#NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Generated on July 12, 2025; 10:59 GMT TreeBASE (cc) 1994-2008 Study reference: Farmer S., & Schilling E. 2002. Phylogenetic analyses of Trilliaceae based on morphological and molecular data. Systematic Botany, 27(4): 674-692. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S953] [ The following blocks are input data for analysis step 1609 ] BEGIN TAXA; TITLE TaxaForAnalysisStep1609; DIMENSIONS NTAX=26; TAXLABELS Daiswa_fargesii Daiswa_polyphylla Daiswa_thibetica Daiswa_violacea Kinugasa_japonica Paris_incompleta Paris_tetraphylla Paris_verticillata Trillium_camschatcense Trillium_chloropetalum Trillium_decipiens Trillium_discolor Trillium_erectum Trillium_govanianum Trillium_grandiflorum Trillium_lancifolium Trillium_maculatum Trillium_ovatum Trillium_petiolatum Trillium_pusillum Trillium_recurvatum Trillium_reliquum Trillium_rivale Trillium_rugelii Trillium_sessile Trillium_undulatum ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M468] TITLE 'small-morphology'; LINK TAXA = TaxaForAnalysisStep1609; DIMENSIONS NCHAR=110; FORMAT DATATYPE=Standard SYMBOLS= "1 2 3 4 5 6 7 8 9 A B C D E F G H I J K L M N O P Q" MISSING=? GAP= -; CHARSTATELABELS 1 hybrid_status / yes no, 2 flowering_time / February March April May June July August September, 3 chromosome_number / '2n=10' '2n=15' '2n=20' '2n=30' '2n=40' '2n=60' '2n=14' '2n=12' '2n=24', 4 geographical_area / east_Asia western_North_America eastern_North_America Europe, 5 genus / outgroup Trillium Paris, 6 subgenus / outgroup Trillium Phyllantherum Paris Kinugasa Daiswa, 7 section / outgroup grandiflorum erectum catesbaei recurvatum sessile maculatum paris axiparis kinugasa daiswa dunnaniana marmorata fargesiana thibetica, 8 Rafinesque / outgroup Paris Daiswa Phyllantherum Trillium Delostylis, 9 PLANT_type / herbs vines, 10 foliaceousness / scapose leafy subscapose, 11 plant_sexuality / bisexual dioecious polygamous, 12 INFLORESCENSE_type / solitary simple_umbel raceme panicle_of_racemes panicle spike cyme, 13 FLOWERS_Num / one more_than_one, 14 composition / tepals 'sepals + petals', 15 PED._vertical_posture / erect above_the_leaves horizontal below_the_leaves none, 16 root_type / rhizome bulb tuber fibrous, 17 rhizome_size / very_thin slender thick very_thick not_applicable, 18 STEM_habit / erect partially_decumbent decumbent twining, 19 vestiture / glabrous puberulent pubescent pilose papillose scabrous striate floccose, 20 stem_color / green 'yellowish-green' reddish_purple greenish_purple purplish brownish_green reddish green_over_purple purple_tinged 'green over brown-red', 21 stem_distribution / throughout geographic suffused, 22 LEAF_number / two three four five six seven eight nine ten eleven_and_up, 23 leaf_location / terminal cauline basal reduced_cauline, 24 leaf_arrangement / whorled alternate opposite spirally_inserted, 25 Num_whorls / one more_than_two none, 26 leaf_attachment / petiolate subsessile sessile, 27 leaf$_widest_point / 'ovate (.25)' 'elliptic-ovate (.375)' 'elliptic-rhombic-oblong (.5)' 'elliptic-obovate (.675)' 'obovate (.75)', 28 'leaf$ width (LxW)' / linear narrow average broad very_broad depressed_or_transverse, 29 leaf$_sides / 'elliptic (curved)' 'oblong-elliptic' 'oblong (parallel)' 'oblong-rhombic' 'rhombic (straight)' 'rhombic-elliptic', 30 leaf_margin / entire undulate serrulate, 31 leaf_distribution / throughout mottled geographic suffused, 32 leaf_color / green more_or_less_purple_mottled green_w_maroon_hue small_brownish_spots white_variegation_on_veins mottled mottled_w_dk_green spots_of_lt_green multiple_shades_of_green shades_of_green_beside_pale_mid dk_green_spots_on_mottled_backg dk_green_between_veins_w_pale_m, 33 leaf_lower_surface / pubescent_on_veins scabrous_on_veins glossy dull purple purple_nerves glabrous pubescent, 34 apex_type / entire sinusus 'mid-rib, midvein or vein exten', 35 apices / acuminate acute obtuse rounded emarginate 'sub-acute' cuspidate