#NEXUS [File created by TreeBASE: 1/22/08 14:27:47] [Matrix accession#: M3676] BEGIN DATA; DIMENSIONS NTAX=26 NCHAR=105; [!This data set was downloaded from TreeBASE, a prototype relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, and UC Davis. Please do not remove this acknowledgment from the Nexus file. TreeBASE © 1994-2008. Study reference: Gernandt, D. S., S. Magallon, G. Geada Lopez, O. Zeron Flores, A. Willyard, and A. Liston. 2008. Use of simultaneous analyses to guide fossil-based calibrations of Pinaceae phylogeny. International Journal of Plant Sciences. in press. Study accession number = S1973 Matrix accession number = M3676 ] FORMAT SYMBOLS = " 0 1 2 3 4 5 6 7 " MISSING = ? GAP = - INTERLEAVE ; CHARLABELS [1] 'shoot_dimorphism' [2] 'primary_leading_shoot' [3] 'sieve_element_plastids' [4] 'stem_phloem_fibers' [5] 'phloem_fiber_sclerids' [6] 'phloem_mucilage' [7] 'secondary_phloem_horizontal_resin_canals' [8] 'phloem_resin_cavities' [9] 'xylem_parenchyma' [10] 'thickenings_on_transverse_tracheid_walls' [11] 'spiral_thickenings_on_axial_tracheid_walls' [12] 'epithelium_of_vertical_resin_canals' [13] 'vertical_secondary_wood_resin_canals' [14] 'horizontal_resin_ducts_in_rays' [15] 'cortical_resin_ducts' [16] 'indentations_horizont_walls_ray_parenchyma' [17] 'ray_tracheids' [18] 'crossfield_pits' [19] 'root_resin_canals' [20] 'brachioblasts' [21] 'leaf_shape' [22] 'leaf_arrangement' [23] 'leaf_attachment' [24] 'leaf_bases' [25] 'leaf_midrib' [26] 'leaf_petiole' [27] 'leaf_thickness' [28] 'leaf_persistence' [29] 'apical_meristems' [30] 'primary_stomatal_bands' [31] 'leaf_endoderm_Casparian_strips' [32] 'mesophyll_parenchyma' [33] 'tracheids_of_leaf_tranfusion_tissue' [34] 'vascular_bundles_in_the_stele_of_the_leaf_2' [35] 'resin_canal_position' [36] 'biflavonoids' [37] 'tropolones' [38] 'chemical_immunology' [39] 'male_strobili_arrangement' [40] 'microsporangial_dehiscence' [41] 'pollen_tetrad_formation' [42] 'pollen_with' [43] 'pollen_exine' [44] 'pollen_triradiate_streaks' [45] 'pollen_saccae_or_frills' [46] 'sperm_nuclei_cell_walls' [47] 'pollination_drop' [48] 'micropyle' [49] 'ventral_canal_cell' [50] 'megaspore_membrane' [51] 'proembryo_wall_formation' [52] 'proembryo_tiers' [53] 'polyembryony' [54] 'orientation_of_mature_cones' [55] 'cones_on_leaved_peducles' [56] 'scale_apex' [57] 'umbo' [58] 'seed_scale_absission' [59] 'disintegration_of_cone_rachis' [60] 'bract' [61] 'bract_length' [62] 'bract_apex' [63] 'cone_scale_shape' [64] 'seed_scales_with_narrowed,_pedicellate_base' [65] 'sclerenchyma_in_pith' [66] 'resin_canals_in_pith' [67] 'secondary_xylem_cone_axis' [68] 'resin_canals_in_secondary_xylem' [69] 'female_cone_maturation' [70] 'sclerenchyma_in_inner_cortex' [71] 'sclerenchyma_in_outer_cortex' [72] 'cortical_resin_canals' [73] 'trichomes' [74] 'vascular_trace_to_each_bract-scale' [75] 'scale_trace' [76] 'scale_trace' [77] 'resin_canal_to_scale' [78] 'bract_scale_separation' [79] 'bract_base_abaxial_lobe' [80] 'bract_sclerenchyma' [81] 'bract_resin_canals' [82] 'bract_trace' [83] 'resin_canals_to_scale_base' [84] 'resin_canals_to_scale_seed_level' [85] 'resin_canals_to_scale_distal' [86] 