Geographic characters---traits relating to the spatial distribution of
a species---may both affect and be affected by processes associated
with lineage birth and death. This is potentially confounding to
comparative analyses of species distributions because current models
do not allow reciprocal interactions between the evolution of traits
and the growth of phylogenetic trees. Here we introduce a
likelihood-based approach to estimating region-dependent rates of
speciation, extinction, and range evolution from a phylogeny, using a
new model in which these processes are interdependent. We demonstrate
the method with simulation tests that accurately recover parameters
relating to the mode of speciation and source-sink dynamics. We then
apply it to the evolution of habitat occupancy in Californian plant
communities, where we find higher rates of speciation in chaparral
than in forests and evidence for expanding habitat tolerances.
habitat character states for Arctostaphylos
1 = chaparral, 2 = forest, 0 = both
arc-states.csv
habitat character states for Ceanothus
1 = chaparral, 2 = forest, 0 = both
cea-states.csv
phylogenetic trees for Arctostaphylos
1000 trees from the posterior set produced by BEAST
arc-trees.tre
phylogenetic trees for Ceanothus
1000 trees from the posterior set produced by BEAST
cea-trees.tre
chaparral analysis script
Fitting the GeoSSE model with this script requires the R package diversitree, written by Rich FitzJohn. A snapshot of the code used for the analyses in the paper is archived by Systematic Biology as a supplemental file to the paper (diversitreeGSE_0.4-5.tar.gz) because its GPL licence is not compatible with Dryad's CC0 requirement. This package is presently undergoing rapid development, so for any new applications, please use the current, improved version of the package, available from: http://cran.r-project.org/web/packages/diversitree/ and http://www.zoology.ubc.ca/prog/diversitree/.
chaparral-analysis.R
simulation analysis script
Simulating trees under the GeoSSE model requires the C program SimTreeSDD. A snapshot of the code used for the analyses in the paper is archived by Systematic Biology as a supplemental file to the paper (SimTreeSDD-2009.tar.gz) because its GPL licence is not compatible with Dryad's CC0 requirement. Extensive further development is not planned, but the current version of the package is available from: http://tigger.uic.edu/~eeg/code/code.html. The R package diversitree is also required by this script. See Description for chaparral-analysis.R.
simulation-analysis.R
alignment for Arctostaphylos
also contains habitat states and maximum clade credibility tree
Arctostaphylos.nex
alignment for Ceanothus
also contains habitat states and maximum clade credibility tree
Ceanothus.nex
BEAST input file for Arctostaphylos
ArctostaphylosBeastfile.xml
BEAST input file for Ceanothus
CeanothusBeastfile.xml
arc & cea supplementary table
GenBank accession numbers and habitat encoding notes and references
ArcCeaSupplementaryTable.xls