#NEXUS [written Tue Nov 11 16:01:14 CET 2014 by Mesquite version 3.01 (build 658) at stickleback.geomar.de/134.245.221.16] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=45; TAXLABELS Astatotilapia_burtoni Aulonocranus_dewindti Callochromis_macrops Grammatotria_lemairii Ophthalmotilapia_ventralis Xenotilapia_spiloptera Cyprichromis_leptosoma Neolamprologus_caudopunctatus Lamprologus_callipterus Lepidiolamprologus_elongatus Neolamprologus_modestus Neolamprologus_tetracanthus Neolamprologus_pulcher Variabilichromis_moorii Boulengerochromis_microlepis Oreochromis_tanganicae Trematocara_nigrifrons Bathybates_graueri Eretmodus_cyanostictus Pseudocrenilabrus_philander Ctenochromis_benthicola Neolamprologus_prochilus Ctenochromis_horei exGnathochromis_pfefferi Lobochilotes_labiatus Tropheus_moorii Cyphotilapia_gibberosa Limnochromis_abeelei Tylochromis_polylepis Gnathochromis_permaxillaris Haplotaxodon_microlepis Perissodus_microlepis Serranochromis_macrocephalus Altolamprologus_compressiceps Julidochromis_ornatus Labrochromis_stone Neochromis_rufocaudalis Pundamilia_nyererei Paralabidochromis_sp._rockkribensis Haplochromis_cf.stappersii Labidochromis_caeruleus Pseudotropheus_sp._acei Cynotilapia_pulpican Rhamphochromis_esox Tilapia_sparrmanii ; END; BEGIN CHARACTERS; TITLE GapsAsBinary; DIMENSIONS NCHAR=167; FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1"; MATRIX Astatotilapia_burtoni 000000000000010000000110000000110001100001000000100001100000000000100001?001100000001011000100100100101001?0000001?0010000011?00001100110001000000000000100000000100001 Aulonocranus_dewindti 000001???000010000000110000000010001000000010000100001100000000001010?01?00100000000100100000011010010100000100001?0010000011?0000111?110000000000000000000000000100000 Callochromis_macrops 000001???000010000000110001?00010001000001010000100001100000000000010?01?0010000000010010?100011010010100000100101?0011?001????0001100110000000000000000010100?10100000 Grammatotria_lemairii 000000000000010000000110001?00010001000001000000100001100000000000010?01?00100000000100100000011010010100000100001?0010000011?0000111?11000000000000000001010000010?100 Ophthalmotilapia_ventralis 000001???000010000000110000000010001000001010000100001100000000001010?01?00100000000100100000011010010100000100001?0010000011?0000111?110000000000010000010100000100000 Xenotilapia_spiloptera 000000000000000000000110000000010001000001010000100001100000000001010?01?00100000000100100000011010010100000100001?0011?00011?00001100110000000000000000010100?10100000 Cyprichromis_leptosoma 000000000000010000000110000000110001000001000000100011100000000100010?01?00100000000100100000011010010100000001001?0011?00011?00001100111000000000000001010100000100000 Neolamprologus_caudopunctatus 0001000001000100000001100000000100010000010000001000011000000000000?1?01?00100000000100100000011010010100000000010110?0100011?00101101110000000000000000010100000100000 Lamprologus_callipterus 0000000000000100010001100000000100010000010000001000011000000000000?1?01?00100000000100100000011010010100000000010110?0100011?00101101110000000000000000000000000100000 Lepidiolamprologus_elongatus 0000000001000100000001100000000100010000010000001000011000000000000?1?01?001000000001001000000110101?0100000000010110?0100011?00101101110000000000000000000000000100000 Neolamprologus_modestus 0000000001000100010001100000000100010000010000001000011000000000000?1?01?00100100000100100000011010010100001000001?0010100011?00101101110000000000000100010100000100000 Neolamprologus_tetracanthus 0000000001000100010001100000000100010000010000001001011000000000000?1?01?00100001000100100000011010010100001000000110?0100011?00001101110000000000000000010100000100000 Neolamprologus_pulcher 0000000000000100000001100000000100010000010000001000011000000000000?1?01?00100001000100100000011010010100000000001?0010100011?00001101110000100000000000010100000100000 Variabilichromis_moorii 0000000000000100000001100000000000000000000000001000011000000000000?1?01?00100000100100100000011010010100001000001?0010100011?00101101110000000000000000010100000100000 Boulengerochromis_microlepis 000000000000000000000110000001010001000001000000100001100000000000010?01?0010000000011010000001101001010000000000010010000011?00000100010000000011??0000010100000100000 Oreochromis_tanganicae 01000000000000000001000100000001001?001001000100100001100000000000010?0001?10000000010010000001101001011000000000010010000010?10000100010010000000000000000000000000000 Trematocara_nigrifrons 