Improved Transcriptome Sampling Pinpoints 26 Ancient and More Recent Polyploidy Events In

1 Supporting Information

2 Article title: Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including 3 two allopolyploidy events 4 5 Authors: Ya Yang, Michael J. Moore, Samuel F. Brockington, Jessica Mikenas, Julia Olivieri, Joseph F. Walker, and Stephen A. 6 Smith 7 8 Article acceptance date: 09 August 2017 9

10 The following Supporting Information is available for this article:

12 Fig. S1 Workflow for the modified phylome approach.

14 Fig. S2 Maximum Quartet Support Species Tree (MQSST) from ASTRAL analysis of individual subclade orthologous gene trees.

15 Numbers on branches are multi-locus bootstrap percentages. Branch length represents coalescent units, with terminal branch lengths

16 artificially fixed to 1 as coalescent units cannot be calculated for terminal branches. (a) PHYT: the phytolaccoid clade and Aizoaceae;

17 (b) PORT: Portulacineae and Molluginaceae; (c) AMAR: Amaranthaceae and Chenopodiaceae; (d) CARY: Caryophyllaceae; and (e)

18 NCORE: the clade sister to rest of the Caryophyllales.

20 Fig. S3 Phylogram from RAxML analysis of the concatenated 624-gene supermatrix from modified phylomes, with ICA scores on

21 branches.

23 Fig. S4 Maximum Quartet Support Species Tree (MQSST) from ASTRAL analysis of 624 orthologous gene trees from modified

24 phylomes. Numbers on branches are multi-locus bootstrap percentages. Branch length represents coalescent units, with terminal

25 branch lengths artificially fixed to 1 as coalescent units cannot be calculated for terminal branches.

27 Fig. S5 Proportion of orthogroups showing duplications filtered by local tree topology in addition to orthogroup-wide average

28 bootstrap support. Bubble diameters are proportional to frequency of gene duplication. (a) PHYT: the phytolaccoid clade and

29 Aizoaceae; (b) PORT: Portulacineae and Molluginaceae; (c) AMAR: Amaranthaceae and Chenopodiaceae; (d) CARY:

30 Caryophyllaceae; and (e) NCORE: the clade sister to rest of the Caryophyllales.

32 Fig. S6 Distribution of within-taxon synonymous distances (Ks) among paralogs gene pairs based on BLASTP hits. Zoomed-in Ks

33 plots from BLASTN hits are shown in addition to the results from BLASTP hits to show more recent Ks peaks. (a) PHYT: the

34 phytolaccoid clade and Aizoaceae; (b) PORT: Portulacineae and Molluginaceae; (c) AMAR: Amaranthaceae and Chenopodiaceae; (d)

35 CARY: Caryophyllaceae; and (e) NCORE: the clade sister to rest of the Caryophyllales.

37 Table S1 Sources of data and settings for assembly and translation.

TAXON TAXON NAME SUB- SOURCE ASSMBLY AND DATA ACCESS CITATION CODE CLADE TRANSLATION MJM1677 Achatocarpaceae AMAR Smith Lab trinity20140413p1stranded, SRA BioProject PRJNA280277 Brockington et Phaulothamnus_spinescens transdecoder16JAN2014stranded al., 2015 HDSY Amaranthaceae Aerva_javanica AMAR 1KP 1KP Matasci et al., 2014 Yang et al., 2015 PDQH Amaranthaceae Aerva_lanata AMAR 1KP 1KP Matasci et al., 2014 Yang et al., 2015 ZBPY Amaranthaceae AMAR 1KP 1KP Matasci et al., 2014 Yang et al., 2015 Alternanthera_brasiliana OHKC Amaranthaceae AMAR 1KP 1KP Matasci et al., 2014 Yang et al., 2015 Alternanthera_caracasana Alph Amaranthaceae AMAR NCBI SRA trinity2.04, transdecoder2 SRR1661509 No information Alternanthera_philoxeroides BWRK Amaranthaceae Alternanthera_sessilis AMAR 1KP 1KP Matasci et al., 2014 Yang et al., 2015 EYRD Amaranthaceae Alternanthera_tenella AMAR 1KP 1KP Matasci et al., 2014 Yang et al., 2015 XSSD Amaranthaceae Amaranthus_cruentus AMAR 1KP 1KP Matasci et al., 2014 Yang et al., 2015 Amhy Amaranthaceae AMAR download translated by transdecoder from resource.ibab.ac.in/Plant_Genomi Sunil et al., 2014

Amaranthus_hypochondriacus downloaded transcriptome cs AmhyPA Amaranthaceae AMAR NCBI SRA trinity2.04, transdecoder2 SRR1698129+SRR1698126 Christin et al., C Amaranthus_hypochondriacus_PAC 2015 WMLW Amaranthaceae Amaranthus_retroflexus AMAR 1KP 1KP Matasci et al., 2014 Yang et al., 2015 Amtr Amaranthaceae Amaranthus_tricolor AMAR NCBI SRA trinity20140413p1, SRR924083 No information transdecoder16JAN2014 CUTE Amaranthaceae Blutaparon_vermiculare AMAR 1KP 1KP Matasci et al., 2014 Yang et al., 2015 MJM1665 Amaranthaceae Froelichia_latifolia AMAR Smith Lab trinity20140413p1stranded, SRA BioProject PRJNA280277 Brockington et transdecoder16JAN2014stranded al., 2015 MJM1807 Amaranthaceae AMAR Smith Lab trinity2.04stranded, SRA BioProject PRJNA388222 This study Gossypianthus_lanuginosus transdecoder2stranded MJM2445 Amaranthaceae AMAR Smith Lab trinity2.03stranded, SRA BioProject PRJNA388222 This study Guilleminea_densa_var_aggregata transdecoder2stranded MJM2259 Amaranthaceae Tidestromia_lanuginosa AMAR Smith Lab trinity2.03stranded, SRA BioProject PRJNA388222 This study transdecoder2stranded Agsq Chenopodiaceae AMAR NCBI SRA trinity2.04, transdecoder2 SRR1559276 Zhao et al., 2014 Agriophyllum_squarrosum ONLQ Chenopodiaceae Atriplex_hortensis AMAR 1KP 1KP Matasci et al., 2014 Yang et al., 2015 AAXJ Chenopodiaceae Atriplex_prostrata AMAR 1KP 1KP Matasci et al., 2014 Yang et al., 2015 CBJR Chenopodiaceae Atriplex_rosea AMAR 1KP 1KP Matasci et al., 2014 Yang et al., 2015 WGET Chenopodiaceae Bassia_scoparia AMAR 1KP 1KP Matasci et al., 2014 Matasci et al., 2014 FVXD Chenopodiaceae Beta_maritima AMAR 1KP 1KP Matasci et al., 2014 Yang et al., 2015

Beta Chenopodiaceae Beta_vulgaris AMAR Genome genome annotation v1.2 http://bvseq.molgen.mpg.de/ Dohm et al., 2014 Bisi Chenopodiaceae Bienertia_sinuspersici AMAR NCBI TSA Download transcripts,transdecoder GCEP01000001-GCEP01073224 No information

Cham Chenopodiaceae AMAR NCBI SRA trinity20140413p1, SRR503600 Zhang et al., Chenopodium_giganteum transdecoder16JAN2014 2012 SMMC Chenopodiaceae Chenopodium_quinoa AMAR 1KP 1KP Matasci et al., 2014 Yang et al., 2015 MJM3214 Chenopodiaceae Extriplex_californica AMAR Smith Lab trinity2.03stranded, SRA BioProject PRJNA388222 This study transdecoder2stranded MJM3268 Chenopodiaceae Grayia_spinosa AMAR Smith Lab trinity2.03stranded, SRA BioProject PRJNA388222 This study transdecoder2stranded Hagl Chenopodiaceae Halogeton_glomeratus AMAR NCBI SRA trinity2.03, transdecoder2; offset SRX643376 all 5 runs combined No information 64 Haam Chenopodiaceae AMAR NCBI SRA trinity2.04, transdecoder2 SRR1697346 Long et al., 2014 Haloxylon_ammodendron MJM2311 Chenopodiaceae AMAR Smith Lab trinity2.04stranded, SRA BioProject PRJNA388222 This study Krascheninnikovia_lanata transdecoder2stranded Saeu Chenopodiaceae Salicornia_europaea AMAR NCBI SRA trinity20140413p1, SRR896619 Fan et al., 2013 transdecoder16JAN2014 SaeuGB Chenopodiaceae AMAR NCBI TSA Download transcripts,transdecoder GAIA01000001-GAIA01083157 Ma et al., 2013 Salicornia_europaeaGB Spol Chenopodiaceae Spinacia_oleracea AMAR Genome Download http://bvseq.molgen.mpg.de/ Dohm et al., 2014 Sufr Chenopodiaceae Suaeda_fruticosa AMAR NCBI SRA trinity2.03, transdecoder2 SRR1946833 Diray-Arce et al., 2015 MJM1679 Chenopodiaceae Suaeda_linearis AMAR Smith Lab trinity2.04stranded, SRA BioProject PRJNA388222 This study transdecoder2stranded YNFJ Microteaceae Microtea_debilis 1KP 1KP Matasci et al., 2014 Yang et al., 2015 RUUB Physenaceae Physena_madagascariensis 1KP 1KP Matasci et al., 2014 Yang et al., 2015 CVDF Simmondsiaceae Simmondsia_chinensis 1KP 1KP Matasci et al., 2014 Yang et al., 2015 Aggi Caryophyllaceae Agrostemma_githago CARY NCBI SRA trinity2.04, transdecoder2 SRX352988 all 4 runs combined Sloan et al., 2014 MJM1164 Caryophyllaceae Arenaria_serpyllifolia CARY Smith Lab trinity2.04stranded, SRA BioProject PRJNA388222 This study transdecoder2stranded MJM1767 Caryophyllaceae Cerastium_arvense CARY Smith Lab trinity20140413p1stranded, SRA BioProject PRJNA280277 Brockington et transdecoder16JAN2014stranded al., 2015 MJM1163 Caryophyllaceae CARY Smith Lab trinity2.04stranded, SRA BioProject PRJNA388222 This study Cerastium_fontanum_subsp_vulgare transdecoder2stranded Coqu Caryophyllaceae Colobanthus_quitensis CARY NCBI TSA Download GCIB01000001-GCIB01165386 Arthofer et al., transcripts,transdecoder2 2015 CorSFB Caryophyllaceae Corrigiola_litoralis CARY Smith Lab trinity2.04stranded, SRA BioProject PRJNA388222 This study transdecoder2stranded Dica Caryophyllaceae Dianthus_caryophyllus CARY Genome genome annotation v1.0 http://carnation.kazusa.or.jp/ Yagi et al., 2014 LCMsn Caryophyllaceae Drymaria_cordata CARY Smith Lab trinity20140413p1stranded, SRA BioProject PRJNA280277 Brockington et transdecoder16JAN2014stranded al., 2015 MJM2503 Caryophyllaceae CARY Smith Lab trinity20140717stranded, SRA BioProject PRJNA388222 This study Drymaria_subumbellata transdecoder20140704stranded

AP35665 Caryophyllaceae CARY Smith Lab trinity2.03stranded, SRA BioProject PRJNA388222 This study Eremogone_hookeri_subsp_desertorum transdecoder2stranded AreSFB Caryophyllaceae Eremogone_procera CARY Smith Lab trinity2.04stranded, SRA BioProject PRJNA388222 This study transdecoder2stranded GypSFB Caryophyllaceae Gypsophila_repens CARY Smith Lab trinity2.04stranded, SRA BioProject PRJNA388222 This study transdecoder2stranded HerSFB Caryophyllaceae Herniaria_latifolia CARY Smith Lab trinity2.04stranded, SRA BioProject PRJNA388222 This study transdecoder2stranded HoncSFB Caryophyllaceae Honckenya_peploides CARY Smith Lab trinity2.04stranded, SRA BioProject PRJNA388222 This study transdecoder2stranded IlleSFB Caryophyllaceae CARY Smith Lab trinity2.04stranded, SRA BioProject PRJNA388222 This study Illecebrum_verticillatum transdecoder2stranded LepySFB Caryophyllaceae CARY Smith Lab trinity2.04stranded, SRA BioProject PRJNA388222 This study Lepyrodiclis_stellarioides transdecoder2stranded RXEN Caryophyllaceae Polycarpaea_repens CARY 1KP 1KP Matasci et al., 2014 Yang et al., 2015 SKNL Caryophyllaceae Saponaria_officinalis CARY 1KP 1KP Matasci et al., 2014 Yang et al., 2015 OLES Caryophyllaceae CARY 1KP 1KP Matasci et al., 2014 Yang et al., 2015 Schiedea_membranacea SclSFB Caryophyllaceae CARY Smith Lab trinity2.04stranded, SRA BioProject PRJNA388222 This study Scleranthus_polycarpos transdecoder2stranded AP01224 Caryophyllaceae Silene_acaulis_subsp_ CARY Smith Lab trinity2.03stranded, SRA BioProject PRJNA388222 This study subacaulescens transdecoder2stranded Sico Caryophyllaceae Silene_conica CARY NCBI SRA trinity2.04, transdecoder2 SRX353031 all 4 runs combined Sloan et al., 2014 FZQN Caryophyllaceae Silene_latifolia CARY 1KP 1KP Matasci et al., 2014 Yang et al., 2015 Sila Caryophyllaceae Silene_latifolia_SRA CARY NCBI SRA trinity20140413p1, SRR404980-SRR404985 6 runs Muyle et al., transdecoder16JAN2014 combined 2012 Sino Caryophyllaceae Silene_noctiflora CARY NCBI SRA trinity2.04, transdecoder2 SRX353048 all 4 runs combined Sloan et al., 2014 Sipa Caryophyllaceae Silene_paradoxa CARY NCBI SRA trinity2.04, transdecoder2 SRX353049 all 4 runs combined Sloan et al., 2014 Sivu Caryophyllaceae Silene_vulgaris CARY NCBI SRA trinity20140413p1, SRR342041 No information transdecoder16JAN2014 Sivu_AL Caryophyllaceae Silene_vulgaris_ALN CARY NCBI SRA trinity2.04, transdecoder2 SRX353050 all 4 runs combined Sloan et al., N 2014 TJES Caryophyllaceae Spergularia_media CARY 1KP 1KP Matasci et al., 2014 Yang et al., 2015 TelSFB Caryophyllaceae Telephium_imperati CARY Smith Lab trinity2.04stranded, SRA BioProject PRJNA388222 This study transdecoder2stranded VeleSFB Caryophyllaceae Velezia_rigida CARY Smith Lab trinity2.04stranded, SRA BioProject PRJNA388222 This study transdecoder2stranded MJM1652 Droseraceae Aldrovanda_vesiculosa NCORE Smith Lab trinity20140413p1stranded, SRA BioProject PRJNA280277 Brockington et transdecoder16JAN2014stranded al., 2015 Dimu Droseraceae Dionaea_muscipula NCORE NCBI SRA trinity20140413p1, SRR916183 Jensen et al., transdecoder16JAN2014 2015

