dataset for Brownie
liquenologo
I'm trying to use Brownie to infer a species tree in my group or
organisms (lichens). I have the following dataset: 3 putative species,
two different markers (with 289 sequences for the first one and 219
for the second, there are 187 individuals with both sequences). The
aim of the study is to delimit the species (using different lines of
evidence: molecular markers, morphology, chemistry, geography). My
question arises at the moment of deciding which trees to use in
Brownie. I've used Beast to generate ultrametric trees. Then, I have
trees with 187 sequences for each marker (with many identical
sequences included, recommended for Beast analysis), and trees with
with only those sequences that are different (haplotypes). My question
is the following: Which dataset could performance better in the
analysis carried out by Brownie?
Thank you very much for your help!
Sergio
Brian O'Meara
trees to work properly, so you'd have to randomly resolve the input
trees or drop the identical haplotypes. Dropping them removes some
useful information (identical haplotypes pointing to possible
existence of a species), but I'd worry that brownie would oversplit
based on random similarities between the two arbitrarily-resolved
trees. How many unique haplotypes do you have per putative species? If
it's something like 2, you'd have trouble, but something like 10 would
be much better.
As a general thing, when faced with two suboptimal choices like this,
I'd be tempted to do both ways and then report both (even if you focus
on one, mention the results from the other in the paper). As a
practical thing, having fewer sample might really speed up the search.
Of course, the optimal thing would be to simulate and test to see
which approach resulted in the best estimates by Brownie (and perhaps
other programs), but that could be a whole separate paper.
Best,
Brian
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------------------------------------------------------
Brian O'Meara
http://www.brianomeara.info
Assistant Prof.
Dept. Ecology & Evolutionary Biology
U. of Tennessee, Knoxville
Sergio Pérez-Ortega
Best,
Sergio