sign in sign up
<<
Home , Buxales, Caryophyllales, Cornales, Dilleniales, Ericales, Gunnerales

Nymphaelaes A Magnolids

Monocots

Ranunculales

Proteales Trochodendrales Vitales FUL-Like Gunnerales Saxifragales Vitales

Rosids FUL

Caryophyllales Cornales Ericales

Asterids

Gunnerales Saxifragales Vitales

Rosids

euAP1 Caryophyllales Cornales Ericales

Asterids

Amborellales Nymphaelaes B

Magnolids

Chloranthales Monocots

Ranunculales

Proteales Trochodendrales Buxales Gunnerales Saxifragales Vitales

Rosids

Dilleniales Santanales TM6 Caryophyllales

Cornales

Ericales

Asterids

Saxifragales

Vitales

Rosids

Dilleniales Caryophyllales Cornales euAP3 Ericales

Asterids Amborellales Nymphaelaes C Austrobaileyales Magnolids

Chloranthales

Monocots

Ranunculales

Proteales

Trochodendrales Buxales Gunnerales Saxifragales Vitales

Rosids

Dilleniales Caryophyllales

Cornales

PI Ericales

Asterids

Amborellales D Nymphaelaes

Magnolids

Monocots

Ranunculales

Proteales Trochodendrales Buxales Gunnerales Saxifragales Vitales

Rosids

euAG

Caryophyllales

Cornales Ericales

Asterids

Gunnerales Saxifragales Vitales

Rosids SHP

Dilleniales

Asterids Amborellales E Chloranthales Magnolids

Monocots

Ranunculales

Proteales Buxales Gunnerales Saxifragales Vitales

Rosids

STK

Caryophyllales

Ericales

Asterids

Amborellales Nymphaelaes F Magnolids

Monocots

Ranunculales Proteales Trochodendrales Buxales Gunnerales Saxifragales Vitales

Rosids

Caryophyllales Cornales FBP9

Ericales

Asterids

Vitales

Rosids

Caryophyllales SEP4 Cornales

Asterids

Gunnerales Saxifragales Vitales

Rosids

SEP1/2

Caryophyllales Cornales Ericales

Asterids Amborellales Chloranthales G Magnolids

Monocots

Ranunculales Proteales Trochodendrales Buxales Gunnerales Vitales

Rosids

Asterids SEP3 Caryophyllales

Cornales

Ericales

Asterids

Amborellales H Nymphaelaes Magnolids

Monocots

Ranunculales

Proteales Buxales Saxifragales Vitales

Rosids SVP

Caryophyllales Cornales Ericales

Asterids

Saxifragales Vitales Rosids Dilleniales Caryophyllales StMADS11 Ericales

Asterids

Gunnerales Vitales

Rosids AGL24

Dilleniales Caryophyllales Cornales Ericales

Asterids Amborellales Nymphaelaes I Magnolids

Monocots

Ranunculales

Proteales Trochodendrales Buxales Saxifragales Vitales

Rosids

Santanales Caryophyllales Cornales FBP22

Asterids

Gunnerales Vitales

Rosids

Berberidopsidales AGL14 Cornales Ericales

Asterids

Saxifragales Vitales

Rosids

TM3

Dilleniales Cornales

Asterids

Supplemental Figure 1: Simplified phylogenetic of the MADS-box gene subfamilies used for ASR and selective pressure estima- tion. AP1- (A), AP3- (B), PI- (C), AG- (D), STK- (E), SEP1/2/4 (F), SEP3 (G), SVP/AGL24 (H), SOC1- (I) gene lineages. Arrows denote the nodes used for ASR before the γ triplication (blue) and at the Rosid/Asterid split (green). Red arrows denote the nodes for which no reliable ancestral genes could be reconstructed. ancAP1 pre-γ ancPI post-γ ancPI

1 1 1

0.8 0.8 0.8

0.6 0.6 0.6

0.4 0.4 0.4

0.2 0.2 0.2

0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 21 31 41 51 61 71 81 91 1 21 31 41 51 61 71 81 91 21 31 41 51 61 71 81 91 11 11 11 2 2 101 121 131 141 151 161 171 181 191 201 101 121 131 141 151 161 171 181 191 201 221 231 241 251 101 121 131 141 151 161 171 181 191 201 MADS I K C MADS I K C MADS I K C

anceuAP1 ancFUL-LIKE ancFUL

1 1 1

0.8 0.8 0.8

0.6 0.6 0.6

0.4 0.4 0.4

0.2 0.2 0.2

0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 21 31 41 51 61 71 81 91 21 31 41 51 61 71 81 91 21 31 41 51 61 71 81 91 11 11 11 2 2 2 101 121 131 141 151 161 171 181 191 201 221 231 241 101 121 131 141 151 161 171 181 191 201 221 231 241 251 101 121 131 141 151 161 171 181 191 201 221 231 241

MADS I K C MADS I K C MADS I K C

ancAP3 anceuAP3 ancTM6

1 1 1

0.8 0.8 0.8

0.6 0.6 0.6

0.4 0.4 0.4

0.2 0.2 0.2

0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 21 31 41 51 61 71 81 91 21 31 41 51 61 71 81 91 21 31 41 51 61 71 81 91 11 11 11 2 2 2 101 121 131 141 151 161 171 181 191 201 221 231 101 121 131 141 151 161 171 181 191 201 221 101 121 131 141 151 161 171 181 191 201 221 MADS I K C MADS I K C MADS I K C

ancAG anceuAG ancSHP

1 1 1

0.8 0.8 0.8

0.6 0.6 0.6 0.4 0.4 C 0.4 0.2 0.2 0.2

0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 21 31 41 51 61 71 81 91 21 31 41 51 61 71 81 91 21 31 41 51 61 71 81 91 11 11 11 2 2 101 121 131 141 151 161 171 181 191 201 101 121 131 141 151 161 171 181 191 201 101 121 131 141 151 161 171 181 191 201 MADS I K C MADS I K C MADS I K C

pre-γ ancSTK post-γ ancSTK

1 1

0.8 0.8

0.6 0.6

0.4 0.4

0.2 0.2

0 0 1 1 1 1 1 1 1 1 1 1 1 1 21 31 41 51 61 71 81 91 21 31 41 51 61 71 81 91 11 11 2 2 101 121 131 141 151 161 171 181 191 201 221 101 121 131 141 151 161 171 181 191 201 221 MADS I K C MADS I K C ancSEP1/2/4 pre-γ ancSEP3 post-γ ancSEP3

