7 angiosperm genomes OrthoMCL 7 taxa, 7-9 genes HaMStR Physcomitrella patens Orthologous groups (size ≥ 300aa, identity ≥ 60%) GO Ontology 15 genomes 3.

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7 angiosperm genomes OrthoMCL 7 taxa, 7-9 genes HaMStR Physcomitrella patens Orthologous groups (size ≥ 300aa, identity ≥ 60%) GO Ontology 15 genomes 3 angiosperm EST 73 species blast 20 genes with other functions 28 genes with DNA/RNA metabolism Gene copy number Single gene trees Gene copy number SMC1, SMC2, MCM5, MLH1, and MSH1 blast PCR 3 gymnosperm EST blast Phylogenetic analyses Divergence time estimation Fig. S1 The workflow applied in this paper. Arabidopsis thaliana, Populus tricocarpa Prunus persica, Vitis vinifera, Mimulus guttatus Oryza sativa, Sorghum bicolor

Glycine max Cucumis sativus Manihot esculenta Ricinus communis Populus trichocarpa Arabidopsis thaliana Arabidopsis lyrata Carica papaya Vitis vinifera Mimulus guttatus Aquilegia coerulea Sorghum bicolor Setaria italica Oryza sativa Brachypodium distachyon 12>=3 AT1G02100AT1G63160AT1G53120AT1G18270 AT2G27680AT2G40760AT3G10370AT3G18140AT4G24270AT4G32910AT4G36390AT3G05040AT5G08400AT5G15920AT5G17620AT5G43710AT5G45380AT5 G AT5G67100AT5G52910 Fig. S2 Gene copy number of 20 randomly selected low-copy nuclear genes in 15 angiosperms with whole sequenced genome. The organismal relationships modified from our results were shown on the left. The gene names were provided at the bottom, gene copy numbers were donated by different colors with green, orange, and red indicating only one, two and 3 or more copies, respectively.

IDLength (AA) identitiesFunctionIDLength (AA) identitiesFunction AT1G MethyltransferaseAT4G unkown AT1G Zinc ion bindingAT4G Transferase activity AT1G RNA bindingAT5G unknown AT1G DNA replicationAT5G adaptin family AT2G OxidoreductaseAT5G ATP binding AT2G PhosphataseAT5G unknown AT3G GlycerophosphateAT5G Glycosyl hydrolase AT3G Nucleotide bindingAT5G Sodium symporter AT3G ARM repeatAT5G Circadian rhythm AT4G Nucleic acid bindingAT5G DNA-directed DNA polymerase Glycine max Cucumis sativus Manihot esculenta Ricinus communis Populus trichocarpa Arabidopsis thaliana Arabidopsis lyrata Carica papaya Vitis vinifera Mimulus guttatus Aquilegia coerulea Sorghum bicolor Setaria italica Oryza sativa Brachypodium distachyon * * * Fig. S3 Single gene tree of 15 species with sequenced genome and information of 20 randomly selected low-copy genes. The tree was generated by PhyML based on AT5G52910 amino acid sequences using JTT model. If other 19 single gene trees were congruent with the AT5G52910 tree at one node, the bar with corresponding color was placed on the node, asterids indicate all 20 single gene trees supporting this combination. Detailed information on support by single gene trees will be provided upon request.

0.1 96/60 22/48 99/- 100/- 98/- 100/99 99/30 100/98 * Cucumis sativus Glycine max Manihot esculenta Ricinus communis Populus trichocarpa Arabidopsis thaliana Arabidopsis lyrata Carica papaya Vitis vinifera Mimulus guttatus Aquilegia coerulea Brachypodium distachyon Oryza sativa Setaria italica Sorghum bicolor * * * Fig. S4 Comparison between the concatenated five good gene tree and the concatenated five bad gene tree. The phylogram is the best ML tree conducted by PhyML 3.0 using five good genes (AT5G15920, AT5G17620, AT5G43710, AT5G52910, and AT5G67100), the two numbers associated with the branch are the supporting values, with the former and the latter being the one of concatenated five good gene tree and the one of concatenated five bad gene tree ( AT1G02100, AT1G18270, AT2G27680, AT2G40760, AT3G10370 ), respectively. Asterisk indicates 100% bootstrap at this node for both trees. *

Fig. S5. Size of SMC1 proteins and sequence identities between species with sequenced genomes. The sizes of amino acid of angiosperm species with whole-sequenced genomes are shown in the diagonal cells of the table. Sequence identities between two proteins are indicated by color. The gene names are abbreviated as follows: Glyma_1, Glycine max_1; Cucsa, Cucumis sativus; Manes, Manihot esculenta; Ricco, Ricinus communis; Poptr, Populus trichocarpa; Arath, Arabidopsis thaliana; Araly, Arabidopsis lyrata; Carpa, Carica papaya; Vitvi, Vitis vinifera; Mimgu, Mimulus guttatus; Aquco, Aquilegia coerulea; Sorbi, Sorghum bicolor; Setit, Setaria italica; Orysa, Oryza sativa; Bradi, Brachypodium distachyon

Aly : tgctcaacgtgagaagaagattgctgagaaaagctcgaaacttggaaaaa Ath : tgctcaacgtgagaagaagattgctgagaaaagctcgaagcttggaaaaa Aly : ttGTGAGTATACCTTGGAAATCTGTGGTTAACAGATTCTATTTTCCCTTT Ath : ttGTGAGTATACCTTGGAAATCTGTGGTTAACAGATTCTATTTTCCCTTT Aly : CAAATATAGCATTAGCATTTCCAGACATCTCTTACAATTTATTTTTTGTT Ath : TAAATATAGCATTTTGAGA-CATGTCTTACATTTTTTTTTATTTTTTGTT Aly : ACCCTCTGGAATTTTACTAA-CGTTCTCACTTGAGTAACTTATATCTGTA Ath : ATCCTCTGGAATTTCACTAAACTTTCTCACTTGAGTAACTTATATCTGTA Aly : CTTTTCCTGTGAGCAGcaacctgagcttctgagatttaaggaggagatag Ath : CCTTTCCTGTGAGCAGcaacctgagcttctgagatttaaggaggagatag Aly : ctcgcattaaagcaaaaattgaga Ath : ctcgcattaaagcaaaaattgaga Arabidopsis lyrata Arabidopsis thaliana Identity (%) intronLength Species (bp) Fig. S6a. Comparison of introns of SMC1 between Arabidopsis thaliana and A. lyrata. The table shows the length of each intron from Arabidopsis thaliana and A. lyrata and the percentage of identity for every intron. The alignment of intron 3 of SMC1 is shown below. The conserved gene sequences are represented by black characters, while the variable regions are shown by red ones. Exon and intron regions are shown by lower case letters and upper case letters, respectively.

