COMPARISON OF METHODS
The methods used in these programs make different assumptions about evolutionary rates, probabilities of different kinds of events, and our knowledge about the characters or about the character state trees. Basic references on these assumptions are my 1979, 1981b and 1983b papers, particularly the latter. The assumptions of each method are briefly described in the documentation file for the corresponding program. In most cases my assertions about what are the assumptions of these methods are challenged by others, whose papers I also cite at that point. Personally, I believe that they are wrong and I am right. I must emphasize the importance of understanding the assumptions underlying the methods you are using. No matter how fancy the algorithms, how maximum the likelihood or how minimum the number of steps, your results can only be as good as the correspondence between biological reality and your assumptions!
The input format is as described in the main documentation file. The
input starts with a line containing the number of species and the number of
characters, then continues with the option information, and then the species
information. One option, the U (user tree) option, will require information to
follow the species information.
The allowable states are, as just mentioned, 0, 1, P, B, and ?. Blanks
may be included between the states (i. e. you can have a species whose data is
DISCOGLOSS0 1 1 0 1 1 1). It is possible for extraneous information to follow
the end of the character state data on the same line. For example, if there
were 7 characters in the data set, a line of species data could read
"DISCOGLOSS0110111 Hello there").
The binary character data can continue to a new line whenever needed. The
characters are not in the "aligned" or "interleaved" format used by the
molecular sequence programs: they have the name and entire set of characters
for one species, then the name and entire set of characters for the next one,
and so on. This is known as the sequential format. Be particularly careful
when you use restriction sites data, which can be in either the aligned or the
sequential format for use in RESTML but must be in the sequential format for
these discrete character programs.
Errors in the input data will often be detected by the programs, and this
will cause them to issue an error message such as 'BAD OUTGROUP NUMBER: '
together with information as to which species, character, or in this case
outgroup number is the incorrect one. The program will them terminate; you
will have to look at the data and figure out what went wrong and fix it. Often
an error in the data causes a lack of synchronization between what is in the
data file and what the program thinks is to be there. Thus a missing character
may cause the program to read part of the next species name as a character and
complain about its value. In this type of case you should look for the error
earlier in the data file than the point about which the program is complaining.
Specific information on options will be given in the documentation file
associated with each program. However, some options occur in many programs.
Many options are selected from the menu in each program, but some require
information to be put into the beginning of the input file (Particularly the
Ancestors, Factors, Weights, and Mixtures options).
Three that require information in the input file are:
Examples:
For example, if there were 20 binary characters that had been generated by
nine multistate characters having respectively 4, 3, 3, 2, 1, 2, 2, 2, and 1
binary factors you would make the auxiliary information be:
The following options are common options that can be selected from the menu:
Note that the A (Ancestors), F (Factors), and M (Mixture of methods)
options not only have information that must be entered in the input file, they
also require you to select options from the interactive menu. The selection
for the mixture option is actually X rather than M because M in most menus
means "multiple data sets".
By intelligent use of the options these programs acquire great
flexibility. The available options are indicated in the document files for
each program.
After each tree is printed out, its numerical evaluation (number of steps
required, for instance) is also given. A table of the number of events
required in each character is also printed, to help in reconstructing the
placement of changes on the tree.
This table may not be obvious at first. A typical example looks like
this:
I cannot emphasize too strongly that just because the tree diagram which
the program prints out contains a particular branch DOES NOT MEAN THAT WE HAVE
EVIDENCE THAT THE BRANCH IS OF NONZERO LENGTH. The procedure which prints out
the tree cannot cope with a trifurcation, nor can the internal data structures
used in my programs. Therefore, even when we have no resolution and a
multifurcation, successive bifurcations will be printed out, although some of
the branches shown will in fact actually be of zero length. To find out which,
you will have to work out character by character where the placements of the
changes on the tree are, under all possible ways that the changes can be placed
on that tree.
In MIX, PENNY, DOLLOP, and DOLPENNY the trees will be (if the user selects
the option to see them) accompanied by tables showing the reconstructed states
of the characters in the hypothetical ancestral nodes in the interior of the
tree. This will enable you to reconstruct where the changes were in each of
the characters. In some cases the state shown in an interior node will be "?",
which means that either 0 or 1 would be possible at that point. In such cases
you have to work out the ambiguity by hand. A unique assignment of locations
of changes is often not possible in the case of the Wagner parsimony method.