'sclerenchyma_in_scale' [87] 'scale_right_angle_to_cone_axis_and_sharply_upturned_distally' [88] 'axillary_complex' [89] 'sterile_appendages_per_dwarf_shoot' [90] 'bract_scale_complexes_per_cone' [91] 'mechanical_tissue_of_scale_base' [92] 'mechanical_tissue_at_scale_base' [93] 'ovule_position' [94] 'ovules_per_scale' [95] 'interseminal_ridge' [96] 'seed_body' [97] 'seed_trace' [98] 'seed_wing_origin' [99] 'seed_wing_attachment' [100] 'seed_wing_overall_shape' [101] 'seed_coat_with_resin_vesicles' [102] 'seed_storage_product' [103] 'seed_maturation' [104] 'seed_germination_hypogeal' [105] 'number_of_cotyledons' ; STATELABELS 1 'absent' 'present', 2 'erect_or_spreading' 'pendulous', 3 'starch_accumulating' 'protein_accumulating', 4 'present' 'absent', 5 'absent' 'present', 6 'absent' 'present', 7 'absent' 'present', 8 'absent' 'present', 9 'absent' 'present', 10 'absent' 'spiral' 'plates', 11 'absent' 'present', 12 'thick' 'thin', 13 'absent' 'present', 14 'absent' 'present', 15 'cavities_only' 'present' 'absent', 16 'absent' 'present', 17 'absent' 'present' 'weakly-developed', 18 'cupressoid_or_taxodioid' 'piceoid' 'pinoid' 'fenestriform', 19 'absent_or_one' 'two', 20 'absent' 'long_with_close_annual_rings' 'long_with_distinct_annual_rings' 'short', 21 'falcate_profile_tetragonal_cross_section' 'linear_lanceolate_bifacially_flattened' 'scalelike' 'bilaterally_flattened' 'needlelike' 'fused' 'fan-shaped', 22 'spread_out_on_branch' 'in_fascicles,_spirally_arranged_on_short_shoots' 'helically_arranged_on_short_shoots', 23 'decurrent' 'stalklike_constrictions' 'shield_shaped', 24 'decurrent' 'fused', 25 'raised' 'sunken_or_absent', 26 'absent' 'present', 27 'thick' 'thin', 28 'persistent' 'deciduous', 29 'without_modified_leaves' 'shorter_leaves,_interrupting_growth' 'scale_leaves' 'winter_buds,_tips_free' 'winter_buds,_scales_overlapping', 30 'abaxial' 'adaxial_or_amphi', 31 'absent' 'present', 32 'smooth' 'plicate', 33 'lateral_to_vascular_bundle' 'all_around_vascular_bundle', 34 'one' 'two' 'more_than_two', 35 'absent' 'central' 'marginal', 36 'present' 'absent', 37 'absent' 'present', 38 'pinoid' 'abietoid', 39 'single' 'clusters_from_a_single_bud' 'grouped_in_racemes', 40 'longitudinal' 'oblique' 'transverse', 41 'simultaneous' 'successive', 42 'shallow_functional_germination_furrow' 'harmomegathus' 'functionless_germ_furrow' 'pore', 43 'tegillate' 'rough_corrugate' 'granular' 'roughened', 44 'absent' 'present', 45 'present' 'absent', 46 'present' 'absent', 47 'present' 'absent' 'microdrops', 48 'symmetric' 'asymmetric', 49 'distinct_cell_wall' 'no_wall_but_nuclei', 50 'uniform_thickness' 'thin_at_micropylar_end', 51 'secondary_type' 'primary_type', 52 'three' 'four', 53 'simple' 'cleavage', 54 'pendant' 'erect', 55 'absent' 'present', 56 'thinning_distally' 'thickening_distally_or_umbo', 57 'dorsal' 'terminal', 58 'absent' 'present' 'semi', 59 'absent' 'present', 60 'not_keeled' 'keeled', 61 'shorter' 'well_developed', 62 'acute_or_rounded' 'trifurcate', 63 'ovate_obovate_orbicular' 'deltoid_triangular' 'flabellate' 'rhombic' 'subcordate' 'tongue_shaped', 64 'absent' 'present', 65 'absent' 'present', 66 'absent' 