gene families.

A rooted phylogenetic tree drawn to emphasize evolutionary divergence from a common ancestor with DRAWGRAM. Note:   Humans are closely related to gorillas and chimpanzees, but it is not true that we are descended from them.  Instead all three species diverged from a shared ancestral species, which has since become extinct, and have evolved independently over the last 10 million years or so.  An analogy is family relationships - second cousins are certainly related to each other, but they are not descended from the same parents. "Creation Scientists" frequently say that evolution claims that "humans descended from apes".  This is an oversimplification and a  distortion of what evolutionary theory really says!