DRAWTREE
and DRAWGRAM
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.
![](7philosophy.GIF) |
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! |
![](7unroottree_small.GIF) |
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.
|
![](7roottree_small.GIF) |
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!
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