A Macintosh® program for the analysis of how
dependent phylogenies are related, by cophylogeny mapping.
© Copyright, 2002 Michael A. Charleston* and
Roderic D. M. Page
Development of this program has been supported by NERC and
the Royal Society
*School of Information Technologies, Sydney
Bioinformatics and the Centre for Mathematical Biology; Sydney
University, Camperdown, Sydney, NSW 2006, Australia.
Division of Environmental and Evolutionary
Biology, Institute of Biomedical and Life Sciences, University of
Glasgow, University Avenue, Glasgow G12 8QQ, U.K.
E-mail Michael Charleston
at m•charleston AT usyd•edu•au or Rod Page at
r•page AT bio•gla•ac•uk
Alert! TreeMap3 is coming. I am re-writing it in Java and it's
coming along nicely. I am willing to let you have a development version, but it comes with NO
TREEMAP is a Macintosh program that performs cophylogeny
mapping from a dependent evolutionary tree (e.g., a group of
parasites) into an independent one (e.g., the
hosts of those parasites), in order to recover the best
possible coevolutionary explanation for the relationship between the
two (Page & Charleston, 1998).
The archetypal example is of the coevolution of pocket gophers and
their chewing lice (Page &
A manual is still hasn't been written. Write to me and ask!
Version 2.02ß Download here
- Was filtering out all guaranteeably non-optimal sub-solutions
during jungle construction, even if the option had not been
checked: this has been fixed.
- New statistical test: the "Cherry Picking Test", to
determine whether the significant part of congruence between H and
P is due to associations between pairs of siblings at the tips of
both trees (manuscript in prep.) "unbound" option on
jungle bounds for each category (number of codivergences /
duplications; number of losses; host switches; total number of
non-codivergence events / total cost).
- Log file "TreeMapLogFile.txt" automatically
- Summary descriptions of all resulting maps listed to the Log
- Now takes into account timing information on host or associate
tree. The relative times taken from branch lengths can be used to
constrain jungle construction (and therefore make it faster!).
- Jungle construction and significance testing dialogs are now
- Numerous speed-ups, mostly from using new branch-and-bound
Version 2.0ß New features, in no particular
- Jungles are
now implemented. This means
- All solutions are found, by exhaustive search
(previous heuristics had to be used).
- All host switches can be dealt with
consistently (including weakly incompatible switches).
- There is no explicit optimality criterion:
all solutions which could be optimal for some event cost scheme
(cost of duplication, host switch and loss events) are
presented; you can also opt to present all feasible maps (but
the number of these grows exponentially!).
- Much faster branch-and-bound search.
- Option to produce all feasible solutions (memory
notwithstanding) prior to filtering out guaranteeably non-optimal
- Plot of relative frequency in presented solutions
of host switches in the host tree.
- Significance testing, by randomizing the associate
tree and measuring how often randomized associate trees fit as
well as the given one. There are several new randomization test
statistics available, and the standard error of the estimation on
significance value is given.
- Tabbed dialog boxes for your viewing pleasure.
- Ability to save Macintosh graphics files (PICT
format) for a selection of reconstructions.
- Temporal information in the host and parasite
trees can now be accommodated.
- Lots of bug fixes.
You are welcome to use this software free of charge
but the authors accept no responsibility for the veracity of the
results and make no representation of the application's
bug-free-ness, correctness, or suitability for your analysis. If you
are in doubt we strongly recommend that you contact Michael
Charleston or Rod Page.
We do assert that the logo is rather
- Once you've downloaded it, just double-click and it should
expand itself with the example files.
- Please join the mailing
list in order to be updated with new versions and bug fixes, and
to let us know if you have suggestions for future versions.
Known Bugs and Problems
This is a beta version. There may still be bugs!
If you really think you've found one, please let us know.
Some of the ones we do know about are listed below.
- We don't know of any bugs at the moment. This will, no
finds all the globally optimal maps it is an exact solution
and requires a lot of memory! If it runs out, try either giving it
more using the Get Info
in the Finder, or constrain the
acceptable solutions more at the outset. Permitting very few
non-codivergence events, particularly host switches, makes the
solution much quicker, but at the expense of not necessarily knowing
that the solutions you get are all of the potentially optimal ones.
Bear in mind that the less restrictive you have to make these bounds
to get a feasible solution, the less likely you are to get a
significant match between the two trees.
THINGS WED LIKE IN TREEMAP
- Ability to draw polytomies. We don't rate this as a high
priority though since we do not believe there are good theoretical
methods of dealing with them.
- Better bounds during jungle construction current ones
are a big improvement but tighter ones are theoretically possible.
- Inclusion of failure to diverge event, without too
much increase in computational complexity.
- Ability to handle reticulate phylogenies (such as caused by
hybridization and recombination).
- Plots showing relative frequencies of host switches on the
host tree among reconstructions.
- Some kind of "consensus" method for maps.
- Inclusion of multiple sets of associations.
- A better Switch Frequency Plot, perhaps just showing the
numbers of times in the current set of solutions that a switch
occurs (at present this is shown by a shade of grey).
Charleston, M. A. 1998. Jungles:
A new solution to the host/parasite phylogeny reconciliation problem.
Mathematical Biosciences 149:191-223. (pdf)
Page, R. D. M., & Hafner,
M.S. 1996. Molecular phylogenies and host-parasite cospeciation:
gophers and lice as a model system. Pages 255-270 in New uses
for new phylogenies (Harvey, P.H., Leigh Brown, A.J., Maynard Smith,
J., & Nee, S., eds.). Oxford University Press, Oxford.
Page, R. D. M. and Charleston, M. A.
1998. Trees within trees: phylogeny and historical associations.
Trends in Ecology and Evolution 13(9):356-359. (pdf)
Last modified: Friday, January 6, 2006