Is Positive Selection Acting on Genes Controlling Arsenic Hyperaccumulation in Pteris Vittata L

Exploring the pattern of phenotypic and genetic polymorphism in the arsenic hyperaccumulator Pteris vittata L. (Chinese brake fern)

Bing Yang1, 3 *, Alessio Mengoni2, *, Ye-Ling Huang1, Xiong-Lei He1, Jin-Tian Li1, Bin Liao1,

Mi Zhou1, Wen-Sheng Shu1, §

1School of Life Sciences and Guangdong Key Laboratory of Plant Resources, State Key

Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China;

2Department of Evolutionary Biology, University of Firenze, Via Romana 17, I-50125

Florence, Italy;

3State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research

Academy of Environmental Sciences, Beijing 100012, China.

*: These authors contributed equally to this paper.

§: Author for correspondence

Wen-sheng Shu

Tel.: +86 20 39332933

Fax: +86 20 39332944

Email: [email protected]

1 Supporting Information

Table S1 List of As-related candidate ‘functional’ genes* and ‘control’ loci analyzed.

Table S2 Characteristics of primers used for the PCR and specific conditions.

Table S3 Results of codon based on Fisher's Exact Test and Bayesian graphical model (BGM)*.

Table S4 Results of Model test on the analyzed genes.

Figure S1 Maximum Likelihood dendrograms for As-related genes. See legend of Figure 2 and Table S4 for more information.

2 Table S1 List of As-related candidate ‘functional’ genes* and ‘control’ loci analyzed. Gene Putative function Reference As-related ‘functional’ genes PvABCT1 Arsenite-phytochelatins transporter He et al., 2004 PvACR2 Arsenate reduction Ellis et al., 2006 PvACR3 Arsenite transporter Indriolo et al., 2009 PvACR31 Arsenite transporter Indriolo et al., 2009 PvcTPI Arsenate reduction Rathinasabapathi et al., 2006 PvGRX5 Reductant for arsenate reductase Sundaram et al., 2007 PvGST1 Glutathione S transferase 1 Csonka et al., NCBI PvGST2 Glutathione S transferase 2 Csonka et al., NCBI PvPCS1 Arsenite chelation Dong et al., 2005

‘Control’ loci PvatpA ATP synthase alpha chain-like gene Schuettpelz et al., 2007 PvatpB ATP synthase beta chain gene Schuettpelz et al., 2007 PvgapCp-L NAD-dependent glyceraldehyde-3-phosphate dehydrogenase Schuettpelz et al., 2008 PvgapCp-S NAD-dependent glyceraldehyde-3-phosphate dehydrogenase Schuettpelz et al., 2008 PvITS Internal transcribed spacer Ma et al., 2010 PvPIXM Protoporphyrin IX magnesium chelatase Indriolo et al., 2009 PvRBCL Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit Prado et al., 2007 PvRPB2 Ribulose bisphosphate carboxylase Sang, 2002 PvTRN TrnL-trnF intergenic spacer Li et al., 2004 PvtrnH TrnH-psbA intergenic spacer Ma et al., 2010 *Gene code and putative function for genes involved in metabolic pathway of As in Pteris vittata are reported.

3 Table S2 Characteristics of primers used for the PCR and specific conditions.

Locus Accession number Primer sequences (5’–3’) Ta (ºC) PvABCT1 AY496966 F: AGAAGCTCACGTAGAAGAAAAT mRNA, complete cds 50 R: TAAAAGTAGATATGGCTATGGC PvACR2 DQ310370 F: CGCGTCGACATGGCCTCGCTTCCATCCC mRNA, complete cds 60 R: CGCGGATCCTCAACACCCCTCACAAAAGGC PvACR3 FJ751631 F: CTAAACAGAAGGCCCCTTCCTCTGA mRNA, complete cds 52 R: ATGGAGAACTCAAGCGCGGAGC PvACR31 FJ751632 F: TTACGTGAAAGGGGTGAAGG mRNA, complete cds 60.7 R: CGGATACATCATCACCCACA PvcTPI DQ333446 F: CGCGTCGACATGGCCCGCAAGTTCTTC mRNA, complete cds 58 R: CGCGGATCCTTAAGATTTCGACACCAACGCTGAT PvGRX5 EF052272 F: CGCGTCGACATGGCGTCCAGGGCC mRNA, complete cds 58 R: CGCGGATCCCTACGAGCACATTGCCTTCTC PvGST1 EU259319 F: GGGCCAATAGAGTAGACT mRNA, complete cds 58 R: TCATTTTGAAGGAGTAGCCAT PvGST2 EU259320 F: GCACTCACACTGTAGCGAGAG mRNA, complete cds 60.7 R: TTTGAGGAGTTGTGTATGCC PvPCS1 AY542894 F: CGCGTCGACATGAATGGATTCTTTAAGCTAGTCAGTACTT mRNA, complete cds 50 R: CGCGGATCCCTAGTTTTTCGTTTCAATTAACGCC PvatpA EF452123 F: GARCARGTTCGACAGCAAGT nrDNA, partial sequence 60 R: GTATAGGTTCRARTCCTATTGGACG PvatpB EF452060 F: TTGATACGGGAGCYCCTCTWAGTGT nrDNA, partial sequence 60 R: GAATTCCAAACTATTCGATTAGG PvgapCp-L EU551452 F: ATYCCAAGYTCAACTGGTGCTGC nrDNA, partial sequence 52 R: GTATCCCCAYTCRTTGTCRTACC PvgapCp-S EU551443 F: ATYCCAAGYTCAACTGGTGCTGC nrDNA, partial sequence 50 R: GTATCCCCAYTCRTTGTCRTACC

