SUPPLEMENTARY FIGURES Supp. Fig. 1a. Venn diagram showing locus overlap across the five datasets (g2, g5, g7, i36, and i57) used to infer species trees. 1b. Histogram showing the number of loci of a given length (number of basepairs) for each of the five datasets (g2, g5, g7, i36, and i57). Supp. Fig. 2a. Heatmap showing the number of paralogs per gene family per individual for photosynthesis genes. 2b. Heatmap showing the number of paralogs per gene family per individual for non-photosynthesis genes. The tree topology for both heatmaps is the ASTRAL g5 topology. Supp. Fig. 3 Co-phylo plot of ASTRAL g5 topology with branch lengths scaled to the number of reconstructed gene duplications in photosynthesis genes (right panel) and those in all other genes (left panel), with scale bar indicated below the trees and total number of gene duplications indicated above each branch, suppressed when zero. Supp. Fig. 4a. ASTRAL topology from the g2 loci dataset. 4b. ASTRAL topology from the g7 loci dataset. 4c. ASTRAL topology from the i36 loci dataset. 4d. ASTRAL topology from the i57 loci dataset. 4e. RAxML topology from the g2 loci dataset. 4f. RAxML topology from the g5 loci dataset. 4g. RAxML topology from the g7 loci dataset. 4h. RAxML topology from the i36 loci dataset. 4i. RAxML topology from the i57 loci dataset. Supp. Fig. 5. Genomic conflict for family-level phylogenetic relationships within Portulacineae, emphasizing the placement of monotypic Halophytaceae. (A) Heatmap of the “calculate-pairs” analysis in BUCKy (i.e., based on a posterior distribution of trees randomly pruned to one exemplar for each of Montiaceae, Basellaceae, Halophytaceae, and Didiereaceae, as well as one member of the Cactaceae + Portulacaceae + Anacampserotaceae + Talinaceae (ACPT) clade), indicating the posterior probability (pp) that a pair of loci support the same topology (red: pp=1; white: pp=0). Thus, each row and column represents a locus; locus names and numbers are given to the left, posterior probability from the MrBayes analysis of individual loci (i.e., based on unpruned trees) for alternative placements of Halophytaceae are given to the right (light grey: pp=0; black: pp=1; clades are indicated by the first letter for each member family), and a dendrogram based on Euclidean distance between pp values is drawn above. (B-D) Topologies for three putative placements of Halophytaceae, with genome-wide concordance factor (bold) and 95% credibility interval (in brackets) indicated. (E-H) Histograms of posterior probability from MrBayes analyses of individual loci for three putative clades (E: Halophytaceae + Basellaceae; F: Halophytaceae + Montiaceae; G: Halophytaceae + the ACPT clade). [Note that although there is one major red block (representing “(M,(BH),(D,(ACPT)))” topology), especially Halophytum keeps jumping around, typically to M, but when that happens, the relations among the other families sometimes change (e.g., some loci that have HM also have DACPT, others don’t). Thus, ultimately, the concordance support for BH (i.e., irrespective of other relations) is only a little larger that the support for MH.] i36 Supp. Fig. 1a 0 0 0 0 0 0 i57 0 0 0 g2 0 0 55 0 0 