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 linea...