1 1 1

0.8 0.8 0.8

0.6 0.6 0.6

0.4 0.4 0.4

0.2 0.2 0.2

0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 21 31 41 51 61 71 81 91 21 31 41 51 61 71 81 91 1 1 21 31 41 51 61 71 81 91 11 11 2 2 11 101 121 131 141 151 161 171 181 191 201 221 231 241 101 121 131 141 151 161 171 181 191 201 221 231 241 2 101 121 131 141 151 161 171 181 191 201 221 231 241 MADS I K C MADS I K C MADS I K C

ancSEP1/2 ancSEP4 ancFBP9

1 1 1

0.8 0.8 0.8

0.6 0.6 0.6

0.4 0.4 0.4

0.2 0.2 0.2

0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 21 31 41 51 61 71 81 91 1 1 1 1 21 31 41 51 61 71 81 91 21 31 41 51 61 71 81 91 11 2 11 101 121 131 141 151 161 171 181 191 201 221 231 241 251 11 2 2 101 121 131 141 151 161 171 181 191 201 221 231 241 251 101 121 131 141 151 161 171 181 191 201 221 231 241 251 MADS I K C MADS I K C MADS I K C

ancSVP/AGL24 ancSVP ancAGL24

1 1 1

0.8 0.8 0.8

0.6 0.6 0.6

0.4 0.4 0.4

0.2 0.2 0.2

0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 21 31 41 51 61 71 81 91 1 1 1 1 21 31 41 51 61 71 81 91 21 31 41 51 61 71 81 91 11 2 11 11 101 121 131 141 151 161 171 181 191 201 221 231 2 2 101 121 131 141 151 161 171 181 191 201 221 231 101 121 131 141 151 161 171 181 191 201 221 231 MADS I K C MADS I K C MADS I K C

ancSOC1 ancFBP22 ancTM3

1 1 1

0.8 0.8 0.8

0.6 0.6 0.6

0.4 0.4 0.4

0.2 0.2 0.2

0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 21 31 41 51 61 71 81 91 1 1 1 1 21 31 41 51 61 71 81 91 21 31 41 51 61 71 81 91 11 2 11 11 101 121 131 141 151 161 171 181 191 201 2 2 101 121 131 141 151 161 171 181 191 201 221 101 121 131 141 151 161 171 181 191 201 221 MADS I K C MADS I K C MADS I K C

Supplemental Figure 2: Ancestral sequences and their accuracy. Dots represent the posterior probabilities (y-axis) for each amino acid site (x-axis) for all reconstructed genes. Arrows denote ambiguous sites defined as sites for which the most likely amino acid has a posterior probability lower than 0.80 and that have an alternative amino acid state with a posterior probability higher than 0.2. Green arrows represent ambiguous sites of which the most likely amino acids are biochemically similar (S and T; V, L and I; D and E; N and Q; K and R were considered similar).

A Gene subfamilies AP1 SQUA/AP1/FUL CAL Overlapping FUL PPIs only in de Folter et al (2005) DEF/AP3 AP3 PPIs only in this study GLO/PI PI No interactions detected AG AG SHP1 SHP2 STK STK SEP1 SEP1/2/4 SEP2 SEP4 SEP3 SEP3 SVP SVP/ StMADS11 AGL24 AGL42 SOC1/TM3 SOC1 AP1 CAL FUL AP3 PI AG SHP1 SHP2 STK SEP1 SEP2 SEP4 SEP3 SVP AGL24 AGL42 SOC1

Gene s ubfamilies

B MC

TM4 Overlapping SQUA/AP1/FU L

SLMBP 7 PPIs only in Leseberg et al (2008) PPIs only in this study SLMBP2 0 No interactions detected

TAP3 DEF/AP 3

TM6

LeP I GLO/P I

TP I

TAG1 AG

TAGL1

SLMBP 3 STK

TAGL1 1

TM29

RIN SEP1/2 /4

LeMADS1

SLMBP21

SEP3 TM5

JOINTLESS SVP/S tMADS11

SLMBP2 4

SLMBP1 8 SOC1/TM 3

TM3

MC TM4 SLMBP7 SLMBP20 TAP3 TM6 LeP I TP I TAG1 TAGL1 SLMBP3 TAGL11 TM29 RIN LeMADS1 SLMBP21 TM5 JOINTLESS SLMBP24 SLMBP18 TM3

C

Arabidopsis Interaction No interaction Total Sensitivity 0,6052632 This study Interaction 23 16 39 Accuracy 0,7973856 No interaction 15 99 114 Precision 0,5897436 Total 38 115 153 Specificity 0,8608696

Solanum Interaction No interaction Total Sensitivity 0,4125 This study Interaction 33 12 45 Accuracy 0,7445887 No interaction 47 139 186 Precision 0,7333333 Total 80 151 231 Specificity 0,9205298

Arabidopsis/Solanum Interaction No interaction Total Sensitivity 0,4745763 This study Interaction 56 28 84 Accuracy 0,765625 No interaction 62 238 300 Precision 0,6666667 Total 118 266 384 Specificity 0,8947368