DrobinSF Droseraceae Drosera_binata NCORE Smith Lab trinity2.04stranded, SRA BioProject PRJNA350559 Walker et al., B transdecoder2stranded combined 3 stages 2017 DrolusSF Drosophyllaceae NCORE Smith Lab trinity2.04stranded, SRA BioProject PRJNA350559 Walker et al., B Drosophyllum_lusitanicum transdecoder2stranded 2017 WPYJ Frankeniaceae Frankenia_laevis NCORE 1KP 1KP Matasci et al., 2014 Yang et al., 2015 WQUF Nepenthaceae Nepenthes_alata NCORE 1KP 1KP Matasci et al., 2014 Yang et al., 2015 NepSFB Nepenthaceae Nepenthes_alata_SFB NCORE Smith Lab trinity2.04stranded, SRA BioProject PRJNA350559 Walker et al., transdecoder2stranded combined 3 stages 2017 WOBD Plumbaginaceae Limonium_spectabile NCORE 1KP 1KP Matasci et al., 2014 Yang et al., 2015 CGGO Plumbaginaceae Plumbago_auriculata NCORE 1KP 1KP (SOAPdenovo- Matasci et al., 2014 Yang et al., 2015 Trans)+trinity20140413p1, transdecoder16JAN2014 MJM1811 Polygonaceae Antigonon_leptopus NCORE Smith Lab trinity20140413p1stranded, SRA BioProject PRJNA280277 Brockington et transdecoder16JAN2014stranded al., 2015 Faes Polygonaceae Fagopyrum_esculentum NCORE NCBI SRA trinity20140413p1, SRX112838 all seven runs No information transdecoder16JAN2014 combined Fata Polygonaceae Fagopyrum_tataricum NCORE NCBI SRA trinityrnaseq_r20140717, SRR1552215 Zhu et al., 2015 transdecoder_r20140704 FYSJ Polygonaceae Fallopia_convolvulus NCORE 1KP 1KP Matasci et al., 2014 Yang et al., 2015 MJM1170 Polygonaceae NCORE Smith Lab trinity2.04stranded, SRA BioProject PRJNA388222 This study Muehlenbeckia_platyclada transdecoder2stranded Pomi Polygonaceae Persicaria_minor NCORE NCBI SRA trinity20140413p1, SRR1536192 No information transdecoder16JAN2014 Pomi2 Polygonaceae Persicaria_minor2 NCORE NCBI SRA trinity20140413p1, SRR1536245 No information transdecoder16JAN2014 Poti Polygonaceae Persicaria_tinctoria NCORE NCBI SRA trinityrnaseq_r20140717, SRR1565474 No information transdecoder_r20140704 MJM1162 Polygonaceae Persicaria_virginiana NCORE Smith Lab trinity2.04stranded, SRA BioProject PRJNA388222 This study transdecoder2stranded MJM2667 Polygonaceae Polygonum_aviculare NCORE Smith Lab trinity2.04stranded, SRA BioProject PRJNA388222 This study transdecoder2stranded PterSFB Polygonaceae Pterostegia_drymarioides NCORE Smith Lab trinity2.04stranded, SRA BioProject PRJNA388222 This study transdecoder2stranded Pocu Polygonaceae Reynoutria_japonica NCORE NCBI SRA trinity20140413p1, SRR292345 Hao et al., 2012 transdecoder16JAN2014 EmexSFB Polygonaceae Reynoutria_japonica 2 NCORE Smith Lab trinity2.04stranded, SRA BioProject PRJNA388222 This study transdecoder2stranded Rhno Polygonaceae Rheum_nobile NCORE NCBI SRA trinity20140413p1, SRR1449867 No information transdecoder16JAN2014 Rhrh Polygonaceae Rheum_rhabarbarum NCORE NCBI SRA trinity20140413p1, SRR867377 No information transdecoder16JAN2014 Ruac Polygonaceae Rumex_acetosa NCORE NCBI SRA trinity20140413p1, ERR216274+ERR216275 No information transdecoder16JAN2014 combined

Ruha Polygonaceae Rumex_hastatulus NCORE NCBI SRA trinity20140413p1, SRR1266797 No information transdecoder16JAN2014 Rupa Polygonaceae Rumex_palustris NCORE NCBI SRA trinity20140413p1, ERR216276+ERR216277 No information transdecoder16JAN2014 combined RuprSFB Polygonaceae Ruprechtia_salicifolia NCORE Smith Lab trinity2.04stranded, SRA BioProject PRJNA350559 Walker et al., transdecoder2stranded 2017 Reso Tamaricaceae Reaumuria_soongarica NCORE NCBI SRA trinity2.03, transdecoder2 SRR1232022 No information Retr Tamaricaceae Reaumuria_trigyna NCORE NCBI SRA trinity20140413p1, SRR350859+SRR364263 No information transdecoder16JAN2014 combined Tama Tamaricaceae Tamarix_hispida NCORE NCBI SRA trinity20140413p1, SRR522908+SRR527758+SRR52 Wang et al., transdecoder16JAN2014 7759+SRR527762+SRR527765+ 2014 SRR527772+SRR527773+SRR52 7780 combined GJNX Aizoaceae Cypselea_humifusa PHYT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 BJKT Aizoaceae Delosperma_echinatum PHYT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 Mecr Aizoaceae PHYT NCBI SRA trinity2.04, transdecoder2 SRR1698355+SRR1701857 Christin et al., Mesembryanthemum_crystallinum combined 2015 HZTS Aizoaceae Sesuvium_portulacastrum PHYT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 EDIT Aizoaceae Sesuvium_verrucosum PHYT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 OMYK Aizoaceae Trianthema_portulacastrum PHYT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 Trpo Aizoaceae PHYT NCBI SRA trinity2.04, transdecoder2 SRR1698227+SRR1698228 Christin et al., Trianthema_portulacastrum_SRA combined 2015 BERS Aizoaceae Zaleya_pentandra PHYT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 MJM2189 Nyctaginaceae Abronia_bigelovii PHYT Smith Lab trinity2.03stranded, SRA BioProject PRJNA388222 This study transdecoder2stranded MJM1751 Nyctaginaceae Abronia_nealleyi PHYT Smith Lab trinity20140413p1stranded, SRA BioProject PRJNA280277 Brockington et transdecoder16JAN2014stranded al., 2015 MJM2247 Nyctaginaceae Acleisanthes_acutifolia PHYT Smith Lab trinity20140717stranded, SRA BioProject PRJNA388222 This study transdecoder20140704stranded MJM2246 Nyctaginaceae PHYT Smith Lab trinity20140717stranded, SRA BioProject PRJNA388222 This study Acleisanthes_chenopodioides transdecoder20140704stranded MJM1741 Nyctaginaceae Acleisanthes_lanceolata PHYT Smith Lab trinity20140413p1stranded, SRA BioProject PRJNA280277 Brockington et transdecoder16JAN2014stranded al., 2015 MJM1697 Nyctaginaceae Acleisanthes_obtusa PHYT Smith Lab trinity20140413p1stranded, SRA BioProject PRJNA280277 Brockington et transdecoder16JAN2014stranded al., 2015 EGOS Nyctaginaceae Allionia_incarnata PHYT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 DVXD Nyctaginaceae Allionia_incarnata2 PHYT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 MJM2362 Nyctaginaceae Anulocaulis_eriosolenus PHYT Smith Lab trinity2.04stranded, SRA BioProject PRJNA388222 This study transdecoder2stranded MJM1070 Nyctaginaceae PHYT Smith Lab trinity20140413p1non-stranded, SRA BioProject PRJNA261527 Yang et al., 2015 Anulocaulis_leiosolenus_var_gypsogen transdecoder16JAN2014 us VJPU Nyctaginaceae Boerhavia_burbidgeana PHYT 1KP 1KP Matasci et al., 2014 Yang et al., 2015

ZBTA Nyctaginaceae Boerhavia_coccinea PHYT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 Boco Nyctaginaceae PHYT NCBI SRA trinity2.04, transdecoder2 SRR1698115+SRR1698114 Christin et al., Boerhavia_coccinea_SRA combined 2015 MJM2201 Nyctaginaceae Boerhavia_purpurascens PHYT Smith Lab trinity20140717stranded, SRA BioProject PRJNA388222 This study transdecoder20140704stranded MJM2202 Nyctaginaceae Boerhavia_torreyana PHYT Smith Lab trinity20140717stranded, SRA BioProject PRJNA388222 This study transdecoder20140704stranded JAFJ Nyctaginaceae PHYT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 Bougainvillea_spectabilis SFB32 Nyctaginaceae Bougainvillea_stipitata PHYT Smith Lab trinity20140413p1non-stranded, SRA BioProject PRJNA261527 Yang et al., 2015 transdecoder16JAN2014 MJM1714 Nyctaginaceae PHYT Smith Lab trinity20140413p1stranded, SRA BioProject PRJNA280277 Brockington et Cyphomeris_gypsophiloides transdecoder16JAN2014stranded al., 2015 SFB27 Nyctaginaceae Guapira_obtusata PHYT Smith Lab trinity20140413p1non-stranded, SRA BioProject PRJNA261527 Yang et al., 2015 transdecoder16JAN2014 JGAB Nyctaginaceae Mirabilis_jalapa PHYT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 Mija Nyctaginaceae Mirabilis_jalapa_SRA PHYT NCBI SRA trinityrnaseq_r20140717, ERR324436 No information transdecoder_r20140704 MJM1771 Nyctaginaceae Mirabilis_multiflora PHYT Smith Lab trinity20140413p1stranded, SRA BioProject PRJNA280277 Brockington et transdecoder16JAN2014stranded al., 2015 MJM2585 Nyctaginaceae Nyctaginia_capitata PHYT Smith Lab trinity20140717stranded, SRA BioProject PRJNA388222 This study transdecoder20140704stranded SFB28 Nyctaginaceae Pisonia_aculeata PHYT Smith Lab trinity20140413p1non-stranded, SRA BioProject PRJNA261527 Yang et al., 2015 transdecoder16JAN2014 SFB29 Nyctaginaceae Pisonia_umbellifera PHYT Smith Lab trinity20140413p1stranded, SRA BioProject PRJNA280277 Brockington et transdecoder16JAN2014stranded al., 2015 MJM3267 Nyctaginaceae PHYT Smith Lab trinity2.03stranded, SRA BioProject PRJNA388222 This study Tripterocalyx_crux_maltae transdecoder2stranded SFKQ Petiveriaceae Hilleria_latifolia PHYT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 AZBL Petiveriaceae Petiveria_alliacea PHYT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 MJM1651 Petiveriaceae Rivina_humilis PHYT Smith Lab trinity20140413p1non-stranded, SRA BioProject PRJNA261527 Yang et al., 2015 transdecoder16JAN2014 SFB30 Petiveriaceae Seguieria_aculeata PHYT Smith Lab trinity20140413p1non-stranded, SRA BioProject PRJNA261527 Yang et al., 2015 transdecoder16JAN2014 AniSFB Phytolaccaceae Anisomeria_littoralis PHYT Smith Lab trinity2.04stranded, SRA BioProject PRJNA388222 This study transdecoder2stranded MJM1649 Phytolaccaceae Ercilla_volubilis PHYT Smith Lab trinity20140413p1stranded, SRA BioProject PRJNA280277 Brockington et transdecoder16JAN2014stranded al., 2015 BKQU Phytolaccaceae Phytolacca_americana PHYT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 MRKX Phytolaccaceae Phytolacca_bogotensis PHYT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 SFB31 Phytolaccaceae Phytolacca_dioica PHYT Smith Lab trinity20140413p1stranded, SRA BioProject PRJNA280277 Brockington et transdecoder16JAN2014stranded al., 2015 GIWN Sarcobataceae Sarcobatus_vermiculatus PHYT 1KP 1KP Matasci et al., 2014 Yang et al., 2015

