I don’t think a lot of people appreciate the degree of variance possible under a simple constant rate speciation extinction model.  I think the natural reaction if we see the third and fifth tree above as sister lineages is that the third must have a significantly higher net speciation rate.  However each of the above trees were generated under the same model.  When I went to the Bodega phylogenetics workshop last year Brian Moore did a nice presentation where he walked us through illustrating this point in R.  I need to do the same thing for a seminar that I am giving soon and I decided that it would be good to generate it on my own and make a few small aesthetic changes.  So here it is:

here is the script

I will try to post the code here in the post for this later but something about it seems to be conflicting with bloggers parser and it comes out all messed up.  For now you can just get the script from dropbox

cheers
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Labels: comparative methods R simulation
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  1. Thank you for the post
    Waiting for the code.

    ReplyDelete

  2. Good post, thanks for that.
    waiting for the code.

    ReplyDelete
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I am broadly interested in the application and development of comparative methods to better understand genome evolution at all scales from nucleotides to chromosomes.
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