Paolo Piras wrote:
> I write you in order to ask a phylosophical opinion in
> applying phylogenetic comparative methods to
> subspecies belonging to the same species for which a
> phylogenetic/phylogeographic scenario is known on the
> basis of molecular studies. I have a number (>10) of
> population samples belonging to two species at
> continental scale. Some OTUs are surely NOT panmittic
> with the others while for some others this is not
> sure. Someone could argument against the use of
> comparative methods when a gene flow is still present
> among OTUs. However, I think that, if possible, AT
> LEAST the covariance due to populations relationships
> should be removed. You dont think that it is always
> better to take in account all possible relatedness
> betwen OTUs? In this paper
>
> D. C. BLACKBURN, G. J. MEASEY. 2009.Dispersal to or
> from an African biodiversity hotspot? Molecular
> Ecology; Volume 18, Issue 9, pages 19041915, May
> 2009.
>
> the authors apply common comparative methods to a
> phylogeography of populations belonging to ONE
> species. I found their strategy appropriate. I wrote
> to ask your opinion about this issue.
Using standard tree-based methods to treat a single species which has
populations that exchange migrants is inappropriate. In a 2002 paper I
discussed how to do this properly using contrasts which are derived from the
eigenvectors and eigenvalues of (an estimate of) the migration matrix between
populations. Such migration matrices can now be inferred using programs LAMARC
and Migrate.
The paper is here:
Felsenstein, J. 2002. Contrasts for a within-species comparative method.
pp. 118-129 in "Modern Developments in Theoretical Population Genetics",
ed. M. Slatkin and M. Veuille. Oxford University Press, Oxford.
Here
http://evolution.gs.washington.edu/papers/spectrum/
is where you can get a PDF of a preprint version of it.
The method is univariate at the moment but a multivariate version is under
development -- the univariate version can be used to see whether a character
has significant covariation with an environmental measurement.
The method is also described in a recent paper by Stone, Nee and me:
Stone, G. N., S. Nee, and J. Felsenstein. 2011. Controlling for
non-independence in comparative analysis of patterns across populations within
species. Philosophical Transactions of the Royal Society B 366 (1569):
1410-1424.
which discusses the general issue. The (other) authors preferred, for greater
comprehensibility, to describe my method slightly incorrectly (I got outvoted).
Anyone considering this issue should consider these two papers carefully. Of
course mixing within- and between-species analyses is more difficult yet. I
hope to release an R package later this year to do the one-character analysis
(it is not too hard to put one together yourself in the meantime).
Joe
----
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
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