MJM1773 Sarcobataceae PHYT Smith Lab trinity2.04stranded, SRA BioProject PRJNA388222 This study Sarcobatus_vermiculatus_MJM transdecoder2stranded DBGStha Stegnospermataceae PHYT Smith Lab trinity2.03stranded, SRA BioProject PRJNA388222 This study Stegnosperma_halimifolium transdecoder2stranded Anfi Anacampserotaceae PORT NCBI SRA trinity2.04, transdecoder2 SRR1698105 Christin et al., Anacampseros_filamentosa 2015 MJM2441 Anacampserotaceae PORT Smith Lab trinity2.04stranded, SRA BioProject PRJNA388222 This study Talinopsis_frutescens transdecoder2stranded CTYH Basellaceae Basella_alba PORT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 Ecpe Cactaceae Echinocereus_pectinatus PORT NCBI SRA trinity2.04, transdecoder2 SRR1698109 Christin et al., 2015 Lebl Cactaceae Leuenbergeria_bleo PORT NCBI SRA trinity2.04, transdecoder2 SRR1698112 Christin et al., 2015 Lely Cactaceae Leuenbergeria_lychnidiflora PORT NCBI SRA trinity2.04, transdecoder2 SRR1698113 Christin et al., 2015 CPKP Cactaceae Lophophora_williamsii PORT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 Noco Cactaceae Nopalea_cochenillifera PORT NCBI SRA trinity2.04, transdecoder2 SRR1698231+SRR1698229 Christin et al., combined 2015 JLOV Cactaceae Pereskia_aculeata PORT 1KP 1KP (SOAPdenovo- Matasci et al., 2014 Yang et al., 2015 Trans)+trinity20140413p1, transdecoder16JAN2014pfamAB Pegr Cactaceae Pereskia_grandifolia PORT NCBI SRA trinity2.04, transdecoder2 SRR1698106 Christin et al., 2015 RNBN Molluginaceae Mollugo_cerviana PORT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 SCAO Molluginaceae Mollugo_nudicaulis PORT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 HURS Molluginaceae Mollugo_pentaphylla PORT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 NXTS Molluginaceae Mollugo_verticillata PORT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 TRS2027 Montiaceae Claytonia_nevadensis PORT Smith Lab trinity2.03stranded, SRA BioProject PRJNA388222 This study transdecoder2stranded MJM1156 Montiaceae Claytonia_virginica PORT Smith Lab trinity2.04stranded, SRA BioProject PRJNA388222 This study transdecoder2stranded MJM2214 Montiaceae Phemeranthus_parviflorus PORT Smith Lab trinity2.04stranded, SRA BioProject PRJNA388222 This study transdecoder2stranded LDEL Portulacaceae Portulaca_amilis PORT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 LLQV Portulacaceae Portulaca_cryptopetala PORT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 CPLT Portulacaceae Portulaca_grandiflora PORT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 UQCB Portulacaceae Portulaca_molokiniensis PORT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 EZGR Portulacaceae Portulaca_oleracea PORT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 Pool Portulacaceae Portulaca_oleracea_SRA PORT NCBI SRA trinity2.04, transdecoder2 SRR1698123+SRR1698125 Christin et al., combined 2015 IWIS Portulacaceae Portulaca_pilosa PORT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 GCYL Portulacaceae Portulaca_suffrutescens PORT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 KDCH Portulacaceae Portulaca_umbraticola PORT 1KP 1KP Matasci et al., 2014 Yang et al., 2015

MJM1789 Talinaceae Talinum_paniculatum PORT Smith Lab trinity2.04stranded, SRA BioProject PRJNA388222 This study transdecoder2stranded Tapo Talinaceae Talinum_portulacifolium PORT NCBI SRA trinity2.04, transdecoder2 SRR1698110 Christin et al., 2015 LKKX Talinaceae Talinum_sp PORT 1KP 1KP Matasci et al., 2014 Yang et al., 2015 Achn Actinidiaceae Actinidia_chinensis outgroup genome genome annotation http://bioinfo.bti.cornell.edu/cgi- Huang et al.,

bin/kiwi/download.cgi 2013

Atrichopo Amborella_trichopoda outgroup genome v1.0 https://phytozome.jgi.doe.gov/ Goodstein et al., da 2012

Acoerulea Aquilegia_coerulea outgroup genome v1.1 https://phytozome.jgi.doe.gov/ Goodstein et al., 2012

Athaliana Arabidopsis_thaliana outgroup genome TAIR10 https://phytozome.jgi.doe.gov/ Goodstein et al., 2012

Elgu Arecaceae Elaeis_guineensis outgroup genome genome annotation v2 http://genomsawit.mpob.gov.my/ Singh et al., 2013 Phoe Arecaceae Phoenix_dactylifera outgroup genome genome annotation v3 http://qatar- Al-Mssallem et weill.cornell.edu/research/datepal al., 2013

mGenome/download

Bstricta Boechera_stricta outgroup genome v1.2 https://phytozome.jgi.doe.gov/ Goodstein et al., 2012

Brapa Brassica_rapa outgroup genome v1.3 https://phytozome.jgi.doe.gov/ Goodstein et al., 2012 Rara Brassicaceae Raphanus_raphanistrum outgroup genome genome annotation http://radish.plantbiology.msu.edu Moghe et al., /index.php/Genome_sequence/ana 2014

lysis

Crubella Capsella_rubella outgroup genome v1.0 https://phytozome.jgi.doe.gov/ Goodstein et al., 2012

Cpapaya Carica_papaya outgroup genome ASGPBv0.4 https://phytozome.jgi.doe.gov/ Goodstein et al., 2012

Cclementi Citrus_clementina outgroup genome v1.0 https://phytozome.jgi.doe.gov/ Goodstein et al., na 2012

Csinensis Citrus_sinensis outgroup genome v1.1 https://phytozome.jgi.doe.gov/ Goodstein et al., 2012

Csativus Cucumis_sativus outgroup genome v1.0 https://phytozome.jgi.doe.gov/ Goodstein et al., 2012 Cila Cucurbitaceae Citrullus_lanatus outgroup genome genome annotation v1 ftp://www.icugi.org/pub/genome/ Guo et al., 2013

watermelon/97103/v1/

Egrandis Eucalyptus_grandis outgroup genome v2.0 https://phytozome.jgi.doe.gov/ Goodstein et al., 2012

Esalsugin Eutrema_salsugineum outgroup genome v1.0 https://phytozome.jgi.doe.gov/ Goodstein et al., eum 2012

Fvesca Fragaria_vesca outgroup genome v1.1 https://phytozome.jgi.doe.gov/ Goodstein et al., 2012

Gmax Glycine_max outgroup genome Wm82.a2.v1 https://phytozome.jgi.doe.gov/ Goodstein et al., 2012

Graimond Gossypium_raimondii outgroup genome v2.1 https://phytozome.jgi.doe.gov/ Goodstein et al., ii 2012

Utri Lentibulariaceae Utricularia_gibba outgroup genome genome https://genomevolution.org/CoGe Ibarra-Laclette et annotation+transdecoder20131117 al., 2013

Lusitatissi Linum_usitatissimum outgroup genome v1.0 https://phytozome.jgi.doe.gov/ Goodstein et al., mum 2012

Mesculent Manihot_esculenta outgroup genome v4.1 https://phytozome.jgi.doe.gov/ Goodstein et al., a 2012

Mtruncatu Medicago_truncatula outgroup genome Mt4.0v1 https://phytozome.jgi.doe.gov/ Goodstein et al., la 2012

Mguttatus Mimulus_guttatus outgroup genome v2.0 https://phytozome.jgi.doe.gov/ Goodstein et al., 2012 Musa Musaceae Musa_acuminata outgroup genome genome annotation DH-Pahang v1 http://banana-genome- D'Hont et al.,

hub.southgreen.fr 2012

Nenu Nelumbonaceae Nelumbo_nucifera outgroup genome genome annotation http://lotus-db.wbgcas.cn/ Ming et al., 2013; Wang et al., 2015 Pheq Orchidaceae Phalaenopsis_equestris outgroup genome genome annotation ftp://ftp.genomics.org.cn/from_B Cai et al., 2015

GISZ/20130120/02.annotation/

Osativa Oryza_sativa outgroup genome v7.0 https://phytozome.jgi.doe.gov/ Goodstein et al., 2012

Ptrichocar Populus_trichocarpa outgroup genome v3.0 https://phytozome.jgi.doe.gov/ Goodstein et al., pa 2012

Ppersica Prunus_persica outgroup genome v2.1 https://phytozome.jgi.doe.gov/ Goodstein et al., 2012

Rcommun Ricinus_communis outgroup genome v0.1 https://phytozome.jgi.doe.gov/ Goodstein et al., is 2012 Coca Rubiaceae Coffea_canephora outgroup genome genome annotation http://coffee- Denoeud et al.,

genome.org/download 2014

Spurpurea Salix_purpurea outgroup genome v1.0 https://phytozome.jgi.doe.gov/ Goodstein et al., 2012 Caan Solanaceae outgroup genome genome annotation v2.0 ftp://ftp.solgenomics.net/genomes/ Qin et al., 2014 Capsicum_annuum_var_glabriusculum Capsicum_annuum/C.annuum_gla

briusculum/

Slycopersi Solanaceae Solanum_lycopersicum outgroup genome iTAGv2.3 https://phytozome.jgi.doe.gov/ Goodstein et al., cum 2012

Spolyrhiz Spirodela_polyrhiza outgroup genome v2 https://phytozome.jgi.doe.gov/ Goodstein et al., a 2012

Tcacao Theobroma_cacao outgroup genome v1.1 https://phytozome.jgi.doe.gov/ Goodstein et al., 2012

Vvinifera Vitis_vinifera outgroup genome Genoscope.12X https://phytozome.jgi.doe.gov/ Goodstein et al., 2012

Zmays Zea_mays outgroup genome 6a https://phytozome.jgi.doe.gov/ Goodstein et al., 2012 38

40 Table S2 Information for the 43 newly sequenced transcriptomes. YY=Ya Yang, MJM=Michael J. Moore, SFB=Samuel F.

41 Brockington, JM=Jessica Mikenas, JO=Julia Olivieri, JFW=Joseph F. Walker. Details for collection, RNA extraction, and library

42 preparation protocols can be found in Yang et al. (2017)

44 Methods S1 All-by-all homology search for subclade datasets. Coding sequences from each transcriptome were reduced using cd-hit-

45 est (-c 0.99 -n 10) as part of the CD-HIT package. Homology searches were carried out using all-by-all BLASTN with an E-value

46 cutoff of 10 and max_target_seqs set to 1000. BLASTN output was filtered by requiring the alignment to cover 40% of both the query

47 and hit sequences. Clustering was performed using Markov CLuster algorithm [MCL v12-068 (van Dongen, 2000; van Dongen &

−5 48 Abreu-Goodger, 2012)] from filtered hits with the E-value cutoff set to 10 and an inflation value of 1.4. Ends of sequences with no

49 interspecific BLASTN hit coverage were clipped. Remaining sequences shorter than 40 characters were removed, and clusters with

50 more than 2 taxa missing were ignored. Each resulting cluster was aligned, alignments were trimmed as in the modified phylome

51 approach, and phylogenetic trees were estimated with RAxML using the model GTRCAT. Spurious tips were trimmed using a relative

52 tip cutoff of 0.2 and an absolute tip length cutoff of 0.4 (0.3 and 0.6 for NCORE and 0.1 and 0.3 for CARY, respectively), and

53 isoforms were removed with the same criteria as in the modified phylome approach. Internal branches longer than 0.3 (0.4 for

54 NCORE and 0.2 for CARY and AMAR) were separated. The same procedure was repeated once before producing the final homolog

55 trees with 200 fast bootstrap replicates.

57 References

58 Al-Mssallem IS, Hu SN, Zhang XW, Lin Q, Liu WF, Tan J, Yu XG, Liu JC, Pan LL, Zhang TW, et al. 2013. Genome sequence 59 of the date palm Phoenix dactylifera L. Nature Communications 4. 60 Arthofer W, Bertini L, Caruso C, Cicconardi F, Delph LF, Fields PD, Ikeda M, Minegishi Y, Proietti S, Ritthammer H, et al. 61 2015. Genomic Resources Notes accepted 1 February 2015 – 31 March 2015. Molecular Ecology Resources 15(4): 1014– 62 1015. 63 Brockington SF, Yang Y, Gandia-Herrero F, Covshoff S, Hibberd JM, Sage RF, Wong GKS, Moore MJ, Smith SA. 2015. 64 Lineage-specific gene radiations underlie the evolution of novel betalain pigmentation in Caryophyllales. New Phytologist 65 207(4): 1170–1180. 66 Cai J, Liu X, Vanneste K, Proost S, Tsai WC, Liu KW, Chen LJ, He Y, Xu Q, Bian C, et al. 2015. The genome sequence of the 67 orchid Phalaenopsis equestris. Nature Genetics 47(1): 65–72.

