A new method for integrating ecological niche modeling with phylogenetics to estimate ancestral distributions

Ancestral range estimation and projection of niche models into the past
have both become common in evolutionary studies where the ancient
distributions of organisms are in question. However, these methods are
hampered by complementary hurdles: discrete characterization of areas in
ancestral range estimation can be overly coarse, especially at shallow
timescales, and niche model projection neglects evolution. Phylogenetic
niche modeling accounts for both of these issues by incorporating
knowledge of evolutionary relationships into a characterization of
environmental tolerances. We present a new method for phylogenetic niche
modeling, implemented in R. Given past and present climate data, taxon
occurrence data, and a time-calibrated phylogeny, our method constructs
niche models for each extant taxon, uses ancestral character estimation to
reconstruct ancestral niche models, and projects these models into
paleoclimate data to provide a historical estimate of the geographic range
of a lineage. Models either at nodes or along branches of the phylogeny
can be estimated. We demonstrate our method on a small group of
dendrobatid frogs and show that it can make inferences given species with
restricted ranges and little occurrence data. We also use simulations to
show that our method can reliably reconstruct the niche of a known
ancestor in both geographic and environmental space. Our method brings
together fields as disparate as ecological niche modeling, phylogenetics,
and ancestral range estimation in a user-friendly package.