Is it possible to enter two different types of information into Mesquite?
I have two sets of species data:
- the divergence times (in millions of years) i.e. how old each species is and the relationships between them i.e. how they are grouped on a tree, using brackets.
- the sexual system status of each species (e.g. 0 = gonochoristic, 1 = hermaphroditic).
It seems I can only open one of the following to make a tree:
- a nexus file containing the divergence times/relationship data (begin trees;)
or
- a nexus file containing character states (begin data;)
I have combined both sets of information (see attachment) into a single nexus file but this doesn't seem to work; I get a brilliant tree with all the species in the correct positions and branching correctly, but the character states are not shown.
It appears the only way to combine them is to open the character nexus file into a tree, re-position every branch/species until they match a reliable existing phylogeny, and then add divergence times manually too.
As the fish families I am studying have upwards of 500 species in them, this is a long, slow and mind-numbing process!
Does anyone know of a better way? I feel I am missing something really obvious that could save me a heap of time!
Many thanks!
Yer you may do that by opening new data manager window, choosing appropriate data type and fi;;ing it in. It must inherit OTU names from the first data set/
You have to do it slightly differently. Mesquite needs to know that the taxa on your tree and those in your matrix refer to the same things. It doesn't assume that the way you have represented it. Instead:
- Create a "taxa" block that has all the names that are both in the tree and the data. If there is only a single taxa block in your file, mesquite will assume that the trees and the characters blocks refer to that taxa block.
- Encode your characters not in a "data" block (which is deprecated) but in a "characters" block.
If you get this sorted out syntactically correct then what you are trying to accomplish is very much possible. To demonstrate the end result I have done this for you and activated the 'trace character history' window so you can see it all lines up. File attached.
There is a Mesquite module for representing stratigraphic data on trees (http://mesquiteproject.org/packages/stratigraphicTools/) by @Michel Laurin and colleagues. I have spent some time with this package and found it difficult to use (so much so that I abandoned the effort), but Michel and @David Marjanovic have used it effectively to publish a huge tree with stratigraphic ranges. However, I do not think the stratigraphic data can be entered automatically from a file, the branches have to be manipulated manually. The best way to answer your question is to consult the online documentation, specifically the e-mail list (http://www.mesquiteproject.org/Getting%20Help.html).
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