blunt attenuate, 36 base_type / entire with_sinusus w_specialized_attachments, 37 bases / cuneate sheathing obtuse rounded attenuate hastate cordate, 38 leaf_texture / herbaceous membranous papery rugose coriaceous fleshy, 39 Num_main_nerves / many three five seven nine eleven, 40 BRACTS / absent present, 41 SEPAL_form / normal petaloid, 42 sepal_fusion / separate fused, 43 sepal_number / three four five six seven eight nine ten, 44 sepal$_widest_point / 'ovate (.25)' 'elliptic-ovate (.375)' 'elliptic-rhombic-oblong (.5)' 'elliptic-obovate (.625)' 'obovate (.75)', 45 'sepal$ width (LxW)' / narrow average broad, 46 sepal$_sides / 'elliptic (curved)' 'oblong-elliptic' 'oblong (parallel)', 47 sepal_duration / persistent deciduous, 48 sepal_texture / herbaceous membranous, 49 sepal_color / reddish_purple yellow purple purplish_green red green reddish_green yellowish_green white white_w_green_veins greenish_w_red_or_purple_veins 'greenish, purple basally' 'greenish, reddish-purple basall' greensih_brown 'greenish, w red veins' greenish_w_reddish_purple_margi greenish_w_purple_margins green_w_white_veins, 50 sepal_distribution / throughout suffused marginal mottled geographic, 51 sepal_apices / acuminate acute obtuse rounded 'acuminate-rounded' 'sub-acute' cuspidate emarginate caudate blunt attenuate, 52 sepal_apex_type / entire 'mid-rib, midvein or vei', 53 PETAL_form / normal foliaceous staminoid none, 54 petal_presence / present absent, 55 petal_number / zero three four five six seven eight, 56 petal_fusion / separate fused, 57 petal$_widest_point / 'ovate (.25)' 'elliptic-ovate (.375)' 'elliptic-rhombic-oblong (.5)' 'elliptic-obovate (.625)' 'obovate (.75)', 58 'petal$ width (LxW)' / filiform linear narrow average broad very_broad, 59 petal$_sides / 'elliptic (curved)' 'oblong-elliptic' 'oblong (parallel)' 'rhombic-elliptic', 60 petal_duration / persistent deciduous, 61 petal_color / white yellow cream pink red purple bronze green 'reddish-purple' 'greenish-yellow' 'purplish-black' brownish_purple 'greenish-purple' purple_w_greenish_claw yellow_w_greenish_claw green_w_purple_claw yellow_w_purple_claw 'yellow-green w purple claw' white_spotted_w_rose white_w_purple_basally white_w_basal_red_V olive purplish_green_w_purple_cl grey_purple_w_purple_veins_and, 62 petal_distribution / throughout spotted geographic, 63 anthocyanins / yes no fading_to_pink, 64 petal_transverse_posture / incurved plane recurved undulate outcurved, 65 petal_vertical_orientation / erect divergent horizontal divergent declined, 66 petal_longitudinal_posture / straight twisted, 67 petal_apices / acuminate acute obtuse rounded blunt 'sub-acute' cuspidate apiculate emarginate mucronate, 68 petal_apex_type / entire 'mid-rib, midvein or vein extens', 69 STAMEN_form / normal 'petaloid-abortive', 70 stamen_number / zero 1X 2X_sepals 3X 4X, 71 stamen_fusion / free adnate_to_petal adnate_to_sepal adnate_to_tepal, 72 stamen_transverse_posture / straight incurved slightly_recurved, 73 stamen_vertical_posture / erect spreading, 74 ANTHERS_dehiscence / introrse lateral extrorse, 75 POLLEN_shape / spherical ellipsoid irregular, 76 pollen_aperture / omniaperturate monosulcate, 77 pollen_ornamentation / granulate echinate corrugate verrucate spinulate clavate foveolate reticulate psilate gemmate rugulate, 78 CONNECTIVE_prolongation / not_prolonged acute truncate dilated round emarginate obtuse, 79 FILAMENT_color / green purple whitish_purple reddish_purple whitish_green 'red-purple-brown' pinkish_white greenish_yellow white pink brown yellow, 80 pollen_color / yellow orange olive brownish 'olive-orange' purple greyish_purple pink yellowish_pale_purple green maroon 'orange-yellow', 81 connective_color / green pink purple pinkish_purple reddish_purple brown whitish_green white 'red-purple-brown', 82 stamen_distribution / throughout pollen_different all_different, 83 PISTIL_form / normal abortive, 84 OVARY_position / inferior superior, 85 Num_locules / one three