Supporting Information Supporting Information Corrected December 28, 2015 Estep et al. 10.1073/pnas.1404177111 SI Materials and Methods inferred to represent a single locus and were combined into Taxon Sampling. We sampled 114 accessions representing two a majority-rule consensus sequence. Clones that did not meet outgroup species (Paspalum malacophyllum and Plagiantha tenella), these criteria were kept separate through another round of two species of Arundinella, and 100 species of Andropogoneae in RAxML analyses. We identified clades with a bootstrap value ≥ 40 genera. Plant material came from our own collections, the US 50 that comprised the same accession for each locus. Accessions Department of Agriculture (USDA) Germplasm Resources In- in these clades were reduced to a single majority-rule consensus formation Network (GRIN), the Kew Millenium Seed Bank, and sequence using the perl script clone_reducer (github.com/ material sent by colleagues. All plants acquired as seeds (e.g., those mrmckain). from USDA and from Kew) were grown to flowering in the Gene trees were estimated using RAxML v.7.3.0 with the greenhouse at the University of Missouri-St. Louis to verify iden- GTR + Γ model and 500 bootstrap replicates for each locus. tification. Vouchers are listed in Table S1. We used individual gene-tree topologies as a guide to identify and concatenate paralogues from the same genome for each acces- Sequencing and Processing. Total genomic DNA was extracted sion. If a polyploid had two paralogues in each gene tree, and one using a modified cetyl triethylammonium bromide (CTAB) paralogue was always sister to a particular diploid or other poly- procedure (1) or Qiagen DNeasy kits, following the manu- ploid, then we inferred that those paralogues represented the facturer’s protocol (Qiagen) (2). Five regions of four loci were same genome and used them to create a concatenated sequence. PCR amplified following Estep et al. (3). The loci are Aberrant If a locus did not have a sequence congruent to the topology, then panicle organization1 (apo1), Dwarf8(d8), two exons of Erect the locus was marked as missing data. Five datasets were assem- panicle2 (ep2), and Retarded palea1 (rep1). In sorghum (a dip- bled. One included only accessions with full sampling of all loci for loid) apo1 and d8 are on chromosomes 1 and 10, respectively. all genomes, a second included accessions that had four out of five ep2 and rep1 are on chromosome 2, 14.5 Mbp apart; based on markers, a third, three out of five, and so forth. Preliminary trees estimated recombination frequency in euchromatic regions, this for all datasets were congruent, but those trees in which some distance could be ca. 50 cM (4). Thus, the four markers are genomes of some taxa were represented by only one or two se- unlinked. Each marker has homologs on two chromosomes in quences were less well supported. The results presented here are maize, as expected in a tetraploid. Importantly for this study, we based on the dataset with a minimum of three out of five loci for found no evidence that these loci are lost after polyploidization; each taxon, which maximized species inclusion while still providing in known polyploids, paralogues are found consistently as long as enough information for robust results. All five datasets are depos- sequence depth is sufficient. ited at Dryad (datadryad.org/resource/doi:10.5061/dryad.5kf38). PCR products were gel purified, cloned using pGEM-T easy kits, and transformed into JM109 high-efficiency competent cells, Phylogenetic Analysis, Divergence Time, and Diversification Estimates. following the manufacturers’ protocols (Promega) or using Concatenated trees were reconstructed using both maximum a Topo-4 cloning vector and transformed into One Shot Top 10 likelihood (ML) and Bayesian approaches and rooted at Paspalum. cells (Invitrogen). At least eight positive clones for each PCR The ML tree was estimated with RAxML using the GTR + Γ product were sequenced in both directions using universal pri- model and 500 bootstrap replicates. The Bayesian tree was esti- mers (M13, Sp6, or T7) on an ABI3730 DNA sequencer at the mated using MrBayes v.3.2.1 (8) using a gamma model with six Penn State Huck Institute of the Life Sciences or Beckman discrete categories. Two independent runs with 50 million gen- Coulter Genomics. Chromatogram files were trimmed of vector erations each were sampled every 1,000 generations. Convergence and low quality sequences manually or using Geneious Pro-5.5.6 of the separate runs was verified using AWTY (9). (BioMatters), and reverse and forward sequences for each clone Divergence times were estimated using BEAST 1.7.5 (10) on were assembled. Only clones with 80% or more double-stranded the CIPRES Science Gateway (11). The concatenated analysis sequence were used for downstream analyses. Internal primers was run for 100 million generations sampling every 1,000 under were designed as necessary for loci over 1,000 bp long (D8 and the GTR + Γ model with six gamma categories. The tree prior Ep2 exon7). All good quality contigs for each sample were then used the birth-death with incomplete sampling model (12), with aligned using Geneious, and primer sequences were removed. the starting tree being estimated using unweighted pair group Recombinants were initially identified by eye and then con- method with arithmetic mean (UPGMA). The site model fol- firmed with networks in SplitsTree (5), and removed from the lowed an uncorrelated lognormal relaxed clock (13). The anal- alignment. Use of computational methods alone missed many ysis was rooted to Paspalum, with the age of the root estimated recombinant sequences that were readily identifiable by eye. as a normal distribution describing an age of 25.5 ± 5 million y Occasionally, it was difficult to determine which sequences were (14). Convergence statistics were estimated using Tracer v.1.5 genomic and which were PCR recombinants; in these cases, we (15) after a burn-in of 50,000 sampled generations. Chain con- compared the problematic sequences with unambiguous se- vergence was estimated to have been met when the effective quences from other species to determine the nonrecombined sample size was greater than 200 for all statistics. Ultimately, sequences. Singletons were identified with MEGA (6) and were 10,000 trees were used in TreeAnnotator v.1.7.5 to produce interpreted as PCR errors. Sequences were translated and the maximum clade credibility tree and to determine the aligned using MUSCLE, as implemented in Geneious Pro-5.5.6. 95% highest posterior density (HPD) for each node. The final tree was drawn using FigTree v.1.4.0 (tree.bio.ed.ac.uk/software/ Data Matrix Assembly. The dataset for each locus consisted of figtree/). numerous redundant clones. To reduce the number of sequences Tests for shifts in the underlying model of diversification were to one per paralogue per locus, preliminary phylogenetic analyses conducted using Bayesian Analysis of Macroevolutionary Mix- were conducted for each marker in RAxML (7) including all tures (BAMM) (16); priors were chosen as recommended using clones for all taxa. Clones that formed a clade in preliminary the function setBAMMpriors. Analyses were conducted on a tree analyses and that differed by fewer than five nucleotides were constructed by pruning the BEAST tree to leave only a single
Estep et al. www.pnas.org/cgi/content/short/1404177111 1of7 paralogue (genome) per species, as well as on the unpruned trees. using standard methods, and the values were averaged (20). Pi- Analyses were run for 10 million and 100 million generations; cograms of DNA/2C cell were converted to megabasepairs 10 million provided an adequate effective sample size for both (Mbp)/1C by multiplying the average experimental value by rate shifts and log-likelihoods (>>500), and additional generations 980 Mbp per 1 picogram of DNA and dividing by two. did not change the results. Incomplete taxon sampling was ac- commodated by assigning a backbone sampling fraction of 0.5, Estimating the Number of Allopolyploidization Events. To obtain corresponding to our sample of 50% of the genera, and assigning a minimum estimate of the number of allopolyploidy events, we specific fractions for the sample for each clade. Preliminary looked for a clear phylogenetic signal of allopolyploidy, in the analyses using a backbone sample of 0.08 or using a global esti- form of a multiple-labeled gene tree (Fig. S1). This method mate of sampling intensity produced largely similar results. provides unambiguous evidence of allopolyploidy, but will Differences in speciation rate for polyploids versus diploids overlook genetic and taxonomic autopolyploidy, allopolyploidy were estimated using the Binary State Speciation and Extinction between two very similar species or populations of the same (BiSSE) model (17) as implemented in Mesquite (18) and di- species, and allopolyploidy for which our sequencing was not versitree (19). Species were coded as allopolyploid or diploid, sufficiently deep to retrieve paralogues. Thus, the number of and the characters were mapped on the pruned BEAST tree. events estimated here is a robust minimum estimate. We also Adjustment for incomplete sampling was implemented in di- report genome size for many of the sequenced specimens (Figs. S2 versitree, using a sample of 0.08 and also 0.5 to correspond to the and S3). Although genome size gives a rough approximation of analyses in BAMM. Analyses were run for 100,000 generations. Values from an unconstrained analysis were compared with ploidy, it cannot distinguish between polyploids and plants whose those of an analysis in which speciation rates were constrained to genomes have expanded via transposon amplification (21). We be equal. did not use published data on chromosome numbers because the literature on these numbers is unreliable; many counts lack Genome-Size Estimation. Genome size was measured by flow photodocumentation or voucher specimens and thus cannot be cytometry at the Flow Cytometry and Imaging Core laboratory verified as to number or species identity. In addition, many at the Benaroya Research Institute, Virginia Mason Research species have several numbers reported; these may represent real Center. Genome sizes were measured a minimum of four times variation or errors.
1. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh 11. Miller MA, Pfeiffer W, Schwartz T (2010) Creating the CIPRES science gateway for leaf tissue. Phytochem Bull 19:11–15. inference of large phylogenetic trees. Proceedings of the 2010 Gateway Computing 2. Teerawatananon A, Jacobs SWL, Hodkinson TR (2011) Phylogenetics of Panicoideae Environments Workshop (GCE) (Institute of Electrical and Electronics Engineers, New (Poaceae) based on chloroplast and nuclear DNA sequences. Telopea (Syd) 13: York), pp 1–8. 115–142. 12. Stadler T (2009) On incomplete sampling under birth-death models and connections 3. Estep MC, Vela Diaz DM, Zhong J, Kellogg EA (2012) Eleven diverse nuclear-encoded to the sampling-based coalescent. J Theor Biol 261(1):58–66. phylogenetic markers for the subfamily Panicoideae (Poaceae). Am J Bot 99(11): 13. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A (2006) Relaxed phylogenetics and e443–e446. dating with confidence. PLoS Biol 4(5):e88. 4. Mace ES, Jordan DR (2011) Integrating sorghum whole genome sequence information 14. Vicentini A, Barber JC, Giussani LM, Aliscioni SS, Kellogg EA (2008) Multiple coincident
with a compendium of sorghum QTL studies reveals uneven distribution of QTL and origins of C4 photosynthesis in the Mid- to Late Miocene. Glob Change Biol 14: of gene-rich regions with significant implications for crop improvement. Theor Appl 2963–2977. Genet 123(1):169–191. 15. Rambaut A, Suchard MA, Xie D, Drummond AJ (2013) Tracer, Version 1.5. Available at 5. Huson DH, Bryant D (2006) Application of phylogenetic networks in evolutionary tree.bio.ed.ac.uk/software/tracer/. studies. Mol Biol Evol 23(2):254–267. 16. Rabosky DL (2014) Automatic detection of key innovations, rate shifts, and diversity- 6. Tamura K, et al. (2011) MEGA5: Molecular evolutionary genetics analysis using max- dependence on phylogenetic trees. PLoS ONE 9(2):e89543. imum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol 17. Maddison WP, Midford PE, Otto SP (2007) Estimating a binary character’s effect on Evol 28(10):2731–2739. speciation and extinction. Syst Biol 56(5):701–710. 7. Stamatakis A (2006) RAxML-VI-HPC: Maximum likelihood-based phylogenetic analy- 18. Maddison WP, Maddison DR (2011) Mesquite: A Modular System for Evolutionary ses with thousands of taxa and mixed models. Bioinformatics 22(21):2688–2690. Analysis, Version 2.75. Available at mesquiteproject.org. 8. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under 19. FitzJohn RG (2012) Diversitree: Comparative phylogenetic analysis of diversification in mixed models. Bioinformatics 19(12):1572–1574. R. Methods Ecol. Evol. 3:1084–1092. 9. Nylander JAA, Wilgenbusch JC, Warren DL, Swofford DL (2008) AWTY (are we there 20. Arumuganathan K, Earle ED (1991) Estimation of nuclear DNA amounts of plants by yet?): A system for graphical exploration of MCMC convergence in Bayesian phylo- flow cytometry. Plant Mol Biol Rep 9:229–241. genetics. Bioinformatics 24(4):581–583. 21. Kellogg EA, Bennetzen JL (2004) The evolution of nuclear genome structure in seed 10. Drummond AJ, Suchard MA, Xie D, Rambaut A (2012) Bayesian phylogenetics with plants. Am J Bot 91(10):1709–1725. BEAUti and the BEAST 1.7. Mol Biol Evol 29(8):1969–1973.
