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 R package surface.

surface builds on the OUCH methodology (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 “Hansen” model using stepwise AIC, without any a priori specification of which taxa are thought to be convergent. This allows for an objective search for adaptive peak shifts, and for tests of whether a clade is characterized by exceptional phenotypic convergence.

These methods were developed in collaboration with Luke Mahler, and are described in detail here and implemented in a study of Anolis lizard convergence here. The R package surface that implements this method is 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 Methods in Ecology and Evoluion YouTube channel.

surface

News

I am not actively developing or updating surface, but if you have questions or find bugs, feel free to email me

Minor update (version 0.4-1) to ensure compatibility with geiger 2.0

Downloads

Current Version

surface_0.4-1

Documentation

surface_manual.pdf

surface_tutorial.pdf

Archived Versions

surface_0.4  notes

surface_0.3  notes