four_to_ten, 86 placentation / axilary parietal combination, 87 ovary_shape / conical 'angular-ovoid' ovoid ellipsoid obovoid 'flask-shaped' subglobose 'oval-globose' fusiform 'ovate-conical', 88 'ovary X-section shape' / round ridged angled winged, 89 ovary_ribs / zero two three four five six seven, 90 ovary_apex / truncate crowned attenuate obtuse, 91 STYLE_presence / present absent, 92 STIGMA_number / three four five six eight ten seven one, 93 shape / linear 'linear-subulate' subulate button, 94 'vertical posture (orie' / divergent erect, 95 stigma_transverse_posture / incurved straight recurved, 96 stigma_duration / deciduous persistent, 97 stigma_size / very_thin thin average thick, 98 ovary_color / yellowish_white green purple pink cream_yellow white 'reddish-purple' purplish_brown yellow_green 'red-purple-brown over green-red' green_over_purple purple_over_green purple_over_yellow purple_over_white pink_over_white green_w_purple_disk green_w_yellow_disk 'green w white disk-green w whit' yellow_w_black_disk 'red-purple-brown' black, 99 ovary_distribution / throughout spotted striped geographic, 100 stigma_color / green purple yellowish_green creamy_white yellow yellowish_white pink black 'green and purple-red' 'brownish-violet' 'red-purple-brown' brown 'purple out, green in' 'brown-purple out, yellow in' 'purple out, yellow in' 'white, basally pink' 'green out, yellow in' 'pinkish-orange' red, 101 stigma_distribution / throughout banded geographic, 102 PISTIL_distribution / throughout geographic_by_part all_different, 103 FRUIT_type / berry capsule fleshy_capsule, 104 fruit_dehisence / indehiscent basally_absicent septicidal irregular loculicidal dehiscent decay, 105 fruit_shape / conical 'angular-ovoid' ovoid globose obovoid elliptic, 106 fruit_color / green maroon greenish_yellow rusty_red greenish_white red black 'bluish-black' brown purple green_w_purple_dots 'purplish-green' 'greenish-brown' green_w_brown_ribs 'black-purple' white pink, 107 fruit_color_distribution / throughout mottled spotted striped geographic, 108 SEED_arils / incomplete absent complete, 109 endosperm_development / helobial nuclear, 110 cotyledon_shape / strap_like leaf_like, ; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170] [ . . . . . . . . . . . . . . . . .] Daiswa_fargesii 2{2345}1136E311111221{23}1111{345}11111{34}1111711{12}{47}2{34}111{234}1111{12}811111{345}13211{AB}1{12}?11?1131??2228{46}B?63121213?213???24?1?113{56}{34}?1322 Daiswa_polyphylla 2{4567}{13}136B31111122131111{5678}1111{123}{23}{123}1117111112111{234}{12}1{12}11611111{345}15131{2A}12??1?1131??22272?1?1121233?21{23}1??24515113{56}?A1322 Daiswa_thibetica 231136F31111122131711{678}111{123}1211117111122111311111611111{234}15131?12?{23}1?1131??22282???1121283?{12}13???23{GH}4{257}133{56}?81122 Daiswa_violacea 2{34}1136?31111122131111{56789}1111121135511111?111{12}1{12}111I51111{23}11131E31??1?1131??222?1C??112124??211?13242121{13}3{56}?61322 Kinugasa_japonica 2{567}5135A21111122141111{6789}111{23}{45}{23}11117111132121{45678}{12}1{12}12{9A}11111{17}15{12}31112?1131131?1322A15172123143?21{457}31324{HI}441311?A12?2 Paris_incompleta 2{2345}1{14}34821111122111111{56789A}1111{25}2{12}1114111112111{123}1{12}11161?1421-------------131??222?{12}???112314??41{123}???2231?1111?81222 Paris_tetraphylla 2{4567}113482111112211111131113{234}{234}{126}11171211121112{123}1{123}116111421-------------131??222A1???1123131?412???2??1?1111481222 Paris_verticillata 2{45}1134821111122111111{567}1112{135}{23}1111711111?111{23}11111611111{34}13131{2A}12351?1131??22272???11231{34}1?31{23}?132{12}81212114F1222 Trillium_camschatcense 2{456}112235111112213111121113{23}3611171{12}131{23}1111{23}2{23}1161{23}11121{123}4{123}1112521{123}1131111111511121212{14}26321?1322{139C}{124}51311{34}{AB}{13}111 Trillium_chloropetalum 2{12}12237411111251?11112111{23}1{345}11{12}{14}71{348}1?2?11111111161{234}111215{34}{12}1{1567AD}1{12}111{2345}1131111111{57}2{14}3212??3364212{12}2243121111311111 Trillium_decipiens 2{123}13236411111251311112111312112A212141311111{12}111612111215{34}11{6AD}11111{234}1131{12}1211?