75 0 0 0 0 0 0 25 0 23 2 38 0 0 0 0 0 g9 g5 Supp. Fig. 1b 1500 matrix raw 1000 g2 count g5 g9 i36 i57 500 0 0 1000 2000 3000 4000 length Supp. Fig. 2a. Photosynthetic Loci per Gene Family none 3 7−8 >15 1 4 9−10 2 5−6 11−15 Oryza sativa cds Trigastrotheca molluginea 137 Trigastrotheca stricta 148 Mollugo verticillata 56 Calandrinia granulifera 46 Calandrinia mirabilis 85 Calandrinia pumila 60 Calandrinia calyptrata 188 Calandrinia flava 79 Calandrinia lehmannii 35 Lewisia congdonii 17 Lewisia triphylla 107 Lewisia rediviva minor 10 Lewisia cotyledon cotyledon 113 Claytonia washingtoniana 26 Claytonia megarhiza 195 Montia parviflora 27 Lewisiopsis tweedyi 4 Calyptridium umbellatum 193 Calyptridium parryi 170 Cistanthe grandiflora 199 Phemeranthus calycinus 173 Phemeranthus brevicaulis 202 Rhipsalis capilliformis 54 Mammillaria plumosa 117 Blossfeldia liliputana 204 Maihuenia poeppigii 205 Pereskiopsis porteri 51 Quiabentia zehntneri 85 Opuntia subulata 208 Pereskia sacharosa 67 Pereskia grandifolia 59 Pereskia horrida 64 Pereskia lychnidiflora 78 Pereskia guamacho 35 Pereskia bleo tr Pereskia quisqueyana 55 Portulaca cf perennis 209 Portulaca cf perennis 213 Portulaca cf filifolia 187 Portulaca cryptopetala 49 Portulaca oleracea tr Portulaca filsonii 186 Portulaca cf digyna 184 Anacampseros baeseckei 91 Anacampseros arachnoides 101 Anacampseros lanceolata 46 Anacampseros papyracea papyracea 100 Anacampseros coahuilensis 68 Grahamia bracteata 62 Talinum triangulare 50 Talinella pachypoda 73 Talinum arnottii 4 Alluaudia dumosa 65 Alluaudia procera 53 Portulacaria afra 50 Ceraria fruticulosa 72 Anredera baselloides 38 Anredera diffusa 211 Ullucus tuberosus 74 Basella alba 61 Halophytum ameghinoi 76 Trianthema portulacastrum tr Mesembryanthemum crystallinum tr Boerhavia coccinea tr Beta vulgaris cds Amaranthus hypochondriacus tr Solanum tuberosum cds Glycine max cds Populus trichocarpa cds Vitis vinifera cds Arabidopsis thaliana cds T dit tdt amk apl asp bass dic nhd pck ppc ppdk ppt rbcs alaA nadme betaCA nadmdh nadpmdhnadpme Supp. Fig 2b. Loci per Gene Family none 3 7−8 >15 1 4 9−10 2 5−6 11−15 Oryza sativa cds Trigastrotheca molluginea 137 Trigastrotheca stricta 148 Mollugo verticillata 56 Calandrinia granulifera 46 Calandrinia mirabilis 85 Calandrinia pumila 60 Calandrinia calyptrata 188 Calandrinia flava 79 Calandrinia lehmannii 35 Lewisia congdonii 17 Lewisia triphylla 107 Lewisia rediviva minor 10 Lewisia cotyledon cotyledon 113 Claytonia washingtoniana 26 Claytonia megarhiza 195 Montia parviflora 27 Lewisiopsis tweedyi 4 Calyptridium umbellatum 193 Calyptridium parryi 170 Cistanthe grandiflora 199 Phemeranthus calycinus 173 Phemeranthus brevicaulis 202 Rhipsalis capilliformis 54 Mammillaria plumosa 117 Blossfeldia liliputana 204 Maihuenia poeppigii 205 Pereskiopsis porteri 51 Quiabentia zehntneri 85 Opuntia subulata 208 Pereskia sacharosa 67 Pereskia grandifolia 59 Pereskia horrida 64 Pereskia lychnidiflora 78 Pereskia guamacho 35 Pereskia bleo tr Pereskia quisqueyana 55 Portulaca cf perennis 209 Portulaca cf perennis 213 Portulaca cf filifolia 187 Portulaca cryptopetala 49 Portulaca oleracea tr Portulaca filsonii 186 Portulaca cf digyna 