Arabidopsis lyrata Arabidopsis thaliana Identity (%) intronLength Species (bp) Aly : ggcattgcttctcttcaaaccggctcctctttatatattagacgagGTAC Ath : ggcattgcttctcttcaaaccggctcctctttatatattagatgagGTAC Aly : GTCTCTGCTTTTCGATTTTTGATT-CTCAGTTCCCAACTGATATTTCAAA Ath : ATCTCTGCTTTTCAATTTCAGATTTCTCAGTTTCCAATTGATATTTCAAA Aly : TTACCATAGAAGATCTCAAGGGTTTGTTTATGTTTTTGATGTGGA----- Ath : TTATCATAGAAGATCTATAGGGTTGGTTTATGTTTCCGATGTGGAACACT Aly : --TTTTCAATAAACAATCAGCGAGTGAAGAGAGAAAATACTCATGATTTTG Ath : GATTTTGCATTAACAATCAGCGAGTGAAGAGAGAAAATACTCATGATTTTG Aly : ATTTATTTCAGgttgatgcagctcttgatctcagtcacacacagaacatag Ath : AATTATATCAGgttgatgcagctcttgatctcagtcacacacagaacatag Aly : gaagaatg Ath : gaagaatg Fig. S6b. Comparison of introns of SMC2 between Arabidopsis thaliana and A. lyrata. The table shows the length of each intron from Arabidopsis thaliana and A. lyrata and the percentage of identity for every intron. (b), The alignment of intron 18 of SMC2 is shown below. The conserved gene sequences are represented by black characters, while the variable regions are shown by red ones. Exon and intron regions are shown by lower case letters and upper case letters, respectively.

Arabidopsis lyrata Arabidopsis thaliana Identity (%) intronLength Species (bp) Aly : tggaagacacaaatgaggccagttcccgtggccctgccaacttcactcct Ath : tggaagacacaaatgaggccagttcccgtggccctgccaacttcactcct Aly : gacgaaGTTAGTATCGCATCATTTGGATCATTTTTTT-CTTCATTTGATA Ath : gacgaaGTTAGTATCGCATCATTTGGTTCTTTTTGTTTTCTCATTTGATA Aly : GCCTATGCCATCCATGGTTTCACAATGGACTGTTAAAGTCAACATGCCTG Ath : GCCTATGTCATCCATGGTTTCACAATGAACTATTAAAGTTAACATGGCTG Aly : AACTACTGTTACTGGAAACCAAATGCCTTACGTAGCTGTTGGCTTTATGA Ath : AATTATTGTTACTGGAAACCAAATGCCTTAGGTAGCTGTTGGCTCTATGA Aly : AATTTGATTCTTTATGTAACTCCCAAATGGATGTGATGGTGTTTTCAGGA Ath : AATT-----CTTTATGTAACTCCCAAATGAATGTGATGGTGTTTTCTGGA Aly : AACATACTCTGTGCTATTAGTTTACTATGAACCATTTAGGCCTGCTTGGA Ath : AATATTCTCTGTGCTACTAGTTTACTATGAAACATTTAGGCCTGCTTGGA Aly : ACATCACTTTATACAGCCTTGTTGTACAATTCCATTTATCAGTTTTGCCT Ath : A GCCTAGTTGTACAATTCCATTTATCAGTTTTGTCT Aly : TTCCTAATATTACTTTTAGgaggaagaattcaaaaagtttgctgatagtc Ath : TCCATAATATTACTTTTAGgaggaagaattcaaaaagtttgctgatagtc Aly : aagatgtatacaagaacatttg Ath : aagatgtatacaagaacatttg Fig. S6c. Comparison of introns of MCM5 between Arabidopsis thaliana and A. lyrata. (a), The table shows the length of each intron from Arabidopsis thaliana and A. lyrata and the percentage of identity for every intron. (b), The alignment of intron 6 of MCM5 is shown below. The conserved gene sequences are represented by black characters, while the variable regions are shown by red ones. Exon and intron regions are shown by lower case letters and upper case letters, respectively.

Arabidopsis lyrata Arabidopsis thaliana % Identity intron Length Species (bp) Aly : ggttacatgcctttttgcaacccaagccacaaagtctccctgacaaggtt Ath : ggttacatgcctttttgcaacccaagccacataatctccctgacaaggtt Aly : tctagtttgagtgtagtaagGTAAGACCCCACCTGATACAAGACGTGTAG Ath : tctagtctgagtgtagttagGTAAGACCTCATGTGATACCGGATATGTAG Aly : TTACATATAAACAACATTGGATCCCATGTCATTACTGTATTCAAAACTCT Ath : TTTCATACAAACAAAATTGGATCCCGAGTCATCACTT--TTCAAAAATCG Aly : CATCTTATTTACCAGTAGATGTTCACTCCTTTAATTTCCGTGAAAATTGT Ath : CATCTTATTTACCAAA-GATGTGCACTCCTTTGATTTCCTTGAAAAGTAT Aly : TTCCTGCAGGTGTTTCTTTGGCATGATTCTTTATTGGTTAGATGTGTTGC Ath : TTGCTGCCGGTGTTACTATGGCTTGATA-----TTTCTTTTATTTTTTAC Aly : GCAACTGCAGTATATTC–ACTTGATCT–TATTACGGAA-TTGCAGgtctt Ath : ---ACTTCATTATATTCCACATGATATATATTACTGAACTTGCAGgtctt Aly : ctgtaaggcaaagaagaaacccaaaggaaactgctgatctttctag Ath : cggtaaggcaaagaagaaacccaaaggaaactgctgatctttctag Fig. S6d. Comparison of introns of MLH1 between Arabidopsis thaliana and A. lyrata. (a), The table shows the length of each intron from Arabidopsis thaliana and A. lyrata and the percentage of identity for every intron. (b), The alignment of intron 9 of MLH1 is shown below. The conserved gene sequences are represented by black characters, while the variable regions are shown by red ones. Exon and intron regions are shown by lower case letters and upper case letters, respectively.

