#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 November 14, 2025; 6:57 GMT TreeBASE (cc) 1994-2008 Study reference: Marcus J., & Mccune A. 1999. Ontogeny and phylogeny in the northern swordtail clade of Xiphophorus. Systematic Biology, 48(3): 491-522. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S2368] [ The following blocks are input data for analysis step 4813 ] BEGIN TAXA; TITLE TaxaForAnalysisStep4813; DIMENSIONS NTAX=28; TAXLABELS Alfaro_hubberi Poecilia_butleri Poecilia_reticulata Priapella_compressa Priapella_intermedia Priapella_olmaceae Xiphophorus_alvarezi Xiphophorus_andersi Xiphophorus_birchmanni Xiphophorus_clemenciae Xiphophorus_continens Xiphophorus_cortezi Xiphophorus_couchianus Xiphophorus_evelynae Xiphophorus_gordoni Xiphophorus_helleri Xiphophorus_maculatus Xiphophorus_malinche Xiphophorus_meyeri Xiphophorus_milleri Xiphophorus_montezumae Xiphophorus_multilineatus Xiphophorus_nezahualcoyotl Xiphophorus_nigrensis Xiphophorus_pygmaeus Xiphophorus_signum Xiphophorus_variatus Xiphophorus_xiphidium ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M4097] TITLE Appendix_1; LINK TAXA = TaxaForAnalysisStep4813; DIMENSIONS NCHAR=86; FORMAT DATATYPE=Standard SYMBOLS= "0 1 2 3 4" MISSING=? GAP= -; CHARSTATELABELS 1 Sword / Complete_absence_of_a_sword 'caudal protrusion or small sword (0.1-0.3 times the length of t' 'large sword (0.7-6 times the length of the caudal fin, generall', 2 Sword_consisting_exclusively_of_unbranched_rays / The_presence_of_branched_rays_in_the_sword absence, 3 Upturned_sword / Straight_swords upturned_swords_were_coded_as_1, 4 Distal_serrae_on_ray_4p_of_the_gonopodium / Serrae_are_absent poorly_developed well_developed well_developed_and_fused., 5 'Well-formed hook on ray 5a of the gonopodium' / Absence_of_a_large_hook presence_of_a_large_hook, 6 Granular_tissue_on_the_dorsal_part_of_the_hook_on_ray_3_of_the_gonopodium / The_absence_of_ray_3_hook_and_granular_tissue 'the presence of a short, slightly decurved hook on ray 3' 'the presence of a short, highly decurved ray 3 hook' 'presence of a short, highly decurved ray 3 hook with the blade' 'presence of a greatly en- larged ray 3 hook', 7 Subdistal_spines_on_ray_3_of_the_gonopodium / Absence_of_subdistal_spines presence_of_elongate_and_peglike_spines presence_of_large_and_angular_spines 'presence of large, angular spines with scalloped or indented di', 8 Size_of_segments_of_the_distal_ramus_of_ray_4a_of_the_gonopodium / ray_4a_segments_not_enlarged segments_somewhat_enlarged segments_very_enlarged_and_flared_was_coded_as_2., 9 Subdistal_serrae_on_ray_4p_of_the_gonopodium / 'presence of a few, small subdistal serrae' 'presence of > 10 well-developed serrae', 10 Head_bump / species_that_lack_a_head_bump species_that_possess_this_tissue, 11 Male_pelvic_fin_fleshy_in_the_distal_third / absent present, 12 'Teeth compressed, spatulate' / 'Large, conical teeth fixed in large, robust jaws' 'compressed, spatulate teeth set in a more delicate set of jaws', 13 Elongate_ventral_caudalfin_rays / absence presence, 14 Width_of_the_base_of_the_dorsalfin / 0 short_dorsal_fin_bases long_dorsal_fin_bases, 15 Growth_rate / All_allelic_variants_at_the_p_locus_grow_at_similar_rates allelic_variants_that_grow_faster, 16 Allometric_growth_of_sword / sword_index_is_constant_intraspecifically the_largest_animals_with_proportionately_larger_swords_for_thei, 17 'Sex-determining mechanism' / 'XX-XY sex determining mechanism' combination_of_both_mechanisms 'WY-YY sex-determining mechanism', 18 Dusky_band_continuous_with_dorsal_pigment_of_sword / absence_of_this_pattern midlateral_band_of_dusky_pigment_that_is_continuous_with_the_da, 19 Proximal_dorsal_pigmentation_of_the_sword / species_that_lack_this_pattern species_that_have_this_pattern, 20 Distal_dorsal_sword_pigment / absence present, 21 Grave_spot / absence_of_any_grave_spot_pigmentation presence_of_the_grave_spot_was_coded_as_1, 