{25}619212??4263211132{23}2151211611111 Trillium_discolor 2{34}1323641111125131{13}1121113{12345}3112B71{12}131311111{12}111612111215{34}11F32{15}12{18A}{12}13121{12}111{25}6{12}9212123363213{12}{23}22{2A}{34}B1311{34}?1111 Trillium_erectum 2{345}1322351111122131111211133451117111113111111111611111211311{13469}1{12}{25}21{12}11313121111{9A}{17}??1212{34}46321?132{34}{378}1211113A1111 Trillium_govanianum 2{345}312225111112212114121111{12}{23}{12}111711{12}{47}221111{23}1{23}11{34}1111121{23}{23}{23}1{689}11{23}{234}1111311132261213212??3?32211{12}32131211114A12?? Trillium_grandiflorum 2{345}13222511111221311112111{23}2{34}{46}11171{12}111311111111161{12}111215{34}11{149}1{13}{45}21{37}11313111151918212138263212{12}32121111{13}1411111 Trillium_lancifolium 2{1234}132354111112512111121113{12}2112A712111311111111161211121{345}331{6GN}{13}11112113121111{12}52?3?12??{24}463211132{23}A4E3311211111 Trillium_maculatum 2{123}132374111112513111121113{123}{234}112671{1238}1{45}1311111111131{46}11121{45}{34}{12}1{26H}{13}11{12}2{234}1131211111{35}2{14}3212133{12}61213212481B11113C1111 Trillium_ovatum 2{1234}12222511111221311112111324611171{12}1?1{23}1111{12}1{12}1181211121{12}{34}{12}1{14}1{13}{25}21{23}11313221151517212123363212{12}3211161131311111 Trillium_petiolatum 2{34}122374111112513111121111{13}{345}111171{34}14141111{2345}{12}{12}1161211121{123}3{123}1{68D}11{15}{12}121131112113{12}2{123}9112123{34}62212132{23}21212{12}13?1111 Trillium_pusillum 2{234}1322{24}611111221211{15}{13}2111{13}{12}{23}{12}1{14}{13}71314121111{12}1{12}11{6H}{13}{23}111211311113421{23}113111{12}111141{48}31212313311?13219131111311111 Trillium_recurvatum 2{234}132354111112512111121111{13}{234}112771{12}131311111{12}11161211121{14}{34}{14}1{29C}11111{23}1131211112526311213{24}46321113222121211{24}11111 Trillium_reliquum 2{23}13236411111251?{23}11121113{13}{34}112{9C}21{23}1?12111111111{3C}{25}{24}11121{35}311{26D}111122113121111?2213112??3463211132?31F33113?1111 Trillium_rivale 2{234}1222251111122131151211111{23}111171{12}{12}{47}52111121211617211212441{14J}{12}1521{12}113111311?111121213313311213226141131411112 Trillium_rugelii 2{345}132235111112413116121113345111711111{23}111111111D51111211{45}11K31321?11311221111273212{12}{12}A46121?13223121131321111 Trillium_sessile 2{234}132364111112513111121113{13}{34}11{12}{147}71{124}141311111{12}111{6CH}{135}611121{13}{34}11{67A}11111{26}1131111111{25}211312??{37}{34}632132?2{23}81F3311{34}C1111 Trillium_undulatum 2{345}13222511111221311{13}121111131{12}117111413111111111H3111121{12}{34}{12}1L31421211311{12}3114277221212313{34}2121321F471311361111 ; END; BEGIN SETS; CHARSET problematic (CHARACTERS = 'small-morphology') = 33 90 103-104; CHARSET non_morf (CHARACTERS = 'small-morphology') = 1-8; CHARSET numbers (CHARACTERS = 'small-morphology') = 22 43 55 70 92; CHARSET color (CHARACTERS = 'small-morphology') = 20 32 49 61 79-81 98 100 106; CHARSET subjective (CHARACTERS = 'small-morphology') = 17 88 97; CHARSET insufficient (CHARACTERS = 'small-morphology') = 37 64-67 72 77 79-81 85-86 89-90 93-94 100 105; END; [ The following blocks are output data for analysis step 1609 ] BEGIN TREES; TITLE Tb6385; LINK TAXA = TaxaForAnalysisStep1609; TREE Fig._3 = [&R] (Trillium_rivale,(((((((Daiswa_fargesii,Daiswa_thibetica),Daiswa_polyphylla),Daiswa_violacea)Daiswa,((Paris_incompleta,Paris_tetraphylla),Paris_verticillata)Paris),Kinugasa_japonica)Paris_s.l.,Trillium_govanianum),((((Trillium_chloropetalum,((Trillium_decipiens,Trillium_lancifolium,Trillium_recurvatum),(Trillium_discolor,Trillium_maculatum,Trillium_sessile),Trillium_reliquum),Trillium_petiolatum)Trillium_subg._Phyllantherum,Trillium_camschatcense,Trillium_erectum,(Trillium_grandiflorum,Trillium_ovatum)Grandiflorum_Group,Trillium_rugelii),Trillium_undulatum),Trillium_pusillum)Trillium)); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr869] END;