This repository contains scripts and data needed to reproduce the species distribution models published in
Kim S, de Medeiros BAS, ..., Farrell BD. 2018. West Meets East: How Do Rainforest Beetles Become Circum-Pacific? Evolutionary Origin of Callipogon Relictus and Allied Species (Cerambycidae: Prioninae) in the New and Old Worlds. Molecular Phylogenetics and Evolution 125:163–76 https://doi.org/10.1016/j.ympev.2018.02.019
Contents of this folder:
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relictus_distribution_final.txt
File with locality data for Callipogon relictus
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SDM_Callipogon.R
Runs all models and projections using biomod2, in an utm map projection
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plot_projections_lonlat.R
Transform the results of previous scripts back to latlon to enable plotting pretty maps
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plots_expansion_loss.R
Plots graphs of area expansion and loss (figure 5)
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figure_ensemble_projection.R
Plots figure 4 (ensemble projection to present and one future scenario)
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supplementary_plots.R
Plots all supplementary figures
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maxent/
Directory with maxent program
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islands_exclude/
Directory with kml file containg polygon to exclude islands.
Initially, we excluded Japan and other islands from figure 4 and supplementary maps, but later decided to include them. Files 5 and 6, with suffix w_islands, are modifications of these scripts to include islands in the plots.
*.sh files are slurm scripts to run some of the scripts above in Harvard's Odyssey Cluster.