Arabidopsis lyrata Arabidopsis thaliana Identity (%) intron Length Species (bp) Aly : gctgtcatcatctattcttacatgcatcgttgaggcacaatgcatcagGT Ath : gctgtcatcatcttttcttacatgcatcgttgaggcacaatgcatcagGT Aly : TTTGTATACAATCT------CTACATTGTATTAGCACCTCTGAACTGT-G Ath : TTTGAATACTATCTTCAATTCTACATTGTATTAGCATCTCTGAACTGTTG Aly : AAGATAATGCCAA ATGTGGACAGTGTGCAATTTTAACATCACA Ath : AAGATAGTGCCAATAATAGAATGTAGACGG-GTGCCATTTTATCCTCACA Aly : TGAACATAAGTACGCCCAGGTGGCAGCATATGATCTAGCAGTCTATTTAA Ath : TGAACATAAGTATTCTCAGGTGGTAGCATATGATCTAGCAAATACTTTAG Aly : AGTGTCAGGAGACTGTTAGAAGCAAAATACTATTCATGATTTTT--CAAC Ath : AGAGTCTGGAGACAGTTACAAGAGAAATACGATTCATGTTTTGTGTCAAC Aly : TTAATTAGCTTTTGAGCTTTATTGTCTTTTACGATAACAATTCTTGAAAA Ath : TTAATTGACTTTTGAGCTTTGTGGTCTTTTCTGATA-CAATTCTTGTTAA Aly : TTAT—-GGTATGCAGggacgtgccgctggggagagtttggggaagggggt Ath : TTTTTTATTATGCAGggacgtgccgctggggagagtttggggaagggggt Aly : cttctctgggg Ath : cttctctgggg Fig. S6e. Comparison of introns of MSH1 between Arabidopsis thaliana and A. lyrata. (a), The table shows the length of each intron from Arabidopsis thaliana and A. lyrata and the percentage of identity for every intron. (b), The alignment of intron 8 of MSH1 is shown below. The conserved gene sequences are represented by black characters, while the variable regions are shown by red ones. Exon and intron regions are shown by lower case letters and upper case letters, respectively. Gunnera manicata

Tetradium ruticarpum Poncirus trifoliata Rhus chinensis Sapindus mukorossi Hibiscus syriacus Stachyurus yunnanensis Arabidopsis lyrata Arabidopsis thaliana Carica papaya Manihot esculenta Ricinus communis Populus tricocarpa Hypericum chinense Euonymus carnosus Pelargonium hortorum Ulmus macrocarpa Morus alba Photinia serrulata Glycine max_2 Glycine max_1 Cyclobalanopsis glauca Oenothera erythrosepala Lagerstroemia limii Cucumis sativus Stellaria media Phytolacca americana Polygonum runcinatum Callicarpa bodinieri Mimulus guttatus Jassminum nudiflorum Vinca major Nerium oleander Galium aparine Solanum lycopersicum Pharbitis nil Ilex purpurea Aucuba japonica Lonicera japonica Pittosporum tobira Hedera nepalensis Ligusticum chuanxiong Lactuca sativa Cornus officinalis Cornus wisoniana Philadelphus incanus Actinidia arguta Diospyros kaki Rhododendron pulchrum Cercidiphyllum japonicum Distylium buxifolium Paeonia lactiflora Vitis vinifera Gunnera manicata Buxus sinica Pachysandra terminalis Platanus acerifolia Meliosma parviflora Aquilegia coerulea Ranunculus muricatus Nandina domestica Dicentra spectabilis Sorghum bicolor Setaria italica Brachypodium distachyon Oryza sativa Dioscorea opposita Canna indica Musa basjoo Asparagus officinalis Yucca filamentosa Iris japonica Lilium brownii Pinellia ternata Cinnamomum camphora Acorus calamus Asarum heterotropoides Aristolochia fimbriata Houttuynia cordata Liriodendron chinese x L. tulipifera Magnolia denudata Chimonanthus praecox Chloranthus elatior & C. spicatus Ceratophyllum demersum Illicium henryi Schisandra propinqua & S. sphenanthera Nuphar advena_2 Nuphar advena_1 Cabomba caroliniana Amborella trichopoda Pinus Picea Zamia fischeri Fig. S7a. ML tree of SMC1 inferred by PhyML 3.0 using the nucleotide matrix. Numbers associated with branches are SH aLRT supporting values. If two copies are found in one species, the gene that evolved faster is marked by gray background, then it will be excluded from further analyses. 100

Tetradium ruticarpum Poncirus trifoliata Rhus chinensis Sapindus mukorossi Arabidopsis thaliana_2 Arabidopsis thaliana_1 Arabidopsis lyrata Hibiscus syriacus Carica papaya Stachyurus yunnanensis Manihot esculenta Ricinus communis Populus tricocarpa_2 Populus tricocarpa_1 Hypericum chinense Euonymus carnosus Ulmus macrocarpa Morus alba Photinia serrulata Glycine max_2 Glycine max_1 Cucumis sativus Cyclobalanopsis glauca Oenothera erythrosepala Lagerstroemia limii Pelargonium hortorum Vitis vinifera Distylium buxifolium Cercidiphyllum japonicum Paeonia lactiflora Callicarpa bodinieri Mimulus guttatus Jassminum nudiflorum Pharbitis nil Solanum lycopersicum Vinca major Nerium oleander Galium aparine Lactuca sativa Pittosporum tobira Hedera nepalensis Ligusticum chuanxiong Lonicera japonica Ilex purpurea Aucuba japonica Cornus officinalis Cornus wisoniana Philadelphus incanus Actinidia arguta Rhododendron pulchrum Diospyros kaki Phytolacca americana Stellaria media Polygonum runcinatum Gunnera manicata Buxus sinica Pachysandra terminalis Aquilegia coerulea Ranunculus muricatus Nandina domestica Meliosma parviflora Platanus acerifolia Dicentra spectabilis Sorghum bicolor Setaria italica Oryza sativa Brachypodium distachyon Canna indica Musa basjoo Trachycarpus fortunei Yucca filamentosa Asparagus officinalis Iris japonica Lilium brownii Alisma plantago-aquatica Pinellia ternata Acorus calamus Chimonanthus praecox Cinnamomum camphora Asarum heterotropoides Liriodendron chinese x L. tulipifera Magnolia denudata Chloranthus elatior & C. spicatus Aristolochia fimbriata Houttuynia cordata Ceratophyllum demersum Illicium henryi Schisandra propinqua & S. sphenanthera Nuphar advena Amborella trichopoda Picea Pinus Fig. S7b. ML tree of SMC2 inferred by PhyML 3.0 using the nucleotide matrix. Numbers associated with branches are SH aLRT supporting values. If two copies are found in one species, the gene that evolved faster is highlighted by gray background, then it will be excluded from further analyses. Cabomba caroliniana

