SURFACE is a method for inferring the macroevolutionary adaptive landscape of a clade given only trait data and a phylogenetic tree. The name is a recursive acronym for “SURFACE Uses Regime Fitting and AIC to model Convergent Evolution”, and the method is implemented in the new R package surface.


SURFACE builds on the OUCH set of methods (Butler and King, 2004, Am. Nat.), which fits Ornstein-Uhlenbeck stabilizing selection models given a hypothesized history of evolutionary regime shifts in a clade. The novel feature of SURFACE is that it constructs such a model using stepwise AIC, without any a priori specification of which taxa are thought to be convergent. This allows for an objective search for evolutionary regime shifts, and for tests of whether a clade is characterized by exceptional phenotypic convergence.


The methods are described in detail in a paper coauthored with Luke Mahler, which is now in press at Methods in Ecology and Evolution. The R package “surface” that implements this method is now available from CRAN as either source files or Windows or Mac binaries. The surface package includes a vignette, produced using Sweave, which explains and demonstrates its most important functions; package source and vignette can also be downloaded from the links below. You can also watch a ~8 minute video tutorial about SURFACE on the MEE YouTube channel. If you have any questions about the methods or discover any bugs or problems, please send me an e-mail.

surface_0.3.tar.gz


surface_tutorial.pdf

Updates in version 0.3:


Some of the functions were buggy when settings other than the defaults were used. Specifically, the “aic_threshold” wasn’t used correctly when set to a value other than zero, and the “sample_shifts” option wasn’t correctly excluding shifts that didn’t improve the model, leading to truncated runs. This update also includes a new function, “surfaceAICMultiPlot” for visualizing the results of multiple runs, and new features in several other functions (see this list of updates for details).