22 Ventral_margin_ofcaudalfin_and_sword_densely_edged_by_melanophores / Absence_of_the_melanophores presence, 23 Yellow_and_orange_carotenoid_sword_pigmentation / Absence_of_yellow_or_orange_pigment_pattern presence_of_either_color, 24 Green_pteridine_sword_pigmentation, 25 Drosopterin / absence_of_the_enzyme presence_of_the_enzyme, 26 'Sex-linked red and yellow patterns' / absent presence_of_any_of_these_patterns, 27 yellow_caudal_fin / Absence_of_pigment_pattern presence, 28 yellow_dorsal_and_ventral_edges_of_the_caudal_fin / Absence_of_pigment_pattern presence, 29 solid_yellow_body_coloration / Absence_of_pigment_pattern presence, 30 Two_or_more_rows_of_red_lateral_marks / absence Presence, 31 Multiple_lateral_stripes / Absence_of_the_pigmentation_pattern a_faintly_visible_pigmentation_pattern a_clearly_visible_pigmentation_pattern, 32 Solid_midlateral_stripe_at_birth / absent present, 33 Vertical_bars / 'Absence of bars or blotches was scored as 0; thin vertical bars' broad_blotches, 34 Body_bicolored / Absence presence_of_a_distinct_bicolor_pattern presence_of_a_sharply_bicolored_pattern_coded_as_2., 35 Dark_subdermal_dashes_of_pigment / Subdermal_pigment_absent subdermal_pigment_present 'subdermal dashes of pigment elaborated into a three-dimensional', 36 Two_or_more_oblique_lines_behind_pectoral_base / absence_of_these_lines presence_of_these_oblique_lines, 37 Middorsal_spots / absence presence_of_middorsal_spots, 38 'Dorsal fin with dark marginal pigment and a sub-basal row of dark spots on the i' / Absence_of_this_pattern presence, 39 Black_or_darkly_pigmented_gonopodium / Species_that_lack_black_gonopodia presence, 40 'Caudal blotch (Cb)' / absence presence, 41 'Spotted caudal (Sc)' / absence presence, 42 'Carbomaculatus (Cam)' / absence presence, 43 Alleles_at_the_tailspot_locus / 'fixed wild-type allele' the_alleles_found_in_X._milleri the_alleles_found_in_X._maculatus the_alleles_found_in_X._variatus the_alleles_found_in_X._xiphidium, 44 'Sex-linked macromelanophore locus' / 'The absence of sex-linked macromelanophore-producing alleles' the_presence_of_such_alleles, 45 'Well-developed precopulatory behavior' / without with, 46 Nipping / absence presence, 47 gonopodial_thrusting / absence presence, 48 slow_approach / absence presence, 49 sneak_chase / absence presence, 50 close_transverse_presenting_behavior / absence presence, 51 side_change_over_head_behavior / absence presence, 52 stiff_frontal_presenting / absence presence, 53 circling_behavior / absence presence, 54 'figure-eight' / absence presence, 55 open_display_behavior / absence presence, 56 arching_display / absence presence, 57 dancing_display / absence presence, 58 RAPD / Absence Presence, 59 RAPD / Absence Presence, 60 RAPD / Absence Presence, 61 RAPD / Absence Presence, 62 RAPD / Absence Presence, 63 RAPD / Absence Presence, 64 RAPD / Absence Presence, 65 RAPD / Absence Presence, 66 RAPD / Absence Presence, 67 RAPD / Absence Presence, 68 RAPD / Absence Presence, 69 RAPD / Absence Presence, 70 RAPD / Absence Presence, 71 RAPD / Absence Presence, 72 RAPD / Absence Presence, 73 RAPD / Absence Presence, 74 RAPD / Absence Presence, 75 RAPD / Absence Presence, 76 RAPD / Absence Presence, 77 RAPD / Absence Presence, 78 RAPD / Absence Presence, 79 RAPD / Absence Presence, 80 RAPD / Absence Presence, 81 RAPD / Absence Presence, 82 RAPD / Absence Presence, 83 RAPD / Absence Presence, 84 RAPD / Absence Presence, 85 RAPD / Absence Presence, 86 'INV-Xmrk EcoR1' / '7-kb fragment' '10-kb fragment', ; MATRIX [ 10 20 30 40 50 60 70 80 90 100 ] [ . . . . . . . . . . ] Alfaro_hubberi 0--000100?00???-?---0?--???????????????0?????????????????????????????????????????????? Poecilia_butleri ?--000001?11???-2---0?--???????????????0?????????????????????????????????????????????? Poecilia_reticulata ?--000001?11???-0---0?--???????????????0?????????????????????????????????????????????? Priapella_compressa 0--001001?11???