DOI: 10.5061/dryad.280gb5n26
title: Data from: Ppgm: an R package for integrating neontological, palaeontological, and climate data in a phylogenetic comparative framework

description: Understanding how changes in climate affect habitat availability for
 species through time is critical for macroevolutionary, ecological, and
 conservation research. When combined with palaeoclimate reconstructions,
 the fossil record provides insights into how species’ geographic
 distributions have responded to past climate shifts, including under
 non-analogous climate conditions. PalaeoPhyloGeographic Models (PPGM)
 offer a framework to integrate modern and palaeontological data into
 phylogenetic comparative analyses of species climate tolerances. The ppgm
 R package is an implementation of PPGM, which estimates species climate
 envelopes, reconstructs ancestral climatic tolerances across phylogenies,
 and projects these onto palaeoclimate maps to identify climatically
 available regions through time. The package also supports direct inclusion
 of fossil occurrences with associated palaeoclimate data, allowing a
 reconstruction of past trends of species climate tolerances projected into
 palaeoclimate maps to pinpoint the locations of climate availability
 through time according to the fossil record. We demonstrate the broad
 applicability of ppgm through detailed case studies, showing its potential
 for addressing research questions in macroevolutionary and conservation
 palaeobiology research. The ppgm package complements existing R packages
 by allowing researchers to use analytical techniques on large integrated
 datasets and facilitates reproducible analyses of species climate niches
 over deep and shallow time.
description: # Data from: Ppgm: an R package for integrating neontological,
 palaeontological, and climate data in a phylogenetic comparative framework
 ## author: Alexandra FC Howard ## date: 2025-10-31 ### Supplementary Files
 This folder contains the supplementary files for the paper "ppgm: an
 R package for integrating neontological, palaeontological, and climate
 data in a phylogenetic comparative framework". Howard, AFC;
 Hurtado-Materon, MA; Rivera, JA; Zuniga-Vega, JJ; Martins, EM; Lawing, AM.
 Both .rda files can be found at the Supplemental Information link in the
 Related Works ### Contents * **simulations.R** - code for performing
 simulations in paper (see notes within script for further information) *
 **examples.R** - code for in-text examples (see notes within script for
 further information) * **pantherophis_occurrences.rda** - data frame
 containing *Pantherophis* occurrences from GBIF (accessed 26 April 2024,
 doi:[https://doi.org/10.15468/dl.dyh8c7](https://doi.org/10.15468/dl.dyh8c7)) * **pantherophis_fossils.rda** - data frame containing fossil *Pantherophis* (*Elaphe*) in North America * Data was downloaded from paleobiodb.org (accessed 26 April 2024) using the following search criteria: base_id = 42023738134, lngmin = -151.9629, lngmax = -17.0508, latmin = 2.8114, latmax = 60.2834, timerule = major, taxon_status = all * Original Data URL: [http://paleobiodb.org/data1.2/occs/list.csv?lngmin=-151.9629&lngmax=-17.0508&latmin=2.8114&latmax=60.2834&base_id=420237,38134&show=coords,attr,loc,prot,time,strat,stratext,lith,lithext,geo,rem,ent,entname,crmod,paleoloc&datainfo](http://paleobiodb.org/data1.2/occs/list.csv?lngmin=-151.9629&lngmax=-17.0508&latmin=2.8114&latmax=60.2834&base_id=420237,38134&show=coords,attr,loc,prot,time,strat,stratext,lith,lithext,geo,rem,ent,entname,crmod,paleoloc&datainfo) * Species without palaeolongitude/palaeolatitude coordinates were excluded, and fossils from same location and time period were trimmed, resulting in 41 occurrence records. * **pantherophis_tree.nex** - tree of 7 *Pantherophis* species, pruned from the time-calibrated tree from Zheng & Wiens (2016) ### References Zheng, Y., Wiens, J.J., 2016. Data from: Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species. [dataset] Dryad. [https://doi.org/10.5061/dryad.tv055](https://doi.org/10.5061/dryad.tv055)