Poncirus trifoliata Rhus chinensis Sapindus mukorossi Euonymus carnosus Arabidopsis thaliana Arabidopsis lyrata Carica papaya Hibiscus syriacus Manihot esculenta Ricinus communis Populus tricocarpa _2 Populus tricocarpa _1 Hypericum chinense Stachyurus yunnanensis Cyclobalanopsis glauca Ulmus macrocarpa Photinia serrulata Morus alba Glycine max_2 Glycine max_1 Lagerstroemia limii Oenothera erythrosepala Cucumis sativus Pelargonium hortorum Cercidiphyllum japonicum Distylium buxifolium Paeonia lactiflora Gunnera manicata Vitis vinifera Callicarpa bodinieri Mimulus guttatus Jassminum nudiflorum Solanum lycopersicum Pharbitis nil Vinca major Nerium oleander Galium aparine Ligusticum chuanxiong Pittosporum tobira Hedera nepalensis Lonicera japonica Lactuca sativa Diospyros kaki Actinidia arguta Aucuba japonica Ilex purpurea Cornus officinalis Cornus wisoniana Philadelphus incanus Phytolacca americana Polygonum runcinatum Stellaria media Dicentra spectabilis Buxus sinica Pachysandra terminalis Aquilegia coerulea Ranunculus muricatus Nandina domestica Platanus acerifolia Meliosma parviflora Sorghum bicolor Setaria italica Brachypodium distachyon Oryza sativa Canna indica Musa basjoo Trachycarpus fortunei Asparagus officinalis Yucca filamentosa Iris japonica Dioscorea opposita Lilium brownii Alisma plantago-aquatica Pinellia ternata Acorus calamus Liriodendron chinese x L. tulipifera Magnolia denudata Chimonanthus praecox Illicium henryi Schisandra propinqua & S. sphenanthera Chloranthus elatior & C. spicatus Nuphar advena Asarum heterotropoides Aristolochia fimbriata Houttuynia cordata Amborella trichopoda Pinus Picea Zamia fischeri Fig. S7c. ML tree of MCM5 inferred by PhyML 3.0 using the nucleotide matrix. Numbers associated with branches are SH aLRT supporting values. If two copies are found in one species, the gene that evolved faster is highlighted by gray background, then it will be excluded from further analyses. Cabomba caroliniana

Tetradium ruticarpum Poncirus trifoliata Rhus chinensis Sapindus mukorossi Stachyurus yunnanensis Arabidopsis lyrata Arabidopsis thaliana Hypericum chinense Hibiscus syriacus Carica papaya Manihot esculenta Ricinus communis Populus tricocarpa Euonymus carnosus Ulmus macrocarpa Morus alba Photinia serrulata Cyclobalanopsis glauca Lagerstroemia limii Glycine max Pelargonium hortorum Cucumis sativus Cercidiphyllum japonicum Paeonia lactiflora Distylium buxifolium Vitis vinifera Callicarpa bodinieri Mimulus guttatus Jassminum nudiflorum Pharbitis nil Solanum lycopersicum Nerium oleander Vinca major Galium aparine Lactuca sativa Ligusticum chuanxiong Pittosporum tobira Hedera nepalensis Lonicera japonica Ilex purpurea Aucuba japonica Cornus officinalis Cornus wisoniana Philadelphus incanus Actinidia arguta Rhododendron pulchrum Diospyros kaki Gunnera manicata Phytolacca americana Stellaria media Polygonum runcinatum Pachysandra terminalis Buxus sinica Platanus acerifolia Meliosma parviflora Ranunculus muricatus Aquilegia coerulea Nandina domestica Aristolochia fimbriata Houttuynia cordata Liriodendron chinese x L. tulipifera Magnolia denudata Cinnamomum camphora Chimonanthus praecox Illicium henryi Schisandra propinqua & S. sphenanthera Amborella trichopoda Sorghum bicolor Setaria italica Brachypodium distachyon Oryza sativa Canna indica Trachycarpus fortunei Lilium brownii Dioscorea opposita Yucca filamentosa Asparagus officinalis Iris japonica Alisma plantago-aquatica Pinellia ternata Acorus calamus Ceratophyllum demersum Nuphar advena Zamia fischeri Pinus Fig. S7d. ML tree of MLH1 inferred by PhyML 3.0 using the nucleotide matrix. Numbers associated with branches are SH aLRT supporting values.

Tetradium ruticarpum Poncirus trifoliata Rhus chinensis Sapindus mukorossi Hibiscus syriacus Stachyurus yunnanensis Euonymus carnosus Arabidopsis lyrata Arabidopsis thaliana Carica papaya Manihot esculenta Ricinus communis Hypericum chinense Populus tricocarpa Ulmus macrocarpa Morus alba Photinia serrulata Cucumis sativus Glycine max Cyclobalanopsis glauca Lagerstroemia limii Oenothera erythrosepala Cercidiphyllum japonicum Paeonia lactiflora Distylium buxifolium Vitis vinifera Callicarpa bodinieri Mimulus guttatus Pittosporum tobira Jassminum nudiflorum Nerium oleander Vinca major Galium aparine Pharbitis nil Solanum lycopersicum Aucuba japonica Ilex purpurea Ligusticum chuanxiong Hedera nepalensis Lonicera japonica Lactuca sativa Actinidia arguta Rhododendron pulchrum Diospyros kaki Cornus officinalis Cornus wisoniana Philadelphus incanus Stellaria media Phytolacca americana Polygonum runcinatum Gunnera manicata Buxus sinica Pachysandra terminalis Platanus acerifolia Meliosma parviflora Aquilegia coerulea Ranunculus muricatus Nandina domestica Dicentra spectabilis Sorghum bicolor Setaria italica Brachypodium distachyon Oryza sativa Canna indica Musa basjoo Trachycarpus fortunei Yucca filamentosa Asparagus officinalis Iris japonica Dioscorea opposita Lilium brownii Alisma plantago-aquatica Pinellia ternata Acorus calamus Chloranthus elatior & C. spicatus Aristolochia fimbriata Houttuynia cordata Asarum heterotropoides Magnolia denudata Liriodendron chinese x L. tulipifera Cinnamomum camphora Chimonanthus praecox Nuphar advena Ceratophyllum demersum Illicium henryi Schisandra propinqua & S. sphenanthera Amborella trichopoda Fig. S7e. ML tree of MSH1 inferred by PhyML 3.0 using the nucleotide matrix. Numbers associated with branches are SH aLRT supporting values. Cabomba caroliniana