68 Christin P-A, Arakaki M, Osborne CP, Edwards EJ. 2015. Genetic enablers underlying the clustered evolutionary origins of C4 69 photosynthesis in angiosperms. Molecular Biology and Evolution 32(4): 846–858. 70 D'Hont A, Denoeud F, Aury JM, Baurens FC, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M, et al. 2012. The 71 banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488(7410): 213–217. 72 Denoeud F, Carretero-Paulet L, Dereeper A, Droc G, Guyot R, Pietrella M, Zheng CF, Alberti A, Anthony F, Aprea G, et al. 73 2014. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science 345(6201): 1181– 74 1184.

75 Diray-Arce J, Clement M, Gul B, Khan MA, Nielsen BL. 2015. Transcriptome assembly, profiling and differential gene expression 76 analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance. BMC Genomics 16 doi: 10.1186/s12864- 77 12015-11553-x. 78 Dohm JC, Minoche AE, Holtgrawe D, Capella-Gutierrez S, Zakrzewski F, Tafer H, Rupp O, Sorensen TR, Stracke R, 79 Reinhardt R, et al. 2014. The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). Nature 505(7484): 80 546–549. 81 Fan PX, Nie LL, Jiang P, Feng JJ, Lv SL, Chen XY, Bao H, Guo J, Tai F, Wang JH, et al. 2013. Transcriptome analysis of 82 Salicornia europaea under saline conditions revealed the adaptive primary metabolic pathways as early events to facilitate salt 83 adaptation. PloS ONE 8(11): e80595. 84 Goodstein DM, Shu SQ, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, et al. 2012. 85 Phytozome: a comparative platform for green plant genomics. Nucleic Acids Research 40(D1): D1178–D1186. 86 Guo SG, Zhang JG, Sun HH, Salse J, Lucas WJ, Zhang HY, Zheng Y, Mao LY, Ren Y, Wang ZW, et al. 2013. The draft 87 genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nature Genetics 45(1): 51–58. 88 Hao DC, Ma P, Mu J, Chen SL, Xiao PG, Peng Y, Huo L, Xu LJ, Sun C. 2012. De novo characterization of the root transcriptome 89 of a traditional Chinese medicinal plant Polygonum cuspidatum. Science China-Life Sciences 55(5): 452–466. 90 Huang S, Ding J, Deng D, Tang W, Sun H, Liu D, Zhang L, Niu X, Zhang X, Meng M, et al. 2013. Draft genome of the kiwifruit 91 Actinidia chinensis. Nat Commun 4: doi:10.1038/ncomms3640. 92 Ibarra-Laclette E, Lyons E, Hernandez-Guzman G, Perez-Torres CA, Carretero-Paulet L, Chang TH, Lan TY, Welch AJ, 93 Juarez MJA, Simpson J, et al. 2013. Architecture and evolution of a minute plant genome. Nature 498(7452): 94–98. 94 Jensen MK, Vogt JK, Bressendorff S, Seguin-Orlando A, Petersen M, Sicheritz-Ponten T, Mundy J. 2015. Transcriptome and 95 genome size analysis of the Venus Flytrap. PloS ONE 10(4): e0123887.

96 Long Y, Zhang JW, Tian XJ, Wu SS, Zhang Q, Zhang JP, Dang ZH, Pei XW. 2014. De novo assembly of the desert tree 97 Haloxylon ammodendron (C. A. Mey.) based on RNA-Seq data provides insight into drought response, gene discovery and 98 marker identification. BMC Genomics 15. 99 Ma JB, Zhang MR, Xiao XL, You JJ, Wang JR, Wang T, Yao YN, Tian CY. 2013. Global transcriptome profiling of Salicornia 100 europaea L. shoots under NaCl treatment. PloS ONE 8(6): e65877. 101 Matasci N, Hung L-H, Yan Z, Carpenter E, Wickett N, Mirarab S, Nguyen N, Warnow T, Ayyampalayam S, Barker M, et al. 102 2014. Data access for the 1,000 Plants (1KP) project. GigaScience 3(1): 17. 103 Ming R, VanBuren R, Liu YL, Yang M, Han YP, Li LT, Zhang Q, Kim MJ, Schatz MC, Campbell M, et al. 2013. Genome of 104 the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biology 14(5): R41. 105 Moghe GD, Hufnagel DE, Tang HB, Xiao YL, Dworkin I, Town CD, Conner JK, Shiu SH. 2014. Consequences of whole- 106 genome triplication as revealed by comparative genomic analyses of the wild radish Raphanus raphanistrum and three other 107 Brassicaceae species. Plant Cell 26(5): 1925–1937. 108 Muyle A, Zemp N, Deschamps C, Mousset S, Widmer A, Marais GAB. 2012. Rapid de novo evolution of X chromosome dosage 109 compensation in Silene latifolia, a plant with young sex chromosomes. PLoS Biology 10(4): e1001308. 110 Qin C, Yu CS, Shen YO, Fang XD, Chen L, Min JM, Cheng JW, Zhao SC, Xu M, Luo Y, et al. 2014. Whole-genome sequencing 111 of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proceedings of the National 112 Academy of Sciences of the United States of America 111(14): 5135–5140. 113 Singh R, Ong-Abdullah M, Low ETL, Manaf MAA, Rosli R, Nookiah R, Ooi LCL, Ooi SE, Chan KL, Halim MA, et al. 2013. 114 Oil palm genome sequence reveals divergence of interfertile species in Old and New Worlds. Nature 500(7462): 335–339. 115 Sloan DB, Triant DA, Wu M, Taylor DR. 2014. Cytonuclear interactions and relaxed selection accelerate sequence evolution in 116 organelle ribosomes. Molecular Biology and Evolution 31(3): 673–682.

117 Sunil M, Hariharan AK, Nayak S, Gupta S, Nambisan SR, Gupta RP, Panda B, Choudhary B, Srinivasan S. 2014. The draft

118 genome and transcriptome of Amaranthus hypochondriacus: A C4 dicot producing high-lysine edible pseudo-cereal. DNA 119 Research 21(6): 585-602. 120 van Dongen S. 2000. Graph clustering by flow simulation. PhD Thesis, University of Utrecht, The Netherlands. 121 van Dongen S, Abreu-Goodger C 2012. Using MCL to extract clusters from networks. In: Helden Jv, Toussaint A, Thieffry D eds. 122 Bacterial Molecular Networks: Methods and Protocols. Heidelberg: Springer, 281–295. 123 Walker JF, Yang Y, Moore MJ, Mikenas J, Timoneda A, Brockington SF, Smith SA. 2017. Widespread paleopolyploidy, gene 124 tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales. American Journal of Botany 104(6): 858– 125 867.

126 Wang C, Gao C, Wang L, Zheng L, Yang C, Wang Y. 2014. Comprehensive transcriptional profiling of NaHCO3-stressed Tamarix 127 hispida roots reveals networks of responsive genes. Plant Molecular Biology 84: 145–157. 128 Wang K, Deng J, Damaris RN, Yang M, Xu LM, Yang PF. 2015. LOTUS-DB: an integrative and interactive database for Nelumbo 129 nucifera study. Database-the Journal of Biological Databases and Curation. 2015:bav2023. doi:2010.1093/database/bav2023. 130 Yagi M, Kosugi S, Hirakawa H, Ohmiya A, Tanase K, Harada T, Kishimoto K, Nakayama M, Ichimura K, Onozaki T, et al. 131 2014. Sequence analysis of the genome of carnation (Dianthus caryophyllus L.). DNA Research 21(3): 231–241. 132 Yang Y, Moore MJ, Brockington SF, Soltis DE, Wong GK-S, Carpenter EJ, Zhang Y, Chen L, Yan Z, Xie Y, et al. 2015. 133 Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing. Molecular 134 Biology and Evolution 32(8): 2001–2014. 135 Yang Y, Moore MJ, Brockington SF, Timoneda A, Feng T, Marx H, Walker JF, Smith SA. 2017. An efficient field and 136 laboratory workflow for plant phylotranscriptomic projects. Applications in Plant Sciences 5(3): 1600128. 137 Zhang YQ, Pei XW, Zhang C, Lu ZF, Wang ZX, Jia SR, Li WM. 2012. De novo foliar transcriptome of Chenopodium 138 amaranticolor and analysis of its gene expression during virus-induced hypersensitive response. PloS ONE 7(9): e45953

139 Zhao PS, Capella-Gutierrez S, Shi Y, Zhao X, Chen GX, Gabaldon T, Ma XF. 2014. Transcriptomic analysis of a psammophyte 140 food crop, sand rice (Agriophyllum squarrosum) and identification of candidate genes essential for sand dune adaptation. BMC 141 Genomics 15: 872. 142 Zhu HF, Wang H, Zhu YF, Zou JW, Zhao FJ, Huang CF. 2015. Genome-wide transcriptomic and phylogenetic analyses reveal 143 distinct aluminum-tolerance mechanisms in the aluminum-accumulating species buckwheat (Fagopyrum tataricum). BMC 144 Plant Biology 15:16. 145

146 Figure S1 The modified phylome approach

Homology search Query: peptides from beet genome Database: peptides from 40 ingroup and 3 outgroup genomes including beet

