Order. GLO-like sequences

Transcription

1 Table S1. DEF and GLO-like sequences employed in this study. This manuscript describes the isolation and characterization of those sequences with names in bold type. DEF-like sequences Species GenBank Accession Number AmAP3 Amborella trichopoda AB DEF1 Elaeis guineensis AY ApDEF Agapanthus praecox AB AODEF Asparagus officinalis AB MADS1 Cymbidium spp DQ DcOAP3A Dendrobium crumenatum DQ DcOAP3B Dendrobium crumenatum DQ GogalDEF1 Gongora galeata FJ GogalDEF2 Gongora galeata FJ GogalDEF3 Gongora galeata FJ HrDEF Habenaria radiata AB MADS1 Hemerocallis hyb AF HyvilDEF1 Hypoxis villosa FJ HyvilDEF2 Hypoxis villosa FJ MaDEF Muscari armeniacum AB OMADS3 Oncidium Gower Ramsey AY PeMADS2 Phalaenopsis equestris AY PeMADS3 Phalaenopsis equestris AY PeMADS4 Phalaenopsis equestris AY PeMADS5 Phalaenopsis equestris AY PhlonDEF1 Phragmipedium longifolium FJ PhlonDEF2 Phragmipedium longifolium FJ PhlonDEF3 Phragmipedium longifolium FJ PhlonDEF4 Phragmipedium longifolium FJ SpodoDEF1 Spiranthes odorata FJ SpodoDEF2 Spiranthes odorata FJ SpodoDEF3 Spiranthes odorata FJ SpodoDEF4 Spiranthes odorata FJ VaplaDEF1 Vanilla planifolia FJ VaplaDEF2 Vanilla planifolia FJ VaplaDEF3 Vanilla planifolia FJ Ap3-1 Illicium floridanum AY IhAP3-1 Illicium henryi AY KjAP3 Kadsura japonica AB CCDEF Commelina communis AB Order Amborellales GLO-like sequences Species GenBank Accession Number PI Acorus calamus DQ PI Alisma plantago-aquatica DQ PI Arum maculatum DQ SmPI Sagittaria montevidensis AF PIa Tofieldia calyculata DQ PIb Tofieldia calyculata DQ AmPI Amborella trichopoda AB PI1 Caryota mitis DQ PI2 Caryota mitis DQ GLO1 Elaeis guineensis AF GLO2 Elaeis guineensis AF ApMADS1 Agapanthus praecox AB PI2 Allium ursinum DQ AOGLOA Asparagus officinalis AB AOGLOB Asparagus officinalis AB PIC2 Crocus sativus DQ DthyrPI Dendrobium thyrsiflorum DQ PI Epipactis palustris DQ GogalGLO1 Gongora galeata FJ HrGLO1 Habenaria radiata AB HrGLO2 Habenaria radiata AB HyvilGLO1 Hypoxis villosa FJ HyvilGLO2 Hypoxis villosa FJ PI1 Muscari botryoides DQ PI2 Muscari botryoides DQ PI1a Narcissus cyclamineus DQ PI1b Narcissus cyclamineus DQ OrcPI Orchis italica AB PeMADS6 Phalaenopsis equestris AY PhlonGLO1 Phragmipedium longofolium FJ PI1a Speirantha convallarioides DQ PI1b Speirantha convallarioides DQ SpodoGLO1 Spiranthes odorata FJ VaplaGLO1 Vanilla planifolia FJ PI Illicium floridanum AY Order Acorales Amborellales