4 PvITS AM920403 F: GGAAGTAAAAGTCGTAACAAGG nrDNA, partial sequence 50 R: TCCTCCTCC2GCTTATTGATATGC PvPIXM HM179992 F: ATGGCTGCAAGCACGGC cpDNA, partial cds 60.7 R: TTCTCACTTGCCGGGGGT PvRBCL EF473709 F: GTTGGATTCAAAGCTGGTGTCAAAGATT cpDNA, partial cds 51.5 R: CTTACTAGCTTCGCGAATGATTTCG PvRPB2 - F: CCYCGTAATACWTAYCARTCWGC nrDNA, partial sequence 48-52 R: CCCATRATACACTCAATGAGYTG PvTRN AY545520 F: GGTTCAAGTCCCTCTATCCC cpDNA, complete sequence 50 R: ATTTGAACTGGTGACACGAG PvtrnH GU135302 F: TGATCCACTTGGCTACATCCGCC cpDNA, partial cds 54 R: GCTAACCTTGGTATGGAAGT

5 Table S3 Results of codon based on Fisher's Exact Test and Bayesian graphical model (BGM)*.

Gene/Loci Codon based on Fisher Exact Test of Spidermonkey/BGM analysis (co-evolving Selection sites) As-related ‘functional’ genes PvABCT1 N.s. pairs No sites PvACR2 N.s. pairs 5 sites PvACR3 N.s. pairs 2 sites PvACR31 N.s. pairs 6 sites PvcTPI N.s. pairs 6 sites PvGRX5 N.s. pairs 9 sites PvGST1 N.s. pairs No sites PvGST2 N.s. pairs No sites PvPCS1 N.s. pairs 2 sites

‘Control’ loci PvatpA N.s. pairs No sites PvatpB N.s. pairs 1 site PvgapCp-S N.s. pairs 3 sites PvgapCp-L N.s. pairs 5 sites PvITS N.a. No sites PvPIXM N.s. pairs No sites PvRBCL N.s. pairs No sites PvRPB2 N.s. pairs No sites PvtrnH N.a. No sites PvTRN N.a. No sites *N.s. pairs: no significant pair of accessions detected. No sites, no co-evolving selected sites at 0.5 posterior probability were found. N.a., not applicable.

6 Table S4 Results of Model test on the analyzed genes. The Maximum Likelihood fits of 24 different nucleotide substitution models is shown. Models with the lowest BIC scores (Bayesian Information

Criterion) are considered to describe the substitution pattern the best. For each model, AICc value (Akaike

Information Criterion, corrected), Maximum Likelihood value (lnL), and the number of parameters

(including branch lengths) are also presented. Non-uniformity of evolutionary rates among sites may be modeled by using a discrete Gamma distribution (+G) with 5 rate categories and by assuming that a certain fraction of sites are evolutionarily invariable (+I). Whenever applicable, estimates of gamma shape parameter and/or the estimated fraction of invariant sites are shown. Assumed or estimated values of transition/transversion bias (R) are shown for each model, as well. All positions containing gaps and missing data were eliminated.

Abbreviations: GTR: General Time Reversible; HKY: Hasegawa-Kishino-Yano; TN93: Tamura-Nei; T92:

Tamura 3-parameter; K2: Kimura 2-parameter; JC: Jukes-Cantor.

