Caio Maximino de Oliveira asked --
> I'm not even sure if I am supposed to send some of those
> questions to this list, but this was the only place where I felt confident
> to ask them.
This is one of the right places.
> I am working with a small comparative data set (8 species), but was thinking
> about including data from other studies using the same species.
> Incorporating phylogenetic information, should I input only one data point,
> estimating the parameter by some meta-analysis method, or should I include
> information of each study as a separate "species", perhaps using polytomies?
> I ask this question because the data from the other studies I wish to use
> come from the same species, but different strains, and I do believe that the
> different genetic background can account for some differences observed in
> the studies...
and Ted Garland said --
> You can certainly keep populations of a species separate for analyses. If
> you know the splitting order, then you are set; if not, then you can use a
> polytomy. Similarly, if you were studying various inbred strains of mice
> then you would keep them separate and use an appropriate phylogenetic tree.
> For example, see:
>
> Ashton, K. G. 2004. Comparing phylogenetic signal in intraspecific and
> interspecific body size datasets. Journal of Evolutionary Biology
> 17:1157-1161.
> Rhodes, J. S., M. M. Ford, C.-H. Yu, L. Brown, D. A. Finn, T. Garland, Jr.,
> and J. C. Crabbe. 2007. Mouse inbred strain differences in ethanol drinking
> to intoxication. Genes, Brain and Behavior 6:1-18.
I would be cautious. Ted's response assumes that the genealogy of the
populations is a branching tree, with no migration among populations.
But within a species many populations often don't have a strictly
branching genealogy. Within the boundary of the species we have to worry
about whether "tree-thinking" is the right thing to do. "Gene-flow-thinking"
may be needed. Casually making polychotomies may not be the best way to
deal with this.
I have tried to make a start on this, for cases where we have an estimate
of the migration rates among populations, and are willing to assume that this
population structure has been around for a long time at equilibrium.
The resulting methods are still not particularly useful. Here is my
paper looking at what needs to be done within species to do comparative
methods. I have got this extended to multiple characters, know how to
extend it to finite samples of individuals, and am working on a program.
Even then it's very idealized:
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.
A PDF of the manuscript is available at:
http://evolution.gs.washington.edu/papers/spectrum/
As for integrating this with between-species comparative methods, I am
pretty sure that can be done but it will be even messier.
For combinations of gene-flow-thinking and tree-thinking see Rasmus Nielsen
and Jody Hey's program IMa, which is still in its early days and does not
yet handle continuous characters.
----
Joe Felsenstein [email protected]
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
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