Ancestral character mapping
We used an algorithm of stochastic mapping of discrete characters via
Bayesian inference (Bollback 2006) to reconstruct the trajectory of diet
states across the rodent phylogenies. We used the functionmake.simmap of the Phytools package (Revell 2012), implemented in
the R environment. Stochastic mapping based on Bayesian inference allows
calculation of the discrete ancestral state (s) of the phylogeny’s nodes
and the timing of changes along the branches. Stochastic mapping output
shows the most probable ancestral state (s) of a node; this output is
based on the mean posterior probability of finding a given state and the
timing of changes along the phylogeny branches. The mean posterior
probability is based on a sample of the posterior probability across a
desired number of simulations; here, we used 100 phylogenies and 100
simulations per phylogeny.
Evolutionary processes can produce both symmetric and asymmetric
transitions across diet states (Joy et al. 2016), so we first defined
whether transitions across diet states are equal (“SYM”, symmetric
model) or different (“ARD”, all-rates-different model) (Table S1, see
Supplementary Methods in the Online Supporting Information). As the
model with symmetric transition rates had more support than the model
with asymmetric rates, we conducted definitive stochastic character
mapping using the complete set of 100 phylogenies, with 100 simulations
per phylogeny, to more robustly estimate parameters under the symmetric
evolutionary model. The output of the stochastic mapping procedure
consisted of a set of 10,000 estimates of diet states and length of time
that a given diet state persisted per node. This time length is based on
the branch length between two nodes with a common diet state. To
attribute diet category and estimated time to each node, we built an
adjacency matrix with phylogeny tips (species) in the rows, and
internal-node numbers in the columns. Values of 1 were attributed to
nodes belonging to the evolutionary history of a species. The first
column is the phylogeny root and is completely filled with 1’s, as it
belongs to the evolutionary history of all species; the last column is
the most recent internal node leading to a tip. These 1’s were then
replaced by the reconstructed diet category and time. When more than one
state was equally probable at a given node, we used the state present
longer at that node.