a) Non coding chloroplast loci

Model #Param BIC AICc lnL Invariant Gamma R T92 63 3329.7 2813.2 -1343.4 n/a n/a 2.6715 K2 62 3333.2 2825 -1350.3 n/a n/a 2.6713 JC 61 3337.3 2837.2 -1357.5 n/a n/a 0.5 T92+G 64 3338.5 2813.8 -1342.8 n/a 0.13737 2.6929 T92+I 64 3339.8 2815.2 -1343.4 0.015813 n/a 2.6716 K2+G 63 3342.1 2825.7 -1349.7 n/a 0.15218 2.6854 K2+I 63 3343.4 2826.9 -1350.3 0.038147 n/a 2.6714 JC+G 62 3346.2 2837.9 -1356.8 n/a 0.15968 0.5 JC+I 62 3347.5 2839.2 -1357.5 0.00001 n/a 0.5 T92+G+I 65 3348.7 2815.9 -1342.8 0 0.13737 2.6929 HKY 65 3349.2 2816.3 -1343 n/a n/a 2.6716 K2+G+I 64 3352.3 2827.7 -1349.7 0 0.15218 2.6854 JC+G+I 63 3356.4 2840 -1356.8 0.00001 0.15969 0.5 HKY+G 66 3358 2816.9 -1342.3 n/a 0.133 2.6946 TN93 66 3359.2 2818.2 -1342.9 n/a n/a 2.6719 HKY+I 66 3359.3 2818.3 -1343 0.011838 n/a 2.6717 TN93+G 67 3368 2818.8 -1342.2 n/a 0.12903 2.6977 HKY+G+I 67 3368.2 2819 -1342.3 0 0.133 2.6946 TN93+I 67 3369.4 2820.2 -1342.9 0.007222 n/a 2.6719 TN93+G+I 68 3378.2 2820.8 -1342.2 0.00001 0.12903 2.6977 GTR 69 3386.8 2821.1 -1341.4 n/a n/a 2.6727

7 GTR+I 70 3396.9 2823.1 -1341.4 0.014295 n/a 2.6725 GTR+G 70 3397 2823.1 -1341.4 n/a 0.30106 1.9126 GTR+G+I 71 3407.1 2825.1 -1341.3 0.00001 0.16751 1.9155

b) Coding chloroplast loci

Model #Param BIC AICc lnL Invariant Gamma R K2+G+I 64 21422 20788 -10330 0.827668 0.58268 1.673 T92+G+I 65 21429 20786 -10328 0.827696 0.58146 1.6781 HKY+G+I 67 21445 20782 -10324 0.827288 0.57825 1.6787 TN93+G+I 68 21453 20780 -10322 0.82737 0.58179 1.6841 T92+I 64 21499 20865 -10368 0.905724 n/a 1.6696 JC+G+I 63 21606 20982 -10428 0.827453 0.58731 0.5 K2+G 63 21650 21026 -10450 n/a 0.05 1.6333 T92+G 64 21658 21024 -10448 n/a 0.05 1.6365 HKY+G 66 21674 21021 -10444 n/a 0.05 1.6365 JC+I 62 21676 21063 -10469 0.905142 n/a 0.5 TN93+G 67 21681 21018 -10442 n/a 0.05 1.6446 GTR+G+I 71 21689 20987 -10422 0.088066 0.05 1.6395 GTR+G 70 21712 21019 -10439 n/a 0.05 1.636 JC+G 62 21833 21219 -10547 n/a 0.05 0.5 K2+I 63 21897 21273 -10573 0.645803 n/a 1.6165 HKY+I 66 21973 21320 -10594 0.604825 n/a 1.616 K2 62 22397 21784 -10830 n/a n/a 1.6044 T92 63 22407 21783 -10829 n/a n/a 1.6046 TN93+I 67 22412 21749 -10808 0.057472 n/a 1.6059 HKY 65 22422 21779 -10824 n/a n/a 1.605 TN93 66 22430 21777 -10823 n/a n/a 1.6054 GTR+I 70 22457 21765 -10812 0.034385 n/a 1.6052 GTR 69 22463 21780 -10821 n/a n/a 1.605 JC 61 22578 21974 -10926 n/a n/a 0.5

c) PvITS

Model #Param BIC AICc lnL Invariant Gamma R K2+G 63 5648 5169.4 -2521.4 n/a 0.22409 1.5715 GTR+G 70 5651.8 5120.1 -2489.7 n/a 0.223 1.5969 T92+G 64 5655.8 5169.6 -2520.5 n/a 0.22426 1.5704 TN93+G 67 5658 5149 -2507.2 n/a 0.22404 1.6585 K2+G+I 64 5658.4 5172.2 -2521.8 0.500261 1.03123 1.5791 GTR+G+I 71 5663.5 5124.2 -2490.7 0.506026 1.16787 1.5757 T92+G+I 65 5666.1 5172.3 -2520.9 0.499112 1.0224 1.5785

