Vol. 67 (2) • April 2018 International Journal of Taxonomy, Phylogeny and Evolution Electronic Supplement to Phylogeny and systematics of the tribe Thlaspideae (Brassicaceae) and the recognition of two new genera Shokouh Esmailbegi, Ihsan A. Al-Shehbaz, Milan Pouch, Terezie Mandáková, Klaus Mummenhoff, Mohammad Reza Rahiminejad, Mansour Mirtadzadini & Martin A. Lysak Taxon 67: 324–340 (https://doi.org/10.12705/672.4) https://doi.org/10.12705/672.4.S1 (DNA sequence alignment: https://doi.org/10.12705/672.4.S2) TAXON 67 (2) • April 2018 Electr. Suppl. to: Esmailbegi & al. • Phylogeny and systematics of Thlaspideae (Brassicaceae) Table S1. ITS and trnL-F primers used in phylogenetic study. Gene Primer Sequence Reference ITS ITS1 TCC GTA GGT GAA CCT GCG G White & al., 1990 ITS4 TCC TCC GCT TAT TGA TAT GC White & al., 1990 ITS-18F GGA AGG AGA AGT CGT AAC AAG G Mummenhoff & al., 1997 trnL-F tabC CGA AAT CGG TAG ACG CTA CG Shaw & al., 2005 tabF ATT TGA ACT GGT GAC ACG AG Shaw & al., 2005 White, T.J., Bruns, T., Lee, S. & Taylor, J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. Pp. 315–322 in: Innis, M.A., Gelfand, D.H., Sninsky, J.J. & White, T.J. (eds.), PCR protocols: A guide to methods and applications. San Diego: Academic Press. Mummenhoff, K., Franzke, A. & Koch, M. 1997. Molecular data reveal convergence in fruit characters used in the classification of Thlaspi s.l. (Brassicaceae). Bot. J. Linn. Soc. 125: 183–199. https://doi.org/10.1111/j.1095-8339.1997.tb02253.x Shaw, J., Lickey, E., Beck, J.T., Farmer, S.B., Liu, W., Miller, J., Siripun, K.C., Winder, C.T., Schilling, E.E. & Small, R.L. 2005. The tortoise and the hare II: Relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Amer. J. Bot. 92: 142–166. https://doi.org/10.3732/ajb.92.1.142 Table S2. List of accessions with chromosome counts. Chromosome Species Collector, number (herbarium) Origin number Alliaria petiolata Esmailbegi 2092 (MIR) Austria, Vienna, Lainzer Tiergarten 2n = 42 Alliaria petiolata Esmailbegi 2093 (MIR) Czech Republic, Brno, near the Lesni bus stop 2n = 42 Alliaria petiolata Esmailbegi & Al-Shehbaz 2091 (MIR) France, Paris, Jardin Botanique 2n = 42 Alliaria petiolata Doostmohammadi 2090 (MIR) Iran, Tehran, Darband 2n = 42 Didymophysa aucheri Mirtadzadini 1759 (MIR) Iran, NW of Tar lake 2n = 14 Elburzia fenestrata Mirtadzadini 1758a (MIR) Iran, 5 km W of Gachsar 2n = 14 Graellsia saxifragifolia Mirtadzadini 1780c (MIR) Iran, Kerman, Rabor 2n = 14 Graellsia stylosa Esmailbegi 1744 (MIR) Iran, Darband 2n = 14 Parlatoria cakiloidea Lysak & al. s.n. (Lysak) Turkey, Antalya, Gazipaşa, Sugözü village, Atçıl hill 2n = 14 Parlatoria cakiloidea Ahmad & al. 17_1107 (MIR) Iraq, Sulaimani Province, Qaiwan mt. 2n = 14 Peltaria turkmena Joharchi 45111 (FUMH) Iran, NW of Neyshabur, Bar waterfall 2n = 14 Peltaria angustifolia Lysak & al. s.n. (Lysak) Turkey, Antalya, Gazipaşa, Sugözü village 2n = 14 Peltariopsis grossheimii Mirtadzadini 1827e (MIR) Iran, Azarbaijan, 15 km S of Tshaldoran 2n = 14 Peltariopsis planisiliqua Mirtadzadini 1777e (MIR) Iran, between Sufian and Marand, SW of Yam village 2n = 14 Pseudocamelina