Estep et al. www.pnas.org/cgi/content/short/1404177111 2of7 Examples of gene trees, Evolutionary history Gene tree, full sampling incomplete sampling
diploids, divergent tetraploid AE AE evolution hybridization A B B E A C AE B D C AE E AE
No diversification after polyploidy D AE B E AE
AE1 AE1 AE3 A E2 AE4 A E3 B AE4 A C AE1 A B E AE2 B C AE1 AE3 C D AE2 AE4 D Diversification after polyploidy E AE4 E E A 1 AE1 AE2 E AE4 A 3 AE1 AE4 AE4
Fig. S1. Gene-tree patterns resulting from hybridization and polyploidy (genetic allopolyploidy). (Left) The actual evolutionary history of divergent evolution at the diploid level, followed by hybridization between taxon A and taxon E (reticulation) and formation of a tetraploid. Subsequent speciation may (Lower)or may not (Upper)occur.(Center) The double-labeled gene trees that will be produced by each pattern of evolution. Tetraploids appear twice in the tree; the A genome (AE) will appear with its A genome progenitor and the E genome (AE) with its E genome progenitor. (Right) Some of the many possible gene trees that will result from incomplete taxon sampling. In this study, any of these patterns were taken as indication of allopolyploidy.
Estep et al. www.pnas.org/cgi/content/short/1404177111 3of7 1 Paspalum_malacophyllum_058 1805 Plagiantha_tenella_060 1/100 Arundinella_nepalensis_115 1975 Arundinella_hirta-099 2819 1/100 Arthraxon_prionodes_103 2185 1/100 Arthraxon_lanceolatus_131 Thelepogon_elegans_170 1/99 Chrysopogon_gryllus_006 1/100 Chrysopogon_zizanoides_104 1058 1 1/100 1/100 Chrysopogon_gryllus_006 1/100 Chrysopogon_serrulatus_056 677 Phacelurus_huillensis_024 0.79 / 34 Chionachne_massiei_133 0.67 / 12 1/100 Tripsacum_dactyloides_041 0.58 / 25 3449 0.86 / 42 Zea_maysA_997 1 / 100 Tripsacum_dactyloides_041 2 Zea_maysB_998 Apluda_mutica_100 1751 0.92 / 42 1 / 100 Coix_lacryma-jobi_053 1878 0.96 / 36 Coix_gasteenii_134 1 / 100 1 / 100 Rottboellia_cochinchinensis_046 Chasmopodium_caudatum_120 1675 0.90 / 64 Chasmopodium_caudatum_120 Phacelurus_digitatus_025 1 / 100 Erianthus_arundinaceum_165 1 / 32 Erianthus_ravennae_110 Eriochrysis_pallida_016 955 1 / 71 Imperata_cylindrica_154 1 / 100 Pogonatherum_crinitum_160 1 / 100 Pogonatherum_paniceum_072 960 0.99 / 54 1 / 100 Apocopis_intermedius_128 1 / 100 1 / 100 Germainia_capitata_145 Apocopis_siamensis_129 3 0.98 / 59 Apocopis_courtllumensis_127 1 / 82 Apocopis_intermedius_128 Miscanthus_sinensis_068 2597 4 1 / 100 Miscanthus_sinensis_068 0.95 / 62 Pseudosorghum_fasciculare_164 0.94 / 66 Miscanthus_ecklonii_089 2171 Saccharum_narenga_166 0.92 / 36 Miscanthus_ecklonii_089 5 0.95 / 43 0.88 / 48 1/100 Saccharum_narenga_166 0.83 / 29 Microstegium_vimineum_124 1563 Kerriochloa_siamensis_157 0.72 / 17 Sehima_nervosum_034 1 / 100 Sorghastrum_nutans_035 Sorghastrum_elliotti_187 posterior 1 / 100 