8 TN93+G+I 68 5669.5 5153 -2508.2 0.482306 0.95789 1.6556 HKY+G 66 5673.8 5172.4 -2519.9 n/a 0.22404 1.5699 K2+I 63 5675.6 5197 -2535.2 0.60503 n/a 1.4291 GTR+I 70 5679.8 5148 -2503.7 0.596647 n/a 1.3975 T92+I 64 5683.6 5197.4 -2534.4 0.604877 n/a 1.4273 HKY+G+I 67 5684 5175.1 -2520.2 0.498874 1.01912 1.5779 TN93+I 67 5689.2 5180.2 -2522.8 0.599579 n/a 1.4388 JC+G 62 5726.9 5255.9 -2565.7 n/a 0.23456 0.5 JC+G+I 63 5737.5 5258.8 -2566.2 0.508929 1.21502 0.5 K2 62 6029.8 5558.8 -2717.1 n/a n/a 1.2071 GTR 69 6030 5505.9 -2683.6 n/a n/a 1.2143 TN93 66 6033.3 5531.9 -2699.7 n/a n/a 1.2149 T92 63 6037.7 5559.1 -2716.3 n/a n/a 1.2068 HKY 65 6056 5562.2 -2715.8 n/a n/a 1.207 HKY+I 66 6065.6 5564.2 -2715.8 0.00001 n/a 1.207 JC 61 6091.8 5628.3 -2752.9 n/a n/a 0.5 JC+I 62 6101.4 5630.4 -2752.9 0.00001 n/a 0.5

d) PvABCT1

Model #Param BIC AICc lnL Invariant Gamma R HKY 65 7329.1 6747.1 -3308.5 n/a n/a 6.4925 K2 62 7330.1 6775 -3325.4 n/a n/a 6.4921 T92 63 7332.3 6768.3 -3321.1 n/a n/a 6.4924 TN93 66 7337.4 6746.5 -3307.2 n/a n/a 6.4922 HKY+G 66 7339.7 6748.8 -3308.3 n/a 2.20058 6.5132 HKY+I 66 7339.9 6749 -3308.4 0.044072 n/a 6.4951 K2+I 63 7340.8 6776.8 -3325.3 0.216531 n/a 6.4993 K2+G 63 7340.9 6776.8 -3325.3 n/a 3.19654 6.499 T92+G 64 7343 6769.9 -3320.9 n/a 2.33907 6.5072 T92+I 64 7343.3 6770.2 -3321.1 0.00636 n/a 6.4927 TN93+G 67 7348.1 6748.2 -3307 n/a 2.42315 6.5067 TN93+I 67 7348.4 6748.5 -3307.2 0.001747 n/a 6.4924 HKY+G+I 67 7350.6 6750.7 -3308.3 0.275837 200 6.5139 K2+G+I 64 7351.8 6778.8 -3325.3 0.21314 200 6.4993 T92+G+I 65 7353.9 6771.9 -3320.9 0.265281 200 6.5079 TN93+G+I 68 7359 6750.1 -3307 0.259166 200 6.5073 GTR 69 7368 6750.2 -3306 n/a n/a 6.4921 GTR+G 70 7378.7 6751.9 -3305.9 n/a 2.72725 6.5145 GTR+I 70 7378.9 6752.2 -3306 0.007753 n/a 6.4926 GTR+G+I 71 7389.6 6753.9 -3305.9 0.238837 200 6.516 JC 61 7456.4 6910.3 -3394.1 n/a n/a 0.5 JC+I 62 7467.2 6912.1 -3394 0.195786 n/a 0.5

9 JC+G 62 7467.2 6912.1 -3394 n/a 3.69203 0.5 JC+G+I 63 7478.2 6914.1 -3394 0.192478 200 0.5

e) PvACR2

Model #Param BIC AICc lnL Invariant Gamma R K2+G 63 2141 1671.5 -772.46 n/a 0.05 1.7585 JC+G 62 2142.5 1680.5 -777.94 n/a 0.05 0.5 K2+G+I 64 2147.6 1670.7 -771.02 0.772056 0.7909 1.7842 K2 62 2148.5 1686.4 -780.92 n/a n/a 1.733 JC+G+I 63 2149.6 1680.1 -776.73 0.770209 0.79764 0.5 T92+G 64 2150.1 1673.2 -772.28 n/a 0.05 1.7592 JC 61 2150.3 1695.7 -786.55 n/a n/a 0.5 K2+I 63 2156.2 1686.7 -780.02 0.130572 n/a 1.7339 T92+G+I 65 2157.1 1672.7 -771.02 0.772284 0.78892 1.7861 T92 63 2158 1688.5 -780.93 n/a n/a 1.733 JC+I 62 2158.9 1696.9 -786.12 0.063778 n/a 0.5 HKY+I 66 2165.4 1673.6 -770.46 0.874728 n/a 1.7973 T92+I 64 2166.2 1689.3 -780.32 0.090822 n/a 1.7336 HKY+G 66 2167.2 1675.4 -771.35 n/a 0.05 1.7698 HKY+G+I 67 2174.1 1674.8 -770.06 0.774267 0.78934 1.8047 HKY 65 2175.1 1690.7 -780.04 n/a n/a 1.7331 TN93+G 67 2176.1 1676.9 -771.09 n/a 0.05 1.8068 TN93+G+I 68 2182.6 1675.9 -769.57 0.783031 0.72108 1.9196 TN93+I 67 2183.1 1683.8 -774.56 0.584882 n/a 1.7538 TN93 66 2184.4 1692.6 -779.96 n/a n/a 1.7334 GTR+G 70 2197.4 1675.9 -767.54 n/a 0.05 1.8047 GTR+G+I 71 2204.1 1675.1 -766.13 0.779668 0.73776 1.8946 GTR 69 2205.5 1691.4 -776.3 n/a n/a 1.7322 GTR+I 70 2213.3 1691.7 -775.45 0.123824 n/a 1.734