184 Anacampseros baeseckei 91 Anacampseros arachnoides 101 Anacampseros lanceolata 46 Anacampseros papyracea papyracea 100 Anacampseros coahuilensis 68 Grahamia bracteata 62 Talinum triangulare 50 Talinella pachypoda 73 Talinum arnottii 4 Alluaudia dumosa 65 Alluaudia procera 53 Portulacaria afra 50 Ceraria fruticulosa 72 Anredera baselloides 38 Anredera diffusa 211 Ullucus tuberosus 74 Basella alba 61 Halophytum ameghinoi 76 Trianthema portulacastrum tr Mesembryanthemum crystallinum tr Boerhavia coccinea tr Beta vulgaris cds Amaranthus hypochondriacus tr Solanum tuberosum cds Glycine max cds Populus trichocarpa cds Vitis vinifera cds Arabidopsis thaliana cds yC ph nGroup 441 nGroup 796nGroup 902 nGroup 1213 nGroup 1537 nGroup 1706 nGroupnGroup 2238 2241 nGroupnGroupnGroup 2489nGroup 2917nGroup 3000nGroup 3058 3292nGroup 4237nGroupnGroup 6043nGroup 6312nGroup 6416nGroup 7264 7482nGroup 7713nGroup 8489nGroup 8998 9112 nGroupnGroupnGroup 10776nGroup 10860 10951nGroup 11253nGroupnGroup 12443nGroup 13658 15299nGroup 15311nGroupnGroup 16142nGroup 16157 16219nGroup 16321nGroupnGroup 17974nGroup 18355nGroup 18627nGroup 18875nGroup 18890nGroup 19153nGroup 19342nGroup 19417nGroup 19448nGroup 20351 20409 22334nGroupnGroupnGroup 22620nGroup 24195 24434 24488 Supp. Fig. 3 Non-photosynthesis genes Photosynthesis genes Beta vulgaris cds 5 Amaranthus hypochondriacus tr 3 4 Solanum tuberosum cds 3 11 Oryza sativa cds 6 Arabidopsis thaliana cds 3 2 Vitis vinifera cds 3 Glycine max cds 1 Populus trichocarpa cds Boerhavia coccinea tr Trianthema portulacastrum tr Mesembryanthemum crystallinum tr 3 Mollugo verticillata 56 1 20 Trigastrotheca molluginea 137 13 Trigastrotheca stricta 148 2 2 Phemeranthus calycinus 173 5 4 Phemeranthus brevicaulis 202 Cistanthe grandiflora 199 1 3 13 Calyptridium umbellatum 193 9 1 Calyptridium parryi 170 3 Calandrinia pumila 60 3 21 4 3 Calandrinia granulifera 46 1 14 4 Calandrinia mirabilis 85 1 2 Calandrinia lehmannii 35 1 5 4 Calandrinia calyptrata 188 3 2 Calandrinia flava 79 Lewisiopsis tweedyi 4 1 6 Montia parviflora 27 4 2 Claytonia washingtoniana 26 12 7 Claytonia megarhiza 195 3 19 6 Lewisia cotyledon cotyledon 113 4 Lewisia rediviva minor 10 1 Lewisia congdonii 17 Lewisia triphylla 107 Halophytum ameghinoi 76 1 Basella alba 61 1 2 Ullucus tuberosus 74 Anredera baselloides 38 Anredera diffusa 211 28 Alluaudia dumosa 65 32 13 4 Alluaudia procera 53 1 5 1 Portulacaria afra 50 5 Ceraria fruticulosa 72 2 Talinum arnottii 4 2 5 Talinum triangulare 50 7 Talinella pachypoda 73 3 3 Grahamia bracteata 62 2 5 Anacampseros coahuilensis 68 2 4 Anacampseros papyracea papyracea 100 1 13 Anacampseros lanceolata 46 5 4 3 1 Anacampseros baeseckei 91 2 4 Anacampseros arachnoides 101 9 Portulaca filsonii 186 11 10 Portulaca cf digyna 184 2 4 Portulaca oleracea tr 1 5 Portulaca cryptopetala 49 8 3 7 Portulaca cf filifolia 187 11 1 3 Portulaca cf perennis 209 Portulaca cf perennis 213 Pereskia lychnidiflora 78 1 Pereskia guamacho 35 1 Pereskia bleo tr Pereskia quisqueyana 55 5 2 Pereskia horrida 64 2 2 Pereskia sacharosa 67 1 1 Pereskia grandifolia 59 2 Opuntia subulata 208 2 Pereskiopsis porteri 51 1 2 Quiabentia zehntneri 85 Maihuenia poeppigii