SUPPORTING INFORMATION for Multi-dimensional biodiversity hotspots and the future of taxonomic, ecological, and phylogenetic diversity: a case study of North American rodents By T.M. Smiley, P.O. Title, M.L. Zelditch, and R.C. Terry Appendix S1 Data Completeness: A taxonomic list of North American rodents was assembled from two main sources: the Smithsonian Field Guild of North American mammals (Smithsonian, 2018) and the IUCN Red List (IUCN, 2017). The total list from these two sources equaled 368 taxa, 18 of which were excluded from our analysis because they were either 1) considered synonymous with other taxa in the analysis (n = 9), classified as extinct in IUCN (n = 6), lacked range data in IUCN (n = 2) or were invasive species (n = 1). The following rodent species were excluded, as they were listed as Extinct by the IUCN Red List: Neotoma anthonyi, Neotoma bunkeri, Neotoma martinensis, Oryzomys nelson, Peromyscus guardia, Peromyscus pembertoni; or as Invasive to North America: Myocastor coypus. Therefore, a total of 350 North American rodent species were included in the analysis, with a high level of data completeness in our dataset. A total of five taxa were additionally excluded from analyses of body-size richness and evenness (taxa indicated in SI Table 1.1); lack of body size data was frequently the case for species with exceptionally low numbers of occurrences and deemed as “Data Deficient” taxa in IUCN and elsewhere. Of the near-complete dataset, an additional two species were excluded from the phylogenetic analysis due to lack of phylogenetic information in the Fabre et al. (2012) tree: Peromyscus schmidlyi (recently split from P. boylii) and Reithrodontomys bakeri. Additional taxonomic considerations: In a small number of cases, both phylogenetic and geographic data did not reflect the most up-to-date taxonomy. For example, Perognathus parvus has recently been split into two, non-sympatric species, P. mollipilosus and P. parvus (Riddle et al., 2014); however, this change has a negligible impact on phylogenetic diversity patterns. The recent generic revision of Holarctic ground squirrels (Helgen et al., 2009) was used to update taxonomic names for the now defunct Spermophilus genus in this analysis. Other changes in rodent taxonomy (e.g., Helgen et al. 2009) did not change taxonomic relationships or phylogenetic branch lengths. SUPPORTING FIGURES Supporting Figure S1.1 Maps of North American rodent diversity metrics, calculated without species above the 90% quantile in geographic range area. The loss of wide-ranging taxa shows similar patterns of diversity across dimensions as demonstrated in the main text Figures 1, 2, 3. Note the lack of color where species have been lost; in particular, ecological diversity metrics were not calculated for cells with less than 5 species present. See also Supporting Table S1.4. Supporting Figure S1.2 Patterns of phylogenetic diversity based on analyses conducted with the pruned Fabre et al. (2012; n = 348) versus the pruned Faurby and Svenning (2015; n = 314) mammal phylogenies. The left and middle panels show spatial patterns of each diversity metric, while the right panels show the correlation between values in the two maps. Correlation coefficients are generated using a Dutilleul’s t-test, and all relationships are highly significant. Supporting Figure S1.3 Species richness difference pre- minus post-extinction, with positive values indicating number of species lost per cell. Simulated extinction is based on removal of species classified as Critically Endangered, Endangered or Vulnerable by the IUCN Red List (IUCN, 2017). Supporting Figure S1.4 Boxplots of the values for each diversity metric, pre- and post-extinction: (a) taxonomic richness, (b) log(range-weighted richness), (c) log(phylo-endemism), (d) body size richness, (e) diet richness, (f) habitat richness, (g) mean pairwise distance, (h) mean nearest neighbor distance, (i) variance of pairwise distances, (j) genus-to-species ratio. Values for this comparison were calculated only for the cells that experience species loss; therefore, a subset of the total grid cells across North America are included in this comparison. Asterisks for metrics indicate significant differences in values pre- and post-extinction, using a Student’s two sample t-test. 4 (a) (b) (c) ● 10 (d) 9 (e) 40 1 3 9 8 8 30 0 2 7 7 6 20 −1 1 6 5 5 0 10 −2 4 4 ● −1 ● ● ● 0 −3 3 3 Pre−Ext Post−Ext Pre−Ext Post−Ext Pre−Ext Post−Ext Pre−Ext Post−Ext Pre−Ext Post−Ext ● 1.0 120 3500 18 (f) (g) (h) (i) (j) 3000 60 ● 0.9 16 100 2500 14 80 0.8 40 2000 12 60 0.7 1500 10 40 20 1000 0.6 8 20 500 0.5 6 0 ● 