f) PvACR3

Model #Param BIC AICc lnL Invariant Gamma R K2+G 63 5524.2 4988.8 -2431.3 n/a 0.14833 5.2129 K2+G+I 64 5532.6 4988.7 -2430.2 0.593391 0.9061 5.2274 T92+G 64 5535 4991.1 -2431.4 n/a 0.14512 5.2227 K2+I 63 5535.9 5000.5 -2437.1 0.535418 n/a 5.1586 HKY+G 66 5537 4976.1 -2421.9 n/a 0.15494 5.197 T92+G+I 65 5543.3 4990.9 -2430.3 0.596604 0.90681 5.2378 HKY+G+I 67 5545.4 4976.1 -2420.9 0.587201 0.9149 5.208 TN93+G 67 5545.7 4976.3 -2421 n/a 0.1576 5.2142

10 K2 62 5550.9 5024 -2449.9 n/a n/a 5.1265 TN93+G+I 68 5554.2 4976.3 -2420 0.582251 0.91295 5.223 T92 63 5561.9 5026.5 -2450.2 n/a n/a 5.1264 HKY 65 5563 5010.6 -2440.2 n/a n/a 5.1262 T92+I 64 5563.9 5020.1 -2445.9 0.204594 n/a 5.1342 HKY+I 66 5571.3 5010.4 -2439.1 0.056479 n/a 5.1277 TN93 66 5571.4 5010.5 -2439.2 n/a n/a 5.1267 TN93+I 67 5571.7 5002.4 -2434.1 0.2437 n/a 5.1377 GTR+G 70 5572.4 4977.6 -2418.6 n/a 0.16222 5.2548 GTR+G+I 71 5581 4977.6 -2417.7 0.578115 0.91717 5.2657 GTR 69 5597.7 5011.4 -2436.6 n/a n/a 5.1271 GTR+I 70 5604.4 5009.5 -2434.6 0.098844 n/a 5.1323 JC+G 62 5645.9 5119 -2497.4 n/a 0.15309 0.5 JC+G+I 63 5654.4 5119 -2496.4 0.590444 0.92842 0.5 JC 61 5672 5153.6 -2515.7 n/a n/a 0.5 JC+I 62 5682.6 5155.7 -2515.7 0.00001 n/a 0.5

g) PvcTPI

Model #Param BIC AICc lnL Invariant Gamma R K2+G 63 3541.4 3031.6 -1452.6 n/a 0.05 4.9367 K2+G+I 64 3541.5 3023.5 -1447.6 0.530167 0.05 5.0957 HKY+G 66 3544 3009.9 -1438.8 n/a 0.05 4.963 HKY+G+I 67 3544.2 3002 -1433.8 0.517945 0.06159 5.0966 T92+G+I 65 3549.4 3023.4 -1446.5 0.534793 0.05 5.1347 T92+G 64 3549.6 3031.7 -1451.7 n/a 0.05 4.9522 TN93+G 67 3550.3 3008.1 -1436.9 n/a 0.05 4.9083 TN93+G+I 68 3551.7 3001.4 -1432.5 0.714458 0.31332 5.0104 HKY+I 66 3572 3038 -1452.8 0.48776 n/a 4.8601 K2 62 3578.3 3076.6 -1476.1 n/a n/a 4.8246 HKY 65 3579.4 3053.4 -1461.5 n/a n/a 4.8232 GTR+G+I 71 3582.2 3007.7 -1432.6 0.714466 0.31182 4.1697 K2+I 63 3583.3 3073.4 -1473.6 0.146889 n/a 4.829 GTR+G 70 3583.8 3017.3 -1438.5 n/a 0.05 3.9764 GTR+I 70 3584 3017.6 -1438.6 0.762734 n/a 3.9097 TN93 66 3585.3 3051.3 -1459.4 n/a n/a 4.8237 T92 63 3586.8 3077 -1475.3 n/a n/a 4.8238 JC+G 62 3592.2 3090.4 -1483.1 n/a 0.05 0.5 T92+I 64 3592.2 3074.3 -1473 0.138589 n/a 4.8285 JC+G+I 63 3592.9 3083.1 -1478.4 0.52223 0.05551 0.5 TN93+I 67 3599.1 3057 -1461.3 0.00001 n/a 4.8249 GTR 69 3619.4 3061.1 -1461.3 n/a n/a 3.8502 JC 61 3628.7 3135 -1506.4 n/a n/a 0.5