'present', 67 'continuous_cylinder' 'separate_strands', 68 'absent' 'present', 69 'one_year' 'two_to_three', 70 'absent' 'present', 71 'absent' 'present', 72 'uniform_in_diameter' 'dilated', 73 'absent' 'present', 74 'separate' 'fused', 75 'clearly_derived_from_two_lateral_strands' 'derived_as_single_abaxially_concave_strand', 76 'abaxially_concave' 'becoming_cylindrical_after_divergence', 77 'single_branch' 'two' 'three' 'four', 78 'first_laterally' 'first_medially', 79 'absent' 'present', 80 'absent' 'present', 81 'absent' 'two' 'greater_than_two', 82 'entering_bract' 'terminating_before', 83 'abaxial' 'adaxial' 'both' 'absent', 84 'abaxial' 'adaxial' 'both' 'both_and_between' 'absent', 85 'abaxial' 'adaxial' 'both' 'between_vascular_bundles' 'absent' 'both_and_between' 'abaxial_and_between' 'adaxial_and_between', 86 'both' 'abaxial' 'adaxial' 'absent' 'both_and_between' 'abaxial_and_between' 'adaxial_and_between', 87 'absent' 'present', 88 'free_from_bract' 'partially_fused' 'fused', 89 'more_than_10' 'less_than_6', 90 'many' 'few' 'one', 91 'modified' 'well_developed', 92 'highly_gelatinous' 'fibrous', 93 'lateral' 'terminal', 94 'more_than_two' 'one' 'two', 95 'absent' 'extending_less_than_half_seed_diameter' 'extending_more_than_half' 'overarching_seeds', 96 'ovoid-obovate' 'triangular_cuneate_oblong' 'oval-ovoid' 'round-obovate', 97 'absent' 'present', 98 'from_lateral_extension_of_integument' 'absent' 'from_scale_epidermis' 'from_bract_and_scale', 99 'absent' 'claws' 'shallow_cup_separable' 'shallow_cup' 'deep_cup', 100 'widening_distally,_blunt_or_rounded_apex' 'elongate,_not_widening_distally,_rounded' 'semi-trullate_sharp', 101 'absent' 'present', 102 'starch' 'oils', 103 '2_years' '1_year', 104 'absent' 'present', 105 'two_to_six' 'four_to_twenty', ; MATRIX 'Ginkgo' 1??00000100?00200001610??111000001000??00000100000000??????????????????????????????????????????0?1?? 'Sciadopitys' 100000??000?00?0000050001000210000?00?1012201000000010?0?1?0002000100000100010002011720100??0000?1?? 'Cryptomeria' 00000000100?0021000000000?00110000100?2003201000000010?0?00020?01000011000??00002034440100??0001?1?? 'Amentotaxus' 000000??110?00?1000010000100400000?00?101220100?00000?0?????????????????????????????????01??11?0?1?? 'Podocarpus' 00000000100?0020000010000100400000100?120000000000001?0????0?0?0????0???????????0?3???0011??11?0?1?? 'Araucaria' 000?0000100?0020000010001000110002100?(01)001301010000001?0?1001020????1???????????0?3???1210??01?0?3?? 'Pityostrobus_corneti' ??????????????1????????????????????????????????????????0?0??0021100001100011?0011123510000??0201?240 'Pityostrobus_californiensis' ??????????????1????????????????????????????????????????0?0??002111010111001010001023500000??0221?2?? 