Poncirus trifoliata Tetradium ruticarpum Rhus chinensis Sapindus mukorossi Arabidopsis thaliana Arabidopsis lyrata Carica papaya Hibiscus syriacus Stachyurus yunnanensis Manihot esculenta Ricinus communis Populus tricocarpa Hypericum chinense Euonymus carnosus Ulmus macrocarpa Morus alba Photinia serrulata Glycine max Cyclobalanopsis glauca Cucumis sativus Oenothera erythrosepala Lagerstroemia limii Pelargonium hortorum Stellaria media Phytolacca americana Polygonum runcinatum Distylium buxifolium Cercidiphyllum japonicum Paeonia lactiflora Vitis vinifera Callicarpa bodinieri Mimulus guttatus Jassminum nudiflorum Solanum lycopersicum Pharbitis nil Nerium oleander Vinca major Galium aparine Ilex purpurea Aucuba japonica Hedera nepalensis Ligusticum chuanxiong Pittosporum tobira Lonicera japonica Lactuca sativa Cornus officinalis Cornus wisoniana Philadelphus incanus Actinidia arguta Rhododendron pulchrum Diospyros kaki Gunnera manicata Buxus sinica Pachysandra terminalis Platanus acerifolia Meliosma parviflora Ranunculus muricatus Aquilegia coerulea Nandina domestica Dicentra spectabilis Oryza sativa Brachypodium distachyon Setaria italica Sorghum bicolor Musa basjoo Canna indica Trachycarpus fortunei Dioscorea opposita Yucca filamentosa Asparagus officinalis Iris japonica Lilium brownii Pinellia ternata Alisma plantago-aquatica Acorus calamus Asarum heterotropoides Aristolochia fimbriata Houttuynia cordata Cinnamomum camphora Chimonanthus praecox Magnolia denudata Liriodendron chinese x L. tulipifera Ceratophyllum demersum Chloranthus elatior & C. spicatus Schisandra propinqua & S. sphenanthera Illicium henryi Nuphar advena Amborella trichopoda Pinus Picea Zamia fischeri 1/2/-/4/5 1/2/3/4/- 1/2/-/4/5 1/2/3/4/5 1/-/3/-/5 -/2/3/4/- 1/2/-/-/- 1/2/3/4/5 1/2/-/4/- 1/2/3/-/5 1/-/-/-/- 1/2/3/4/5 1/2/-/4/5 1/2/3/4/5 1/-/-/-/ 1/-/-/-/- -/2/-/-/5 -/2/3/-/- 1/2/-/?/5 1/2/-/?/- 1/2/-/4/5 1/2/3/4/5 1/-/-/-/- 1/2/3/-/- 1/2/3/-/5 1/-/-/4/5 -/2/-/-/- 1/2/3/4/5 -/2/-/-/- 1/2/3/4/5 1/2/-/-/- 1/-/-/-/- -/-/-/-/5 1/2/3/4/? 1/2/3/4/5 1/-/3/-/5 1/2/-/-/5 1/2/3/4/5 1/-/3/-/5 -/2/-/4/5 1/2/-/-/- 1/2/3/4/5 1/-/-/-/- 1/2/-/4/5 1/2/3/4/5 1/-/-/?/5 1/-/-/-/5 1/2/3/4/5-/-/3/-/5 1/2/-/-/5 1/2/3/4/5 1/2/3/?/5 -/-/-/4/5 ?/2/-/4/5 1/-/-/-/- 1/2/3/4/5 1/2/3/-/5 -/2/-/-/5 1/2/3/4/5 ?/-/-/-/5 -/2/3/-/5 1/-/3/?/- 1/-/3/4/5 -/2/?/4/5 1/2/3/4/5 -/-/3/-/5 1/-/-/?/- -/-/-/-/- 1/-/-/-/- 1/2/-/-/- 1/2/3/4/5 1/2/3/-/5 1/2/3/?/? 1/-/-/-/- -/2/3/-/5 -/2/-/-/5 Fig. S8. Comparison of five single gene trees with the concatenated 5 gene tree. The tree is the best ML tree inferred by RAxML using the concatenated five genes. Numbers above the branch indicate different genes, with 1, 2, 3, 4, and 5 indicating SMC1, SMC2, MCM5, MLH1 and MSH1, respectively. If the single gene tree is congruent with the concatenated gene tree, the corresponding number was placed on the branch. The gap (-) indicates different topology at this node when compared with the concatenated tree. Question mark (?) indicates missing data at this node for one single gene tree. Cabomba caroliniana 1/?/3/4/? 1/2/3/4/5 -/2/-/4/5 1/2/3/4/5 BP_RM_N: SMC1/SMC2/MCM5/MLH1/MSH1