Polytrias_indica_073 717 6 probabtility Polytrias_indica_073 0.81 / 26 1 0.99 / 89 Eulalia_aurea_098 1760 Ischaemum_afrum_020 Andropterum_stolzii_050 0.85 / 23 1 / 100 Ischaemum_indicum_155 Ischaemum_muticum_156 0.73 / 18 1.0 / 73 1 / 100 Ischaemum_santapaui_021 7 1 / 96 Ischaemum_santapaui_021 1 / 98 0.98 / 71 Ischaemum_rugosum_186 Dimeria_fuscescens_137 1 / 100 8 1 / 100 Dimeria_fuscescens_137 1 / 100 Dimeria_ornithopoda_138 Dimeria_sinensis_139 Spodiopogon_sibiricus_169 Sorghum_bicolor_182 1 / 100 1161 Sorghum_bicolor_1_037 0.83 / 16 Sorghum_nervosum_039 0.99 / 94 Sorghum_bicolor_2_038 0.82 / 29 0.5163 0.99 / 64 Sorghum_bicolor_g_999 1 / 71 core Andropogoneae (Andropogoninae) (Figure S2)
0.03
Fig. S2. Bayesian phylogeny of Andropogoneae, species not included in the “core Andropogoneae.” Numbers on branches are posterior probability (pp)/ML. Branch color reflects pp values. Genome-size estimates as Mbp/1C nucleus are indicated after species names, where available. Numbered polyploidization events correspond to those in Fig. 1, Figs. S2 and S3, and Table 1. Accession numbers follow the species name for all accessions.
Estep et al. www.pnas.org/cgi/content/short/1404177111 4of7 Outgroups 1 / 100 Arundinella 1 / 100 1 / 100 Arthraxon 1 / 100 1 / 99 Chrysopogon/Thelepogon 0.67 / 12 Phacelurus/Tripsacum/Zea 0.92 / 42 0.58 / 25 Apluda/Coix 0.96 / 36 Phacelurus_digitatus 1 / 100 Erianthus 1 / 32 1 / 71 Germainiinae 0.99 / 54 0.83 / 29 Saccharum/Ischaemum Spodiopogon_sibiricus Sorghum 1 / 100 0.95 / 43 1 / 100 Diheteropogon_amplectens_055 993 Diheteropogon_hagerupii_183 0.99 / 67 1 / 100 Hyparrhenia_diplandra_152 9 0.73 / 18 1 / 100 Hyparrhenia_diplandra_152 Hyparrhenia_diplandra_177 1 / 100 Hyparrhenia_rufa_108 1973 1 / 100 Hyparrhenia_rufa_153 10 Hyparrhenia_rufa_153 0.83 / 16 1 / 100 1 / 100 Hyparrhenia_hirta_095 11 Hyparrhenia_hirta._185 1 / 90 Hyparrhenia_hirta_189 1 / 90 Hyparrhenia_hirta_018 1819 Hyparrhenia_hirta_095 1 / 100 2175 0.60 / 50 Hyparrhenia_hirta_018 A 1 / 100 Hyparrhenia_rufa_108 1 / 78 1 / 81 Hyparrhenia_hirta_018 A’ Hyparrhenia_hirta_189 0.82 / 29 Hyparrhenia_hirta_189 1 / 71 1 / 96 12 Hyparrhenia_hirta_018 0.64 / 50 Hyparrhenia_hirta_185 1 / 100 Schizachyrium_exile_45 1 / 100 Schizachyrium_sanguineum_var_hirtiflorum_007 1 / 100 Schizachyrium_brevifolium_167 13 Schizachyrium_sanguineum_168 1 / 100 Schizachyrium_sanguineum_168 B 0.52 / 49 Schizachyrium_sanguineum_032 0.99 / 71 1 / 100 Schizachyrium_sanguineum_var_hirtiflorum_007 Schizachyrium_sanguineum_168 14 0.95 / 58 1 / 96 Schizachyrium_sanguineum_032 1 / 88 Andropogon_chinensis_125 C Andropogon_gayanus_051 Andropogon_perligulatus_003 0.52 / 41 1 / 96 Andropogon_gerardii_002 15 1 / 71 Schizachyrium_sanguineum_var_hirtiflorum_007 0.83 / 45 1 / 100 Andropogon_gerardii_002 Andropogon_hallii_052 Andropogon_eucomus_001 1 / 