'Pityostrobus_bernissartensis' ??????????????1???????????????????????????0?0??????????0?0??0050110000000010100?0100210000110200?211 'Pseudoaraucaria_heeri' ??????????????1????????????????????????????????????????110000001001000100000100110112010000002311240 'Pinus_belgica' ?????????2????1????????????????????????????????????????10000005010011(01)100110100(01)11005400001102100211 'Pinus_sylvestris' 1?110011020111101(23)10420?1000411111210020000001001111100100000050(01)0011(01)1(01)0110100(01)100(03)5400001102100211 'Pinus_ponderosa' 1?110011020111101210420?1000411111210020000001001111100100000050(01)0011(01)(01)(01)0110100(01)100(03)5400001102100211 'Pinus_strobus' 1?110011000111101310420?1000411110210020000001001111100110000050(01)0011(01)0(01)0110100(01)100(03)5400001102100211 'Pinus_cembroides' 10110011000111101110420?1000411110210020000001001111100100000050(01)0011(01)0(01)0110100(01)102(03)5400001102100211 'Picea' 001100110(01)1011111110?0100000411?102110000000010011110000?0010030(01)0(01)(01)0(01)10(01)0101010(12)023(57)400001102(12)00221 'Cathaya' 1011001011101110111010211100401110210?0000?0011011111010?0000000000000101?10??10112?500000??0210?231 'Pseudotsuga' 00111011111011111110102111004010102100010121111111110010?000110010010(01)10(01)010100(01)10115000001102100231 'Larix' 10111011101011011113111011114010102100001120111111110110?0001100100(01)0(01)10101011(01)0(12)(01)115000001102(12)00231 'Tsuga' 01110000100?00111000101011004000101101020010011011111000?001000110000(01)(01)0101031(01)110115000001102101241 'Nothotsuga' 11??00011000101110?0101011004000101???12???00????????110?0111021????0???1??????11?1?5?0000?10210?241 'Pseudolarix_erensis' 1??????????????????1111?011????????????????????????????1?0??0011???????????????????????000??02?0?242 'Pseudolarix' 10110101100?00010001111001114000102101120000011011110111?0100011101001101010?00110235100000102001242 'Keteleeria' 00110101100010110000102101004000102101120000011011111110?011114100000011(01)011101111222010001102111240 'Abies' 00110101100?00110000102111004000112101020001011011110100?1011121101(01)011(01)(01)(01)1011(01)110115010001102011240 'Cedrus' 1(01)110010100?00011002011011104(01)10112111000000012011111100?100002100101(01)10(01)0103001012?5410000002(01)11240 'Ginkgo' 000?0 'Sciadopitys' 010?0 'Cryptomeria' 01100 'Amentotaxus' 000?0 'Podocarpus' 00??0 'Araucaria' 0?010 'Pityostrobus_corneti' 1???? 'Pityostrobus_californiensis' 0???? 'Pityostrobus_bernissartensis' 0???? 'Pseudoaraucaria_heeri' 1???? 'Pinus_belgica' ????? 'Pinus_sylvestris' 01001 'Pinus_ponderosa' 01001 'Pinus_strobus' 01001 'Pinus_cembroides' 01001 'Picea' 01101 'Cathaya' 01100 'Pseudotsuga' 01101 'Larix' 01100 'Tsuga' 11100 'Nothotsuga' 1?1?? 'Pseudolarix_erensis' ????? 'Pseudolarix' 11100 'Keteleeria' 11110 'Abies' 11101 'Cedrus' 11101 ; END; BEGIN TREEBASE; END; BEGIN TREES; [! 1 trees. TreeBASE accession#: Tree5632 ] TRANSLATE 1 'Pityostrobus_bernissartensis', 2 'Pityostrobus_californiensis', 3 'Pseudoaraucaria_heeri', 4 'Pityostrobus_corneti', 5 'subfamily_Pinoideae', 6 'Pseudolarix_erensis', 7 'Pinus_cembroides', 8 'Pinus_sylvestris', 9 'Pinus_ponderosa', 10 'Pinus_belgica', 11 'Pinus_strobus', 12 'Pseudolarix', 13 'Amentotaxus', 14 'Cryptomeria', 15 'Sciadopitys', 16 'Pseudotsuga', 17 'Keteleeria', 18 'Nothotsuga', 19 'Podocarpus', 20 'Araucaria', 21 'Conifers', 22 'Pinaceae', 23 'Cathaya', 24 'Cedrus', 25 'Ginkgo', 26 'Tsuga', 27 'Picea', 28 'Abies', 29 'Larix', ; TREE 'parsimony1A' = [&R] (((24,((((28,17),(((12,6),4),(18,26))),(2,((29,16),(23,(27,(((7,11),(9,(8,10))),1)))))),3)),((20,19),((13,14),15))),25); END;