11 JC+I 62 3636.9 3135.2 -1505.4 0.105969 n/a 0.5

h) PvGRX5

Model #Param BIC AICc lnL Invariant Gamma R K2+G 63 2856.8 2367.2 -1120.4 n/a 0.12341 2.7282 K2 62 2859.5 2377.6 -1126.6 n/a n/a 2.6576 T92+G 64 2866.5 2369.1 -1120.3 n/a 0.12298 2.7292 K2+G+I 64 2866.6 2369.2 -1120.3 0.462975 0.49882 2.7333 K2+I 63 2868.5 2378.9 -1126.2 0.056272 n/a 2.6587 T92 63 2869.2 2379.5 -1126.5 n/a n/a 2.6577 T92+G+I 65 2876.2 2371 -1120.3 0.468403 0.50855 2.7344 T92+I 64 2877.6 2380.2 -1125.9 0.095332 n/a 2.6598 JC+G 62 2880.4 2398.6 -1137.1 n/a 0.13155 0.5 JC 61 2882.4 2408.3 -1142.9 n/a n/a 0.5 HKY+G 66 2885.5 2372.6 -1120.1 n/a 0.12383 2.7249 HKY 65 2888.2 2383 -1126.3 n/a n/a 2.6581 JC+G+I 63 2889.8 2400.2 -1136.9 0.405105 0.42548 0.5 JC+I 62 2890.6 2408.7 -1142.1 0.115005 n/a 0.5 TN93+G 67 2893.1 2372.4 -1119 n/a 0.13895 2.7266 TN93 66 2895.2 2382.3 -1124.9 n/a n/a 2.6596 HKY+G+I 67 2895.3 2374.6 -1120 0.469146 0.51284 2.7298 HKY+I 66 2895.7 2382.7 -1125.1 0.164037 n/a 2.6618 TN93+G+I 68 2902.9 2374.4 -1118.9 0.401167 0.43469 2.7298 TN93+I 67 2904 2383.3 -1124.4 0.077042 n/a 2.6615 GTR+G 70 2921.8 2377.9 -1118.6 n/a 0.13903 2.7282 GTR 69 2923.9 2387.7 -1124.6 n/a n/a 2.667 GTR+G+I 71 2931.6 2379.8 -1118.6 0.289246 0.30528 2.7299 GTR+I 70 2931.9 2388 -1123.7 0.130106 n/a 2.6703

i) PvPCS1

Model #Param BIC AICc lnL Invariant Gamma R T92 63 6236.4 5686.7 -2780.3 n/a n/a 2.6287 T92+G 64 6238 5679.5 -2775.7 n/a 0.44792 2.6464 K2 62 6238.4 5697.3 -2786.6 n/a n/a 2.6285 K2+G 63 6240.2 5690.4 -2782.1 n/a 0.44792 2.641 T92+I 64 6243.2 5684.7 -2778.3 0.264705 n/a 2.633 HKY 65 6244.6 5677.4 -2773.6 n/a n/a 2.6284 HKY+G 66 6246.1 5670.2 -2769 n/a 0.44792 2.6475 T92+G+I 65 6248.3 5681.1 -2775.5 0.342839 0.7345 2.6526 K2+I 63 6248.7 5699 -2786.4 0.025281 n/a 2.6287

12 K2+G+I 64 6250.6 5692.1 -2782 0.334108 0.74904 2.6449 TN93 66 6252.9 5677 -2772.4 n/a n/a 2.6286 TN93+G 67 6254.6 5669.9 -2767.9 n/a 0.44792 2.6468 HKY+I 66 6255.1 5679.1 -2773.5 0.016165 n/a 2.6286 HKY+G+I 67 6256.5 5671.8 -2768.8 0.340607 0.73838 2.654 TN93+I 67 6263.4 5678.7 -2772.3 0.016699 n/a 2.6288 TN93+G+I 68 6264.9 5671.6 -2767.7 0.337047 0.74484 2.6525 GTR 69 6282 5679.9 -2770.9 n/a n/a 2.6287 GTR+G 70 6283.9 5673.1 -2766.4 n/a 0.44792 2.6517 GTR+I 70 6292.1 5681.3 -2770.5 0.04806 n/a 2.6296 JC 61 6294.5 5762.2 -2820 n/a n/a 0.5 GTR+G+I 71 6294.7 5675.1 -2766.4 0.306482 0.69434 2.6625 JC+G 62 6296.3 5755.3 -2815.6 n/a 0.44792 0.5 JC+I 62 6305.1 5764 -2819.9 0.008999 n/a 0.5 JC+G+I 63 6306.8 5757.1 -2815.4 0.330127 0.75528 0.5

