Class I-A Class II-A Class II-B Class II- Basal Class I-B Class I Class II 0.1 Arabidopsis thaliana PHO1;H2 Capsella rubella PHO1;H11 100 Thellungiella.

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Class I-A Class II-A Class II-B Class II- Basal Class I-B Class I Class II 0.1 Arabidopsis thaliana PHO1;H2 Capsella rubella PHO1;H Thellungiella halophila PHO1;H9 64 Brassica rapa PHO1;H17 Brassica rapa PHO1;H Capsella rubella PHO1;H10 Arabidopsis thaliana PHO1;H6 100 Thellungiella halophila PHO1;H10 Brassica rapa PHO1;H Brassica rapa PHO1;H21 Brassica rapa PHO1;H Brassica rapa PHO1;H18 Brassica rapa PHO1;H13 86 Thellungiella halophila PHO1;H11 59 Arabidopsis thaliana PHO1;H5 Capsella rubella PHO1;H Brassica rapa PHO1;H15 Brassica rapa PHO1;H23 50 Brassica rapa PHO1;H22 Brassica rapa PHO1;H14 Brassica rapa PHO1;H Thellungiella halophila PHO1;H8 90 Arabidopsis thaliana PHO1;H3 Capsella rubella PHO1;H Carica papaya PHO1;H3 100 Citrus clementina PHO1;H5 70 Linum usitatissimum PHO1;H8 Linum usitatissimum PHO1;H6 99 Linum usitatissimum PHO1;H7 66 Linum usitatissimum PHO1;H5 100 Linum usitatissimum PHO1;H10 Linum usitatissimum PHO1;H9 100 Linum usitatissimum PHO1;H Ricinus communis PHO1;H3 Ricinus communis PHO1;H2 91 Manihot esculenta PHO1;H3 74 Populus trichocarpa PHO1;H7 Populus trichocarpa PHO1;H4 99 Populus trichocarpa PHO1;H6 100 Populus trichocarpa PHO1;H Thellungiella halophila PHO1;H7 Thellungiella halophila PHO1;H2 88 Brassica rapa PHO1;H5 69 Brassica rapa PHO1;H7 83 Capsella rubella PHO1;H2 Arabidopsis thaliana PHO1;H Arabidopsis thaliana PHO1;H7 Capsella rubella PHO1;H1 100 Capsella rubella PHO1;H5 Arabidopsis thaliana PHO1;H4 100 Brassica rapa PHO1;H4 62 Thellungiella halophila PHO1;H1 100 Carica papaya PHO1;H Glycine max PHO1;H9 Phaseolus vulgaris PHO1;H6 67 Glycine max PHO1;H10 79 Glycine max PHO1;H Glycine max PHO1;H2 Glycine max PHO1;H7 100 Phaseolus vulgaris PHO1;H7 100 Cucumis sativus PHO1;H1 Cucumis sativus PHO1;H Malus domestica PHO1;H8 Malus domestica PHO1;H9 50 Malus domestica PHO1;H7 100 Malus domestica PHO1;H10 99 Prunus persica PHO1;H3 100 Vitis vinifera PHO1;H6 20 Mimulus guttatus PHO1;H6 Vitis vinifera PHO1;H3 Vitis vinifera PHO1;H2 100 Vitis vinifera PHO1;H5 85 Vitis vinifera PHO1;H Citrus sinensis PHO1;H1 Citrus clementina PHO1;H7 100 Citrus clementina PHO1;H6 100 Populus trichocarpa PHO1;H Aquilegia coerulea PHO1;H1 Aquilegia coerulea PHO1;H2 Aquilegia coerulea PHO1;H Citrus clementina PHO1;H4 Citrus sinensis PHO1;H2 100 Populus trichocarpa PHO1;H9 Manihot esculenta PHO1;H5 98 Eucalyptus