NEXUS
[File created by TreeBASE:  1/16/09  15:07:17]
[Matrix accession#: M644]

BEGIN TAXA;
	TITLE M644;
	DIMENSIONS  NTAX=28;
	TAXLABELS
		Xiphophorus_xiphidium	Xiphophorus_variatus	Xiphophorus_signum	Xiphophorus_pygmaeus	Xiphophorus_nigrensis	Xiphophorus_nezahualcoyotl	Xiphophorus_multilineatus	Xiphophorus_montezumae	Xiphophorus_milleri	Xiphophorus_meyeri	Xiphophorus_malinche	Xiphophorus_maculatus	Xiphophorus_helleri	Xiphophorus_gordoni	Xiphophorus_evelynae	Xiphophorus_couchianus	Xiphophorus_cortezi	Xiphophorus_continens	Xiphophorus_clemenciae	Xiphophorus_birchmanni	Xiphophorus_andersi	Xiphophorus_alvarezi	Priapella_olmaceae	Priapella_intermedia	Priapella_compressa	Alfaro_hubberi	Poecilia_butleri	Poecilia_reticulata
	;
END;

BEGIN CHARACTERS;
	TITLE M644;
	DIMENSIONS NCHAR=86;
	FORMAT 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 / _ 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
		Xiphophorus_xiphidium            10020420101111?-0-000000?1???020100100100041111111010000000110?00001100001000001101110
		Xiphophorus_variatus             0--20420101111?-0---00--11???020100100102031111111100000000(01)(01)1000(01)1110(01)0010(01)(01)011101010
		Xiphophorus_signum               2002232210111??0?11021?1?0???0000000000000001111110010011????????????????????????????0
		Xiphophorus_pygmaeus             1--1142010111?0-0-0-00--00101001000001000000111111001000010000010111011101010101010110
		Xiphophorus_nigrensis            2111142010111?110011111?00110001000001010000111111001100010?10010111011?01010111010?10
		Xiphophorus_nezahualcoyotl       2112142010111?000011111?1000002010000?0100?1?111110011100111110101011111110101110?011?
		Xiphophorus_multilineatus        2111142010111?110011111?0011100110000?0100?01?????????????000001011101110101011111111?
		Xiphophorus_montezumae           2112142010111?00?011111?10000020100000000000111111001110011011110111011111010111111110
		Xiphophorus_milleri              0--204201011120-0---00--?1???0001000001000110111111000000????????????????????????????0
		Xiphophorus_meyeri               0--3043010110??-?---00--?0???000?12?0?1000??0111111000000????????????????????????????1
		Xiphophorus_malinche             2112142011111?00?011111?10??000020001?01???0?????????????11(01)110(01)01(01)100010010110110011?
		Xiphophorus_maculatus            0--204201011120-1---00--11???000100000100021011110000000001011011101100000000110101010
		Xiphophorus_helleri              2002232210111?002110211110???100100000000000111111001001101110001000110001101001110000
		Xiphophorus_gordoni              0--3043010110??-?---01--10???0001210001000000111111000000????????????????????????????1
		Xiphophorus_evelynae             0--20420101111?-?---00--11???0201001000000010111111000000????????????????????????????0
		Xiphophorus_couchianus           0--4043010110?0-0---00--10???0001110001000001111111000000????????????????????????????1
		Xiphophorus_cortezi              2112142010111?000011111?101100001000000111001111110010100111001101110011001(01)(01)(01)001101(01)0
		Xiphophorus_continens            1--2142010111?0-?-0-10--1000001000000?0000?0??????????????1001??0111011111010111?1011?
		Xiphophorus_clemenciae           2012142010111?00?111111?10000100000000000000111111000001010110000001(01)1(01)10(01)(01)00011110100
		Xiphophorus_birchmanni           1--2142011111?0-?-0-11--1011000020001?0011?0?11111001110011(01)110101110(01)0100101101100110
		Xiphophorus_andersi              2002042010111?0000000000?????000?00?0??000??1111110100000????????????????????????????0
		Xiphophorus_alvarezi             2002222110111?002110211110???1000000000000001111110000010?????????????????????????????
		Priapella_olmaceae               0--001001?11???-?---0?--???????????????0??????????????????????????????????????????????
		Priapella_intermedia             0--001001?11???-?---0?--???????????????0??????????????????????????????????????????????
		Priapella_compressa              0--001001?11???-?---0?--???????????????0??????????????????????????????????????????????
		Alfaro_hubberi                   0--000100?00???-?---0?--???????????????0??????????????????????????????????????????????
		Poecilia_butleri                 ?--000001?11???-2---0?--???????????????0??????????????????????????????????????????????
		Poecilia_reticulata              ?--000001?11???-0---0?--???????????????0??????????????????????????????????????????????
	;
END;

BEGIN ASSUMPTIONS;
USERTYPE tailspot STEPMATRIX = 5 
 0 1 2 3 4 
 . 3 8 5 3 
 3 . 7 7 6 
 8 7 . 7 9 
 5 7 7 . 3 
 3 6 9 3 . 
 ; 
 
USERTYPE GRANULAR STEPMATRIX= 5
0 1 2 3 4
. 1 2 3 2
1 . 1 2 1
2 1 . 1 2
3 2 1 . 3
2 1 2 3 .
;
 
 OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS ; 
 CHARSET Phenotypic = 1 - 86 ; 
 CHARSET MORPH_GROWTH_SEX = 1 - 17 ; 
 CHARSET PIGMENT = 18 - 44 ; 
 CHARSET BEHAVIOR = 45 - 57 ; 
 CHARSET RAPD_RFLP = 58 - 86 ; 
 TAXSET OUTGROUP = 1 - 6 ; 
 TAXSET MALEDATA = 9 11 - 12 16 21 - 22 25 ; 
 TAXSET FEMALEDATA = 9 11 - 12 16 21 - 22 24 - 25 ; 
 TYPESET * chartypes = unord: 2 - 3 5 9 - 16 18 - 20 22 - 30 32 34 36 - 42 44 - 86 , ord: 1 4 7 - 8 17 21 31 33 35 , tailspot: 43 , GRANULAR: 6 ; 
 
 END;