I have molecular data and morphological data. I want to compare molecular phylogenies with morphological data, but I do not how to make the morphological phylogeny. Can you help? How to work it? And need some software?
To generate a morphological phylogeny you need to code your morphological data in a matrix. If you already have such matrix, you can generate a parsimony or a likelihood tree using PAUP in the same way as you generate a molecular phylogeny http://people.sc.fsu.edu/~dswofford/paup_test/
If you want, you can also generate your morphological tree using MrBayes.
Dear Dr. Coiro,
I do not know how to get the matrix, can you give me a mode of the matrix? you can contact with me by email [email protected].
Thanks for your answer.
Warm regards
Lin
Unfortunately, to generate a morphological matrix is not a straightforward process. There is plenty of literature discussing coding strategies. Here are some examples:
http://onlinelibrary.wiley.com/doi/10.1111/j.1096-0031.1995.tb00092.x/abstract
http://www.wienslab.com/Publications_files/characteranalysis2001.pdf
http://onlinelibrary.wiley.com/doi/10.1111/j.1096-0031.1999.tb00272.x/abstract
However, if some morphological analyses have already been published for the group you are working on, you could use the published matrix and code the morphology of your taxa in their framework.
Which group are you currently studying?
Kind Regards
You should probably work on the morphological characteristics by compiling the character states for each of the characters of the target species, and data input using NEXUS Editor for the analysis.
Cheers, HongChang
Dear Lim,
Thanks for your letter. I can not work the NEXUS.
Warm regards
Lin
To build a matrix, you just have to compare the characters shown by the terminals. For example, if one character would be the number of pairs of legs presented by some animals (the terminals you are comparing), you should compare this character in each of them: terminal A – 2 (pairs), terminal B – 1, terminal C – 3, terminal D – 2, and so on.
At the lines of the matrix, you have the character state of each terminal, at the columns, you have this information displayed by each character.
After that step, you can code your characters using different possible methods. You may begin using the outgroup method. You choose a group that you know that is outside (but not too far away) from the group of the terminals you are comparing. If the outgroup would have two pairs of legs, in comparing it with each one of the terminals in the above example, you would have tA – 0, tB -1, tC – 1, tD -0 (for if the character state equals that of the outgroup, you code as 0, if not, 1).
Doig this for all characters, you will have your matrix.
Oh, many answers were already arrived... Make a data matrix file (binary data) in the MacClade program, and open it in the PAUP program, and then choose the outgroup, and choose parsimony option; general search options; character state optimization; ACCTRAN (or DELTRAN) option, and choose Heuristic search; Branch-and Bound search...
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