Poncirus trifoliata Tetradium ruticarpum Rhus chinensis Sapindus mukorossi Arabidopsis thaliana Arabidopsis lyrata Carica papaya Hibiscus syriacus Stachyurus yunnanensis Manihot esculenta Ricinus communis Populus tricocarpa Hypericum chinense Euonymus carnosus Ulmus macrocarpa Morus alba Photinia serrulata Glycine max Cyclobalanopsis glauca Cucumis sativus Oenothera erythrosepala Lagerstroemia limii Pelargonium hortorum Stellaria media Phytolacca americana Polygonum runcinatum Distylium buxifolium Cercidiphyllum japonicum Paeonia lactiflora Vitis vinifera Callicarpa bodinieri Mimulus guttatus Jassminum nudiflorum Solanum lycopersicum Pharbitis nil Nerium oleander Vinca major Galium aparine Ilex purpurea Aucuba japonica Hedera nepalensis Ligusticum chuanxiong Pittosporum tobira Lonicera japonica Lactuca sativa Cornus officinalis Cornus wisoniana Philadelphus incanus Actinidia arguta Rhododendron pulchrum Diospyros kaki Gunnera manicata Buxus sinica Pachysandra terminalis Platanus acerifolia Meliosma parviflora Ranunculus muricatus Aquilegia coerulea Nandina domestica Dicentra spectabilis Oryza sativa Brachypodium distachyon Setaria italica Sorghum bicolor Musa basjoo Canna indica Trachycarpus fortunei Dioscorea opposita Yucca filamentosa Asparagus officinalis Iris japonica Lilium brownii Pinellia ternata Alisma plantago-aquatica Acorus calamus Asarum heterotropoides Aristolochia fimbriata Houttuynia cordata Cinnamomum camphora Chimonanthus praecox Magnolia denudata Liriodendron chinese x L. tulipifera Ceratophyllum demersum Chloranthus elatior & C. spicatus Schisandra propinqua & S. sphenanthera Illicium henryi Nuphar advena Amborella trichopoda Pinus Picea Zamia fischeri */97/*/*/* 78/68/64/91/* */97/*/*/* */*/*/*/* 52/95/*/*/* 43/66/95/99/* -/-/-/-/59 -/-/-/-/82 83/99/*/*/* -/-/-/88/81 -/72/*/*/* -/42/-/93/81 41/56/74/*/* 99/*/*/*/* 57/81/95/88/* -/-/-/-/84 -/-/-/-/80 -/24/22/22/* 50/-/49/-/44 -/*/*/*/* -/-/-/-/35 -/76/96/88/* */*/*/*/* 98/*/*/*/* -/-/-/35/78 -/-/72/99/* 64/99/*/*/* 63/77/50/88/* -/-/-/43/76 */*/*/*/* 99/43/*/*/* 89/*/*/*/* -/32/-/-/51 */*/*/*/* 98/*/*/*/* 99/32/99/*/* -/-/-/-/74 -/18/61/64/* -/81/-/-/51 99/31/97/*/* -/-/-/-/63 24/25/85/98/* 51/88/93/*/* */*/*/*/* 56/99/99/98/* 97/99/99/93/* -/-/-/62/* 90/90/97/*/* -/-/-/62/70 -/-/-/*/* 98/87/*/98/* 99/*/*/*/* 98/*/*/*/* -/97/98/*/* 65/81/98/89/* 97/87/*/*/* 28/82/96/98/84 -/-/35/53/87 */99/*/*/* ?/99/*/*/* 41/25/97/-/81 -/19/82/-/85 -/-/23/33/62 */95/*/*/* 83/95/*/*/* 17/12/-/-/54 -/36/*/*/* -/20/75/75/* 55/81/78/93/* 56/22/71/98/* -/50/52/90/87 17/74/99/*/* 68/99/*/*/* */*/*/*/* -/59/60/-/* ?/-/-/68/59 13/-/-/31/42 34/-/-/66/59 56/-/-/97/* */88/*/*/* ?/96/*/*/* ?/?/*/*/* 29/-/-/98/94 80/91/98/91/83 39/-/-/51/92 Fig. S9. Comparison of five trees reconstructed by one gene and the concatenated 2-5 genes. The tree is the best ML tree inferred by RAxML using the concatenated five genes. Numbers above the branch are bootstrap (BP) values estimated by RAxML using one gene (MLH1), concatenated two genes (MLH1 and MSH1), three genes (MLH1, MSH1 and MCM5), four genes (MLH1, MSH1, MCM5 and SMC1), five genes (MLH1, MSH1, MCM5, SMC1 and SMC2), respectively. Asterisk (*) indicates BP = 100%. The gap (-) indicates different topology at this node when compared with the concatenated five genes. Question mark (?) indicates missing data at this node for one tree. Cabomba caroliniana */*/*/*/* BP_RM_N: 1 gene/2 genes/3 genes/4 genes/5genes

Poncirus trifoliata Tetradium ruticarpum Rhus chinensis Sapindus mukorossi Arabidopsis thaliana Arabidopsis lyrata Carica papaya Hibiscus syriacus Stachyurus yunnanensis Manihot esculenta Ricinus communis Populus tricocarpa Hypericum chinense Euonymus carnosus Ulmus macrocarpa Morus alba Photinia serrulata Glycine max Cyclobalanopsis glauca Cucumis sativus Oenothera erythrosepala Lagerstroemia limii Pelargonium hortorum Stellaria media Phytolacca americana Polygonum runcinatum Distylium buxifolium Cercidiphyllum japonicum Paeonia lactiflora Vitis vinifera Callicarpa bodinieri Mimulus guttatus Jassminum nudiflorum Solanum lycopersicum Pharbitis nil Nerium oleander Vinca major Galium aparine Ilex purpurea Aucuba japonica Hedera nepalensis Ligusticum chuanxiong Pittosporum tobira Lonicera japonica Lactuca sativa Cornus officinalis Cornus wisoniana Philadelphus incanus Actinidia arguta Rhododendron pulchrum Diospyros kaki Gunnera manicata Buxus sinica Pachysandra terminalis Platanus acerifolia Meliosma parviflora Ranunculus muricatus Aquilegia coerulea Nandina domestica Dicentra spectabilis Oryza sativa Brachypodium distachyon Setaria italica Sorghum bicolor Musa basjoo Canna indica Trachycarpus fortunei Dioscorea opposita Yucca filamentosa Asparagus officinalis Iris japonica Lilium brownii Pinellia ternata Alisma plantago-aquatica Acorus calamus Asarum heterotropoides Aristolochia fimbriata Houttuynia cordata Cinnamomum camphora Chimonanthus praecox Magnolia denudata Liriodendron chinese x L. tulipifera Ceratophyllum demersum Chloranthus elatior & C. spicatus Schisandra propinqua & S. sphenanthera Illicium henryi Nuphar advena Amborella trichopoda Pinus Picea Zamia fischeri */*/*/* */*/*/87 */*/*/* */0.99/*/42 */-/59/- */-/82/- */*/*/* */-/81/- */-/*/- */-/81/28 */*/*/* */-/84/- */-/80/- */*/*/89 0.9/-/44/35 */*/*/* 0.9/*/35/- */*/*/* */0.98/78/70 */*/*/* */*/*/56 */-/76/- */*/*/* 0.86/*/51/72 */*/*/* 0.99/-/74/- */-/*/- 0.92/-/51/- */*/*/* 0.99/-/63/65 */*/*/* */*/*/71 */*/*/* */*/*/90 */*/*/* 0.96/*/70/* */*/*/* */*/*/89 */*/*/* */-/84/- */*/87/74 */*/*/* */*/81/90 */*/85/ /*/62/60 */*/*/* 0.85/0.98/54/46 */*/*/* */*/*/89 */*/*/* */0.99/87/73 */*/*/* */*/*/93 */*/59/65 */-/42/- */*/59/64 */*/*/* */*/94/* */*/83/* */*/*/* */*/92/89 */*/*/* 0.99/-/*/ /*/*/* */*/*/* 0.99/*/*/* 0.99/-/*/ /0.66/56/- 0.99/-/76/28 */*/*/* 0.5/0.42/68/- */*/*/- 0.99/-/76/ /*/*/* */*/*/* */0.99/*/* 0.77/0.76/76/ /*/87/ /-/35/- */*/*/* -/-/31/- 0.98/*/*/* */0.99/*/* 0.88/0.99/55/ /*/*/* */*/*/* 0.99/0.72/*/ /-/56/- */*/*/* 0.48/0.93/53/66 */*/*/* -/-/72/- -/-/86/ /-/57/- */*/*/* 0.58/0.72/68/72 */*/88/84 */*/*/* */0.99/*/ /*/*/* 0.99/0.99/*/* 0.99/0.84/*/ /0.99/*/* */*/*/* 0.98/*/*/* 0.94/0.62/63/46 */*/*/* 0.98/*/*/* 0.66/-/68/- 0.97/0.87/83/ /*/*/* */*/*/* 0.99/*/90/* 0.5/-/76/ /*/*/* */*/*/* 0.97/0.97/73/ /0.99/76/ /0.71/46/60 */*/*/* 0.98/*/*/* -/0.5/41/ /0.61/82/ /0.99/*/92 */*/*/* 0.96/0.55/89/66 */*/*/* 0.98/*/*/* */*/*/* 0.98/*/*/ /0.99/94/ /0.81/42/- 0.91/-/31/- 0.97/0.77/ /*/93/ /*/*/* 0.97/*/*/* 0.98/*/*/* 0.97/0.99/89/ /0.99/69/ /*/*/* -/-/81/39 Fig. S10. Cladogram of the best ML tree conducted by RAxML based on the concatenated 5 gene nucleotide sequences. Asterisks indicate supporting values of posterior probabilities (PP) = 1 or bootstrap (BP) > 95.Totally, 8 kinds of supporting values were shown. The first two numbers above the branch are PPs estimated by MrBayes using nucleotide and amino acid matrixes, respectively. While the latter ones are BPs estimated by RAxML using nucleotide and amino acid matrixes, respectively. The first two numbers below the branches are PPs estimatated by PhyloBayes using nucleotide and amino acid matrixes, respectively. The latter ones are BPs estimated by PhyML using nucleotide and amino acid matrixes, respectively. Gap indicates different topology at this node when compared with the best ML tree shown here. Scale bar indicates number of changes per site. Different colors of species names indicate different sources of data, red indicates that data was generated by PCR in this study, black and blue indicate genomic data and EST data retrieved from public databases, respectively. PP_MB_N/PP_MB_P/BP_RM_N/BP_RM_P PP_PB_N/PP_PB_P/BP_PM_N/BP_PM_P Cabomba caroliniana