j) PvACR31

Model #Param BIC AICc lnL Invariant Gamma R T92+G 66 6530.1 5967.7 -2917.7 n/a 0.18413 2.0033 T92+G+I 67 6536.5 5965.6 -2915.7 0.49038 0.61673 2.0337 HKY+G 68 6540.7 5961.3 -2912.5 n/a 0.18752 1.991 K2+G 65 6541 5987.1 -2928.4 n/a 0.18702 1.9841 HKY+G+I 69 6547.6 5959.6 -2910.7 0.48716 0.62053 2.0216 K2+G+I 66 6547.8 5985.4 -2926.6 0.486048 0.6146 2.0143 TN93+G 69 6550.8 5962.9 -2912.3 n/a 0.18504 1.9931 TN93+G+I 70 6557.8 5961.4 -2910.6 0.484978 0.61275 2.0209 GTR+G 72 6577.1 5963.6 -2909.7 n/a 0.18503 2.0036 GTR+G+I 73 6584.4 5962.4 -2908 0.479975 0.6069 2.0284 T92+I 66 6610.6 6048.2 -2958 0.124763 n/a 1.7579 T92 65 6611.9 6058 -2963.9 n/a n/a 1.7457 K2 64 6620.9 6075.6 -2973.7 n/a n/a 1.744 JC+G 64 6622.4 6077 -2974.4 n/a 0.20506 0.5 HKY 67 6622.4 6051.5 -2958.6 n/a n/a 1.7502 K2+I 65 6626.3 6072.4 -2971.1 0.053111 n/a 1.7483 TN93+I 69 6626.3 6038.4 -2950.1 0.16499 n/a 1.7663 GTR+I 72 6626.9 6013.4 -2934.6 0.374227 n/a 1.801 JC+G+I 65 6629.4 6075.5 -2972.6 0.474559 0.6505 0.5 TN93 68 6632.9 6053.4 -2958.6 n/a n/a 1.75 HKY+I 68 6634.1 6054.6 -2959.2 0.00001 n/a 1.7502 GTR 71 6658.7 6053.7 -2955.7 n/a n/a 1.7503 JC+I 64 6697.4 6152 -3011.9 0.10823 n/a 0.5 JC 63 6697.5 6160.6 -3017.2 n/a n/a 0.5

13 k) PvGST1

Model #Param BIC AICc lnL Invariant Gamma R K2 62 3778.2 3286.2 -1580.9 n/a n/a 1.4171 K2+I 63 3787.7 3287.7 -1580.7 0.053871 n/a 1.4217 T92 63 3788.2 3288.2 -1580.9 n/a n/a 1.4171 K2+G 63 3794.2 3294.2 -1583.9 n/a 0.8688 2.5717 T92+I 64 3796.3 3288.3 -1580 0.346292 n/a 1.4628 JC 61 3799.1 3314.9 -1596.3 n/a n/a 0.5 K2+G+I 64 3799.3 3291.4 -1581.5 0.00001 1.02795 2.0952 T92+G 64 3804.2 3296.2 -1583.9 n/a 0.86785 2.5717 HKY 65 3805.2 3289.3 -1579.4 n/a n/a 1.4182 JC+G 62 3807.6 3315.5 -1595.6 n/a 1.81245 0.5 JC+I 62 3808.7 3316.7 -1596.1 0.044035 n/a 0.5 T92+G+I 65 3809.3 3293.4 -1581.5 0.00001 1.02687 2.0952 TN93 66 3813.3 3289.5 -1578.5 n/a n/a 1.422 HKY+I 66 3814.1 3290.3 -1578.9 0.131655 n/a 1.4306 JC+G+I 63 3817.6 3317.6 -1595.6 0.21719 7.91605 0.5 HKY+G 66 3821 3297.2 -1582.4 n/a 0.87032 2.5642 TN93+G 67 3821.5 3289.8 -1577.7 n/a 2.28226 1.4506 TN93+I 67 3822.3 3290.6 -1578.1 0.132915 n/a 1.4345 HKY+G+I 67 3826.2 3294.5 -1580 0.00001 1.02881 2.0891 TN93+G+I 68 3831.4 3291.8 -1577.7 0.253139 6.97287 1.4636 GTR 69 3842.6 3295 -1578.3 n/a n/a 1.422 GTR+G 70 3850.8 3295.3 -1577.4 n/a 2.28226 1.4515 GTR+I 70 3851.7 3296.2 -1577.8 0.118624 n/a 1.4333 GTR+G+I 71 3860.6 3297.1 -1577.3 0 1.45775 1.4673

