Hello,
I'm trying to reconstruct the major biogeographic region from which
different families have originated. I have data on the proportion of each
family's range that falls within each biogeographic region, as well as (of
course) a phylogeny.
My approach so far has been to assign, if possible, each family to ONE
biogeographic region. I do so by finding which region contains >= 50% of
the family's range. The problem (potentially among many!) is that some
families occur in multiple regions and no single region contains >= 50% of
their range. So I have assigned these families to a new category
"cosmopolitan." I then have a discrete variable of "biogeographic affinity"
and reconstruct this along the phylogeny using the ace function in package
ape.
I assume that each ancestor is from a single region and so I take the scaled
likelihood for from the cosmopolitan state and redistribute it evenly to all
other states. My rational is that from a coalescent perspective the
ancestor is a single individual so being "cosmopolitan" is not possible.
That being said, I have no idea if this practice of "redistributing" scaled
likelihoods is legitimate, and my intuition is that it is not. So...does
anyone know of a better way? I am not wedded to using a discrete state
reconstruction, and if it's possible to explicitly reconstruct the
proportion of each range in each region that would probably be better. My
concern there would be that the reconstructed "proportions" would not sum to
1 at every node, and then what--rescale them? That seems no better than
redistributing likelihoods in the discrete case. But I don't know!
Thanks in advance for any help--
Andy
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