In Paleo, you can (well, arguably) see the ancestor and descendent pair, so you can assess the amount of change and the ancestral state. Using just info at the tips, you are inferring from N taxa N-1 ancestral states and 2N-2 rates of change. That seems a lot to ask from data, especially since the rates and states affect each other and so aren't independent. You're also using a model that assumes an even rate of change over the tree, so an ancestor will tend to be between its descendants (exactly between, if you have a two taxon tree with coeval taxa). You could try more exotic models that allow multiple Brownian rates or even multiple Ornstein-Uhlenbeck rates, but there's a limit there, as well. There are Bayesian approaches that can paint a smear (estimated from post-burnin samples) of rates over multiple branches, but I'd be careful interpreting them as robust estimates of rate that are independent of the states.
If you have separate traits, you could ask does trait X lead to higher rates (or OU mean, or OU alpha) of evolution in trait Y. Basically this involves painting a tree with discrete trait X (generalist vs specialist predator, say) and estimating different rates for the other trait (i.e., mouth volume) on the branches painted in different states (and seeing if these rates are biologically and statistically significantly different). Best, Brian _______________________________________ Brian O'Meara Assistant Professor Dept. of Ecology & Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Postdoc collaborators wanted: http://nimbios.org/postdocs/ Calendar: http://www.brianomeara.info/calendars/omeara On Fri, Apr 24, 2015 at 3:14 PM, Milton Tan <[email protected]> wrote: > Hello all, > > I have a question that is perhaps esoteric, since it's on a method I don't > see used often. I am looking at the dynamics of body size evolution, and > have come upon ancestor-vs-change plots described in Alroy 2000 > ("Understanding the dynamics of evolutionary trends", Paleobiology). This > is interesting because it will allow me to see if rate of body size change > depends on body size. I haven't seen this method widely used, so for anyone > unaware how this works: for each branch, you plot the ancestral state vs. > the amount/rate of change along the branch. In theory, by looking at a > scatterplot of ancestral size vs. change, I can answer questions such as > "Are smaller taxa more likely to evolve to a larger size?" I don't see too > many people using this method, so I thought I'd ask why. Is there a > particular reason for it not being used? Are there more powerful methods to > answer this same question that have supplanted it? > > I also have a more specific question, assuming that ancestor-vs-change > plots are valid. For my dataset, I have reconstructed ancestral states for > my clade from tip data and pic, and then plotted ancestral states versus > the rate of change along every branch (attached). While there are a couple > outliers, you can see the distribution roughly hangs around 0 along the > entire graph, but I'd like to fit a line so I can present if the slope > significantly differs from 0 (ie. body size evolutionary rate truly does > not depend on body size of ancestors). Alroy (2000) describes that the > shape of the plot can be informative on different dynamics of evolutionary > change, implying fitting of linear and polynomial lines, but doesn't really > discuss how to test this statistically. Alroy seems to use this method and > fits a polynomial line in Alroy 1998 ("Cope's Rule and the Dynamics of Body > Mass Evolution in North American Fossil Mammals", Science), but he doesn't > really describe his statistics ! > in depth. > > So my question is how can I fit a line to this data? Problematically, > since each branch has a sister branch that shares the same ancestral node, > each ancestral state is represented twice. I think this makes the > observations non-independent. If they are, this makes me think that a > linear regression is inappropriate, but I'm not sure. I could average the > amount of change along each branch for every ancestral node, but I'm not > sure if that's the best way. Does anyone have any insight on an appropriate > way to determine a best fit line statistically? > > Thanks in advance, > > Milton Tan > Auburn University > Department of Biological Sciences > PhD Candidate > > [[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]/ > [[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]/