aphragmodes Mirtadzadini 1787 (MIR) Iran, between Sisakht and Padena 2n = 14 Pseudocamelina campylocarpa Mirtadzadini 1754 (MIR) Iran, Kerman, Khane-Sorkh neck 2n = 14 Pseudocamelina glaucophylla Maroofi 12763 (Sanandaj) Iran, Kurdistan 2n = 14 Pseudocamelina kermanica Mirtadzadini 1784 (MIR) Iran, Kerman, Shahrbabak, Meymand 2n = 14 Thlaspi arvense Lysak & al. s.n. (Lysak) Czech Republic, Brno 2n = 14 Thlaspi ceratocarpum Özüdoğru 3661 (HUB) Turkey, Erzincan, Refahiye, SW of Sağlık village 2n = 14 S1 TAXON 67 (2) • April 2018 Electr. Suppl. to: Esmailbegi & al. • Phylogeny and systematics of Thlaspideae (Brassicaceae) Fig. S1. Bayesian 50% majority- genus tribe lineage S. caucasica Georgia rule consensus tree inferred from 0.99/92 S. caucasica Georgia S. truncata Georgia ITS. Numbers above branches are 1.0/84 S. caucasica Georgia S. clavata Armenia Sobolewskia 1.0/100 Bayesian posterior probabilities S. sibirica Ukraine S .clavata Armenia A. petiolata Georgia 2x and ML bootstrap values (support 0.76/56 A. petiolata Iran 0.59/– < 50% marked by “–”). An asterisk 1.0/78 A. petiolata Armenia Alliaria 1.0/81 A. taurica Georgia (*) represents collapsed nodes in 0.55/– A. petiolata Iran 6x Asia A. petiolata Iran the ML analysis. Clades B to D 1.0/100 P. rostrata Iran 0.99/55 1.0/93 P. rostrata Iran were used to compare the congru- 1.0/100 P. rostrata Iran Lysakia P. rostrata Iran ency between ITS and trnL-F P. macrophyllum Georgia 1.0/100 P. macrophyllum Armenia cladograms. The generic names 0.98/64 P. macrophyllum Pachyphragma reflect the new taxonomy applied in B 1.0/100 P. digitata Georgia 1.0/57 P. digitata Georgia Pseudovesicaria the present study. 0.59/79 A. petiolata France 1.0/97 A. petiolata Austria A. petiolata Czech Republic A. petiolata Austria Alliaria 0.99/89 A. petiolata U.S.A. A. petiolata Slovakia Europe & U.S.A. 1.0/96 A. petiolata Austria A. petiolata P. cakiloidea Iran 1.0/99 P. cakiloidea Iran Parlatoria 0.98/60 P. cakiloidea Iran 1.0/69 G. stylosa Iran 0.9/65 G. stylosa Iran G. saxifragifolia Iran 0.99/77 G. longistyla W Iran 0.78/ G. longistyla W Iran Thlaspideae * 0.67/65 G. saxifragifolia Iran G. isfahan Iran 1.0/99 G. saxifragifolia SE Iran Graellsia C G. saxifragifolia SE Iran G. integrifolia Iran 1.0/100 0.94/60 G. integrifolia Iran 0.9/56 G. integrifolia Afghanistan 1.0/96 G. graellsiifolia Tajikistan G. graellsiifolia Tajikistan 1.0/100 G. davisiana Turkey G. davisiana Turkey exp. 1.0/91 P. campylocarpa Iran P. campylocarpa Iran 0.66/67 P. glaucophylla Iran II P. campylopoda Iran P. glaucophylla Iran P. glaucophylla Iran 0.95/63 P. glaucophylla Iran 1.0/92 P. glaucophylla Iran P. aphragmodes Iran Pseudocamelina P. campylocarpa Iran P. kleinii Iran 1.0/91 P. glaucophylla Iran P. kermanica Iran 1.0/95 P. kurdica Iran P. kermanica Iran A P. bakhtiarica Iran 0.52/– D. fedtschenkoana Afghanistan 1.0/100 D. fedtschenkoana Tajikistan 0.58/– D. fedtschenkoana Uzbekistan D. aucheri Iran Didymophysa 1.0/99 1.0/100 E. fenestrata Iran E. fenestrata Iran D. aucheri Iran 1.0/89 0.92/59 P. alliacea 1.0/100 P. alliacea Austria P. alliacea Croatia 1.0/99 P. angustifolia Iran A1.0/87 