Filter hits by evalue and bitscore

Multiple sequece alignment

Phylogenetic tree inference

Trim spurious branches

Combine trees representing the same Caryophyllales orthogroup

Backbone homolog groups with 43 genomes

Homology search Query: peptides from 175 transcriptomes Database: beet proteome

Add peptides from transcriptomes to backbone homolog groups according to top hit

Multiple sequece alignment

Phylogenetic tree inference

Trim spurious branches

Final homolog groups with 218 genomes and transcriptomes Figure S2 3 5 Boerhavia_torreyana 100 100 100 Portulaca_surutescens 100 Boerhavia_purpurascens Portulaca_pilosa Boerhavia_coccinea_SRA 100 Portulaca_amilis 9 0 Boerhavia_burbidgeana 100 100 Atriplex_hortensis 100 8 2 Portulaca_grandi ora Boerhavia_coccinea 100 100 Atriplex_prostrata 100 Portulaca_umbraticola Atriplex_rosea 9 5 100 Anulocaulis_leiosolenus_var_gypsogenus 100 Anulocaulis_eriosolenus 100 Portulaca_cryptopetala 100 Extriplex_californica Grayia_spinosa 100 Nyctaginia_capitata 100 Portulaca_oleracea_SRA 100 100 9 7 100 Chenopodium_giganteum Cyphomeris_gypsophiloides Portulaca_oleracea 100 100 Allionia_incarnata Portulaca_molokiniensis Chenopodium_quinoa 9 2 100 Spinacia_oleracea Allionia_incarnata2 100 Anacampseros_lamentosa 100 Krascheninnikovia_lanata Mirabilis_jalapa Talinopsis_frutescens 9 9 100 Agriophyllum_squarrosum Mirabilis_jalapa_SRA 100 100 Lophophora_williamsii (c) AMAR 100 100 100 Suaeda_linearis PHYT Mirabilis_multi ora Echinocereus_pectinatus 9 8 Suaeda_fruticosa (a) 100 Abronia_nealleyi 7 8 100 100 Nopalea_cochenillifera Bienertia_sinuspersici 100 Abronia_bigelovii 100 3.0 6 9 Pereskia_aculeata 100 Salicornia_europaeaGB Tripterocalyx_crux_maltae 100 100 Salicornia_europaea 100 Acleisanthes_lanceolata 100 Pereskia_grandifolia 100 3.0 100 100 Leuenbergeria_lychnidi ora 9 8 100 Halogeton_glomeratus 100 Acleisanthes_chenopodioides Haloxylon_ammodendron Leuenbergeria_bleo Acleisanthes_acutifolia 100 Bassia_scoparia Acleisanthes_obtusa 100 Talinum_sp 100 100 100 100 Beta_maritima Bougainvillea_stipitata Talinum_paniculatum Beta_vulgaris Bougainvillea_spectabilis 100 Talinum_portulacifolium 100 100 100 Alternanthera_philoxeroides Guapira_obtusata Basella_alba 100 100 Alternanthera_brasiliana 100 100 Pisonia_aculeata 100 Claytonia_nevadensis 100 Alternanthera_sessilis Pisonia_umbellifera 100 5 0 100 100 Claytonia_virginica Alternanthera_caracasana 100 Hilleria_latifolia 100 Phemeranthus_parvi orus Alternanthera_tenella Rivina_humilis 100 100 Mollugo_cerviana 100 Tidestromia_lanuginosa 8 1 Petiveria_alliacea 100 Gossypianthus_lanuginosus 6 5 Mollugo_nudicaulis 100 Seguieria_aculeata 100 100 100 Blutaparon_vermiculare 100 Phytolacca_americana Mollugo_verticillata Guilleminea_densa_var_aggregata 100 (b) PORT 100 Phytolacca_bogotensis Mollugo_pentaphylla Froelichia_latifolia 100 Anisomeria_littoralis 100 Spinacia_oleracea 100 100 100 Aerva_javanica Phytolacca_dioica Beta_vulgaris 3.0 Aerva_lanata Ercilla_volubilis 100 Dianthus_caryophyllus 100 Amaranthus_hypochondriacus_PAC 100 100 Sarcobatus_vermiculatus 100 Amaranthus_hypochondriacus 100 Sarcobatus_vermiculatus_MJM Amaranthus_retro exus 100 100 100 Sesuvium_portulacastrum Amaranthus_cruentus 100 Sesuvium_verrucosum Amaranthus_tricolor Phaulothamnus_spinescens 100 Cypselea_humifusa Zaleya_pentandra Dianthus_caryophyllus 100 Trianthema_portulacastrum 100 Reynoutria_japonica 2 Trianthema_portulacastrum_SRA 100 Honckenya_peploides 8 0 Reynoutria_japonica 100 100 100 Delosperma_echinatum 100 Fallopia_convolvulus 100 Schiedea_membranacea 100 Mesembryanthemum_crystallinum Muehlenbeckia_platyclada 100 Spinacia_oleracea Scleranthus_polycarpos Colobanthus_quitensis 100 Polygonum_aviculare Beta_vulgaris 100 100 Dianthus_caryophyllus 100 Cerastium_fontanum_subsp_vulgare Rumex_acetosa 100 100 Stegnosperma_halimifolium Cerastium_arvense Rumex_hastatulus 100 100 Lepyrodiclis_stellarioides Rumex_palustris 100 9 3 100 Rheum_rhabarbarum Arenaria_serpyllifolia Rheum_nobile 100 Dianthus_caryophyllus 100 6 3 100 Fagopyrum_tataricum 100 Velezia_rigida Fagopyrum_esculentum Saponaria_ocinalis 100 Persicaria_minor2 Gypsophila_repens 100 100 100 Persicaria_minor (d) CARY 100 Silene_latifolia Persicaria_tinctoria 100 100 Silene_latifolia_SRA Persicaria_virginiana Silene_nocti ora 100 100 100 7 7 Ruprechtia_salicifolia 3.0 Silene_conica 100 Pterostegia_drymarioides 100 100 Silene_vulgaris Antigonon_leptopus 100 Silene_vulgaris_ALN Limonium_spectabile 100 100 100 Silene_acaulis_subsp_subacaulescens 8 0 Plumbago_auriculata 100 Silene_paradoxa 100 Reaumuria_trigyna 100 Agrostemma_githago 100 Reaumuria_soongarica 100 Eremogone_hookeri_subsp_desertorum Tamarix_hispida 100 100 Frankenia_laevis Eremogone_procera 100 Dionaea_muscipula (e) NCORE Spergularia_media 100 Aldrovanda_vesiculosa 100 Drymaria_cordata 9 7 100 100 Drosera_binata 100 Drymaria_subumbellata 100 100 Nepenthes_alata 3.0 Illecebrum_verticillatum 100 Nepenthes_alata_SFB Polycarpaea_repens Drosophyllum_lusitanicum Herniaria_latifolia 100 Spinacia_oleracea 100 100 Corrigiola_litoralis 100 Beta_vulgaris Telephium_imperati 100 Dianthus_caryophyllus 100 Beta_vulgaris Microtea_debilis 100 Spinacia_oleracea Physena_madagascariensis 100 Phaulothamnus_spinescens Simmondsia_chinensis 0.42 0.52 Nyctaginaceae_Boerhavia_torreyana 2n=52 Nyctaginaceae_Boerhavia_purpurascens 0.69 Nyctaginaceae_Boerhavia_coccinea_SRA 2n=52 0.4 Nyctaginaceae_Boerhavia_burbidgeana 0.67 Nyctaginaceae_Boerhavia_coccinea 2n=52 0.52 0.23 0.49 Nyctaginaceae_Anulocaulis_eriosolenus 2n=24 Nyctaginaceae_Anulocaulis_leiosolenus_var_gypsogenus 2n=24 0.44 Nyctaginaceae_Nyctaginia_capitata Nyctaginaceae_Cyphomeris_gypsophiloides 0.99 0.18 Nyctaginaceae_Allionia_incarnata2 2n=40 Nyctaginaceae_Allionia_incarnata 2n=40 0.83 0.82 Nyctaginaceae_Mirabilis_jalapa_SRA 2n=58 Figure S3 0.37 Nyctaginaceae_Mirabilis_jalapa 2n=58 Nyctaginaceae_Mirabilis_multi ora 2n=66 0.97 0.59 Nyctaginaceae_Abronia_bigelovii 0.97 Nyctaginaceae_Abronia_nealleyi 2n=92 Nyctaginaceae_Tripterocalyx_crux_maltae 0.4 0.62 Nyctaginaceae_Acleisanthes_chenopodioides 0.54 0.81 Nyctaginaceae_Acleisanthes_lanceolata Nyctaginaceae_Acleisanthes_acutifolia Nyctaginaceae_Acleisanthes_obtusa 0.94 0.69 Nyctaginaceae_Bougainvillea_spectabilis 2n=34 Nyctaginaceae_Bougainvillea_stipitata 2n=34 0.6 0.82 Nyctaginaceae_Pisonia_aculeata 2n=134_136 0.18 Nyctaginaceae_Guapira_obtusata Nyctaginaceae_Pisonia_umbellifera 2n=134_136 0.98 0.51 Petiveriaceae_Hilleria_latifolia 2n=36 0.37 Petiveriaceae_Rivina_humilis 2n=108_126 0.35 Petiveriaceae_Petiveria_alliacea 2n=36 Petiveriaceae_Seguieria_aculeata 0.69 Phytolaccaceae_Phytolacca_bogotensis 2n=36 0.45 0.44 Phytolaccaceae_Phytolacca_americana 2n=18 0.83 0.46 Phytolaccaceae_Anisomeria_littoralis Phytolaccaceae_Phytolacca_dioica 2n=36 Phytolaccaceae_Ercilla_volubilis 1 Sarcobataceae_Sarcobatus_vermiculatus 2n=36 Sarcobataceae_Sarcobatus_vermiculatus_MJM 2n=36 0.46 0.58 0.9 Aizoaceae_Sesuvium_portulacastrum 2n=16 0.5 Aizoaceae_Sesuvium_verrucosum 2n=16 Aizoaceae_Cypselea_humifusa 0.97 Aizoaceae_Zaleya_pentandra 2n=16 0.45 0.83 Aizoaceae_Trianthema_portulacastrum 2n=26_28 Aizoaceae_Trianthema_portulacastrum_SRA 2n=26_28 0.7 Aizoaceae_Mesembryanthemum_crystallinum 2n=18 Aizoaceae_Delosperma_echinatum 2n=54 0.82 0.67 Portulacaceae_Portulaca_surutescens 2n=8 0.62 Portulacaceae_Portulaca_pilosa 2n=8 0.47 Portulacaceae_Portulaca_amilis 2n=18 0.46 Portulacaceae_Portulaca_grandi ora 2n=10_18 Portulacaceae_Portulaca_umbraticola 2n=18 0.98 Portulacaceae_Portulaca_cryptopetala 0.38 0.56 Portulacaceae_Portulaca_oleracea 2n=18 0.06 0.31 Portulacaceae_Portulaca_oleracea_SRA 2n=18 Portulacaceae_Portulaca_molokiniensis 2n=40 0.81 Anacampserotaceae_Talinopsis_frutescens Anacampserotaceae_Anacampseros_lamentosa 2n=18 0.31 0.68 0.38 Cactaceae_Lophophora_williamsii 2n=22 Cactaceae_Echinocereus_pectinatus 2n=22 0.04 Cactaceae_Nopalea_cochenillifera 2n=22 0.11 0.34 0.54 Cactaceae_Pereskia_grandifolia 2n=22 Cactaceae_Pereskia_aculeata 2n=22 0.18 Cactaceae_Leuenbergeria_lychnidi ora 2n=22 Cactaceae_Leuenbergeria_bleo 2n=22 0.37 0.98 0.66 Talinaceae_Talinum_sp Talinaceae_Talinum_paniculatum 2n=24 0.7 Talinaceae_Talinum_portulacifolium 2n=48 Basellaceae_Basella_alba 2n=44_48 0.97 0.55 Montiaceae_Claytonia_virginica 2n=12 to 191 0.18 Montiaceae_Claytonia_nevadensis 2n=14 Montiaceae_Phemeranthus_parvi orus 2n=24 0.33 0.19 Molluginaceae_Mollugo_cerviana 2n=18 0.42 Molluginaceae_Mollugo_nudicaulis 2n=54 Molluginaceae_Mollugo_verticillata 2n=64 Molluginaceae_Mollugo_pentaphylla 2n=18 0.42 0.63 Chenopodiaceae_Atriplex_prostrata 2n=18 Chenopodiaceae_Atriplex_hortensis 2n=18 0.61 Chenopodiaceae_Atriplex_rosea 2n=18 0.94 0.69 Chenopodiaceae_Grayia_spinosa 2n=36 Chenopodiaceae_Extriplex_californica 2n=18 0.4 0.9 Chenopodiaceae_Chenopodium_quinoa 2n=36 0.52 Chenopodiaceae_Chenopodium_giganteum 2n=54 0.66 Chenopodiaceae_Spinacia_oleracea 2n=12 Chenopodiaceae_Krascheninnikovia_lanata 2n=18 Chenopodiaceae_Agriophyllum_squarrosum 2n=18 0.51 0.32 0.47 Chenopodiaceae_Suaeda_fruticosa 2n=18 Chenopodiaceae_Suaeda_linearis 2n=54 0.58 Chenopodiaceae_Bienertia_sinuspersici 2n=18 0.04 0.94 Chenopodiaceae_Salicornia_europaea 2n=18 0.34 0.68 Chenopodiaceae_Salicornia_europaeaGB 2n=18 0.9 0.69 Chenopodiaceae_Haloxylon_ammodendron 2n=18 Chenopodiaceae_Halogeton_glomeratus 2n=18 Chenopodiaceae_Bassia_scoparia 2n=18 0.99 Chenopodiaceae_Beta_maritima 2n=18 Chenopodiaceae_Beta_vulgaris 2n=18 0.54 0.94 Amaranthaceae_Alternanthera_brasiliana Amaranthaceae_Alternanthera_philoxeroides 2n=64 0.61 0.62 Amaranthaceae_Alternanthera_sessilis 2n=28_32_34_40_88 0.94 Amaranthaceae_Alternanthera_caracasana 2n=96 0.19 Amaranthaceae_Alternanthera_tenella 2n=28 0.52 0.68 Amaranthaceae_Blutaparon_vermiculare 2n=30 0.47 0.9 Amaranthaceae_Gossypianthus_lanuginosus Amaranthaceae_Guilleminea_densa_var_aggregata 0.69 Amaranthaceae_Froelichia_latifolia 2n=54 or 58 0.39 Amaranthaceae_Tidestromia_lanuginosa 2n=20 0.58 Amaranthaceae_Aerva_lanata 2n=16 0.63 Amaranthaceae_Aerva_javanica 2n=32 0.82 0.82 Amaranthaceae_Amaranthus_hypochondriacus 2n=32 Amaranthaceae_Amaranthus_hypochondriacus_PAC 2n=32 0.9 Amaranthaceae_Amaranthus_retro exus 2n=32_34 0.9 Amaranthaceae_Amaranthus_tricolor 2n=32_34 Amaranthaceae_Amaranthus_cruentus 2n=32_34 Achatocarpaceae_Phaulothamnus_spinescens 0.61 0.9 Caryophyllaceae_Schiedea_membranacea 2n=44-60 0.2 Caryophyllaceae_Honckenya_peploides 2n=68 0.15 Caryophyllaceae_Scleranthus_polycarpos 2n=44 Caryophyllaceae_Colobanthus_quitensis 2n=80 0.13 1 0.82 Caryophyllaceae_Cerastium_arvense 2n=36 0.21 Caryophyllaceae_Cerastium_fontanum_subsp_vulgare 2n=72 0.13 Caryophyllaceae_Lepyrodiclis_stellarioides 2n=68 Caryophyllaceae_Arenaria_serpyllifolia 2n=20 0.82 0.38 Caryophyllaceae_Velezia_rigida 2n=28 0.45 0.61 Caryophyllaceae_Dianthus_caryophyllus 2n=30 Caryophyllaceae_Gypsophila_repens 2n=34 Caryophyllaceae_Saponaria_ocinalis 2n=28 0.25 Caryophyllaceae_Silene_nocti ora 2n=24 0.49 0.21 Caryophyllaceae_Silene_conica 2n=20_24 0.35 0.81 Caryophyllaceae_Silene_latifolia_SRA 2n=24 Caryophyllaceae_Silene_latifolia 2n=24 0.94 0.7 Caryophyllaceae_Silene_vulgaris 2n=24 0.66 0.7 Caryophyllaceae_Silene_vulgaris_ALN 2n=24 0.82 0.82 Caryophyllaceae_Silene_acaulis_subsp_subacaulescens 2n=24 0.32 Caryophyllaceae_Silene_paradoxa 2n=24 Caryophyllaceae_Agrostemma_githago 2n=24 1 0.5 Caryophyllaceae_Eremogone_hookeri_subsp_desertorum 2n=44_66 Caryophyllaceae_Eremogone_procera 2n=22 Caryophyllaceae_Spergularia_media 2n=18 0.7 0.5 0.49 0.47 Caryophyllaceae_Drymaria_cordata 2n=24_36 0.94 Caryophyllaceae_Drymaria_subumbellata 2n=40_42_44 Caryophyllaceae_Illecebrum_verticillatum 2n=10 0.58 Caryophyllaceae_Polycarpaea_repens 2n=18 Caryophyllaceae_Herniaria_latifolia 2n=18 0.58 0.5 Caryophyllaceae_Corrigiola_litoralis 2n=18 Caryophyllaceae_Telephium_imperati 2n=18 Stegnospermataceae_Stegnosperma_halimifolium Microteaceae_Microtea_debilis 2n=18 Physenaceae_Physena_madagascariensis Simmondsiaceae_Simmondsia_chinensis 2n=52 0.9 0.83 Polygonaceae_Rumex_acetosa 2n=14_15 Polygonaceae_Rumex_hastatulus 2n=18 0.82 Polygonaceae_Rumex_palustris 2n=60 0.9 Polygonaceae_Rheum_rhabarbarum 2n=22 0.68 Polygonaceae_Rheum_nobile 0.58 Polygonaceae_Reynoutria_japonica 2 2n=44 0.47 Polygonaceae_Reynoutria_japonica 2n=44 0.41 0.71 0.33 Polygonaceae_Muehlenbeckia_platyclada 2n=20 Polygonaceae_Fallopia_convolvulus 2n=20 Polygonaceae_Polygonum_aviculare 2n=40_60 0.9 0.94 Polygonaceae_Fagopyrum_tataricum 2n=16 Polygonaceae_Fagopyrum_esculentum 2n=16 0.61 0.97 Polygonaceae_Persicaria_minor 2n=40 0.94 0.97 Polygonaceae_Persicaria_minor2 2n=40 Polygonaceae_Persicaria_tinctoria 2n=40_42_44 Polygonaceae_Persicaria_virginiana 2n=44 0.55 0.57 0.49 Polygonaceae_Pterostegia_drymarioides 2n=28 Polygonaceae_Ruprechtia_salicifolia 2n=28 Polygonaceae_Antigonon_leptopus 2n=14_40_44_48 0.36 0.12 Plumbaginaceae_Limonium_spectabile 2n=18 Plumbaginaceae_Plumbago_auriculata 2n=14 0.94 0.82 Tamaricaceae_Reaumuria_soongarica 2n=22 0.71 Tamaricaceae_Reaumuria_trigyna 2n=22 Tamaricaceae_Tamarix_hispida 2n=24 0.58 Frankeniaceae_Frankenia_laevis 2n=30 0.61 0.71 Droseraceae_Aldrovanda_vesiculosa 2n=48 Droseraceae_Dionaea_muscipula 2n=32 0.29 Droseraceae_Drosera_binata 2n=32 0.54 1 Nepenthaceae_Nepenthes_alata 2n=80 Nepenthaceae_Nepenthes_alata_SFB 2n=80 Drosophyllaceae_Drosophyllum_lusitanicum 2n=12 Nyctaginaceae_Boerhavia_purpurascens 100 12 Nyctaginaceae_Boerhavia_coccinea_SRA 2n=52 100 Nyctaginaceae_Boerhavia_torreyana 2n=52 Nyctaginaceae_Boerhavia_burbidgeana 100 99 Nyctaginaceae_Boerhavia_coccinea 2n=52 Figure S4 100 Nyctaginaceae_Anulocaulis_leiosolenus_var_gypsogenus 2n=24 97 100 Nyctaginaceae_Anulocaulis_eriosolenus 2n=24 100 Nyctaginaceae_Nyctaginia_capitata Nyctaginaceae_Cyphomeris_gypsophiloides 100 75 Nyctaginaceae_Allionia_incarnata2 2n=40 Nyctaginaceae_Allionia_incarnata 2n=40 100 Nyctaginaceae_Mirabilis_jalapa_SRA 2n=58 100 100 Nyctaginaceae_Mirabilis_jalapa 2n=58 Nyctaginaceae_Mirabilis_multi ora 2n=66 100 Nyctaginaceae_Abronia_nealleyi 2n=92 100 100 Nyctaginaceae_Abronia_bigelovii Nyctaginaceae_Tripterocalyx_crux_maltae 100 Nyctaginaceae_Acleisanthes_chenopodioides 100 100 100 Nyctaginaceae_Acleisanthes_lanceolata Nyctaginaceae_Acleisanthes_acutifolia Nyctaginaceae_Acleisanthes_obtusa 100 100 Nyctaginaceae_Bougainvillea_stipitata 2n=34 Nyctaginaceae_Bougainvillea_spectabilis 2n=34 100 Nyctaginaceae_Guapira_obtusata 100 100 Nyctaginaceae_Pisonia_aculeata 2n=134_136 Nyctaginaceae_Pisonia_umbellifera 2n=134_136 100 Petiveriaceae_Hilleria_latifolia 2n=36 100 100 Petiveriaceae_Rivina_humilis 2n=108_126 94 Petiveriaceae_Petiveria_alliacea 2n=36 Petiveriaceae_Seguieria_aculeata 100 Phytolaccaceae_Phytolacca_dioica 2n=36 100 100 Phytolaccaceae_Anisomeria_littoralis 100 100 Phytolaccaceae_Phytolacca_bogotensis 2n=36 Phytolaccaceae_Phytolacca_americana 2n=18 Phytolaccaceae_Ercilla_volubilis 100 Sarcobataceae_Sarcobatus_vermiculatus 2n=36 100 Sarcobataceae_Sarcobatus_vermiculatus_MJM 2n=36 100 Aizoaceae_Sesuvium_portulacastrum 2n=16 100 100 Aizoaceae_Sesuvium_verrucosum 2n=16 Aizoaceae_Cypselea_humifusa 100 Aizoaceae_Zaleya_pentandra 2n=16 100 100 Aizoaceae_Trianthema_portulacastrum_SRA 2n=26_28 Aizoaceae_Trianthema_portulacastrum 2n=26_28 100 Aizoaceae_Delosperma_echinatum 2n=54 Aizoaceae_Mesembryanthemum_crystallinum 2n=18 100 Portulacaceae_Portulaca_surutescens 2n=8 100 100 Portulacaceae_Portulaca_pilosa 2n=8 100 Portulacaceae_Portulaca_amilis 2n=18 100 Portulacaceae_Portulaca_grandi ora 2n=10_18 Portulacaceae_Portulaca_umbraticola 2n=18 100 Portulacaceae_Portulaca_cryptopetala 100 Portulacaceae_Portulaca_oleracea 2n=18 100 100 100 Portulacaceae_Portulaca_oleracea_SRA 2n=18 Portulacaceae_Portulaca_molokiniensis 2n=40 100 Anacampserotaceae_Anacampseros_lamentosa 2n=18 Anacampserotaceae_Talinopsis_frutescens 100 100 Cactaceae_Lophophora_williamsii 2n=22 99 32 Cactaceae_Echinocereus_pectinatus 2n=22 Cactaceae_Nopalea_cochenillifera 2n=22 28 Cactaceae_Leuenbergeria_lychnidi ora 2n=22 100 100 96 Cactaceae_Pereskia_grandifolia 2n=22 Cactaceae_Pereskia_aculeata 2n=22 99 Cactaceae_Leuenbergeria_bleo 2n=22 100 Talinaceae_Talinum_sp 100 Talinaceae_Talinum_paniculatum 2n=24 100 Talinaceae_Talinum_portulacifolium 2n=48 Basellaceae_Basella_alba 2n=44_48 100 Montiaceae_Claytonia_nevadensis 2n=14 100 Montiaceae_Claytonia_virginica 2n=12 to 191 93 Montiaceae_Phemeranthus_parvi orus 2n=24 100 Molluginaceae_Mollugo_nudicaulis 2n=54 91 100 Molluginaceae_Mollugo_cerviana 2n=18 Molluginaceae_Mollugo_verticillata 2n=64 Molluginaceae_Mollugo_pentaphylla 2n=18 98 Chenopodiaceae_Atriplex_hortensis 2n=18 100 Chenopodiaceae_Atriplex_prostrata 2n=18 100 Chenopodiaceae_Atriplex_rosea 2n=18 100 100 Chenopodiaceae_Grayia_spinosa 2n=36 Chenopodiaceae_Extriplex_californica 2n=18 100 100 Chenopodiaceae_Chenopodium_quinoa 2n=36 100 Chenopodiaceae_Chenopodium_giganteum 2n=54 100 Chenopodiaceae_Spinacia_oleracea 2n=12 Chenopodiaceae_Krascheninnikovia_lanata 2n=18 Chenopodiaceae_Agriophyllum_squarrosum 2n=18 100 Chenopodiaceae_Suaeda_fruticosa 2n=18 25 100 Chenopodiaceae_Suaeda_linearis 2n=54 100 Chenopodiaceae_Bienertia_sinuspersici 2n=18 93 100 Chenopodiaceae_Salicornia_europaea 2n=18 100 100 Chenopodiaceae_Salicornia_europaeaGB 2n=18 100 Chenopodiaceae_Halogeton_glomeratus 2n=18 100 Chenopodiaceae_Haloxylon_ammodendron 2n=18 Chenopodiaceae_Bassia_scoparia 2n=18 100 Chenopodiaceae_Beta_vulgaris 2n=18 Chenopodiaceae_Beta_maritima 2n=18 100 Amaranthaceae_Alternanthera_philoxeroides 2n=64 100 Amaranthaceae_Alternanthera_brasiliana 100 100 Amaranthaceae_Alternanthera_sessilis 2n=28_32_34_40_88 100 Amaranthaceae_Alternanthera_caracasana 2n=96 81 Amaranthaceae_Alternanthera_tenella 2n=28 100 Amaranthaceae_Blutaparon_vermiculare 2n=30 100 100 100 Amaranthaceae_Gossypianthus_lanuginosus Amaranthaceae_Guilleminea_densa_var_aggregata 100 Amaranthaceae_Froelichia_latifolia 2n=54 or 58 100 Amaranthaceae_Tidestromia_lanuginosa 2n=20 100 Amaranthaceae_Aerva_javanica 2n=32 100 Amaranthaceae_Aerva_lanata 2n=16 100 Amaranthaceae_Amaranthus_hypochondriacus_PAC 2n=32 100 Amaranthaceae_Amaranthus_hypochondriacus 2n=32 100 Amaranthaceae_Amaranthus_retro exus 2n=32_34 100 Amaranthaceae_Amaranthus_tricolor 2n=32_34 Amaranthaceae_Amaranthus_cruentus 2n=32_34 Achatocarpaceae_Phaulothamnus_spinescens 100 Caryophyllaceae_Schiedea_membranacea 2n=44-60 100 99 Caryophyllaceae_Honckenya_peploides 2n=68 45 Caryophyllaceae_Scleranthus_polycarpos 2n=44 100 Caryophyllaceae_Colobanthus_quitensis 2n=80 100 Caryophyllaceae_Cerastium_fontanum_subsp_vulgare 2n=72 100 Caryophyllaceae_Cerastium_arvense 2n=36 90 88 Caryophyllaceae_Lepyrodiclis_stellarioides 2n=68 Caryophyllaceae_Arenaria_serpyllifolia 2n=20 100 Caryophyllaceae_Dianthus_caryophyllus 2n=30 98 100 100 Caryophyllaceae_Velezia_rigida 2n=28 Caryophyllaceae_Gypsophila_repens 2n=34 Caryophyllaceae_Saponaria_ocinalis 2n=28 71 Caryophyllaceae_Silene_conica 2n=20_24 100 100 Caryophyllaceae_Silene_nocti ora 2n=24 100 100 Caryophyllaceae_Silene_latifolia_SRA 2n=24 Caryophyllaceae_Silene_latifolia 2n=24 100 100 Caryophyllaceae_Silene_vulgaris_ALN 2n=24 100 Caryophyllaceae_Silene_vulgaris 2n=24 100 100 100 Caryophyllaceae_Silene_paradoxa 2n=24 Caryophyllaceae_Silene_acaulis_subsp_subacaulescens 2n=24 100 Caryophyllaceae_Agrostemma_githago 2n=24 100 100 Caryophyllaceae_Eremogone_procera 2n=22 Caryophyllaceae_Eremogone_hookeri_subsp_desertorum 2n=44_66 Caryophyllaceae_Spergularia_media 2n=18 100 Caryophyllaceae_Drymaria_cordata 2n=24_36 100 100 100 100 Caryophyllaceae_Drymaria_subumbellata 2n=40_42_44 Caryophyllaceae_Illecebrum_verticillatum 2n=10 100 Caryophyllaceae_Polycarpaea_repens 2n=18 Caryophyllaceae_Herniaria_latifolia 2n=18 100 100 Caryophyllaceae_Telephium_imperati 2n=18 Caryophyllaceae_Corrigiola_litoralis 2n=18 Stegnospermataceae_Stegnosperma_halimifolium Microteaceae_Microtea_debilis 2n=18 Physenaceae_Physena_madagascariensis Simmondsiaceae_Simmondsia_chinensis 2n=52 100 Polygonaceae_Rumex_acetosa 2n=14_15 100 Polygonaceae_Rumex_hastatulus 2n=18 100 Polygonaceae_Rumex_palustris 2n=60 100 Polygonaceae_Rheum_rhabarbarum 2n=22 100 Polygonaceae_Rheum_nobile 100 Polygonaceae_Fallopia_convolvulus 2n=20 95 Polygonaceae_Muehlenbeckia_platyclada 2n=20 100 100 100 Polygonaceae_Reynoutria_japonica 2 2n=44 Polygonaceae_Reynoutria_japonica 2n=44 Polygonaceae_Polygonum_aviculare 2n=40_60 100 100 Polygonaceae_Fagopyrum_esculentum 2n=16 Polygonaceae_Fagopyrum_tataricum 2n=16 100 Polygonaceae_Persicaria_minor2 2n=40 100 100 100 Polygonaceae_Persicaria_minor 2n=40 Polygonaceae_Persicaria_tinctoria 2n=40_42_44 Polygonaceae_Persicaria_virginiana 2n=44 100 100 Polygonaceae_Ruprechtia_salicifolia 2n=28 100 Polygonaceae_Pterostegia_drymarioides 2n=28 Polygonaceae_Antigonon_leptopus 2n=14_40_44_48 100 75 Plumbaginaceae_Limonium_spectabile 2n=18 Plumbaginaceae_Plumbago_auriculata 2n=14 100 Tamaricaceae_Reaumuria_soongarica 2n=22 100 100 Tamaricaceae_Reaumuria_trigyna 2n=22 Tamaricaceae_Tamarix_hispida 2n=24 100 Frankeniaceae_Frankenia_laevis 2n=30 100 Droseraceae_Aldrovanda_vesiculosa 2n=48 100 Droseraceae_Dionaea_muscipula 2n=32 98 Droseraceae_Drosera_binata 2n=32 100 100 Nepenthaceae_Nepenthes_alata 2n=80 Nepenthaceae_Nepenthes_alata_SFB 2n=80 Drosophyllaceae_Drosophyllum_lusitanicum 2n=12 3 . 0 Figure S5