grandis PHO1;H4 75 Capsella rubella PHO1;H3 Arabidopsis thaliana PHO1;H10 72 Brassica rapa PHO1;H3 Thellungiella halophila PHO1;H Prunus persica PHO1;H5 27 Medicago truncatula PHO1;H4 Medicago truncatula PHO1;H3 100 Phaseolus vulgaris PHO1;H2 Glycine max PHO1;H Cucumis sativus PHO1;H7 78 Mimulus guttatus PHO1;H Eucalyptus grandis PHO1;H1 Eucalyptus grandis PHO1;H2 100 Eucalyptus grandis PHO1;H3 100 Citrus clementina PHO1;H2 Citrus sinensis PHO1;H5 100 Manihot esculenta PHO1;H6 Manihot esculenta PHO1;H4 100 Ricinus communis PHO1;H1 Populus trichocarpa PHO1;H Cucumis sativus PHO1;H3 Cucumis sativus PHO1;H2 100 Vitis vinifera PHO1;H7 56 Capsella rubella PHO1;H4 Arabidopsis thaliana PHO1;H9 100 Thellungiella halophila PHO1;H3 51 Brassica rapa PHO1;H1 Brassica rapa PHO1;H6 100 Carica papaya PHO1;H4 99 Mimulus guttatus PHO1;H3 Mimulus guttatus PHO1;H2 100 Glycine max PHO1;H6 Glycine max PHO1;H3 100 Phaseolus vulgaris PHO1;H1 100 Medicago truncatula PHO1;H5 Medicago truncatula PHO1;H6 100 Malus domestica PHO1;H2 Malus domestica PHO1;H1 100 Malus domestica PHO1;H Prunus persica PHO1;H Selaginella moellendorffii PHO1;H4 Selaginella moellendorffii PHO1;H10 81 Selaginella moellendorffii PHO1;H3 95 Selaginella moellendorffii PHO1;H8 79 Selaginella moellendorffii PHO1;H Glycine max PHO1;H8 Glycine max PHO1;H5 99 Phaseolus vulgaris PHO1;H5 100 Medicago truncatula PHO1;H1 98 Glycine max PHO1;H4 Glycine max PHO1;H1 84 Phaseolus vulgaris PHO1;H3 100 Medicago truncatula PHO1;H Cucumis sativus PHO1;H4 Citrus clementina PHO1;H1 Citrus sinensis PHO1;H Mimulus guttatus PHO1;H5 Aquilegia coerulea PHO1;H4 78 Vitis vinifera PHO1;H8 Linum usitatissimum PHO1;H4 Linum usitatissimum PHO1;H1 100 Populus trichocarpa PHO1;H3 Populus trichocarpa PHO1;H Manihot esculenta PHO1;H1 Manihot esculenta PHO1;H7 51 Ricinus communis PHO1;H Malus domestica PHO1;H3 Malus domestica PHO1;H6 81 Prunus persica PHO1;H2 100 Capsella rubella PHO1;H7 Arabidopsis thaliana PHO1 86 Brassica rapa PHO1;H10 Brassica rapa PHO1;H8 Thellungiella halophila PHO1;H6 100 Eucalyptus grandis PHO1;H8 Eucalyptus grandis PHO1;H6 Eucalyptus grandis PHO1;H Zea mays PHO1;H2 Sorghum bicolor PHOH2 100 Setaria italica PHO1;H2 100 Oryza sativa PHO1;H2 91 Brachypodium distachyon PHO1;H Pinus taeda PHO1;H2 Pinus taeda PHO1;H1 100 Picea glauca PHO1;H3 Picea glauca PHO1;H Glycine max PHO1;H14 Glycine max PHO1;H12 96 Phaseolus vulgaris PHO1;H4 100 Cucumis sativus PHO1;H5 Eucalyptus grandis PHO1;H5 Malus domestica PHO1;H4 Malus domestica PHO1;H5 100 Prunus persica PHO1;H4 100 Populus trichocarpa