PaleoPhyloGeographic Modeling of Climate Niches and Species Distributions

Reconstruction of paleoclimate niches using phylogenetic comparative methods and projection reconstructed niches onto paleoclimate maps. The user can specify various models of trait evolution or estimate the best fit model, include fossils, use one or multiple phylogenies for inference, and make animations of shifting suitable habitat through time. This model was first used in Lawing and Polly (2011), and further implemented in Lawing et al (2016) and Rivera et al (2020). Lawing and Polly (2011) "Pleistocene climate, phylogeny and climate envelope models: An integrative approach to better understand species' response to climate change" Lawing et al (2016) "Including fossils in phylogenetic climate reconstructions: A deep time perspective on the climatic niche evolution and diversification of spiny lizards (Sceloporus)" Rivera et al (2020) "Reconstructing historical shifts in suitable habitat of Sceloporus lineages using phylogenetic niche modelling.".

ppgm

This package, ppgm allows the user to produce PaleoPhyloGeographic Models (PPGM). This method reconstructs the evolutionary history of climate envelopes using phylogenetic comparative methods, incorporating both neontological and paleontological data.

Installation

You can install the development version of ppgm from GitHub with:

# install.packages("devtools")
devtools::install_github("michellelawing/ppgm")

You can install the current CRAN version using:

# install.packages("ppgm")
library(ppgm)