I converted my PowerPoint slides to a Quicktime
movie that you can download and play to review. This should be possible
on both Macs and PC's.
The assignment is to enter and analyze the Laurin and Reisz matrix. First,
see if you can duplicate his results. Second, constrain temnospondyls
and Lissamphibia to be a clade and analyze the data set under that constraint.
Third, get down and funky and do something interesting with the data matrix.
I assigned groups as follows (we will switch in the
Greg and Holly
Rafe and Amy
Emily and Jonathan
Cat and Jackson
Alisha and Gabe
Ted and Nina
I'd like each group to present their results on the
23rd. Two overheads maximum, no more than about 5 minutes talking so that
we can discuss this adequately. Don't re-hash the general stuff about
I paired folks up so that those who know how to run
PAUP can help the others, but it's my intent that everyone learn how to
use it. So don't totally depend on your partner to do everything for you.
Some notes on running PAUP:
You can run PAUP using either the menus or commands
embedded in the PAUP file. I like the latter way because it gives running
record of what I've done. Knowing which commands to use can be daunting,
but here are some tips.
- PAUP and MacClade data files are just plain old ASCII text files.
They can be edited using MS Word, the PAUP editor, BBEdit, etc.
- The PAUP data file is structured into blocks; there is a TAXA block,
a CHARACTERS block, etc. The commands to analyze the matrix are in a
PAUP block. A block is a chunk of text that starts with "BEGIN
keyword" and ends with "END;" For example:
This PAUP block does a heuristic search, and then
displays all of the trees found in that search. There are many implicit
options for which the default value is used. We can change these as
in the example below. Note that comments can be embedded anywhere in
the datafile using brackets . Also the datafile is in free format,
meaning that the position of linebreaks and the number of spaces between
commands does not matter.
||[begin the block; note the semicolon]
|log file=dataset1.log append=yes;
||[log all the output into a text
file named dataset1.log, but append this output to the file if it
already exists, so that I don't overwrite it by mistake]
8 10 45-67;
command excludes certain characters from the analysis; the opposite
command is include]
|[you can put comments almost anywhere]
|constraints AmphibianMonophyly = (1-9,13,(10,11,12));
||[define a constraint tree in which
taxa 10,11,12 must be a clade]
|constraints FrogMonophyly = (1-10,13,(11,12));
||[define another constraint tree;
you can do as many as you need]
||[delete the specified taxa from
the analysis; the opposite command is restore;]
||[do a heuristic search, but note
that the constraint is not enforced]
||[show only the first tree from
||[re-include all of the characters]
||[do another analysis with the
following subcommands: use TBR branch swapping; note there is no semicolon]
constraints = AmphibianMonophyly
|[this time, enforce this particular
constraint tree; note again, no semicolon]
|[ no semicolon]
|[to get a more through search
of possible trees, select the next taxon to be added to the tree at
random; then repeat the search 100 times in hopes of finding a shorter
tree; note the semicolon, which ends the subcommands of HSEARCH]
||[save all the shortest trees found
in a file named dataset1.trees; this file will contain the tree description
in parenthetical notation; you can re-use these trees later for printing,
||[stop logging to the file]
|[!Because this comment starts with
a !, it will be echoed (written) to the log file]
- After you add or edit a PAUP block to your datafile, you must save
the file (apple-S) and then execute the datafile (apple-R for RUN).
Executing the datafile will check the syntax of the commands first,
and alert you if there are errors. If there are no errors, the program
executes the PAUP block. If you have just created a datafile but have
no PAUP block, executing the datafile will just check the data and then
terminate normally. This is useful for checking syntax errors in the
- You can keep your old PAUP blocks in the datafile by just adding [
] around the entire block, which converts it to a comment; this is handy.
You can also define several PAUP blocks in a row, each with different
analyses, log files, etc. and then run all in one session, like overnight.
- You can use a SETS block to define sets of characters or taxa. Then,
you can use the name of the set in include/exclude and delete/restore
statements rather than having to list all of the numbers.
Charset Skull = 1-50;
Charset Postcranial = 51-75;
Taxset Lissamphibia = 23-29;
Taxset Lepospondyls = 31-45;
- After you start PAUP you should see a window that has "PAUP*
4.0b8" or something similar as the title. At the bottom of this
window you should see a one-line blank rectangle. This is the command-line
box, and you can enter PAUP commands here. One very useful command is
"?", a question mark, which will give you a list of the possible
PAUP commands. If you enter a command followed by a ? then PAUP will
give you the syntax of the command. This is useful in setting up PAUP
You can also execute PAUP commands by typing them in here, rather than
putting them in a PAUP block or using the menu.