Phylogeny
We used one of the most updated and complete sets of phylogenies of
sigmodontine rodents (Upham et al. 2019) for ancestral diet mapping and
phylogenetic uncertainty analysis. The phylogenies have dated branches
and were built from a supermatrix alignment of 11 genes which were
extracted from a more inclusive mammalian supermatrix of 31 genes (Upham
et al. 2019). The phylogenies were built using the multigene-approach
for 279 of 413 extant sigmodontine species; the remaining 134 species
were randomly placed at the tips of the phylogeny according to
prevailing taxonomy. To consider phylogenetic uncertainty, we used a
random sample of 100 phylogenies. An ancestral state was estimated for
each node included in the evolutionary history of the 413 species, but
we focused our analysis on the 350 species with distribution data that
were included in the phylogeny. The mapping of ancestral characters was
repeated for the 100 phylogenies in order to assess uncertainty in
tip-based metrics (see below Ancestral character mapping ).