Fig. S11a. Phylogram of 42 species inferred by MrBayes 3.0 based on the concatenated 5 gene nucleotide sequences. Number associate with branches are supporting values with the former and the latter being posterior possibilities give by Mrbayes 3.0 and bootstrap values estimated by RAxML, respectively. When PP = 1.0 and bootstrap value > 95 at the same time, asterisk is placed on the node. The gap indicates that difference exists between ML tree and Bayes tree. Cucumis sativus Ulmus macrocarpa Populus tricocarpa Sapindus mukorossi Lagerstroemia limii Mimulus guttatus Solanum lycopersicum Pittosporum tobira Cornus wisoniana Actinidia arguta Gunnera manicata Pachysandra terminalis Buxus sinica Ranunculus muricatus Aquilegia coerulea Nandina domestica Dicentra spectabilis Musa basjoo Canna indica Trachycarpus fortunei Dioscorea opposita Asparagus officinalis Yucca filamentosa Iris japonica Lilium brownii Pinellia ternata Alisma plantago-aquatica Acorus calamus Asarum heterotropoides Aristolochia fimbriata Houttuynia cordata Magnolia denudata Liriodendron chinese X L. tulipifera Cinnamomum camphora Chimonanthus praecox Chloranthus elatior & C. spicatus Ceratophyllum demersum Schisandra propinqua & S. sphenanthera Illicium henryi Nuphar advena Amborella trichopoda 1.0/89 1.0/ / / / / /80 0.9/27 * 0.52/ * * * * * * * * * * * * * * * * * * * * * * * * * Eudicots Monocots Magnoliids Chloranthaceae Ceratophyllaceae Early-diverging angiosperms * * * Cabomba caroliniana

Tetradium ruticarpum Poncirus trifoliata Rhus chinensis Sapindus mukorossi Arabidopsis thaliana Arabidopsis lyrata Carica papaya Hibiscus syriacus Stachyurus yunnanensis Manihot esculenta Ricinus communis Populus tricocarpa Hypericum chinense Euonymus carnosus Ulmus macrocarpa Morus alba Photinia serrulata Glycine max Cyclobalanopsis glauca Cucumis sativus Oenothera erythrosepala Lagerstroemia limii Pelargonium hortorum Stellaria media Phytolacca americana Polygonum runcinatum Distylium buxifolium Cercidiphyllum japonicum Paeonia lactiflora Vitis vinifera Callicarpa bodinieri Mimulus guttatus Jassminum nudiflorum Solanum lycopersicum Pharbitis nil Vinca major Nerium oleander Galium aparine Aucuba japonica Ilex purpurea Ligusticum chuanxiong Hedera nepalensis Pittosporum tobira Lonicera japonica Lactuca sativa Cornus wisoniana Conus officinalis Philadelphus incanus Rhododendron pulchrum Actinidia arguta Diospyros kaki Gunnera manicata Pachysandra terminalis Buxus sinica Platanus acerifolia Meliosma parviflora Ranunculus muricatus Aquilegia coerulea Nandina domestica Dicentra spectabilis 1.0/69 1.0/ /85 1.0/87 * 1.0/52 1.0/ / /25 1.0/51 1.0/ / /65 1.0/ / /93 1.0/ / * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Rosidae Caryophyllales Saxifragales Vitaceae Asteridae Basal eudicots Fig. S11b. Phylogram of eudicot species inferred by MrBayes 3.0 based on the concatenated 5 gene nucleotide sequences. Number associate with branches are supporting values with the former and the latter being posterior possibilities give by Mrbayes and bootstrap values estimated by RAxML, respectively. When PP =1.0 and bootstrap value > 95 at the same time, asterisk is placed on the node. The gap indicates that difference exists between ML tree and Bayes tree * * * * *

