Supplementary Information for Ecological causes of uneven diversification and richness in the mammal tree of life Nathan S. Upham, Jacob A. Esselstyn, and Walter Jetz Nathan S. Upham Email: [email protected] This PDF file includes: Table of Contents Supplementary Methods Supplementary Results Figs. S1 to S24 Tables S1 to S12 Captions for Datasets S1 to S7 References for SI reference citations Other supplementary materials for this manuscript include the following: Datasets S1 to S7 i Table of Contents (click to navigate) Supplementary Methods .............................................................................................................. 1 0. Experimental design ................................................................................................................. 1 0.1 Overview of tree-building strategy...................................................................................................... 1 Fig. S1. ............................................................................................................................................. 1 0.2 Our tree relative to other inference methods ....................................................................................... 2 Fig. S2. ............................................................................................................................................. 2 1. DNA gathering pipeline ............................................................................................................ 3 1.1. Targeted gene fragments .................................................................................................................... 3 1.2. BLAST-based gathering of DNA sequences...................................................................................... 3 1.3. Parsing output for redundancy ........................................................................................................... 4 Table S1. .......................................................................................................................................... 4 2. Taxonomic matchup of mammalian species names ............................................................... 5 2.1 NCBI to IUCN..................................................................................................................................... 5 Fig. S3 .............................................................................................................................................. 6 2.2 Master taxonomy for this study ........................................................................................................... 6 Table S2. .......................................................................................................................................... 7 3. Error-checking via iterative DNA sequence alignment and gene tree construction .......... 7 3.1 DNA alignments and pseudogenes...................................................................................................... 7 3.2 Gene tree construction and rogue taxon identification ........................................................................ 7 3.3 Visual error-checking of gene trees..................................................................................................... 8 3.4 Final gene alignments and gene trees .................................................................................................. 9 Table S3. ........................................................................................................................................ 10 4. Global genetic scaffold tree using maximum likelihood ...................................................... 11 4.1 Supermatrix concatenation ................................................................................................................ 11 4.2 PartitionFinder ................................................................................................................................... 11 Table S4. ........................................................................................................................................ 12 4.3 Global ML tree in RAxML ............................................................................................................... 12 5. Patch clade trees and PASTIS completion of missing species ............................................ 12 5.1 Delimitation of patch clades .............................................................................................................. 12 Table S5. ........................................................................................................................................ 14 5.2 Genetic missingness, taxonomic constraints, and species completion .............................................. 15 5.3 Patch clade estimation in MrBayes ................................................................................................... 16 6. Fossil-dated backbone trees ................................................................................................... 17 6.1 Node-dating backbone analyses ........................................................................................................ 17 6.2 Tip-dating backbone analyses ........................................................................................................... 19 7. Construction of full dated mammalian phylogenies ............................................................ 20 7.1 Summary of patch clade and backbone posteriors ............................................................................ 20 7.2 Consensus trees and their pitfalls for taxonomically completed trees .............................................. 20 7.3 Patch-to-backbone grafting for full Mammalia trees ........................................................................ 21 8. Tests of diversification-rate variation or constancy ............................................................ 22 8.1 Tip-level diversification rates ............................................................................................................ 22 8.2 Tip DR compared to model-based estimators ................................................................................... 23 Fig. S4 ............................................................................................................................................ 24 8.3 Lineage-specific rate shifts in BAMM .............................................................................................. 25 ii 8.4 Tree-wide rate shifts in CoMET and TreePar ................................................................................... 26 8.5 Lineages-through-time (LTT) plots................................................................................................... 26 8.6 Simulation of rate-constant trees ....................................................................................................... 27 8.7 Likelihood tests of RC and RV models of diversification ................................................................ 27 8.8 Time-sliced clades ............................................................................................................................. 28 Fig. S5 ............................................................................................................................................ 29 8.9 Clade-level PGLS to test RC versus RV diversification ................................................................... 30 8.10 Fossil genus diversification ............................................................................................................. 30 9. Tests for causes of diversification-rate variation ................................................................. 31 9.1 Mammalian trait data......................................................................................................................... 31 Fig. S6 ............................................................................................................................................ 31 Fig. S7 ............................................................................................................................................ 34 9.2 Tip-level correlates of diversification rates ....................................................................................... 35 9.3 Clade-level correlates of diversification rates ................................................................................... 35 9.4 Phylogenetic path analyses: clade-level causes of diversification and richness ............................... 36 Fig. S8 ............................................................................................................................................ 37 Supplementary Results and Discussion .................................................................................... 38 1. Appropriate use of trees ......................................................................................................... 38 2. Comparisons to previous mammal studies ........................................................................... 38 2.1 Topological relationships .................................................................................................................. 38 2.2 Backbone divergence times ............................................................................................................... 39 2.3 Tip-level rates in mammal supertrees ..............................................................................................