Difference between revisions of "Phylogenetics: Distances Lab"

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== Part B: Analysis of algae.nex ==
 
== Part B: Analysis of algae.nex ==
  
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'''Download the data file algae.nex from [http://hydrodictyon.eeb.uconn.edu/phylogenetics/labs/Spring2005/data/algae.nex here].''' This data file was originally used in a 1994 study by Lockhart et al.<ref>Lockhart, P. J., M. A. Steel, M. D. Hendy, and D. Penny. 1994. Recovering evolutionary trees under a more realistic model of sequence evolution. ''Molecular Biology and Evolution'' 11:605-612.</ref> and comprises eight 16S ribosomal RNA sequences:
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=== Create the data file algae.nex ===
 +
Click [http://hydrodictyon.eeb.uconn.edu/phylogenetics/labs/Spring2005/data/algae.nex here] to get the data, then use Ctrl-a to copy all of it from your browser window and save it to a file named algae.nex in a folder on your local hard drive. These data were originally used in a 1994 study by Lockhart et al.<ref>Lockhart, P. J., M. A. Steel, M. D. Hendy, and D. Penny. 1994. Recovering evolutionary trees under a more realistic model of sequence evolution. ''Molecular Biology and Evolution'' 11:605-612.</ref> and comprise eight 16S ribosomal RNA sequences:
 
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| ''Nicotiana'' || a chloroplast from a dicot (the flowering plant tobacco)
 
| ''Nicotiana'' || a chloroplast from a dicot (the flowering plant tobacco)
 
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All of these organisms except ''Anacystis'' and ''Olithodiscus'' have both chlorophylls a and b. It is probable (based on independent evidence) that all chlorophyll a/b-containing chloroplasts have a common endosymbiotic origin, so we would expect trees constructed from these data to show a branch separating ''Anacystis'' and ''Olithodiscus'' from everything else. The cyanobacterium ''Anacystis'' uses phycobilin accessory pigments rather than chlorophylls for photosynthesis, and the chromophyte alga ''Olithodiscus'' has chlorophylls a and c (but not b).
+
All of these organisms except ''Anacystis'' and ''Olithodiscus'' have chlorophylls a ''and'' b. It is probable (based on independent evidence) that all chlorophyll a/b-containing chloroplasts have a common endosymbiotic origin, so we would expect trees constructed from these data to show a branch separating ''Anacystis'' and ''Olithodiscus'' from everything else. The cyanobacterium ''Anacystis'' uses phycobilin accessory pigments rather than chlorophylls for photosynthesis, and the chromophyte alga ''Olithodiscus'' has chlorophylls a and c (but not b).
 +
 
 +
=== Create a PAUP* command file.===
 +
Instead of executing the file algae.nex directly in PAUP*, start PAUP* (cancel the dialog box that appears) and choose File &gt; New from the main menu to create a blank text file. Copy the following text and paste it into the new text file window, then save this file as runalgae.nex, placing it in the same directory as algae.nex:<pre>
 +
#nexus
 +
 
 +
begin paup;
 +
  log file=lab3.txt start replace;
 +
  set torder=right autoclose;
 +
  execute algae.nex;
 +
  outgroup Anacystis_nidulans;
 +
  set criterion=distance;
 +
 
 +
  [!
 +
  ******************************
 +
  ** JC69 Model, ME Criterion **
 +
  ******************************
 +
  ]
 +
  dset distance=jc objective=me;
 +
  alltrees;
 +
  describe 1;
 +
 
 +
  [other commands here]
 +
  log stop;
 +
end;</pre>
 +
 
 +
During the course of this lab, you can simply add commands to this paup block rather than creating a paup block in the data file itself. The <tt>set torder=right</tt> command simply causes trees to be displayed so that the outgroup is at the top and the tree appears to flow to the right (this is often called ''ladderizing right''). Try changing this to <tt>set torder=left</tt> to see what ''ladderizing left'' looks like. The <tt>set autoclose</tt> command just makes the analysis run more quickly because PAUP* closes the progress dialog box automatically after a search is done rather than requiring you to press the "Close" button.
  
 
== References cited ==
 
== References cited ==

Revision as of 19:25, 30 January 2007

Under construction.png This article is still under construction.
Expect it to change frequently until this notice is removed.
This article is part of an EEB course.
Please do not edit the content of this page without the approval of the course instructor.
Adiantum.png EEB 349: Phylogenetics
The goal of this lab exercise is to show you how to conduct various distance based analyses in PAUP* and SplitsTree

Part A: Using PAUP* to check your answers for homework #3

Part B: Analysis of algae.nex

Create the data file algae.nex

Click here to get the data, then use Ctrl-a to copy all of it from your browser window and save it to a file named algae.nex in a folder on your local hard drive. These data were originally used in a 1994 study by Lockhart et al.[1] and comprise eight 16S ribosomal RNA sequences:

Anacystis a cyanobacterium (has chlorophyll a but not b or c)
Olithodiscus a chloroplast from a chromophyte alga (chlorophylls a and c)
Euglena a chloroplast from a photosynthetic euglenophyte protist
Chlorella a chloroplast from a a chlorophyte green alga
Chlamydomonas a chloroplast from a chlorophyte green alga
Marchantia a chloroplast from a thallose liverwort (non-vascular bryophyte land plant)
Oryza a chloroplast from a monocot (the flowering plant rice)
Nicotiana a chloroplast from a dicot (the flowering plant tobacco)

All of these organisms except Anacystis and Olithodiscus have chlorophylls a and b. It is probable (based on independent evidence) that all chlorophyll a/b-containing chloroplasts have a common endosymbiotic origin, so we would expect trees constructed from these data to show a branch separating Anacystis and Olithodiscus from everything else. The cyanobacterium Anacystis uses phycobilin accessory pigments rather than chlorophylls for photosynthesis, and the chromophyte alga Olithodiscus has chlorophylls a and c (but not b).

Create a PAUP* command file.

Instead of executing the file algae.nex directly in PAUP*, start PAUP* (cancel the dialog box that appears) and choose File > New from the main menu to create a blank text file. Copy the following text and paste it into the new text file window, then save this file as runalgae.nex, placing it in the same directory as algae.nex:
#nexus

begin paup;
  log file=lab3.txt start replace;
  set torder=right autoclose;
  execute algae.nex;
  outgroup Anacystis_nidulans;
  set criterion=distance;
  
  [!
  ******************************
  ** JC69 Model, ME Criterion **
  ******************************
  ]
  dset distance=jc objective=me;
  alltrees;
  describe 1;
  
  [other commands here]
  log stop;
end;

During the course of this lab, you can simply add commands to this paup block rather than creating a paup block in the data file itself. The set torder=right command simply causes trees to be displayed so that the outgroup is at the top and the tree appears to flow to the right (this is often called ladderizing right). Try changing this to set torder=left to see what ladderizing left looks like. The set autoclose command just makes the analysis run more quickly because PAUP* closes the progress dialog box automatically after a search is done rather than requiring you to press the "Close" button.

References cited

  1. ↑ Lockhart, P. J., M. A. Steel, M. D. Hendy, and D. Penny. 1994. Recovering evolutionary trees under a more realistic model of sequence evolution. Molecular Biology and Evolution 11:605-612.
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