Supplemental Figure 3: Comparison of the PPIs obtained in this study with the determined PPIs from previous published literature. (A-B) Colored blocks indicate PPI between two proteins. PPIs that have been detected in one direction are not differentiated from reciprocal ones. Black represents PPIs present in both studies. Yellow refers to PPIs detected only by previous studies (de Folter, 2005; Leseberg et al., 2008). Red indicates the PPIs only found in this study. (A) Ara-PIN compared to Folter et al. 2005 (de Folter, 2005; Leseberg et al., 2008). (B) Sol-PIN compared to Leseberg et al. 2008 (Leseberg et al., 2008). (C) Comparison between the Arabidopsis or Solanum network from this study to those reconstructed in de Folter et al (2005) or Leseberg et al (2008) respectively (de Folter, 2005; Leseberg et al., 2008). A

B C

1.0 ● 0.8 ● Ck = 0.329 Ck = 0.586 2 0.7 ● 2 0.8 R = 0.12 R = 0.251 0.6 ● p-value = 0.270 p-value = 0.0815 0.6 0.5 ● ● ● 0.4 ● ● ● 0.4 0.3 ● ● ● ●● 0.2

0.2 ● Ara-PIN ● Sol-PIN ● ●

1 2 5 10 20 50 1 2 5 10 20 50 Ck 0.500 ● Ck = 1.493 Ck = 1.815 R2 = 0.52 0.50 R2 = 0.613 ● P-value = 0.00813 P-value = 0.00155 0.200 ● ● ● 0.20 0.100 ● ● 0.10 0.050 ● ●

0.05 0.020 ● ● 0.010 0.02

0.005 0.01 Upscaled Ara-PIN ● Upscaled Sol-PIN 5 10 20 5 10 20

k Supplemental Figure 4: C(k) and P(k) distribution for tracing of elementary process in network evolution from Pre-PIN, via Post-PIN until extant Ara-PIN and Sol-PIN by simulation models (A) The flowchart of simulation process based on the actual ancestral and extant MADS-box PIN parameters for two models, namely the initial upscaled Pre-PIN model and the initial Erdős–Rényi (ER) random Pre-PIN model. Red arrows indicate critical steps: 1. Actual Pre-PIN with 7 nodes (i) was upscaled into simulated Pre-PIN with 1000 nodes (ii). This step is only achieved for the initial upscaled Pre-PIN model; 2. The network size of upscaled Pre-PIN (ii) or new builded initial ER random Pre-PIN (ii) were three fold upscaled into simu- lated Pre-PIN with 3000 nodes (iii) by γ triplication; 3. (iii) evolved to simulated Post-PIN (iv) through 37% node deletion followed by 27% edge deletion and 73% edge addition; 4. The network size of (iv) was two fold upscaled into simulated Ara-PIN (v) by β WGD; 5. (v) evolved to simulated Ara-PIN (vi) through 52% node deletion followed by 47.2% edge dele- tion and 22.7% edge addition; 6. The network size of (vi) was subsequently two fold upscaled into simulated Ara-PIN (vii) by α WGD; 7. After 23% node deletion followed by 20.3% edge deletion and 9.8% edge addition, (vii) evolved to final simu- lated Ara-PIN (viii); 8. The network size of (iv) was three fold upscaled into simulated Sol-PIN (ix) by T WGT; 9. (ix) evolved to final simulated Sol-PIN (x) through 59% node deletion followed by 58% edge deletion and 42% edge addition. (B) C(k) distribution of each simulated network from the initial upscaled Pre-PIN model (left) and from the initial ER random Pre-PIN model (right) corresponding to simulation process discussed in (A). (C) C(k) distribution of the original Ara-PIN and Sol-PIN, and from their directly upscaled versions (without following all intermediate steps shown in (A). ● ● ● ● ● ● ●●● ● ● ● ● ● (ii) Simulated Pre-PIN A ● ● B Triplicated simulated Pre-PIN after node deletion ● ● ● ●

● 0.12 ● ● ● (iv) Simulated Post-PIN ●●● ●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● (viii) Final simulated Ara-PIN ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ● (x) Final simulated Sol-PIN ● ●