69 1 / 100 Andropogon_virginicus _105 921 1 / 91 Andropogon_glomeratus_192 0.57 / 49 Andropogon_virginicus_075 765 “core 1 / 100 Eulalia_quadrinervis_142 16 Eulalia_quadrinervis_142 Andropogoneae” 0.78 / 45 Eulalia_villosa_047 Cymbopogon_martinii_048 1770 1 / 91 0.98 / 78 Cymbopogon_citratus_135 1 / 100 Cymbopogon_flexuosus_009 1 / 100 Cymbopogon_obtectus_010 872 1 / 100 Cymbopogon_refractus_012 1034 0.95 / 98 Cymbopogon_obtectus_091 470 D 1 / 72 1 / 90 Cymbopogon_parkeri_011 1523 Cymbopogon_citratus_135 17 Cymbopogon_distans_008 0.98 / 43 785 Cymbopogon_citratus_135 0.78 / 29 18 0.96 / 34 Cymbopogon_parkeri_011 0.99 / 51 Cymbopogon_jwarancusa_ssp_olivieri_049 779 Heteropogon_triteceus_151 1 / 82 1 / 100 1 / 100 Themeda_villosa_172 Themeda_arundinacea_171 19 1 / 100 0.99 / 100 Themeda_villosa_172 1 / 98 Themeda_triandra_101 1 / 100 Themeda_triandra_116 20 Themeda_triandra_101 2121 0.83 / 72 Themeda_triandra_116 2106 1 / 96 Iseilema_macratherum_061 821 1 / 100 Eremopogon_foveolatum_181 1 / 100 Bothriochloa_barbinodis_078 Bothriochloa_alta_077 4125 Bothriochloa_woodrovii_083 1 / 99 Bothriochloa_exaristata_094 1 / 88 0.99 / 84 Bothriochloa_hybrida_092 posterior 1 / 100 TK132_Capillipedium_assimile_132 1 / 95 Capillipedium_parviflorum_005 probability 542 1 / 100 0.59 / 8 Bothriochloa_bladhii_093 21 1 1 / 100 Bothriochloa_bladhii_076 1036 Bothriochloa_bladhii_082 3082 E 0.98 / 31 0.99 / 54 Capillipedium_spicigerum_090 0.59 / 29 Capillipedium_parviflorum_005 1 / 93 22 0.59 / 44 Capillipedium_spicigerum_090 1510 1 / 100 Dichanthium_aristatum_014 1253 1 / 100 Dichanthium_theinlwinii_136 1 / 100 Dichanthium annulatum_188 Bothriochloa_ischaemum_102 1762 23 Dichanthium_annulatum_054 1105 24 0.95 / 69 Bothriochloa_bladhii_087 0.92 / 43 Dichanthium_annulatum_013 0.59 / * Dichanthium_annulatum_054 “BCD clade” 0.98 / 44 0.79 / 58 Bothriochloa_insculpta 2005 F 1 / 100 Bothriochloa_insculpta 921 26 1 / 100 Bothriochloa_insculpta 25 1 / 100 Bothriochloa_insculpta 1 / 99 Bothriochloa_bladhii_093 Bothriochloa_bladhii_082 Bothriochloa_ischaemum_063 1548 27 1 / 92 Bothriochloa_ischaemum_063 0.87 / 68 Bothriochloa_bladhii_076 0.98 / 46 1 / 100 Bothriochloa_bladhii_087 1236 Bothriochloa_bladhii_093 1881 1 / 100 Bothriochloa_decipiens_086 Bothriochloa_hybrida_092 Bothriochloa_macra_079 1 / 89 0.59 / * Bothriochloa_woodrovii_083 0.57 / 47 Bothriochloa_laguroides_085 0.93 / 73 28 Bothriochloa_exaristata_094 0.98 / 72 1 / 99 1 / 100 Bothriochloa_macra_079 2053 0.5163 Bothriochloa_decipiens_086 1427 1 / 98 Bothriochloa_woodrovii_083 3130 1 / 98 Bothriochloa_hybrida_092 3880 Bothriochloa_laguroides_085 0.99 / 71 Bothriochloa_barbinodis_078 0.92 / 63 2273 0.52 / 51 Bothriochloa_exaristata_094 1151
0.03
Fig. S3. Bayesian phylogeny of core Andropogoneae. Branch numbers, colors, and genome sizes are as in Fig. S2.