Tetradium ruticarpum Poncirus trifoliata Rhus chinensis Sapindus mukorossi Arabidopsis thaliana Arabidopsis lyrata Carica papaya Hibiscus syriacus Stachyurus yunnanensis Manihot esculenta Ricinus communis Populus tricocarpa Hypericum chinense Euonymus carnosus Ulmus macrocarpa Morus alba Photinia serrulata Glycine max Cyclobalanopsis glauca Cucumis sativus Oenothera erythrosepala Lagerstroemia limii Pelargonium hortorum Stellaria media Phytolacca americana Polygonum runcinatum Callicarpa bodinieri Mimulus guttatus Jassminum nudiflorum Solanum lycopersicum Pharbitis nil Vinca major Nerium oleander Galium aparine Aucuba japonica Ilex purpurea Ligusticum chuanxiong Hedera nepalensis Pittosporum tobira Lonicera japonica Lactuca sativa Cornus wisoniana Conus officinalis Philadelphus incanus Rhododendron pulchrum Actinidia arguta Diospyros kaki Gunnera manicata Pachysandra terminalis Buxus sinica Platanus acerifolia Meliosma parviflora Ranunculus muricatus Aquilegia coerulea Nandina domestica Dicentra spectabilis 1.0/ /82 1.0/87 1.0/76 * 1.0/52 1.0/ / /- 0.98/ / / / / * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Rosidae Caryophyllales Asteridae Basal eudicots Fig. S11c. Phylogram of eudicot species excluding Saxifragales and Vitaceae species inferred by MrBayes 3.0 based on the concatenated 5 gene nucleotide sequences. Number associate with branches are supporting values with the former and the latter being posterior possibilities give by Mrbayes 3.0 and bootstrap values estimated by RAxML, respectively. When PP =1.0 and bootstrap value > 95 at the same time, asterisk is placed on the node. The gap indicates that difference exists between ML tree and Bayes tree. * * * * * * *

Tetradium ruticarpum Poncirus trifoliata Rhus chinensis Sapindus mukorossi Arabidopsis thaliana Arabidopsis lyrata Carica papaya Hibiscus syriacus Stachyurus yunnanensis Manihot esculenta Ricinus communis Populus tricocarpa Hypericum chinense Euonymus carnosus Ulmus macrocarpa Morus alba Photinia serrulata Glycine max Cyclobalanopsis glauca Cucumis sativus Oenothera erythrosepala Lagerstroemia limii Pelargonium hortorum Distylium buxifolium Cercidiphyllum japonicum Paeonia lactiflora Vitis vinifera Callicarpa bodinieri Mimulus guttatus Jassminum nudiflorum Solanum lycopersicum Pharbitis nil Vinca major Nerium oleander Galium aparine Aucuba japonica Ilex purpurea Ligusticum chuanxiong Hedera nepalensis Pittosporum tobira Lonicera japonica Lactuca sativa Cornus wisoniana Conus officinalis Philadelphus incanus Rhododendron pulchrum Actinidia arguta Diospyros kaki Gunnera manicata Pachysandra terminalis Buxus sinica Platanus acerifolia Meliosma parviflora Ranunculus muricatus Aquilegia coerulea Nandina domestica Dicentra spectabilis 1.0/71 1.0/ /91 1.0/90 * 1.0/60 1.0/ / /14 1.0/ / / / /72 1.0/ / * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Rosidae Saxifragales Vitaceae Asteridae Basal eudicots Fig. S11d. Phylogram of eudicot species excluding Caryophyllales inferred by MrBayes 3.0 based on the concatenated 5 gene nucleotide sequences. Number associate with branches are supporting values with the former and the latter being posterior possibilities give by Mrbayes 3.0 and bootstrap values estimated by RAxML, respectively. When PP =1.0 and bootstrap value > 95 at the same time, asterisk is placed on the node. The gap indicates that difference exists between ML tree and Bayes tree. * * * * *

Tetradium ruticarpum Poncirus trifoliata Rhus chinensis Sapindus mukorossi Arabidopsis thaliana Arabidopsis lyrata Carica papaya Hibiscus syriacus Stachyurus yunnanensis Manihot esculenta Ricinus communis Populus tricocarpa Hypericum chinense Euonymus carnosus Ulmus macrocarpa Morus alba Photinia serrulata Glycine max Cyclobalanopsis glauca Cucumis sativus Oenothera erythrosepala Lagerstroemia limii Pelargonium hortorum Cercidiphyllum japonicum Distylium buxifolium Paeonia lactiflora Vitis vinifera Mimulus guttatus Callicarpa bodinieri Jassminum nudiflorum Solanum lycopersicum Pharbitis nil Vinca major Nerium oleander Galium aparine Aucuba japonica Ilex purpurea Ligusticum chuanxiong Hedera nepalensis Pittosporum tobira Lonicera japonica Lactuca sativa Conus officinalis Cornus wisoniana Philadelphus incanus Actinidia arguta Rhododendron pulchrum Diospyros kaki Stellaria media Phytolacca americana Polygonum runcinatum Gunnera manicata Pachysandra terminalis Buxus sinica Platanus acerifolia Meliosma parviflora Ranunculus muricatus Aquilegia coerulea Nandina domestica Dicentra spectabilis Sorghum bicolor Setaria italica Oryza sativa Brachypodium distachyon Musa basjoo Canna indica Trachycarpus fortunei Dioscorea opposita Yucca filamentosa Asparagus officinalis Iris japonica Lilium brownii Alisma plantago-aquatica Pinellia ternata Acorus calamus Aristolochia fimbriata Asarum heterotropoides Houttuynia cordata Chimonanthus praecox Cinnamomum camphora Magnolia denudata Liriodendron chinese x L. tulipifera Chloranthus elatior & C. spicatus Ceratophyllum demersum Schisandra propinqua & S. sphenanthera Illicium henryi Nuphar advena Amborella trichopoda Picea Pinus Zamia fischeri 38/ / /0.7 93/1.0 73/1.0 43/ /1.0 88/ / / /- 27/- 92/1.0 80/ / /1.0 48/ / / /- 30/- 51/ /0.6 89/1.0 81/0.9 92/1.0 93/1.0 92/1.0 86/1.0 84/1.0 49/1.0 45/1.0 * 65/ Eudicots Monocots Magnoliids Chloranthaceae Ceratophyllaceae Early-diverging angiosperms Fig. S12. Phylogram of the best ML tree conducted by RAxML based on the concatenated 5 gene nucleotide matrix excluding the 3 rd codon positions. Asterisks indicate supporting values of posterior probabilities (PP) = 1 and bootstrap (BP) > 95. Numbers associated with internal branches are also supporting values (BP/PP). The gap indicates that difference exists between ML tree and Bayes tree. Scale bar represents number of changes per site. Basal eudicots Rosidae Asteridae Pentapetalae * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Cabomba caroliniana