Boerhavia_torreyana 1.85% Boerhavia_purpurascens 5.16% Boerhavia_coccinea_SRA Boerhavia_coccinea 4.98% Boerhavia_burbidgeana Anulocaulis_leiosolenus_var_gypsogenus 0.08% 3.55% Anulocaulis_eriosolenus 1.07% Nyctaginia_capitata 3.08% Allionia_incarnata2 2.31% 0.98% Allionia_incarnata (a) PHYT Cyphomeris_gypsophiloides 2.08% Mirabilis_jalapa_SRA 3.22% 5.27% Mirabilis_jalapa 0.04 Mirabilis_multiflora 1.64% 1.76% Abronia_bigelovii 45.46% Abronia_nealleyi Tripterocalyx_crux_maltae 0.07% Acleisanthes_lanceolata 2.51% 1.11% Acleisanthes_chenopodioides 2.26% Acleisanthes_acutifolia Acleisanthes_obtusa 4.77% 0.99% Bougainvillea_stipitata Bougainvillea_spectabilis 0.23% Pisonia_aculeata 0.68% 1.55% Guapira_obtusata Pisonia_umbellifera 1.93% Hilleria_latifolia 1.08% Rivina_humilis 1.2% 7.42% Petiveria_alliacea Seguieria_aculeata 0.26% 0% (b) PORT Portulaca_suffrutescens Anisomeria_littoralis 1.56% 2.26% Phytolacca_dioica Portulaca_pilosa 31.28% 1.81% Phytolacca_bogotensis Portulaca_amilis 9.68% 0.04 0.48% 0.41% Phytolacca_americana Portulaca_grandiflora 0.93% Ercilla_volubilis Portulaca_umbraticola 4.73% Sarcobatus_vermiculatus 4.52% Portulaca_cryptopetala Sarcobatus_vermiculatus_MJM 3.17% 2.38% Portulaca_oleracea Sesuvium_portulacastrum 1.27% 5.76% Sesuvium_verrucosum 0.19% Portulaca_oleracea_SRA 0.49% Cypselea_humifusa Portulaca_molokiniensis 3.1% Zaleya_pentandra 0.06% Talinopsis_frutescens 7.81% 0.6% Trianthema_portulacastrum Anacampseros_filamentosa 1.82% outgroup Trianthema_portulacastrum_SRA 0.4% Lophophora_williamsii 0.55% Delosperma_echinatum 0.24% Echinocereus_pectinatus Mesembryanthemum_crystallinum 1.34% Nopalea_cochenillifera Pereskia_aculeata 3.86% 6.66% Pereskia_grandifolia Leuenbergeria_lychnidiflora Leuenbergeria_bleo 1.6% 1.85% Talinum_paniculatum 0.73% Talinum_sp 17.18% Talinum_portulacifolium Basella_alba 18.27% Claytonia_nevadensis 0.39% 22.06% Claytonia_virginica Phemeranthus_parviflorus Mollugo_nudicaulis 0.48% Mollugo_cerviana 1.97% Mollugo_verticillata outgroup Mollugo_pentaphylla Figure S5

