Lab 08

Contents:

• Overview
• Detailed Model
• Your Tasks
• Files You Need
• Examples
• Submitting Your Assignment
• Grading Standards

The cladograms drawn in our previous lab illustrate the presume phylogenetic relationships between model species and their presumed ancestors, but the horizontal axis of those diagrams did carry any additional information. In particular, there was no presumption about how long ago in the past neighboring species may have diverged from their common ancestor.

In this lab, we refine our visualizations to produce what are known as chronograms, as we will use the horizontal axis to denote a sense of evoluationary time. If working with modern species, we will typically align all of the leaf nodes in the rightmost column, as those represent the present day. Presumed common ancestors from the past will be denoted to the left at a distance that depends on the presumed amount of time that has since passed. As an example, here is a figure taken from a 2011 article Megacycles of atmospheric carbon dioxide concentration correlate with fossil plant genome size.

While our illustration will not be quite as pretty (and uses a different convention for the y-coordinates of the internal edges), this example will be rendered as

The key to developing chronograms is that we must be given information about the presumed evolutionary scale. In the previous lab, you may recall that some of the sample trees included numeric labels for the internal nodes. For example, there was a "tree frog" tree that appeared as follows.

For whatever timescale is being used, the 5 at the node connecting Hyla versicolor and Hyla avivoca is to suggest that they diverged 5 evolutionary time units ago, while the 20 at the node connecting Triprion petasalus and Anotheca spinosa suggest they were more distant relatives. The node with label 35 that connects those two clades suggests that the common ancestor of all four of those modern species existed 35 time units ago.

In our chronograms, we will draw the horizontal lines with lengths that are proportional to those evolutionary times, thus rendering the above tree as follows.

(Note that we no longer explicitly render the numeric labels now that the branch lengths portrays such information.)

As a much smaller example, here is a raw tree in our Python format:

(50,
    (30,
        ("A", (), ()),
        ("B", (), ())
    ),
    ("C", (), ())
)

As a starting point this lab, we will soon provide you with a working implementation for the previous lab. The vertical placement of all the leaves and intermediate lines will be the same for our new figures, so your focus should be on the nubmers provided at internal nodes and how to use those to alter the lengths of the horizontal segments. However, in order to do this properly, when drawing a segment from a parent to a child, you must be aware of the evolutionary age of the parent and the evolutionary age of the child (with leaves assumed to have age 0).

In order to convey this extra information, we would like for you to change the recursive signature of the draw function to the following.

def draw(tree, xScale, yScale, parentTime):

With this new information, you should be able to determine the appropriate distance to advance (and later retreat) when tracing a horizontal edge. Of course, because we are relying on recursion, it is not just that you gain this additional information; you now have a responsibility to send the appropriate information when making recursive calls.

Finally, since the new figure style portrays the age information with edge lengths, you should modify the code so that the numeric labels are not explicitly rendered at internal nodes (though you must continue to render the labels for the leaf nodes).

We are providing you with two files:

• chronograms.py
  This is a working solution to the previous lab. this should be your starting point for this lab, though you will need to understand what modifications to make in order to produce the new illustration style.

• samples.py
  A subset of the samples from the previous lab, including the four trees that include evoluationary time as integer labels for internal nodes.

The samples file includes four example trees.

• The biggest one, named complex is the one used to generate the rendering in the overview. Specifically, we rendered that with an original call to draw(complex, 1.19, 20, 462).

• The tree frog example was rendered with an original call to draw(treeFrogs, 5, 20, 70).

• The relatively small example above was rendered with an original call to draw(small, 5, 20, 55).

• Finally, we offer a reproduction of a chronogram shown on page 118 of our text book, which if rendered as draw(p118, 5, 20, 44) should produce the image
  

One member of your partnership should electronically submit your modified file chronograms.py. The comments at the beginning of the file should clearly identify the member(s) of the partnernship.

The assignment is worth 25 points, which will be assessed as follows:

• (10 points) Correct modification to the recursive signature, including sending appropriate information to further recursive calls
• (10 points) Correct use of all the numeric information to affect the horizontal edge lengths.
• (5 points) Avoiding the rendering of internal node labels.