Speciation rates are governed by ecological limits and their associated niche dynamics
Creators: name: Araujo, Matheus
Publisher: name: figshare
Year: 2024
Subjects: classificationCode: 310405
subject: Evolutionary ecology

description: <b>### README ###</b>The following repository contains the following contents:<br><i>1) "Algorithms.R" (R script)</i> ---------------------------------------------------------------------------------------------------------------<br>An R script containing the algorithms used to compute the tip diversification rates sensu Jetz et al. (2012) for 100 bird phylogenies and the standadized effect sizes for functional variables.<br><br><i>2) "Assemblage_data.txt"</i> ---------------------------------------------------------------------------------------------------------------<br>A data table containing all the variables used within the study to assess the drivers of speciation rates at the assemblage level. Each line corresponds to an assemblage cell, and each column contains the variables computed within it.<br>The columns available within the data table:"Cell_ID" - Assemblage cell ID"pet_chs" - Potential Evapotranspiration (PET) obtained from CHELSA Climatology"Eco_lim" - Ecological limits (i.e., ratio between mean annual precipitation and PET)"Fric" - Standardized effect size for functional richness (i.e., niche expansion)"MNND" - Standardized effect size for the functional mean nearest neighborhood distance (i.e., niche packing)"m100_mpd" - Mean of the mean phylogenetic distances obtained for 100 bird phylogenies"m100_mpd_ses" - Mean of the standardized effect size for the mean phylogenetic distances obtained for 100 bird phylogenies (i.e., evolutionary time)"DR_m100t" - Mean tip-diversification rates (sensu Jetz et al., 2012) obtained from 100 bird phylogenies"BAMM_m100t" - Mean speciation rates obtained from 100 bird phylogenies using BAMM (Rabosky et al., 2014)<br><br><i>3) "Species_data.txt"</i> ---------------------------------------------------------------------------------------------------------------<br>A data table containing all the variables used within the study to assess the drivers of speciation rates at the species level. Each line corresponds to a species, and each column contains the variables computed within its range.<br>The columns available within the data table:"Species" - Species name"Order" - Species order"Family" - Species familiy"pet_chs" - Potential Evapotranspiration (PET) obtained from CHELSA Climatology"Eco_lim" - Ecological limits (i.e., ratio between mean annual precipitation and PET)"Fric" - Standardized effect size for functional richness (i.e., niche expansion)"MNND" - Standardized effect size for the functional mean nearest neighborhood distance (i.e., niche packing)"m100_mpd" - Mean of the mean phylogenetic distances obtained for 100 bird phylogenies"m100_mpd_ses" - Mean of the standardized effect size for the mean phylogenetic distances obtained for 100 bird phylogenies (i.e., evolutionary time)"DR_m100t" - Mean tip-diversification rates (sensu Jetz et al., 2012) obtained from 100 bird phylogenies"BAMM_m100t" - Mean speciation rates obtained from 100 bird phylogenies using BAMM (Rabosky et al., 2014)<br><br><b>References:</b>Jetz, W., Thomas, G. H., Joy, J. B., Hartmann, K., &amp; Mooers, A. O. 2012. The global diversity of birds in space and time. Nature, 491(7424): 444–448. doi:10.1038/nature11631Rabosky, D. L., Grundler, M., Anderson, C., Title, P., Shi, J. J., Brown, J. W., Huang, H., &amp; Larson, J. G. 2014. BAMMtools: an R package for the analysis of evolutionary dynamics on phylogenetic trees. Methods in Ecology and Evolution, 5: 701-707. doi:10.1111/2041-210X.12199