0.94/64 P. angustifolia Iran Peltaria P. angustifolia Turkey 1.0/100 P. turkmena Iran P. turkmena 0.99/97 T. arvense U.S.A. A 0.98/89 T. arvense Japan 1.0/100 T. huetii Turkey Thlaspi 0.53/69 T. ceratocarpum 0.62/57 T. ceratocarpum Turkey P. grossheimi Iran 1.0/100 D P. grossheimii Turkey 1.0/100 P. planisiliqua Peltariopsis 1.0/99 P. planisiliqua Iran P. planisiliqua Turkey 0.98/100 T. alliaceum 0.99/– A T. alliaceum U.S.A. 1.0/99 T. alliaceum U.S.A. Mummenhoffia T. oliveri Ethiopia Sisymbrium altissimum Sisymbrieae Isatis tinctoria Isatideae 0.96/72 Streptanthus glandulosus Thelypodieae II Brassica nigra Raphanus sativus Brassiceae 1.0/79 Eutremaedwardsii Eutremeae Eutrema salsugineum Heliophila coronopifolia Heliophileae 0.64/ Cochlearia officinalis Cochlearieae * Calepina irregularis Calepineae 0.94/ Arabis alpina Draba nuda Arabideae 1.0/100* Brayopsis colombiana exp. 0.91/– Eudema nubigena Eudemeae 1.0/96 Mathewsia peruviana II 0.76/– Schizopetalon walkeri Schizopetaleae Noccaea caerulescens Coluteocarpeae Aphragmus oxycarpus 0.88/52 Aphragmeae 0.83/ Lobularia libyca Anastaticeae * Cremolobus subscandens Cremolobeae 1.0/84 Berteroa incana Alysseae Alyssum lenense Dontostemon integrifolius Dontostemoneae 0.88/– Hesperis sibirica Hesperideae Chorispora tenella Chorisporeae III S2 TAXON 67 (2) • April 2018 Electr. Suppl. to: Esmailbegi & al. • Phylogeny and systematics of Thlaspideae (Brassicaceae) Fig. S2. Bayesian 50% majority-rule consen- genus tribe lineage sus tree inferred from trnL-F. Numbers above P. kermanica Iran branches are Bayesian posterior probabili- P. campylocarpa Iran 0.83/88 P. aphragmodes Iran ties and ML bootstrap values (support < 50% P. kermanica Iran marked by “–”). An asterisk (*) represents 1.0/97 P. campylocarpa Iran P. glaucophylla Iran collapsed nodes in the ML analysis. Clades A P. bakhtiarica Iran Pseudocamelina to D were used to compare the congruency be- P. glaucophylla Iran P. glaucophylla Iran tween ITS and trnL-F clado- 1.0/100 P. glaucophylla Iran P. campylocarpa Iran grams. The generic names P. glaucophylla Iran 1.0/84 reflect the new taxonomy P. kleinii Iran applied in the present study. 1.0/92 P. turkmena Iran 1.0/99 P. angustifolia Turkey Peltaria P. alliacea Austria A 1.0/92 D. aucheri Iran 1.0/88 1.0/100 E. fenestrata Iran D. aucheri Iran 1.0/100 D. fedtschenkoana Uzbekistan Didymophysa D. fedtschenkoana Afghanistan 0.89/77 D. fedtschenkoana Tajikistan 1.0/100 T. alliaceum U.S.A 1.0/100 T. alliaceum U.S.A 1.0/69 Mummenhoffia T. oliveri Ethiopia T. arvense Japan 1.0/93 T. arvense U.S.A 1.0/100 T. huetii Turkey Thlaspi T. huetii Turkey T. ceratocarpum Turkey A. petiolata U.S.A A. petiolata 0.99/68 A. petiolata Croatia Alliaria A. petiolata France Europe & U.S.A. Thlaspideae A. petiolata Austria A. petiolata Czech Republic A. petiolata Armenia 0.96/60 A. petiolata Iran A. taurica Georgia Alliaria Asia exp. 1.0/84 A. petiolata Georgia 2x A. petiolata Iran 6x S. clavata Armenia II 1.0/58 S. clavata Armenia S. truncata Georgia Sobolewskia 0.6/ S. caucasica Georgia * 1.0/100 P. rostrata Iran P. rostrata Iran Lysakia B P. rostrata Iran 0.66/ 1.0/99 P.