0.05% Atriplex_prostrata 1.11% Atriplex_hortensis AMAR 1.26% Atriplex_rosea (c) 0.23% 3.57% Extriplex_californica Grayia_spinosa 0.27% 1.6% Chenopodium_giganteum 0.04 0.28% Chenopodium_quinoa 0.29% Spinacia_oleracea Krascheninnikovia_lanata Agriophyllum_squarrosum Suaeda_fruticosa 0.79% 0.15% Suaeda_linearis 5.34% Bienertia_sinuspersici 3.56% Salicornia_europaea 1.16% 0.47% Salicornia_europaeaGB 0.57% Haloxylon_ammodendron 0.42% Halogeton_glomeratus Bassia_scoparia 0.56% Beta_vulgaris Beta_maritima 3.21% Alternanthera_philoxeroides 11.07% Alternanthera_brasiliana 4.69% Alternanthera_sessilis 2.82% 0.93% Alternanthera_caracasana 1.51% Alternanthera_tenella 0.11% Blutaparon_vermiculare 1.14% Gossypianthus_lanuginosus 5.08% 2.36% Guilleminea_densa_var_aggregata 35.09% Froelichia_latifolia Tidestromia_lanuginosa 0.25% Aerva_lanata outgroup 0.59% Aerva_javanica 5.25% Amaranthus_hypochondriacus 2.41% Amaranthus_hypochondriacus_PAC 1.9% Cerastium_arvense 24.18% 1.44% Amaranthus_retroflexus Cerastium_fontanum_subsp_vulgare 0.27% Amaranthus_cruentus Lepyrodiclis_stellarioides 0.68% Amaranthus_tricolor Arenaria_serpyllifolia 0.41% 5.02% Honckenya_peploides 1.42% Schiedea_membranacea Scleranthus_polycarpos 1.05% 0.27% Colobanthus_quitensis 0.63% Velezia_rigida 0.14% Dianthus_caryophyllus 0.9% Gypsophila_repens Saponaria_officinalis 0.41% Silene_latifolia (d) CARY 20.32% 0.53% Silene_latifolia_SRA Silene_conica 1.64% Silene_noctiflora 0.94% 0.04 5.53% Silene_vulgaris_ALN Silene_vulgaris 20.19% 2.89% 0.57% Silene_paradoxa Silene_acaulis_subsp_subacaulescens Agrostemma_githago 0.97% 2.55% Eremogone_procera 0.39% Eremogone_hookeri_subsp_desertorum Spergularia_media 2.39% Drymaria_cordata 0.24% 0.33% Drymaria_subumbellata 0.51% Illecebrum_verticillatum 1.37% Polycarpaea_repens Herniaria_latifolia 0.07% Telephium_imperati outgroup Corrigiola_litoralis Figure S5

0.5% Rumex_hastatulus 0.44% Rumex_acetosa 2.51% Rumex_palustris 1.31% Rheum_nobile Rheum_rhabarbarum 2.83% 4.19% Reynoutria_japonica (e) NCORE 2.64% Reynoutria_japonica 2 2.08% 6.96% Fallopia_convolvulus Muehlenbeckia_platyclada Polygonum_aviculare 0.04 2.22% Fagopyrum_tataricum 16.5% Fagopyrum_esculentum 3.19% Persicaria_minor2 6.28% Persicaria_minor 34.21% 7.38% Persicaria_tinctoria Persicaria_virginiana

1.25% 0.74% Ruprechtia_salicifolia 3.64% Pterostegia_drymarioides Antigonon_leptopus 0.38% Plumbago_auriculata 0.29% Limonium_spectabile 0.94% Reaumuria_trigyna 5.21% Reaumuria_soongarica 3.89% Tamarix_hispida 1.15% Frankenia_laevis 0.19% Aldrovanda_vesiculosa 2.95% Dionaea_muscipula 1.73% Drosera_binata 1.26% 14.5% Nepenthes_alata_SFB Nepenthes_alata Drosophyllum_lusitanicum Figure S6 (a) PHYT Aizoaceae Aizoaceae Aizoaceae Aizoaceae Aizoaceae Aizoaceae Cypselea_humifusa Delosperma_echinatum Mesembryanthemum_crystallinum Sesuvium_portulacastrum Sesuvium_verrucosum Trianthema_portulacastrum 200 600 300 250 3000 800 500 250 150 200 400 600 200 2000 150 100 300 150 400 100 200 100 1000 50 200 50 50 100 500 0 0 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0

Nyctaginaceae Nyctaginaceae Aizoaceae_Zaleya_pentandra Nyctaginaceae Aizoaceae Abronia_bigelovii Abronia_nealleyi Acleisanthes_acutifonia Nyctaginaceae 300 2500

8000 Acleisanthes_chenopodioides 800 Trianthema_portulacastrum_SRA 2500 10000

250 PHYT1 2000 PHYT1 PHYT1 2000 8000 6000 600 200 PHYT2 1500 1500 6000 150 4000 400

PHYT1 1000 PHYT2 1000 4000 PHYT2 100 PHYT2 200 2000 500 500 50 2000 0 0 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0

Nyctaginaceae PHYT1 Nyctaginaceae Nyctaginaceae Nyctaginaceae Nyctaginaceae PHYT1 Allionia_incarnata2 Nyctaginaceae PHYT1 Acleisanthes_lanceolata Acleisanthes_obtusa 350 Allionia_incarnata Anulocaulis_eriosolenus Anulocaulis_leiosolenus PHYT1 PHYT1 2000 var_gypsogenus 3000 800 800 300 PHYT2 PHYT2 300 250 PHYT1 1500 600 600 PHYT2 PHYT2 200 2000 200

1000 PHYT2 400 400 150

PHYT2 100 1000 100 500 200 200 50 500 0 0 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0

PHYT1 PHYT1 Nyctaginaceae Nyctaginaceae Nyctaginaceae Nyctaginaceae Nyctaginaceae Nyctaginaceae 700 800 2500 1000 Boerhavia_burbidgeana Boerhavia_coccinea 2500 Boerhavia_coccinea_SRA Boerhavia_purpurascens Boerhavia_torreyana Bougainvillea_spectabilis 1500 600 2000 800 2000 600 PHYT1 500 PHYT1 1000 1500 PHYT1

PHYT2 PHYT2 600 400 1500

400 PHYT2

300 PHYT2 1000 400

1000 PHYT2 PHYT2 500 200 200 500 200 500 100 0 0 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 Figure S6 (a) PHYT (continued) Nyctaginaceae Nyctaginaceae Nyctaginaceae Nyctaginaceae Nyctaginaceae Nyctaginaceae PHYT1 PHYT1 1000

Bougainvillea_stipitata Cyphomeris_gypsophiloides Guapira_obtusata 1000 Mirabilis_jalapa Mirabilis_jalapa_SRA PHYT1 Mirabilis_multiflora 1200 500 2500 800 1500 800 PHYT1 PHYT2 1000 400 2000 PHYT2 600 800 600 1000 300 1500 PHYT2 PHYT2 PHYT2 600

PHYT2 400 400 200 1000 400 500 200 200 100 500 200 0 0 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0

PHYT2 Nyctaginaceae Nyctaginaceae Nyctaginaceae Nyctaginaceae Phytolaccaceae PHYT2 Phytolaccaceae 5000

Nyctaginia_capitata Pisonia_aculeata 600 Pisonia_umbellifera Tripterocalyx_crux_maltae Anisomeria_littoralis Ercilla_volubilis 3000 4000 600 1500 4000 500 3000