Estep et al. www.pnas.org/cgi/content/short/1404177111 5of7 Chrysopogon serrulatus 69 Chrysopogon zizanioides Chrysopogon gryllus Thelepogon elegans Arthraxon lanceolatus 35 Arthraxon prionodes Zea mays genome A Tripsacum dactyloides
Density Chionachne massiei Phacelurus huillensis 0 Phacelurus digitatus Erianthus ravennae Erianthus arundinaceum 0.00 0.31 Saccharum narenga Miscanthus ecklonii Pseudosorghum fasciculare Evolutionary Rate Miscanthus sinensis Ischaemum muticum Ischaemum indicum Ischaemum rugosum Ischaemum santapaui Dimeria sinensis Dimeria ornithopoda Dimeria fuscescens Andropterum stolzii Microstegium vimineum Kerriochloa siamensis Eulalia aurea Polytrias indica Sorghastrum elliotti Sorghastrum nutans Ischaemum afrum Sehima nervosum Spodiopogon sibiricus Schizachyrium sanguineum Schizachyrium sanguineum var. hirtiflorum Schizachyrium exile Schizachyrium brevifolium Andropogon hallii Andropogon gerardii Andropogon eucomus Andropogon virginicus Andropogon glomeratus Andropogon perligulatus Andropogon chinensis Diheteropogon hagerupii Diheteropogon amplectens Hyparrhenia diplandra Hyparrhenia rufa Hyparrhenia hirta Eulalia quadrinervis Eulalia villosa Cymbopogon distans Cymbopogon jwarancusa ssp. olivieri Cymbopogon parkeri Cymbopopogon martiniii Cymbopogon citratus Cymbopogon flexuosus Cymbopogon refractus Cymbopogon obtectus Heteropogon triticeus Themeda villosa Themeda arundinacea Themeda triandra Dichanthium theinlwinii Dichanthium aristatum Dichanthium annulatum Capillipedium parviflorum Capillipedium spicigerum Capillipedium assimile Bothriochloa decipiens Bothriochloa macra Bothriochloa laguroides Bothriochloa insculpta Bothriochloa ischaemum Bothriochloa bladhii Bothriochloa alta Bothriochloa exaristata Bothriochloa hybrida Bothriochloa woodrovii Bothriochloa barbinodis Eremopogon foveolatum Iseilema macratherum Sorghum bicolor genome Germainia capitata Apocopis intermedius Apocopis siamensis Apocopis cortallumensis Pogonatherum paniceum Pogonatherum crinitum Imperata cylindrica Eriochrysis pallida Coix lacryma-jobi Coix gasteenii Chasmopodium caudatum Rottboellia cochinchinensis Apluda mutica Arundinella nepalensis Arundinella hirta
Fig. S4. Phylorate tree from BAMM (16), with species sample frequency adjusted for each clade, and backbone sampling of 0.5. Models of rate shifts with the highest posterior probability indicate either no shifts or one. The marginal probabilities of a shift are similar across much of the tree; in other words, the position of the shift cannot be assigned with certainty.
Estep et al. www.pnas.org/cgi/content/short/1404177111 6of7 12
Diploid 10 Polyploid
8
6
Probability density 4
2
0
0.0 0.2 0.4 0.6 0.8 Net Diversification Rate
Fig. S5. Net diversification rates (speciation minus extinction) for diploids (blue) and polyploids (yellow), calculated using BiSSE, as implemented in diversitree (19). ML estimates of the rates are significantly different (P < 0.02) compared with a model in which speciation rates are constrained to be equal. Analysis assumes a species sample of 8%.
Other Supporting Information Files
Table S1 (DOCX)
Estep et al. www.pnas.org/cgi/content/short/1404177111 7of7