PHO1;H8 Populus trichocarpa PHO1;H2 100 Populus trichocarpa PHO1;H5 99 Linum usitatissimum PHO1;H2 Linum usitatissimum PHO1;H3 100 Ricinus communis PHO1;H5 Manihot esculenta PHO1;H2 97 Brassica rapa PHO1;H11 Brassica rapa PHO1;H9 59 Brassica rapa PHO1;H12 82 Thellungiella halophila PHO1;H5 80 Capsella rubella PHO1;H6 Arabidopsis thaliana PHO1;H Citrus sinensis PHO1;H3 Citrus clementina PHO1;H3 100 Carica papaya PHO1;H1 Vitis vinifera PHO1;H1 58 Mimulus guttatus PHO1;H4 Mimulus guttatus PHO1;H Aquilegia coerulea PHO1;H3 100 Sorghum bicolor PHOH3 Zea mays PHO1;H1 100 Setaria italica PHO1;H3 100 Brachypodium distachyon PHO1;H1 Oryza sativa PHO1;H Setaria italica PHO1;H1 Sorghum bicolor PHOH1 100 Oryza sativa PHO1;H Picea glauca PHO1;H1 Pinus taeda PHO1;H Selaginella moellendorffii PHO1;H6 86 Physcomitrella patens PHO1;H4 Physcomitrella patens PHO1;H7 100 Physcomitrella patens PHO1;H1 100 Physcomitrella patens PHO1;H6 Physcomitrella patens PHO1;H Selaginella moellendorffii PHO1;H7 Selaginella moellendorffii PHO1;H2 100 Selaginella moellendorffii PHO1;H9 97 Selaginella moellendorffii PHO1;H1 85 Physcomitrella patens PHO1;H5 Physcomitrella patens PHO1;H Micromonas pusilla PHO1 Ostreococcus lucimarinus PHO Saccharomyces cerevisiae SYG1 Caenorhabditis elegans SYG-1 Homo sapiens XPR1 Mus musculus XPR Arabidopsis thaliana PHO1;H2 Capsella rubella PHO1;H Thellungiella halophila PHO1;H9 63 Brassica rapa PHO1;H17 Brassica rapa PHO1;H Capsella rubella PHO1;H10 Arabidopsis thaliana PHO1;H6 100 Thellungiella halophila PHO1;H10 Brassica rapa PHO1;H Brassica rapa PHO1;H21 Brassica rapa PHO1;H Brassica rapa PHO1;H18 Brassica rapa PHO1;H13 79 Thellungiella halophila PHO1;H11 54 Arabidopsis thaliana PHO1;H5 Capsella rubella PHO1;H Brassica rapa PHO1;H23 Brassica rapa PHO1;H22 Brassica rapa PHO1;H15 52 Brassica rapa PHO1;H14 Brassica rapa PHO1;H Thellungiella halophila PHO1;H8 91 Arabidopsis thaliana PHO1;H3 Capsella rubella PHO1;H Carica papaya PHO1;H3 100 Citrus clementina PHO1;H5 74 Linum usitatissimum PHO1;H8 Linum usitatissimum PHO1;H6 99 Linum usitatissimum PHO1;H7 60 Linum usitatissimum PHO1;H5 100 Linum usitatissimum PHO1;H10 Linum usitatissimum PHO1;H9 100 Linum usitatissimum PHO1;H Ricinus communis PHO1;H3 Ricinus communis PHO1;H2 90 Manihot esculenta PHO1;H Populus trichocarpa PHO1;H7 Populus trichocarpa PHO1;H4 98 Populus trichocarpa PHO1;H6 100 Populus trichocarpa PHO1;H Thellungiella halophila PHO1;H7 Thellungiella halophila PHO1;H2 84 Brassica rapa PHO1;H5 75 Brassica rapa PHO1;H7 87 Capsella rubella PHO1;H2 Arabidopsis