Relatedness, trait evolution, and climatic niche divergence in mammalian island endemics
The code and datasets used to conduct analyses presented in our manuscript entitled : "Relatedness, trait evolution, and climatic niche divergence in mammalian island endemics":
Taxonomy_Corrections_Islands: a taxonomy crosswalk between the taxonomy of the relatedness data (Phylacine), the species range data (IUCN) and the trait data (COMBINE dataset).
WorldEcoregions: a list of WWF ecoregions and whether or not they include or are entirely on islands (i.e., not entirely continental).
Ecoregion_Residents_WWF: a list of all species with IUCn ranges and the ecoreigons they live in
01_Island_Endemics.R: code to determine which species are endemic to islands, which ones live on islands but are not endemic to them, and which ones only live on mainlands.
02_Sister_Species.R: code that uses a phylogeny from PHYLACINE to determine which species are sister taxa, whether or not the sister taxa are island-island, island-mainland, or mainland-mainland, whether they are sympatrics or not, and other factors.
Island_Endemics_Final.csv: a list of all speices and their closest relatives, and whether or not they live exclusively on islands (made from 02_Sister_Species.R)
03_Niche_Comparison.R: Code to generate metrics of niche evolution between species pairs (niche overlap and distance as described in the manuscript)
04_Analysis.R: Code to conduct the statistical analyses presented in the manuscript, relating to the three different categories of species pairs, sympatry, and relatedness.
04_Trait_Niche.R: Code to conduct the statistical analyses presented in the manuscript relating to the covariance of climatic niche and trait evolution
Niche_Geography.R: Code to conduct the statistical analyses presented in the manuscript relating to the covariane of climatic niche and geography
NicheComparison_IUCN_Full.csv: The dataset created from 04_Niche_Comparison, 04_Analysis, and Niche_Geography.R that has every species pair, their lcimatic niche overlaps and distance, geographic distance, and relatedness (see 04_Trait_Niche.R for tait differences).
