For rate estimation between temperate and tropical, I'd suggest using OUwie, as it's made for exactly this question: map tropical/temperate on the tree, try the "BMS" model to estimate the rate of evolution in temperate and tropical taxa (note that I'm one of the authors, so take this bias into account). There are other models, too, to allow you to test things like whether temperate and tropical taxa have different evolutionary means, and you can compare these models to Brownian motion models, depending on your question. Note that in theory, these methods should be robust to random sampling of taxa.
For your first question, you could estimate the amount of phylogenetic signal, create a much larger tree under some branching process, transform the branch lengths to match your phylogenetic signal, simulate traits on this transformed tree, then subsample back and estimate the phylogenetic signal on the untransformed but pruned simulated tree. Ideally, the parameter estimate you get from the simulated data matches the true parameter, suggesting that sampling does not matter for phylogenetic signal. Frankly, I'd be surprised if random sampling does matter for signal, though some biased sampling (even from taxonomic bias, of not separating two populations into different species until they are "different enough") could have an effect. Best, Brian _______________________________________ Brian O'Meara Assistant Professor Dept. of Ecology & Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Postdoc collaborators wanted: Check NIMBioS' website Calendar: http://www.brianomeara.info/calendars/omeara On Mon, May 5, 2014 at 11:33 AM, [email protected] < [email protected]> wrote: > Hi Imran, > > I'm by no means an expert on phylogenetic signal with incomplete > phylogenies but I would check out the GEIGER package, specifically the > "mecca" function. I think mecca is set up to do estimates based on > incomplete tip sampling. > > Cheers, > -Dan Gates > PhD candidate > Smith/Pilson Lab University of Colorado/Nebraska > http://ec2-54-186-114-109.us-west-2.compute.amazonaws.com:8080/DanielJGates > ________________________________________ > From: [email protected] <[email protected]> > on behalf of imran khaliq <[email protected]> > Sent: Monday, May 5, 2014 5:15 AM > To: [email protected] > Subject: [R-sig-phylo] Phylogenetic signal, variation in rates and > sample size > > Dear All, > I am trying to understand the effects of incomplete phylogenies on the > phylogenetic signal. I am using different trees and I have at least 100 > species in each tree but still these are only 2 % of total species. So how > can I be sure that results are generalize enough to apply on the whole > group? Secondly, if I want to compare varaition in trait's rates in two > groups e.g. tropical and temperate, what methods are appropriate to > estiamte the evolutionary rates. I tried Brownian rate parameter estimation > by tranforming the branch lengths according to the lambda values of trait > in each group. It gives me lower varaince for the group that has higher > lambda value and that is confusing. In fact with the same trait values, if > I transform the branch lengths of the tree with different lamda values it > gives me higher varaince for higher lambda value. > Can anyone help me? > > Best regards, > Imran > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/[email protected]/ > _______________________________________________ > R-sig-phylo mailing list - [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/[email protected]/ > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