● ● 0.10 ● ●● ● i ● ● ● ● ●● ● ● ● ● ● ● ●● ● ●● ● ● ● ●●● ● ● ● ● ●●● ● ● ● ● ● ● ● ● ● C(k) = 0 ● ● ● ●● ● i ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ●●● ●● ● ● ● ● ● ● ● 0.08 ● ● ●● ● ● ● ● ●● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ●● ● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ●● ● ● ● ●● ●● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●● ● ● ● ● ● ●● ● ●● ● ● ● ● ●●●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ●● ● ● ●● ●● ●●●● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ●● ● ● ● ● ● ● ●● ● ● ● ●● ● ● ● ● ● ● ● ●●● ● ● ● ● ● ● ● ● ● ● ● ● ●●●● ● ● i ● ●● ●● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ●● ● ●● ● 0.06 ●●● ●●● ● ● ● ● ● ● ● ● ●● ● ●● ●● ●● ● ● ●● ● ● ● ● ● ● ●●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ●● ●● C(k) = 0.17 ● ● ● ● ● ● ● ● ● ● ● ● ●●● ● ●●● ● ●● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●● ● i ● ● ●●●● ● ● ● ● ● ● ● ● ● ● ● ●●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ●● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ●● ● ● ● ● ● ● ●● ● ● ● ● ● ●● ●●● ● ● ●●●●● ● ●● ● ● ● ●● ●● ● ● ●●● ● ● ●● ● ● ● ● ● ●● ● ● ● ● ● ●● ● ● ●●● ●● ●●●● ● ●● ● ● ● ● ●● ● ● ●● ● ● ● ●●● ● ● ● ● ●●●● ● ● ●●● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ●● ● ●●● ● ● ● ● ● ●● ● ● ● ● ●● ● ●● ●● ● ● ● ● ● ● ●● ●● ● ● ● ● ● ●● ● ● ● ● ●●● ● ● ● ● ● ● ● ● ● ●●●● ● ● ● ● ● ● ●● ● ● ● ● ●● ● ●● ● ●●●●● ● ● ●● ● ●●●● ● ● ●●● ● ●● ●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ●●● ● ● ● ● ● ● ● ● ● 0.04 ● ●● ● ● ●●● ● ●● ● ●● ● ● ● ● ●●● ● ● ● ● ● ● ●●●● ● ● ●● ●●● ● ●● ● ● ●● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ●●● ●●● ● ● ● ● ●● ● ● ● ● ● ● ●● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ●● ● ●●● ● ●●●● ● ● ● ● ● ● ● ● ● ●● ● ● ●● ● ● ● ●● ● ● ● ● ● ● ●● ● ● ●● ●● ● ●●● ● ● ● ● ● ●●● ● ●● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ●● ● ● ●● ● ● ● ● ●● ●● ● ● ● ● ● ● ●● ●● ● ●● ● ● ● ● ● ● ●● ● ● ●● ● ● ●●● ● ● ● ● ● ● ● ● ●●●● ● ● ●●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ●● ●● ●● ● ● ● ●● ● ● ● i ● ● ● ● ● ● ●● ● ●● ●● ● ● ● ● ● ● ● ● ● ● Degree distribution P(k) ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●●● ● ● ● ●●● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● C(k) = 0.50 ● ●● ● ●● ● ●● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ●● ● 0.02 ● ● ● ● ● ● ●● ● ●● ● ●● ● ● i ● ● ●● ● ● ●● ● ●● ● ● ● ●● ● ●●●●● ● ● ● ● ● ● ●●●● ● ●● ● ●● ● ● ●●●● ● ● ● ●● ● ● ● ● ●●● ●● ●●● ● ● ●● ● ● ●● ● ● ● ● ● ●● ● ● ● ●● ●● ●● ● ● ●●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ●● ● ● ● ●● ● ●● ● ● ●● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● 0 ● 0 20 40 60 80 100 Degree k C D (iv) (iv) 3 0.10 3 0.10 = -0.165 0.05 R 2 = 0.011 0.05 0.02 2 0.01

2 0.005 0.02 = 0.883 Clustering coefficient C(k) Clustering coefficient 1 C(k) Clustering coefficient 0.002 R 2 = 0.090 1 2 5 10 20 50 1 2 5 10 20 50 100 200 500 Degree k Degree k

1 0

(iv)

(iv) 0

-1

0 0 E 2000 4000 6000 F 2000 4000 6000 0.10 (viii) (viii) 3 3 0.10 0.05 0.05

= -0.032 0.02 0.02 R 2 = 0 2 0.01 0.01 0.005 2 0.005 0.002 = 0.944 Clustering coefficient C(k) Clustering coefficient

Clustering coefficient C(k) Clustering coefficient R 2 = 0.103 1 1 2 5 10 20 50 1 2 5 10 20 50100 200 500 Degree k Degree k

1 0

(viii) (viii) 0 -1 0 2000 4000 6000 8000 0 2000 4000 6000 8000 G H 3 0.10 (x) 3 0.10 = -0.240 0.05 0.05 R 2 = 0.016 (x) 0.02 Exponent β 2 0.02 0.01 2 0.005 0.01 0.002 = 0.856 0.005 Clustering coefficient C(k) Clustering coefficient R 2 = 0.073 1 C(k) Clustering coefficient 1 2 5 10 20 50 100200 500 1 2 5 10 20 50 Degree k

Degree k 1 0

(x)

-1 (x) 0 0

0 2000 4000 6000 2000 4000 6000 Random Random Random Random I edge deletion 27% edge addition 73% J edge addition 73% edge deletion 27%

● 3 1 1 ● (iv) = 2.242 (iv) = 2.351 2 3 0.50 R = 0.963 0.50 R 2 = 0.953 ●

● ● 0.20 ● ● ● ● 0.20 2 ●

● 0.10 ● 2 ● ● ● 0.10 ●

● 0.05 ● (iv) ● ● ● (iv) 0.05 ● 1 ● 0.02 ● 1 ●

●

0.01 ● 0.02 ●

●

●

Clustering coefficient C(k) Clustering coefficient 0.005

Clustering coefficient C(k) Clustering coefficient 0.01 ● 0 ● 0 ● 0 500 1000 1500 2000 1 2 5 10 20 50 0 500 1000 1500 2000 1 2 5 10 20 50 Degree k Degree k Simulation steps 3 K L 1 1 40:60 0.30 47:53 73:27 98:2 47:53 0.90 0.50 0.10 0.80 0.25 0.05 2 0.70 0.20 0.20 0.60 0.10 0.15 0.02 73:27 0.05 1 0.50

