[Mesquitelist] mapping continuous character onto NJ tree
wmaddisn at interchange.ubc.ca
Tue Feb 15 13:27:14 PST 2011
I won't comment on whether this is an appropriate analysis, but rather whether Mesquite can do calculations of the exact sort you want. Mesquite, combined with the PDAP package of modules, can ask whether there is a correlation between two continuous valued characters observed for a set of taxa related by a tree. The one continuous character, by the sound of it, would be the distance to a refuge. I am unclear though what would be the second continuous character in your case. How would you assign to a taxon (i.e. plot) a value summarizing its position in the tree?
On 10 Feb 2011, at 7:01 AM, Tonya Lander wrote:
> I am trying to figure out whether Mesquite is an appropriate program
> for what we want to do.
> We're looking at genetic diversity and differentiation in beech
> populations on Mt Ventoux in France. There are two refuge areas on
> the top of the mountain, areas that weren't logged when the rest of
> the mountain was more or less cleared about 200 years ago, and we
> think there has probably been a pattern of multidirectional beech
> population expansion out of a refuge area.
> We generated a Neighbour-Joining tree based on pairwise Fst values (in
> the program TreeFit (Kalinowski 2009)) and if I just number the
> terminals of the tree or the nodes of the tree from top to bottom then
> there is a significant positive correlation between numbered position
> and distance to the NE refuge and a significant negative correlation
> between numbered position and distance to the NW refuge. However, I
> know I can't just number the nodes or terminals that way.
> So, if distance from each sample plot to both the NE and NW refugia is
> like a continuous character of the sample plots, can I use Mesquite to
> determine whether there is a significant relationship between distance
> to the two refuges and position in the NJ tree?
> Any help or advice will be much appreciated.
> Thank you.
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