There may be multiple ways of assigning changes to segments of the tree with
that method. Printing only one would be misleading, as it might imply that
certain segments of the tree had no change, when another equally valid
assignment would put changes there. It must be emphasized that all these
multiple assignments have exactly equal numbers of total changes, so that none
is preferred over any other.
I have followed the convention of having a "." printed out in the table of
character states of the hypothetical ancestral nodes whenever a state is 0 or 1
and its immediate ancestor is the same. This has the effect of highlighting
the places where changes might have occurred and making it easy for the user to
reconstruct all the alternative patterns of the characters states in the
hypothetical ancestral nodes.
On the line in that table corresponding to each branch of the tree will
also be printed "yes", "no" or "maybe" as an answer to the question of whether
this branch is of nonzero length. If there is no evidence that any character
has changed in that branch, then "no" will be printed. If there is definite
evidence that one has changed, then "yes" will be printed. If the matter is
ambiguous, then "maybe" will be printed. You should keep in mind that all of
these conclusions assume that we are only interested in the assignment of
states that requires the least amount of change. In reality, the confidence
limit on tree topology usually includes many different topologies, and
presumably also then the confidence limits on amounts of change in branches are
also very broad.
In addition to the table showing numbers of events, a table may be printed
out showing which ancestral state causes the fewest events for each character.
This will not always be done, but only when the tree is rooted and some
ancestral states are unknown. This can be used to infer states of ancestors.
For example, if you use the O (Outgroup) and A (Ancestral states) options
together, with at least some of the ancestral states being given as "?", then
inferences will be made for those characters, as the outgroup makes the tree
rooted if it was not already.
In programs MIX and PENNY, if you are using the Camin-Sokal parsimony
option with ancestral state "?" and it turns out that the program cannot decide
between ancestral states 0 and 1, it will fail to even attempt reconstruction
of states of the hypothetical ancestors, printing them all out as "." for those
characters. This is done for internal bookkeeping reasons -- to reconstruct
their changes would require a fair amount of additional code and additional
data structures. It is not too hard to reconstruct the internal states by
hand, trying the two possible ancestral states one after the other. A similar
comment applies to the use of ancestral state "?" in the Dollo or Polymorphism
parsimony methods (programs DOLLOP and DOLPENNY) which also can result in a
similar hesitancy to print the estimate of the states of the hypothetical
ancestors. In all of these cases the program will print "?" rather than "no"
when it describes whether there are any changes in a branch, since there might
or might not be changes in those characters which are not reconstructed.
For further information see the documentation files for the individual
programs.
INPUT FORMAT
OPTIONS GENERALLY AVAILABLE
ANCESTOR 001??11
or:
A 001??11
The ancestor information can be continued to a new line and can have blanks
between any of the characters in the same way that species character data can.
When the ancestor option is used, the ancestor is not counted as one of the
species in stating the number of species in the data. The exception is program
CLIQUE where the ancestor is to be included as a regular species and no A
option is available. (This can also be done in programs MIX, MOVE, and PENNY,
although I do not advise doing this since it is only correct if the characters
are all following the Wagner Parsimony rules, and the same end can be achieved
by using the A option).
Mixture WWWCC WWCWC
Note that blanks in the seqence of characters (after the first ones that are as
long as the species names) will be ignored, and the information can go on to a
new line at any point. So this could equally well have been specified by
Mixture WW
CCCWWCWC
F 11112223334456677889
although it could equivalently be:
Factors aaaabbbaaabbabbaabba
All that is important is that the first character be an F, that the length of
species name be filled out with characters or blanks, and that the symbol for
each binary character change only when adjacent binary characters correspond to
different mutlistate characters. The F auxiliary information can continue to a
new line at any time except during the initial characters filling out the
length of a species name.
OUTPUT FORMAT
steps in each character:
0 1 2 3 4 5 6 7 8 9
*-----------------------------------------
0! 2 2 2 2 1 1 2 2 1
10! 1 2 3 1 1 1 1 1 1 2
20! 1 2 2 1 2 2 1 1 1 2
30! 1 2 1 1 1 2 1 3 1 1
40! 1
The numbers across the top and down the side indicate which character is being
referred to. Thus character 23 is column "3" of row "20" and has 2 steps in
this case.
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Maintained 15 Jul 1996 -- by Martin Hilbers(e-mail:M.P.Hilbers@dl.ac.uk)