Exponent β 40:60 0.01 98:2 0.10 0.02 0.40 = 2.710 = 2.328 0.01 = 2.048 0.005 = 1.734 2 Clustering coefficient C(k) Clustering coefficient R = 1 R 2 = 1 R 2 = 0.889 R 2 = 0.682 0 0.005 0:100 24:76 49:51 75:25 99:1 1 2 5 10 20 50 1 2 5 10 20 50 1 2 5 10 20 50 1 2 5 10 20 50 Ratio of edge addition frequency (%) to edge deletion frequency (%) Degree k Supplemental Figure 5: Additional simulations for understanding the consequence of initialization network size and topology, the role of γ triplication and the dominance of random edge addition. Roman numerals in brackets are representing each simulated network according to the flowchart of simulation process in Supplemental Figure 5A. (A) Schematic explanation of individual node i’s C(k)i value increasing through random edge addition dynamics by network evolving from simulated Pre-PIN (iii) to simulated Post-PIN (iv). (B) Degree distribution P(K) for the initial ER random Pre-PIN model. (C), (E) and (G) Exponent β distribution for the initial upscaled Pre-PIN model without γ triplication. The simulation process began with upscaled Pre-PIN with 1000 nodes (ii) from actual Pre-PIN (i) where Pre-PIN (ii) was not subsequently upscaled to 3000 nodes to Post-PIN (iii) by γ triplication, but the network size kept at 1000 nodes for further simulation process. (D), (F) and (H) Exponent β distribution for the initial ER random Pre-PIN model. For both models, the average value of exponent β distribution with the standard deviation (plots in black, yellow and red and error bars in gray) of total 10 replicated simulations are shown following the simulation process. The C(k) distribution of simulated networks (iv), (viii) and (x) are demonstrated as the additional plots in inset. Blue arrows indicate positions of several important simulated networks following the simulation steps corresponding to the simulation process from (A). (I) and (J) The dominance of random edge addition was demon- strated by the average value of exponent β distribution and the standard deviation of total 10 replicated simulations from Pre-PIN (ii) to Post-PIN (iv). The additional plots in inset show the C(k) distribution of Post-PIN (iv) for random edge deletions preceded random edge additions (left) and random edge additions prior to random edge deletions (right). (K) Exponent β distribution in function of edge dynamic ratios (edge addition frequency (%) to edge deletion frequency (%), from 0:100 to 100:0). Blue arrows indicate exponent β values by several main ratios. (L) C(k) distribution for each simulated network by the annotated ratios from (K). 100 100 Amborel2 AmboLich Amborellales A Amborel1 100 NuphAdve Nupharxx AcorAmer 100 OryzSat1 10OryzS0 at2 6 100 OryzSat3 PhylEdul 6 5 4 8 TritAes1 TritAes2 1 7 100 3 6 2 0 100 HordVul1 3 7 HordVul3 HordVul2 TritAes3 Monocots 100 MusaAcum 5 9 ZingOffi 100 ElaeGuin 9 9 BrodSier 5 1 2 4 AloeVera AlliSati 1 5 PosiOcea VaniPlan SaruHenr EupoBenn 5 6 5 3 100 Lirioden 9 4 LiriTuli 5 7 100 MagnPra2 MagnPra1 CalyFlor 8 5 100 5 3 Persea2x Persea1x PersAmer 7 0 3 8 MalDoSVP VitViSVP PolCoSVP 5 9 9 1 BetVuAGL 9 8 PorcrSVP 6 9 4 8 TalSpSVP PhyAmSVP 6 NepAlSVP 100 ActChSVP ActDeSVP DauCaSVP 7 2 1 9 5 1 PauKaSVP 100 ConAmSVP 2 0 7 8 RosOfSVP OciBaSVP 1 5 3 9 2 4 TaPaAGL2 100 MisOrSVP 4 6 AntMaSVP 3 4 OleEuSVP 100 NicBeSVP 5 1 PetHySVP 4 9 4 0 100 SolLySVP CapAnSVP 1 1 5 6 IpoBaSVP IpoNiSVP SVP CofArSVP 9 9 PisSaSVP 8 5 GlyMaSVP 2 6 GleTrSVP 4 4 ManEsSVP 100 PopTrSVP 2 4 PopToSVP 8 6 MorOlSVP 1 1 2 7 CarPaSVP 100 PonTrSVP CitSiSVP 100 CasSiSVP 6 5 QueRoSVP 1 6 CasMoSVP 1 100 EucGrSVP 2 6 EucOcSVP 4 7 RibNiSVP 8 4 100 GunMSVP1 GunMaSVP2 100 DaeSpSVP SanAcSVP 3 5 100 9 4 HamViSVP LorChSVP DapMaSVP 100 NelumSp1 NelumSp2 8 4 100 GrevRob2 100 HakeaPr1 8 2 HakeaPr2 Proteales 8 5 PlatOcci 100 Platanu2 Platanu1 MyrTeAGL 8 CorCaAGL 8 3 CamelAGL 4 5 100 AcChAGL2 AcChAGL1 3 4 SouExAGL PanQuAGL 4 3 8 6 HelPaAGL 2 3 8 8 CicInAGL 100 LacPeAGL 7 3 EspBaAGL 100 GuiAbAGL 3 5 CynCaAGL 100 PetHyAGL 7 9 SolTuAGL 9 1 100 2 1 6 5 IpoCoAGL 4 3 IpoPuAGL IpoQuAGL 100 CoArAGL2 9 9 CoArAGL1 PsyIpAGL 100 DaeSpAGL 2 3 SanAcAGL 7 GunMaAGL 7 7 100 ViViAGL2 ViViAGL1 VitShAGL AGL24 6 BegonAGL 2 MyrCeAGL 3 7 BetPlAGL 3 4 100 CasMoAGL 100 3 7 QuePeAGL QueRoAGL 100 PruPeAGL 4 PruMuAGL 7 5 ManEsAGL 1 8 PoTrAGL1 9 9 9 9 PoTrAGL2 9 8 PopDeAGL 5 2 PopToAGL 100 PopTrAGL 1 3 PopulAGL 3 5 AraThAGL 1 5 PorOlAGL 9 CarPaAGL 2 7 TheCaAGL 7 100 CitSiAGL CitLiAGL 5 4 CepFoAGL CunCaAGL 3 7PachSVP2 100 5 2PachSVP3 100 PachJOI3 6 5 PachJOI2 BuxSemp2 Buxales 9 9 PachMA20 BuxSemp1 6 5 Trocho56 4 Trocho52 Trochodendrales Trocho89 100 HydrCana 9 9 AnemHu24 3 100 AquiFor2 5 5 AquFoPu2 100 ChelMaj1 100 ChelMaj2 9 9 ArgeMexi 3 4 9 9 PapaBra1 1 0 100 PapaBra2 Ranunculales PapaRho2 100 AnemHu83 9 9 Thali766 2 7 8 0 AquiFor1 AquFoPu1 100 PapaSomn PapaRho1 9 7 DiInStM2 2 0 2 7 DiInStM1 IteViStM PhlDrStM 9 6 9 0 RorGoStM 4 3 ActDeStM 4 7 DioMaStM GalUrStM NicTaStM 100 9 8 SolMaStM 7 7 SolToStM 9 8 100 4 2 9 8 SolHaStM SolTuStM 8 0 PhyAlStM 6 6 100 PhyPuStM PhyPeStM 8 1 OciBaStM 9 8 TriPuStM StMADS11 5 5 3 7 MimGuStM 6 4 HelCStM2 3 3 100 CofCaStM CofArStM 4 9 GleTrStM 2 1 HelCStM1 9 9 KocScStM 9 3 BouSpStM NepAlStM 100 ViViStM2 100 ViViStM3 3 2 ViViStM1 9 8 EupEsStM 100 MaEsStM1 9 3 MaEsStM2 HevBrStM