-?---0?--???????????????0?????????????????????????????????????????????? Priapella_intermedia 0--001001?11???-?---0?--???????????????0?????????????????????????????????????????????? Priapella_olmaceae 0--001001?11???-?---0?--???????????????0?????????????????????????????????????????????? Xiphophorus_alvarezi 2002222110111?002110211110???1000000000000001111110000010????????????????????????????? Xiphophorus_andersi 2002042010111?0000000000?????000?00?0??000??1111110100000????????????????????????????0 Xiphophorus_birchmanni 1--2142011111?0-?-0-11--1011000020001?0011?0?11111001110011{01}110101110{01}0100101101100110 Xiphophorus_clemenciae 2012142010111?00?111111?10000100000000000000111111000001010110000001{01}1{01}10{01}{01}00011110100 Xiphophorus_continens 1--2142010111?0-?-0-10--1000001000000?0000?0??????????????1001??0111011111010111?1011? Xiphophorus_cortezi 2112142010111?000011111?101100001000000111001111110010100111001101110011001{01}{01}{01}001101{01}0 Xiphophorus_couchianus 0--4043010110?0-0---00--10???0001110001000001111111000000????????????????????????????1 Xiphophorus_evelynae 0--20420101111?-?---00--11???0201001000000010111111000000????????????????????????????0 Xiphophorus_gordoni 0--3043010110??-?---01--10???0001210001000000111111000000????????????????????????????1 Xiphophorus_helleri 2002232210111?002110211110???100100000000000111111001001101110001000110001101001110000 Xiphophorus_maculatus 0--204201011120-1---00--11???000100000100021011110000000001011011101100000000110101010 Xiphophorus_malinche 2112142011111?00?011111?10??000020001?01???0?????????????11{01}110{01}01{01}100010010110110011? Xiphophorus_meyeri 0--3043010110??-?---00--?0???000?12?0?1000??0111111000000????????????????????????????1 Xiphophorus_milleri 0--204201011120-0---00--?1???0001000001000110111111000000????????????????????????????0 Xiphophorus_montezumae 2112142010111?00?011111?10000020100000000000111111001110011011110111011111010111111110 Xiphophorus_multilineatus 2111142010111?110011111?0011100110000?0100?01?????????????000001011101110101011111111? Xiphophorus_nezahualcoyotl 2112142010111?000011111?1000002010000?0100?1?111110011100111110101011111110101110?011? Xiphophorus_nigrensis 2111142010111?110011111?00110001000001010000111111001100010?10010111011?01010111010?10 Xiphophorus_pygmaeus 1--1142010111?0-0-0-00--00101001000001000000111111001000010000010111011101010101010110 Xiphophorus_signum 2002232210111??0?11021?1?0???0000000000000001111110010011????????????????????????????0 Xiphophorus_variatus 0--20420101111?-0---00--11???020100100102031111111100000000{01}{01}1000{01}1110{01}0010{01}{01}011101010 Xiphophorus_xiphidium 10020420101111?-0-000000?1???020100100100041111111010000000110?00001100001000001101110 ; END; BEGIN SETS; CHARSET PIGMENT (CHARACTERS = Appendix_1) = 18-44; CHARSET BEHAVIOR (CHARACTERS = Appendix_1) = 45-57; CHARSET Phenotypic (CHARACTERS = Appendix_1) = 1-86; CHARSET MORPH_GROWTH_SEX (CHARACTERS = Appendix_1) = 1-17; CHARSET RAPD_RFLP (CHARACTERS = Appendix_1) = 58-86; END; [ The following blocks are output data for analysis step 4813 ] BEGIN TREES; TITLE Tb9590; LINK TAXA = TaxaForAnalysisStep4813; TREE Fig._3 = [&R] ((Poecilia_reticulata,Poecilia_butleri,(Priapella_compressa,Priapella_intermedia,Priapella_olmaceae)),Alfaro_hubberi,(((((Xiphophorus_alvarezi,(Xiphophorus_helleri,Xiphophorus_signum)),(Xiphophorus_clemenciae,((((Xiphophorus_birchmanni,Xiphophorus_malinche),Xiphophorus_cortezi),(Xiphophorus_multilineatus,Xiphophorus_nigrensis,Xiphophorus_pygmaeus)),(Xiphophorus_continens,(Xiphophorus_montezumae,Xiphophorus_nezahualcoyotl))))),Xiphophorus_andersi),(Xiphophorus_couchianus,Xiphophorus_gordoni,Xiphophorus_meyeri)),(Xiphophorus_evelynae,(Xiphophorus_variatus,Xiphophorus_xiphidium)),(Xiphophorus_maculatus,Xiphophorus_milleri))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr3580] END;