thaliana PHO1;H Arabidopsis thaliana PHO1;H7 Capsella rubella PHO1;H1 100 Capsella rubella PHO1;H5 Arabidopsis thaliana PHO1;H4 100 Brassica rapa PHO1;H4 Thellungiella halophila PHO1;H1 100 Carica papaya PHO1;H Phaseolus vulgaris PHO1;H6 Glycine max PHO1;H9 60 Glycine max PHO1;H10 85 Glycine max PHO1;H Glycine max PHO1;H2 Glycine max PHO1;H7 100 Phaseolus vulgaris PHO1;H7 100 Cucumis sativus PHO1;H1 Cucumis sativus PHO1;H6 77 Malus domestica PHO1;H8 Malus domestica PHO1;H9 58 Malus domestica PHO1;H7 100 Malus domestica PHO1;H10 99 Prunus persica PHO1;H3 100 Vitis vinifera PHO1;H6 Mimulus guttatus PHO1;H6 Vitis vinifera PHO1;H3 Vitis vinifera PHO1;H2 100 Vitis vinifera PHO1;H5 83 Vitis vinifera PHO1;H4 82 Citrus sinensis PHO1;H1 Citrus clementina PHO1;H7 100 Citrus clementina PHO1;H6 100 Populus trichocarpa PHO1;H Aquilegia coerulea PHO1;H1 Aquilegia coerulea PHO1;H2 Aquilegia coerulea PHO1;H Capsella rubella PHO1;H4 Arabidopsis thaliana PHO1;H9 100 Thellungiella halophila PHO1;H3 64 Brassica rapa PHO1;H1 56 Brassica rapa PHO1;H6 100 Carica papaya PHO1;H4 99 Citrus clementina PHO1;H2 Citrus sinensis PHO1;H Manihot esculenta PHO1;H6 Manihot esculenta PHO1;H4 100 Ricinus communis PHO1;H1 Populus trichocarpa PHO1;H Eucalyptus grandis PHO1;H1 Eucalyptus grandis PHO1;H2 100 Eucalyptus grandis PHO1;H3 100 Mimulus guttatus PHO1;H3 Mimulus guttatus PHO1;H2 100 Cucumis sativus PHO1;H3 Cucumis sativus PHO1;H2 100 Vitis vinifera PHO1;H Glycine max PHO1;H6 Glycine max PHO1;H3 100 Phaseolus vulgaris PHO1;H1 100 Medicago truncatula PHO1;H5 Medicago truncatula PHO1;H6 100 Malus domestica PHO1;H2 Malus domestica PHO1;H1 100 Malus domestica PHO1;H Prunus persica PHO1;H Citrus clementina PHO1;H4 Citrus sinensis PHO1;H2 100 Populus trichocarpa PHO1;H9 Manihot esculenta PHO1;H5 96 Eucalyptus grandis PHO1;H4 68 Capsella rubella PHO1;H3 Arabidopsis thaliana PHO1;H10 84 Brassica rapa PHO1;H3 Thellungiella halophila PHO1;H Cucumis sativus PHO1;H7 Prunus persica PHO1;H5 Medicago truncatula PHO1;H4 Medicago truncatula PHO1;H3 100 Phaseolus vulgaris PHO1;H2 Glycine max PHO1;H Mimulus guttatus PHO1;H Selaginella moellendorffii PHO1;H4 Selaginella moellendorffii PHO1;H10 82 Selaginella moellendorffii PHO1;H3 96 Selaginella moellendorffii PHO1;H8 80 Selaginella moellendorffii PHO1;H Glycine max PHO1;H8 Glycine max PHO1;H5 100 Phaseolus vulgaris PHO1;H5 100 Medicago truncatula PHO1;H1 97 Glycine max PHO1;H4 Glycine max PHO1;H1 82 Phaseolus vulgaris PHO1;H3 100 Medicago truncatula PHO1;H Cucumis sativus PHO1;H4 Citrus clementina PHO1;H1 Citrus