PHYT1 400 2000 3000 400 1000 PHYT1 PHYT2 300 2000

2000 PHYT2

PHYT2 200

1000 PHYT2 500 200 1000 1000 100 500 0 0 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0

PHYT2 Phytolaccaceae PHYT2 Phytolaccaceae PHYT2 Phytolaccaceae Petiveriaceae Petiveriaceae Petiveriaceae Phytolacca_americana Phytolacca_bogotensis Phytolacca_dioica PHYT2 Hilleria_latifolia Petiveria_alliacea Rivina_humilis PHYT2 400 600 6000 300 400 400 500 5000 250 300 300 300 400 4000 200 200 300 3000 150 200 200 PHYT2 200 2000 100 100 100 100 50 100 1000 0 0 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0

Sarcobataceae Rivinaceae Sarcobataceae Stegnospermataceae Sarcobatus_vermiculatus Sarcobatus_vermiculatus_MJM Stegnosperma_halimifolium

Seguieria_aculeata 12000 2500 12000 10000 300 10000 2000 PHYT2 8000 8000

1500 PHYT2 200 6000 6000 1000 4000 Backbone 4000

100 PHYT2 500 2000 2000 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 Figure S6 (b) PORT Anacampserotaceae Anacampserotaceae Basellaceae Cactaceae Cactaceae Cactaceae Anacampseros_filamentosa Talinopsis_frutescens Basella_alba Echinocereus_pectinatus Leuenbergeria_bleo Leuenbergeria_lychnidiflora 400 2000 5000 5000 5000 4000 PORT2 300 4000 1500 4000 PORT1 4000 3000 3000 3000 3000 200 1000 2000 2000 2000

PORT1 PORT1 2000 PORT1 PORT1 PORT1 500 100 1000 1000 1000 1000 0 0 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0

Cactaceae Cactaceae Cactaceae Cactaceae Caryophyllaceae Molluginaceae PORT1 Lophophora_williamsii Nopalea_cochenillifera Pereskia_aculeata Pereskia_grandifolia Dianthus_caryophyllus Mollugo_cerviana 2500 4000 30 300 250 200 25 2000 250 200 3000 20 150 200 1500 150 15 2000 150 PORT1 100

PORT1 1000 100 PORT1 10 100 1000 50 500 50 5 50 0 0 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0

Molluginaceae Molluginaceae Molluginaceae Montiaceae Montiaceae Montiaceae Mollugo_nudicaulis Mollugo_pentaphylla Mollugo_verticillata Claytonia_nevadensis Claytonia_virginica Phemeranthus_parviflorus 5000 1400 1200 200 10000 3000 1200 4000 1000 8000 1000 150 800 3000 2000 800 PORT3 6000

600 PORT4 100 600 PORT3 PORT1 2000

PORT1 4000

400 PORT1 400 1000 50 1000 2000 200 500 200 0 0 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0

Portulacaceae Portulacaceae Portulacaceae Portulacaceae Portulacaceae Portulacaceae

300 Portulaca_amilis Portulaca_cryptopetala Portulaca_grandiflora Portulaca_molokiniensis Portulaca_oleracea Portulaca_oleracea_SRA 500 800 800 200

250 PORT1 4000 PORT1 400 600 600 200 150 3000 300 PORT1

150 PORT1 PORT1 400 400 100 2000 200

100 PORT1 200 200 50 1000 100 50 0 0 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 Figure S6 (b) PORT continued PORT1 Portulacaceae Portulacaceae Portulacaceae Talinaceae Talinaceae Talinaceae Portulaca_pilosa Portulaca_suffrutescens Portulaca_umbraticola Talinum_paniculatum Talinum_portulacifolium Talinum_sp 250 400 600 PORT1 PORT1 2500 200 200 PORT1 200 500 2000 300 150 150 400 150

1500 PORT1 200 300 PORT1 100 100 100 1000 200 100 50 50 50 500 100 0 0 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 Figure S6 (c) AMAR Achatocarpaceae Amaranthacea Amaranthaceae Amaranthaceae Amaranthaceae Amaranthaceae Phaulothamnus_spinescens Aerva_javanica Aerva_lanata Alternanthera_brasiliana Alternanthera_caracasana Alternanthera_philoxeroides 350 14000 1400 1000 800 300 1200 800

800 AMAR2 250 1000 10000 600 600 600 Backbone 200 800 AMAR1 AMAR1 AMAR1 400 150 600 6000 400 400 100 400 200 200 200 50 200 2000 0 0 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0

AMAR1 AMAR1 Amaranthaceae Amaranthacea Amaranthaceae Amaranthacea Amaranthaceae Amaranthaceae

Alternanthera_sessilis Alternanthera_tenella AMAR3Amaranthus_cruentus Amaranthus_hypochondriacus_PAC Amaranthus_retroflexus 300 Amaranthus_tricolor 300 3000 600 500 AMAR3 250 400 250 2500 500 400 AMAR3 200 200 300 2000 400 300 150 150 300 1500

200 AMAR3 200 100 100 200 1000 100 100 50 50 500 100 0 0 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0

Amaranthaceae Amaranthacea Amaranthaceae Amaranthaceae Amaranthaceae Chenopodiaceae Blutaparon_vermiculare Froelichia_latifolia Gossypianthus_lanuginosus Guilleminea_densa_var_aggregata Tidestromia_lanuginosa Agriophyllum_squarrosum 600

AMAR1 3000 3000

AMAR1 500 4000 6000 300 2500 2500 400 3000 2000 2000 4000 200 300 1500 1500

2000 AMAR1 AMAR1

200 AMAR1 1000 1000 2000 100 1000 100 500 500 0 0 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0

Chenopodiaceae Chenopodiaceae Chenopodiaceae Chenopodiaceae Chenopodiaceae Chenopodiaceae

Atriplex_hortensis Atriplex_prostrata 400 Atriplex_rosea Bassia_scoparia Beta_maritima Beta_vulgaris 250 400 400 300 150 200 300 300 300 150 200 100 200 200 200 100 50 100 100 100 100 50 0 0 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 Figure S6 (c) AMAR continued Chenopodiaceae Chenopodiaceae Chenopodiaceae Chenopodiaceae Chenopodiaceae Chenopodiaceae Bienertia_sinuspersici Chenopodium_giganteum Chenopodium_quinoa Extriplex_californica Grayia_spinosa Halogeton_glomeratus 1000 5000 4000 4000 1500 3000 800 4000 3000 3000 600 3000 1000 2000 2000 2000 400 2000 500 1000 1000 1000 200 1000 0 0 0 0 0 0

0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0

Chenopodiaceae Chenopodiaceae Chenopodiaceae Chenopodiaceae Chenopodiaceae Chenopodiaceae Haloxylon_ammodendron_W Krascheninnikovia_lanata Salicornia_europaeaGB Salicornia_europaea Spinacia_oleracea Suaeda_fruticosa 5000 8000 4000 400 400 800 4000 6000 3000 300 300 600 3000 4000 2000 200 200 400 2000 2000 100 1000 100 200 1000 0 0 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0

Chenopodiaceae Suaeda_linearis 10000 5000 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 Figure S6 (d) CARY CARY2 Caryophyllaceae CARY6 Caryophyllaceae Achatocarpaceae Caryophyllaceae Caryophyllacea Caryophyllaceae Cerastium_fontanum_subsp_vulgare Colobanthus_quitensis Phaulothamnus_spinescens Agrostemma_githago Arenaria_serpyllifolia CARY1 Cerastium_arvense CARY2 CARY6 10000 6000 1000 25000 4000 (BLASTN, (BLASTN, 6000

400 zoomed in) zoomed in) 5000 12000 8000 800 20000 3000 300 4000 6000 8000 600 AMAR4 (outgroup) 3000 15000 3000 2000 200 4000 400 10000 CARY1 4000 1000 2000 CARY1

CARY1 0

1000 CARY1 100 0

200 0.0 0.2 0.4 0.6 0.8 2000 5000

1000 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0 0 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0

CARY7 Caryophyllaceae Caryophyllaceae Caryophyllaceae Caryophyllaceae Caryophyllaceae Caryophyllaceae Corrigiola_litoralis Dianthus_caryophyllus Drymaria_cordata Drymaria_subumbellata_H Eremogone_hookeri_subsp_desertorum Eremogone_procera 7000 800 30 2000 10000 3000

25 CARY1 8000 600 5000 1500 20 2000 6000 400 15 1000

CARY7 3000 4000

10 CARY1 CARY1 1000 200 500 2000 5 500 1000 0 0 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0

CARY3 Caryophyllaceae Caryophyllaceae Caryophyllaceae Caryophyllaceae Caryophyllaceae Caryophyllaceae Gypsophila_repens Herniaria_latifolia Honckenya_peploides Illecebrum_verticillatum Lepyrodiclis_stellarioides Polycarpaea_repens 10000 8000 2000 4000 200 1500 8000 6000 1500 3000 150 6000 1000

4000 CARY1 1000 2000 100 CARY1 4000 CARY1 500 500 2000 50 1000 2000 0 0 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0

CARY1 CARY5 Caryophyllaceae Caryophyllaceae Caryophyllaceae Caryophyllaceae Caryophyllaceae Caryophyllaceae Saponaria_officinalis Schiedea_membranacea Scleranthus_polycarpos Silene_acaulis_subsp_subacaulescens Silene_conica CARY1 Silene_latifolia 1200 300 1200 200 8000 4000 1000 250 1000 CARY4 150 800 6000 800 200 3000 CARY1 CARY1 600 600 150 100 4000 2000 CARY1 400 400 CARY1 100 50 2000 1000 50 200 200 0 0 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 Figure S6 (d) CARY (continued) Caryophyllaceae Caryophyllaceae Caryophyllaceae Caryophyllaceae Caryophyllaceae Caryophyllaceae Silene_latifolia_SRA Silene_noctiflora Silene_paradoxa Silene_vulgaris Silene_vulgaris_ALN Telephium_imperati 3000 1200 2000 2000 2000 1500 2500 1000 1500 1500 2000 1500

800 CARY1 CARY1 1000 CARY1 CARY1 CARY1 1500 600 1000 1000 1000 1000 400 500 500 500 500 500 200 0 0 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0

Caryophyllaceae Caryophyllaceae Velezia_rigida Spergularia_media 2000 200 1500 150 1000 CARY1 100 500 50 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 Figure S6 (e) NCORE Droseraceae Droseraceae Droseraceae Drosophyllaceae Frankeniaceae Microteaceae

600 NCORE4 Aldrovanda_vesiculosa Dionaea_muscipula Drosera_binata Drosophyllum_lusitanicum Frankenia_laevis Microtea_debilis 500 250 20000

NCORE5 4000 500 400 1500 200 15000 3000 400 300 150 1000 300 10000 2000 200 100 200 NCORE5 500 5000 1000 50 NCORE5 100 100 0 0 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0

NCORE6 Backbone NCORE1 Nepenthaceae Nepenthaceae Physenaceae Plumbaginaceae Plumbaginaceae Polygonaceae Nepenthes_alata Nepenthes_alata_SFB Physena_madagascariensis Limonium_spectabile Plumbago_auriculata Antigonon_leptopus 120 300 400 8000 800 100 300 250

300 NCORE2 80 6000 200 600 200 60 150 200 NCORE2 4000 400

NCORE6 40 100 100 100 2000 200 20 50 0 0 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0

Polygonaceae Polygonaceae Polygonaceae NCORE1 Polygonaceae Polygonaceae Polygonaceae Reynoutria_japonica 2 Fagopyrum_esculentum Fagopyrum_tataricum Fallopia_convolvulus Muehlenbeckia_platyclada Persicaria_minor2 1500 250 2500 3000 6000 1500 200 2500 2000 5000 1000 2000 4000 150 1000 NCORE1 NCORE1 1500 NCORE1 NCORE1 1500 3000 100

NCORE1 1000 500 1000 500 2000 50 500 500 1000 0 0 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0

Polygonaceae Polygonaceae Polygonaceae Polygonaceae Polygonaceae Polygonaceae Persicaria_minor Persicaria_tinctorium Persicaria_virginiana Polygonum_aviculare Pterostegia_drymarioides Reynoutria_japonica 12000 8000 5000 2500 2500 1000 10000 4000 2000 6000 2000 800 8000 NCORE1 3000 1500 1500 600 6000 NCORE1 NCORE1 4000 NCORE1 2000 1000 1000 NCORE1 400 4000 NCORE1 2000 500 1000 500 200 2000 0 0 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 Figure S6 (e) NCORE continued Polygonaceae Polygonaceae Polygonaceae Polygonaceae Polygonaceae Polygonaceae Rheum_nobile Rheum_rhabarbarum Rumex_acetosa Rumex_hastatulus Rumex_palustris Ruprechtia_salicifolia 3000 2000 6000 1500 2000 2500 2500

5000 NCORE1 2000 1500 1500 2000 4000 1000

NCORE1 1500 1500 1000 3000 1000 NCORE1 NCORE1 NCORE1 NCORE1 1000 1000 500 2000 500 500 500 500 1000 0 0 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0

Simmondsiaceae Tamaricaceae Tamaricaceae Tamaricaceae Simmondsia_chinensis Reaumuria_soongarica Reaumuria_trigyna Tamarix_hispida 300 600 2000 250 500 3000 Backbone 1500 200

400 NCORE3 2000 150 300 NCORE3 1000 NCORE3 100 200 1000 500 50 100 0 0 0 0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0