0.2 B

chrUn: 22834605-22841892 MscS OFUT SVP

chr18 : 5694915-5711044 MscS MscS OFUT AGL24

chr3 : 12256979-12294427 StMADS11

chr3 : 14652602-14682728 StMADS11

chr15 : 8056559-8087084 StMADS11

C D

Amborella tricopoda evm_27.TU.AmTr_v1.0_scaffold00033.247 trichopoda evm_27.TU.AmTr_v1.0_scaffold00033.249 Musa acuminata GSMUA_AchrUn_randomG08110_001 ROAP-2004925-Illicium_parviflorum Musa acuminata GSMUA_Achr8G34270_001 XQWC-2163750-Michelia_maudiae Brachypodium stacei Brast02G217200 Liriodendron tulipifera DT596775.1 Brachipodium distachyon Bradi1g15920 WBOD-2014030-Magnolia_grandiflora WTKZ-2005457-Nuphar_advena Brachipodium stacei Brast07G206600 WTKZ-2006300-Nuphar_advena Brachipodium distachyon Bradi1g32757 WTKZ-2006301-Nuphar_advena Zea mays GRMZM2G028914 Musa acuminata GSMUA_Achr5G23260_001 Panicum hallii Pahal.D00909 Oryza sativa LOC_Os09g24570 Panicum hallii Pahal.J00661 Brachypodium stacei Brast05G122800 Setaria viridis Sevir.9G361200 Brachypodium distachyon Bradi4g30070 Zea mays GRMZM2G057037 Setaria italica Seita.9G355200 Panicum hallii Pahal.B02756 BCGB-2002434-Cinnamomum_camphora Setaria viridis Sevir.2G210900 WAIL-2004339-Laurelia_sempervirens Setaria italica Seita.2G202800 CSSK-2006191-Houttuynia_cordata Nelumbo nucifera XM_010256228.1 CCID-2009702-Akebia_trifoliata Nelumbo nucifera XM_010279195.1 VQFW-2005328-Platanus_occidentalis IWMW-2013388-Buxus_sempervirens VQFW-2005329-Platanus_occidentalis CCID-2011407-Akebia_trifoliata VQFW-2005327-Platanus_occidentalis NJKC-2019354-Eschscholzia_californica-stem mexicana JG572398.1 coerulea Aquca_010_00284 MVTX-2023655-Papaver_rhoeas-developing_fruit Aquca_007_00488 somniferum FG606859.1 Vitis vinifera GSVIVG01005929001 nervosa JG622405.1 YHFG-2003690-Nandina_domestica Mimulus guttatus Migut.K00797 VGHH-2009538-Hydrastis_canadensis Mimulus guttatus Migut.H02291 Aquilegia coerulea Aquca_010_00285 Solanum lycopersicum Solyc11g010610.1 GBVZ-2004526-Thalictrum_thalictroides Solanum tuberosum PGSC0003DMG400016133 IWMW-2007628-Buxus_sempervirens-green_branch_with_leaves Eucalyptus grandis Eucgr.I00558 SWOH-2001394-Trochodendron_araliodes Linum usitatissimum Lus10012733.g SWOH-2001393-Trochodendron_araliodes EHNF-2004976-Dillenia_indica Linum usitatissimum Lus10002652.g Vitis vinifera GSVIVG01009174001 Prunus persica Prupe.6G201500 Solanum lycopersicum Solyc04g076290.2 Fragaria vesca gene20812-v1.0-hybrid Solanum tuberosum PGSC0003DMG400009362 Citrus clementina Ciclev10024979m.g Eucalyptus grandis Eucgr.F02148 Manihot esculenta Manes.12G126300 Prunus persica Prupe.1G531800 Salix purpurea SapurV1A.0166s0110 Fragaria vesca gene12123-v1.0-hybrid Medicago truncatula Medtr3g100310 Populus trichocarpa Potri.007G011100 Phaseolus vulgaris Phvul.009G037100 Gossypium raimondii Gorai.003G037900 Glycine max Glyma.06G095900 Gossypium raimondii Gorai.008G092700 Glycine max Glyma.04G094100 Theobroma cacao Thecc1EG000988 Citrus clementina Ciclev10000880m.g Theobroma cacao Thecc1EG000986 Theobroma cacao Thecc1EG034508 Gossypium raimondii Gorai.009G229500 Medicago truncatula Medtr5g032090 Salix purpurea SapurV1A.0004s1120 Phaseolus vulgaris Phvul.002G147200 Populus trichocarpa Potri.002G105800 Glycine max Glyma.09G199100 Manihot esculenta Manes.02G144900 Glycine max Glyma.01G023200 Linum usitatissimum Lus10015890.g Carica papaya evm.TU.supercontig_55.26 Linum usitatissimum Lus10009276.g γ Brassica rapa Brara.J02304 Carica papaya evm.TU.supercontig_21.17 Eutrema salsugineum Thhalv10024936m.g Brassica rapa Brara.C00426 γ Brassica rapa Brara.A01459 Eutrema salsugineum Thhalv10012873m.g Capsella rubella Carubv10006569m.g Boechera stricta Bostr.13175s0050 Boechera stricta PF10250 Capsella rubella Carubv10003006m.g Arabidopsis thaliana AT4G24530 Arabidopsis thaliana AT5G10490 Arabidopsis lyrica PF10250 Arabidopsis lyrata 940518 XMQO-2012027-Gunnera_manicata XMQO-2012026-Gunnera_manicata Solanum lycopersicum Solyc04g076300.2 Solanum lycopersicum Solyc11g010600.1 Solanum tuberosum PGSC0003DMG401009344 Solanum tuberosum PGSC0003DMG400016201 Vitis vinifera GSVIVG01009177001 Sesamum indicum XM_011101682.1 Vitis vinifera GSVIVG01009175001 Sesamum indicum XM_011099176.1 Prunus persica Prupe.1G531900 Mimulus guttatus Migut.K00796 Fragaria vesca gene12124-v1.0-hybrid Erythranthe guttatus XM_012989660.1 Mimulus guttatus Migut.H02292 Citrus clementina Ciclev10000465m.g EHNF-2000400-Dillenia_indica Carica papaya evm.TU.supercontig_21.18 Vitis vinifera GSVIVG01005930001 Theobroma cacao Thecc1EG034509 Prunus persica Prupe.6G201400 Gossypium raimondii Gorai.010G034900 Fragaria vesca gene20811-v1.0-hybrid Manihot esculenta Manes.18G058900 Medicago truncatula Medtr5g032100 Phaseolus vulgaris Phvul.002G147300 Populus trichocarpa Potri.005G154000 Glycine max Glyma.09G199000 Salix purpurea SapurV1A.0004s1110 Glycine max Glyma.01G023300 Populus trichocarpa Potri.002G105900 Eucalyptus grandis Eucgr.I00557 Eucalyptus grandis Eucgr.F02149 Citrus clementina Ciclev10025329m.g Linum usitatissimum Lus10009277.g Carica papay evm.TU.supercontig_55.27 Eutrema salsugineum Thhalv10023336m.g Theobroma cacao Thecc1EG000989 Gossypium raimondii Gorai.008G092600 Brassica rapa Brara.A02293 Gossypium raimondii Gorai.007G232700 Capsella rubella Carubv10019907m.g Manihot esculenta Manes.13G099700 Boechera stricta Bostr.30057s0097 Manihot esculenta Manes.12G126600 Arabidopsis thaliana AT1G58200 Salix purpurea SapurV1A.0166s0100 Arabidopsis lyrata 475431 Populus trichocarpa Potri.007G011000 Medicago truncatula Medtr3g100280 Linum usitatissimum Lus10012732.g Linum usitatissimum Lus10002653.g Phaseolus vulgaris Phvul.009G036900 Eutrema salsugineum Sevir.2G210900 Glycine max Glyma.06G096100 Brassica rapa Brara.F02414 Glycine max Glyma.04G094300 Brassica rapa Brara.B03957 Medicago truncatula Medtr3g100320 Capsella rubella Carubv10026260m.g Phaseolus vulgaris Phvul.009G037000 Boechera stricta Bostr.0568s0241 Glycine max Glyma.06G096000 Arabidopsis thaliana AT5G65470 Arabidopsis lyrata 496780 Org_Alyrata Glycine max Glyma.04G094200

