Reconstructing Ecological Niche Evolution via Ancestral State
Reconstruction with Uncertainty Incorporated
Abstract
Study of species’ ecological niches through evolutionary history can
elucidate speciation mechanisms, yet current comparative phylogenetic
methods consistently overestimate niche evolution. Here we propose a
method by which to characterize species’ fundamental ecological niches
for comparative phylogenetic analysis using a bin-based approach that
incorporates uncertainty in niche estimates. Simulation analysis using a
traditional characterization method (median value calculated from
species’ known occurrences) estimated a significantly higher rate of
niche evolution than using our proposed method, and differences in rate
estimates were consistent regardless of the number of simulated taxa in
a phylogeny. We also demonstrate how to perform ancestral state
reconstructions under the new coding system; reconstructions are
performed for each bin individually, and ancestral fundamental niches
inferred by smoothing each node’s reconstructions across all bins.
Finally, we provide a worked empirical example of our method,
investigating ecological niche evolution in 34 species of New World
orioles (Icterus spp.). Ecological niches were generally conserved in
the group, and only a few lineages appear to have experienced niche
reduction and specialization.