sinensis PHO1;H4 100 Mimulus guttatus PHO1;H5 Aquilegia coerulea PHO1;H4 72 Vitis vinifera PHO1;H8 Linum usitatissimum PHO1;H4 Linum usitatissimum PHO1;H1 100 Populus trichocarpa PHO1;H3 Populus trichocarpa PHO1;H10 98 Manihot esculenta PHO1;H1 Manihot esculenta PHO1;H7 59 Ricinus communis PHO1;H Malus domestica PHO1;H3 Malus domestica PHO1;H6 83 Prunus persica PHO1;H2 100 Arabidopsis thaliana PHO1 Capsella rubella PHO1;H7 94 Brassica rapa PHO1;H10 Brassica rapa PHO1;H8 Thellungiella halophila PHO1;H6 100 Eucalyptus grandis PHO1;H8 Eucalyptus grandis PHO1;H6 Eucalyptus grandis PHO1;H7 96 Zea mays PHO1;H2 Sorghum bicolor PHOH2 100 Setaria italica PHO1;H2 100 Oryza sativa PHO1;H2 95 Brachypodium distachyon PHO1;H Pinus taeda PHO1;H2 Pinus taeda PHO1;H1 100 Picea glauca PHO1;H3 Picea glauca PHO1;H Linum usitatissimum PHO1;H2 Linum usitatissimum PHO1;H3 100 Ricinus communis PHO1;H5 Manihot esculenta PHO1;H2 100 Populus trichocarpa PHO1;H8 Populus trichocarpa PHO1;H2 100 Populus trichocarpa PHO1;H5 100 Carica papaya PHO1;H1 10 Brassica rapa PHO1;H9 Brassica rapa PHO1;H11 52 Brassica rapa PHO1;H12 75 Thellungiella halophila PHO1;H5 82 Arabidopsis thaliana PHO1;H1 Capsella rubella PHO1;H Citrus sinensis PHO1;H3 Citrus clementina PHO1;H3 100 Glycine max PHO1;H14 Glycine max PHO1;H12 98 Phaseolus vulgaris PHO1;H4 100 Cucumis sativus PHO1;H5 Eucalyptus grandis PHO1;H5 Malus domestica PHO1;H4 Malus domestica PHO1;H5 100 Prunus persica PHO1;H4 100 Vitis vinifera PHO1;H1 59 Mimulus guttatus PHO1;H4 Mimulus guttatus PHO1;H Aquilegia coerulea PHO1;H3 100 Sorghum bicolor PHOH3 Zea mays PHO1;H1 99 Setaria italica PHO1;H3 99 Brachypodium distachyon PHO1;H1 Oryza sativa PHO1;H Setaria italica PHO1;H1 Sorghum bicolor PHOH1 100 Oryza sativa PHO1;H Picea glauca PHO1;H1 Pinus taeda PHO1;H Selaginella moellendorffii PHO1;H6 72 Physcomitrella patens PHO1;H4 Physcomitrella patens PHO1;H7 100 Physcomitrella patens PHO1;H1 100 Physcomitrella patens PHO1;H6 Physcomitrella patens PHO1;H Selaginella moellendorffii PHO1;H7 Selaginella moellendorffii PHO1;H2 100 Selaginella moellendorffii PHO1;H9 97 Selaginella moellendorffii PHO1;H1 86 Physcomitrella patens PHO1;H5 Physcomitrella patens PHO1;H Micromonas pusilla PHO1 Ostreococcus lucimarinus PHO Saccharomyces cerevisiae SYG1 Caenorhabditis elegans SYG-1 Homo sapiens XPR1 Mus musculus XPR1 Out-groups Green algae ab Plants Land Plants Seed Plants Angiosperm Dicotyledon Gymnosperm Plants Land Plants Seed Plants Angiosperm Dicotyledon Gymnosperm Figure S1. ML trees generated using both WAG and LG models.