Supplemental Figure 6: Phylogenetic relationships of SVP, AGL24 and StMADS11. (A) Maximum likelihood phylogeny of the StMADS11-subfamily with bootstrap support values. Three subclades of SVP, AGL24 and StMADS11 can be distinguished. Since all three contain only core (including Gunnerales for SVP and AGL24, highlighted in orange) and Buxales and other eudi- cots don’t fall within any , these results suggest these originated from the γ triplication. (B) Synteny of Vitis vinifera SVP-like genes further supports the idea that SVP, AGL24 and STMADS11 are sister-clades. (left) AGL24 and two out of three StMADS11 genes are located on chr18 and chr3 (blue) which are known to contain syntenic blocks (Jaillon et al., 2007). Because SVP is positioned on an contig unmapped to a chromosome, we looked at some of it’s colinear genes (marked in orange (O-FUCOSYL- TRANSFERASE (OFUT)), green ((MECHANOSENSITIVE ION CHANNEL PROTEIN 3 MscS) and magenta (Chaperone DnaJ-do- main protein)) which were also found in the proximity of AGL24. (C) and (D) ML-trees of OFUT and MscS show that both genes dupli- cated at the γ event, indicating that SVP and AGL24 are indeed sister genes. and accession numbers are shown in both trees. Supplemental Table 1. LRT and parameter estimations of different Branch models LRT and parameter estimations of different branch models. M0 estimates one ω over all branches. M2 allows ω to vary among select- ed branches (foreground = ωf) compared to the rest of the branches (background = ωb). p-values < 0.05 indicate a significant differ- ence between the M0 and M2 model and thereby implies that there was a difference in selective pressure on the foreground branches compared to the rest of the gene . Simplified phylogenetic trees used in these analyses are shown in Supplemental Figure 1.