0 ● 0 ● Pre−Ext Post−Ext Pre−Ext Post−Ext Pre−Ext Post−Ext Pre−Ext Post−Ext Pre−Ext Post−Ext Supporting Figure S1.5 Maps of residuals from a regression model of (a) log(range-weighted richness), (b) log(phylo-endemism), (c) body size richness, (d) diet richness, (e) habitat richness, (f) mean pairwise distance (MPD), (g) variance of pairwise distances (VPD), (h) mean nearest neighbor distance (PNN), and (i) genus-to-species ratio (GSR) against taxonomic richness. Log(range-weighted richness), log(phylo-endemism), and MPD are positively and strongly correlated with taxonomic richness (r = 0.8, r = 0.9, and r = 0.5, respectively). PNN and GSR are negatively correlated (r = -0.5, r = -0.8, respectively) with taxonomic richness. VPD does not exhibit a strong relationship (r = 0.4) with taxonomic richness. See also Supporting Table S1.3. SUPPORTING TABLES Supporting Table S1.1 The body size (mean and body size class), diet (category), habitat (category), geographic range area (km2), and IUCN Red List status of species included in this study, as well as references from which data were compiled. See accompanying Excel File: “Master_SpeciesData_SI.xlsx” Supporting Table S1.2 Ecological categories determined for this study, including: a) body size class and associated body mass range; b) diet categories; and c) habitat categories. See accompanying Excel File: “Master_SpeciesData_SI.xlsx” These data files are also openly available in the Dryad repository at https://doi.org/10.5061/dryad.4xgxd2559. Supplementary Table S1.3. Correlation values (lower triangle) and adjusted p- values (upper triangle) from Dutilleul’s t-test, for pairwise comparison between dimensions of biodiversity calculated at a 100 x 100 km grid cell size. Significant correlations at ⍺ < 0.05 are bolded (per Bonferroni sequential adjustment). Pairwise log(Range- Mean Variance Faith’s Genus: Taxonomic Body Size Dietary Habitat Nearest log(Phylo- weighted Pairwise Pairwise Phylogenetic Species Richness Richness Richness Richness Neighbor Endemism) Richness) Distance Distance Diversity Ratio Distance Taxonomic Richness - 0.177 0.118 0.056 0.001 0.404 0.476 1 0.001 0.091 0.174 log(Range-weighted Richness) 0.825 - 0.734 1 0.348 1 0.535 1 0.368 0.003 0.179 Body Size Richness 0.753 0.638 - 1 0.271 1 0.476 1 0.133 0.599 1 Dietary Richness 0.675 0.394 0.435 - 0.060 0.391 1 1 0.014 0.788 1 Habitat Richness 0.926 0.747 0.717 0.694 - 1 0.528 1 0.005 0.183 0.476 Mean Pairwise Distance 0.507 0.338 0.295 0.459 0.336 - 1 1 0.008 0.528 1 Pairwise Nearest Neighbor Distance -0.502 -0.509 -0.507 -0.188 -0.516 0.255 - 1 1 1 0.060 Variance Pairwise Distance -0.373 -0.285 -0.294 -0.352 -0.422 -0.213 0.238 - 0.746 1 1 Faith’s Phylogenetic Diversity 0.944 0.751 0.747 0.740 0.887 0.701 -0.268 -0.474 - 0.103 0.734 log(PhyloEndemism) 0.860 0.965 0.652 0.461 0.778 0.465 -0.419 -0.356 0.831 - 0.271 Genus:Species Ratio -0.810 -0.820 -0.555 -0.36 -0.696 -0.236 0.643 0.116 -0.661 -0.794 - Supplementary Table S1.4. Correlation values (lower triangle) and adjusted p- values (upper triangle) from Dutilleul’s t-test, for pairwise comparison between dimensions of biodiversity calculated at a 100 x 100 km grid cell size, excluding wide-ranging taxa. A total of 35 species with ranges > 2,620,000 km2 were removed proir to analysis. Significant correlations at ⍺ < 0.05 are bolded (per Bonferroni sequential adjustment). Pairwise log(Range- Mean Variance Faith’s Genus: Taxonomic Body Size Dietary Habitat Nearest log(Phylo- weighted Pairwise Pairwise Phylogenetic Species Richness Richness Richness Richness Neighbor Endemism) Richness) Distance Distance Diversity Ratio Distance Taxonomic Richness - 0.069 0.018 0.020 <0.001 1 0.196 1 0.004 0.091 0.028 log(Range-weighted Richness) 0.890 - 0.088 0.426 0.040 1 0.078 1 0.062 0.018 0.096 Body Size Richness 0.651 0.571 - 0.759 0.028 1 0.006 0.426 0.045 0.088 0.173 Dietary Richness 0.783 0.582 0.400 - 0.028 1 0.240 1 0.045 0.426 0.162 Habitat Richness 0.887 0.725 0.595 0.738 - 1 0.035 1 0.008 0.069 0.020 Mean Pairwise Distance 0.153 0.106 0.320 0.432 0.239 - 0.018 0.311 1 1 1 Pairwise Nearest Neighbor Distance -0.590 -0.636 -0.538 -0.483 -0.575 0.493 - 1 0.426 0.308 0.062 Variance Pairwise Distance 0.182 0.217 0.436 0.204 0.277 0.456 -0.198 - 1 1 1 Faith’s Phylogenetic Diversity 0.971 0.911 0.638 0.774 0.812 0.301 -0.526 0.203 - 0.045 0.096 log(PhyloEndemism) 0.896 0.951 0.568 0.577 0.687 0.229 -0.528 0.146 0.939 - 0.196 Genus:Species Ratio -0.843 -0.764 -0.501 -0.639 -0.726 -0.015 0.592 -0.289 -0.792 -0.737 - References for Supporting Information (see Supporting Excel File for additional references) Fabre, P.