l) PvGST2

Model #Param BIC AICc lnL Invariant Gamma R K2 66 3960.9 3433 -1650.3 n/a n/a 1.8792 K2+I 67 3969.5 3433.6 -1649.6 0.065917 n/a 1.887 T92 67 3970.9 3435 -1650.3 n/a n/a 1.8792 K2+G 67 3971.9 3435.9 -1650.8 n/a 0.54574 3.5589 K2+G+I 68 3972.8 3428.9 -1646.2 0.352907 2.84273 1.9905 T92+I 68 3972.8 3428.9 -1646.3 0.481188 n/a 1.9928 T92+G 68 3981.9 3438 -1650.8 n/a 0.54462 3.5588 T92+G+I 69 3982.8 3430.9 -1646.2 0.353355 2.84286 1.9908 HKY 69 3985.3 3433.4 -1647.5 n/a n/a 1.8807 HKY+I 70 3991.1 3431.2 -1645.4 0.204123 n/a 1.9096

14 TN93 70 3993.1 3433.2 -1646.4 n/a n/a 1.8821 TN93+G 71 3995.9 3428 -1642.8 n/a 1.15382 1.9519 HKY+G 70 3996.5 3436.6 -1648.1 n/a 0.56179 3.5498 HKY+G+I 71 3997.4 3429.6 -1643.5 0.338006 2.67725 1.989 TN93+I 71 3998.4 3430.5 -1644 0.229608 n/a 1.9167 TN93+G+I 72 4005.2 3429.3 -1642.4 0.473608 200 1.9957 JC 65 4007.1 3487.2 -1678.4 n/a n/a 0.5 JC+G 66 4009.7 3481.8 -1674.7 n/a 1.15382 0.5 JC+I 66 4015.5 3487.6 -1677.6 0.077684 n/a 0.5 JC+G+I 67 4019.1 3483.2 -1674.4 0.00001 0.72808 0.5 GTR 73 4022.4 3438.5 -1646 n/a n/a 1.881 GTR+G 74 4025.3 3433.5 -1642.5 n/a 1.15382 1.953 GTR+I 74 4028.4 3436.5 -1644 0.194278 n/a 1.9095 GTR+G+I 75 4034.6 3434.8 -1642.1 0.470488 200 1.997

15 Figure S1 Maximum Likelihood dendrograms for As-related genes. See legend of Figure 2 and Table S4 for more information.

a) PvABCT1

DC LD 83 WX NS DP 68 LY 86 54 GY SG KM 45 SD CY SY NN GZ TL 58 SL KH YC WZ CP 64 SM

77 HZ CZ JA LZ 63 WQ YW YX HK SS CX 99 GM

16 b) PvACR2

JA TL 63 CZ LZ 82 YW

56 KM CX 45 GY GZ KH YX SM SD NN 33 CP GM WS YC SL SS 97 HK

58 HZ WQ SY

82 CY 38 51 SG LD DC

17 DP LY NS 64 WX

17 c) PvACR3

65 SS WS HK GZ CP 55 GM 82 LZ 61 WQ SD TL 76 HZ NN JA 76 KH CY WX LY 81 SG NS 45 LD DC DP 72 SM SY GY CZ 84 94 CX

56 KM YW 71 YX

18 d) PvcTPI

GM JA LD SD 59 CX SG SM WX KM 8 LZ

42 NS LY

46 79 DC DP 60 NN CP 43 WS CY YC GY YW 64 YX

97 KH TL CZ

39 SY HK

74 SL GZ 92 WQ HZ SS

19 e) PvGRX5

61 GM WX WQ GY 56 CP SG CY LY 51 NS LD SD SM YC YX TL

65 CX 74 KM YW CZ JA

48 WS GZ HK 54 SS SY HZ LZ KH NN 98 SL

20 f) PvPCS1

TL WS SY JA

65 HZ KM KH CX 62 LZ YC 63 CY SD CP 62 YX NS WX LY 61 DC 99 DP

68 SG SM GZ GM 62 GY

99 YW CZ 98 LD SL NN HK 90 93 SS 86 WQ

21 g) PvACR31

66 SS WS HK GZ CP 53 GM 83 LZ 65 WQ SD TL 78 HZ NN JA 82 KH CY WX DP 79 71 SM DC 46 LD NS LY SG SY GY

94 CX 85 KM CZ 62 YW 70 YX

22 h) PvGST1

SM 62 SY 67 NN NS 28 LD LY 47 42 SG CY DC

69 83 DP CP CX GM KM HZ SD TL YW JA 50 95 WX LZ SS HK GZ SL GY KH WQ WS YC CZ YX

23 i) PvGST2

64 DC DP 59 LD LY 59 57 SM 70 WX 64 SG 93 SL

75 CP CX 53 KM WQ CY WS GM GZ HZ NN SS SY 58 TL CZ HK KH YC LZ YW JA SD YX GY NS