2 TRDEF Tradescantia reflexa AB AP3 Tacca chantrieri AF AlsDEFa Alstromeria ligtu AB AlsDEFb Alstromeria ligtu AB MADS1 Lilium longiflorum AF LRDEF1 Lilium regale AB TriaDEF Tricyrtis affinis AB TGDEFA Tulipa gesneriana AB TGDEFB Tulipa gesneriana AB MagrAP3 Magnolia grandiflora AY BsAP3 Brasenia schreberi AB EfAP3 Euryale ferox AB NjAP3-2 Nuphar japonica AB AP3-1 Nuphar variegata AY NymAP3 Nymphaea tetragona AB AP3 Elegia elephas DQ AP3b Elegia elephas DQ HvAP3 Hordeum vulgare AY AP3 Joinvillea ascendens DQ SPW1 Oryza sativa NM_ AP3 Streptochaeta angustifolia DQ TaMADS51 Triticum aestivum AB TaMADS82 Triticum aestivum AB SILKY1 Zea mays AF MADS5 Alpinia hainanensis AY Dioscoreales Magnoliales IhPI-1 Illicium henryi AY KjPI Kadsura japonica AB CCGLO Commelina communis AB TcPI Tacca chantrieri AF PI Alstromeria ligtu DQ GLO1 Lilium longiflorum DQ PI1 Lilium martagon DQ LRGLOA Lilium regale AB TriaGLO Tricyrtis affinis AB TGGLO Tulipa gesneriana AB PIa Veratrum californicum DQ PIb Veratrum californicum DQ BsPI Brasenia schreberi AB CcPI Cabomba caroliniana AB EfPI Euryale ferox AB NjPI-1 Nuphar japonica AB NjPI-2 Nuphar japonica AB NtPI Nymphaea tetragona AB PI1 Cortaderia selloana DQ PI2 Cortaderia selloana DQ PI Elegia elephas DQ HvPI Hordeum vulgare AY PI Joinvillea ascendens DQ MADS2 Oryza sativa AY MADS4 Oryza sativa L37527 PI1 Pharus virescens DQ PI2 Pharus virescens DQ PI1 Streptochaeta angustifolia DQ PI2 Streptochaeta angustifolia DQ WPI1 Triticum aestivum AB WPI2 Triticum aestivum AB ZMM16 Zea mays NM_ ZMM18 Zea mays AJ ZMM29 Zea mays NM_ MADS8 Alpinia hainanensis AY PI Alpinia oblongifolia DQ PI Globba marantina DQ MADS1 Musa acuminata AY PIa Musa ornata DQ PIb Musa ornata DQ Dioscoreales

3 Table S2. Parameter estimates and s analyses with models M7 vs. M8 from monocots. Model Estimate of parameters L DEF-like M7 (beta) p= q= M8 (beta and ω) p 0 = p= q= (p 1 = ) ω= M7 vs M8 : 2δ = df=2 P=0.729 GLO-like Model Estimate of parameters L M7 (beta) p= q= M8 (beta and ω) p 0 = p= q= (p 1 = ) ω= M7 vs M8 : 2δ = df=2 P=0.8805

4 Table S3. Parameter estimates and of MA1 vs. MA in DEF-like genes from Orchidaceae. The branches tested are those labeled with cursive fonts in Figure 3. Clade Model Estimate of parameters Positive selection L C1 (O1) 73 Q 0.752, 114 L 0.546, 125 N 0.608, 131 K δ = 0 df=1 P=1 C2 (O2) C3 (O3) A ω 0 = , f 0 = ω 1 = , f 1 = ω 2a fore = , ω 2a back = , f 2a = ω 2b fore = , ω 2b back = , f 2b = A1 ω 0 = , f 0 = ω 1 = , f 1 = ω 2a fore = , ω 2a back = , f 2a = δ = df=1 P= δ =0 df=1 P=1 C4 (O4) 2δ =0 df=1 P=1 C1-C2 (O5) A1 ω 0 = , f 0 = ω 1 = , f 1 = ω 2a fore = , ω 2a back = , f 2a = δ = df=1 P=1 C3-C4 (O6) A ω 0 = , f 0 = δ =0 df=1 P=1 16 N 0.966*, 51 T 0.982*, 69 D 0.511, 79 L 0.980*, 130 L 0.615, 170 N 0.588, 171 Y 0.972* 33 T 0.505, 43 V 0.628, 68 F 0.641, 178 D R

5 Table S4. Parameter estimates and of MA1 vs. MA in GLO-like genes from Orchidaceae and. The branches tested are those labeled with cursive fonts in Figure 4. Clade Model Estimate of parameters Positive selection L (P1) A ω 0 = , f 0 = ω 1 = , f 1 = V Q ω 2a fore= , ω 2a back= , f 2a = ω 2b fore= , ω 2b back= , f 2b = Q A1 ω 0 = , f 0 = ω 1 = , f 1 = ω 2a fore= , ω 2a back= , f 2a = (P2) ω 2b fore= , ω 2b back= , f 2b = δ= df=1 P= A ω 0 = , f 0 = ω 1 = , f 1 = ω 2a fore= , ω 2a back= , f 2a = ω 2b fore= , ω 2b back= , f 2b = A1 ω 0 = , f 0 = ω 1 = , f 1 = ω 2a fore= , ω 2a back= , f 2a = ω 2b fore= , ω 2b back= , f 2b = (P3) A ω 0 = , f 0 = A1 ω 0 = , f 0 = (P4) A ω 0 = , f 0 = ω 1 = , f 1 = ω 2a fore= , ω 2a back= , f 2a = ω 2b fore= , ω 2b back= , f 2b = A1 ω 0 = , f 0 = ω 1 = , f 1 = ω 2a fore= , ω 2a back= , f 2a = ω 2b fore= , ω 2b back= , f 2b = Orchids (O1) A ω 0 = , f 0 = A1 ω 0 = , f 0 =