Pre gene-clade Post Gene-subclade Foreground Model b f tree length np lnL H0 LRT p / M0 0,179 / 1,45 89,98 410,00 -62103,15 / / / paleo Buxales - M2 0,179 0,096 1,45 89,98 411,00 -62102,67 M0 0,96 0,33 AP1 FUL-Like - A/R split M2 0,178 0,375 1,45 90,00 411,00 -62100,86 M0 4,59 0,032** FUL - A/R split M2 0,179 0,120 1,45 89,97 411,00 -62102,64 M0 1,02 0,31 euAP1 - A/R split M2 0,178 0,396 1,45 90,00 411,00 -62098,04 M0 10,23 0,001** / M0 0,173 / 1,57 89,67 360,00 -54858,36 / / / paleo Buxales - M2 0,173 0,189 1,57 89,67 361,00 -54858,36 M0 0,01 0,92 AP3 euAP3 - A/R split M2 0,173 0,297 1,57 89,70 361,00 -54856,97 M0 2,78 0,096* TM6 - A/R split M2 0,172 0,413 1,57 89,72 361,00 -54853,97 M0 8,79 0,003** / M0 0,153 / 1,44 65,02 300,00 -37891,65 / / / PI paleo Buxales - Gunnerales M2 0,153 0,160 1,44 65,02 301,00 -37891,65 M0 0,01 0,92 PI Buxales - A/R split M2 0,153 0,159 1,44 65,02 301,00 -37891,65 M0 0,01 0,93 / M0 0,117 / 1,39 51,18 214,00 -32058,29 / / / paleo Buxales - M2 0,116 1,061 1,39 51,21 215,00 -32055,97 M0 4,63 0,031** AG euAG - A/R split M2 0,116 0,156 1,39 51,19 215,00 -32058,01 M0 0,55 0,46 SHP - A/R split M2 0,117 0,131 1,39 51,19 215,00 -32058,24 M0 0,10 0,75 / M0 0,088 / 1,33 29,12 136,00 -17607,41 / / / STK paleo Buxales - Gunnerales M2 0,087 0,160 1,33 29,12 137,00 -17606,57 M0 1,67 0,20 STK Buxales - A/R split M2 0,086 0,218 1,33 29,14 137,00 -17604,29 M0 6,23 0,013** / M0 0,119 / 1,49 51,04 302,00 -35135,56 / / / SEP3 paleo Buxales - Gunnerales M2 0,119 0,322 1,49 51,06 303,00 -35133,22 M0 4,69 0,030** SEP3 Buxales - A/R split M2 0,119 0,235 1,49 51,06 303,00 -35133,78 M0 3,56 0,059* / M0 0,180 / 1,63 89,00 444,00 -61131,01 / / / paleo Buxales - M2 0,180 0,114 1,63 89,00 445,00 -61130,85 M0 0,32 0,57 SEP1/2/4 FBP9 - A/R split M2 0,180 0,235 1,63 89,01 445,00 -61130,85 M0 0,32 0,57 SEP4 - A/R split M2 0,180 0,241 1,63 89,01 445,00 -61130,71 M0 0,59 0,44 SEP1/2 - A/R split M2 0,180 0,236 1,63 89,01 445,00 -61130,65 M0 0,72 0,39 / M0 0,214 / 1,39 101,70 430,00 -64469,65 / / / paleo Buxales - M2 0,214 0,091 1,39 101,69 431,00 -64469,49 M0 0,33 0,56 SOC1 FBP22 - A/R split M2 0,214 0,226 1,39 101,70 431,00 -64469,63 M0 0,04 0,84 AGL14 NA M2 NA NA NA NA NA NA / NA NA TM3 - A/R split M2 0,215 0,145 1,39 101,69 431,00 -64468,98 M0 1,34 0,25 / M0 0,176 / 1,73 91,73 438,00 -51796,53 / / / paleo Buxales - M2 NA NA NA NA NA NA / NA NA SVP/AGL24 SVP - A/R split M2 0,176 0,196 1,73 91,74 439,00 -51796,48 M0 0,09 0,76 StMADS11 - A/R split M2 NA NA NA NA NA NA / NA NA AGL24 - A/R split M2 0,176 0,293 1,73 91,77 439,00 -51795,37 M0 2,31 0,13 Legend: *, significant (p < 0.05); **, significant (p < 0.01); paleo, is the last branch before the triplication; ωb, selection pressure on the background branches; ωf, selection pressure on the foreground branches; κ, transition/transversion rate; np, number of parameters; NA = not available Note: Stability of ωb, κ and tree length over different models and different runs indicates the reliability of the results.

Supplementary Table 2. Pearson correlations between edge rewiring (gained or lost interactions) or degree, and rate of protein evolu- tion (sequence similarity, selection pressure of foreground branches and selective pressure of background branches) Rate of protein evolution b f sequence similarity r P-value r P-value r P-value Pre to Post Gain 0.4712 0.056 0.0056 0.983 -0.3057 0.233 Loss -0.6422 0.005** -0.3412 0.180 0.4663 0.059 k (Pre) -0.5938 0.012* -0.3738 0.139 0.4371 0.079 k (Post) 0.0150 0.954 -0.1380 0.597 0.0026 0.992 Post to Ara Gain 0.4017 0.110 / / 0.0710 0.786 Loss 0.1836 0.481 / / 0.1433 0.583 k (Post) 0.0815 0.756 / / 0.3265 0.201 k (Ara) 0.2858 0.266 / / 0.2976 0.246 Post to Sol Gain 0.1920 0.405 / / 0.1126 0.627 Loss 0.2378 0.299 / / 0.3664 0.102 k (Post) 0.1314 0.570 / / 0.3742 0.095 k (Sol) 0.0635 0.784 / / 0.2633 0.249 r, Pearson correlation coefficient; ωf, selection pressure on the foreground branches; ωb selection pressure on the background branches; *, significant (p < 0.05); **, significant (p < 0.01); k, degree in Pre-PIN, Post-PIN, Ara-PIN or Sol-PIN