Dear all,
many thanks to Joe Felsenstein for his advice about
this point. I took a couple of days to study the two
papers (Felsenstein, 2002 and Stone et al, 2011);
well..... the directions are exciting....th problem is
that it is not easy at all to estimate ALWAYS the
migration matrix, mainly if one deal with
morphological data (my case for example). If a
moecular phylogeography is available one could use
that topology but time divergences are often estimated
on other source of data (paleontological, for
example). And the populations for which morphology is
under study could not be EXACTLY THE SAME (they can
come from close localities but not the same) of
molecular topoloy. In this situation one could have a
rather good estimate of phylogenetic relationships
between populations but no estimate at all of
migration matrix. So...probably, given two sources of
covariance, i.e. phylogeny and gene flow, if one is
not available (gene flow) one should at least
incorporate the other one (phylogeny), rather than
ignoring both. But ocourse aknowledging the potential
limitations due to the lack of gene flow informations.
Thus, as Joe said, one should carefully take in
account the two contributions.
Thanks again
Paolo
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 [email protected]
Department of Genome Sciences and Department of
Biology,
University of Washington, Box 355065, Seattle, WA
98195-5065 USA
_______________________________________________
R-sig-phylo mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