00100000001001001000011000000000000100000100000011?001100000001000010?0010010000000011010000011101000000000000000010010000011?01???100010000000010000010010100000100010 Bathybates_graueri 0010100000100110101?0110000000010001000001000000101001100000000000010?01?0010000000011000000001?11001010000000000010010000011?00010100010000000010000000000100000000010 Eretmodus_cyanostictus 0000000000001?0000000110000000010001000000000010100001100000000000010?1??00100000000100100001?11010010101000000001?01?0000011?00001100110000000000000000010100000100001 Pseudocrenilabrus_philander 000000000000000000000110000000010001010001000000100001110010000000100001?00110000000100100000011010010100000000001?0010001011?00001100110000000000000000010100000101001 Ctenochromis_benthicola 000000000000010000000110000000110001000001000001000001100000000000010?01?00100000000100100000011010010100000000001?0010000011?00001100110000000000000000010100000100000 Neolamprologus_prochilus 0000000001000100000001100000000100010000010000001000011000000000000?1?01?00100000000100100000011010010100000000000110?0100011?00001100110000000000000000010100000100000 Ctenochromis_horei 001000000000010000000110000000110001100001000000100001100000000010100001?001100000001001000000110100101001?0000001?0010010011?00001100110000000000000000010000000101001 exGnathochromis_pfefferi 000000000000010000000110000000110001100001000000100001100000000010100001?001100000001001000000110100101001?0000001?0010000011?00001100110000000000100000011000000101000 Lobochilotes_labiatus 001000100000010000000110000000110001000001000000100001100000000000100001?001100000001001000000110100101001?0000001?0010000011?00001100110000000000000000000000000101001 Tropheus_moorii 000000000000010000000110000000110001100001000000100001100000000000100001?001100000001001100000110100101001?0000001?0010000011?00001100110000000000000000011000000101001 Cyphotilapia_gibberosa 100000000000010000000110000000110001000001000001000001100000000000010?01?00100000000000100000011010010100000000001?0010000011?00001100110000000000000000010110000100000 Limnochromis_abeelei 000000000000010000001110000000010001000001000000100001101000000000010?01?00100000000100100000011010010100000000001?0010000011?00001100110000000000000000010100000100000 Tylochromis_polylepis 000000000000000000000100110010011000000100100000000000000000000000010?0000110001000110010000000100100110001001000010000000000000000000000010010100000000000000000100000 Gnathochromis_permaxillaris 00000000000001000000011000000001000100000100000010000110?100000000010?01?00100000000100100000011010010100000000001?0010000011?00001100110000001000000000010100000100000 Haplotaxodon_microlepis 000000000000010000000110000000010001000001000000100001100000000000010?01?00000000010100101000011010010100000000001?0010000011?00001100110000000000000000010100000100000 Perissodus_microlepis 000000000000010000000110000000010001000001000000100001100000000000010?01?00000000010100101000011010010100000000001?0010000011?00001100110000000000000000010100000100000 Serranochromis_macrocephalus 000000000000000100000110000000010001000011000000100001100001000000000000000110000000100100000011010010100000000001?0010000011?00001100110000000000000000110101100101001 Altolamprologus_compressiceps 0000000010000100000001100000000100010000010000001000011000000000000?1?01?00100000000100100000011010010100000000010110?0100011?00101101110000000000000000010100000100000 Julidochromis_ornatus 0000000000000100000001100001000000000000010000001000011000000000000?1?01?00100100000100100000011010010100000000001?10?0100011?00001101110000000000000000010100000100000 Labrochromis_stone 000000000000010000000110000000110101000001001000100001100000000000100101?001?1?000001001000000110100101001?0000001?0010000011?00001100110100000000000000110101101111001 Neochromis_rufocaudalis 000000000000010000000110000000110101000001001000100001100000110000100101?001?1?000001001000000110100101001?0000001?0010000011?00001100110100000000000000110101101111001 Pundamilia_nyererei 000000010000010000000110000000110101000001001000100001100000000000100101?001?1?000001001000000110100101001?0000001?0010000011?00001100110100000000000000110101101111001 Paralabidochromis_sp._rockkribensis 000000000000010000000110000000110101000001001000100001100000110000100101?001?1?000001001000000110100101001?0000001?0010000011?00001100110100000000000000110101101111001 Haplochromis_cf.stappersii 000000010000010000000110000000110101000001001000100001100000000000100101?001?1?00000100100000011010000000000000001?0010000011?00001100110100000000000000110100001111001 Labidochromis_caeruleus 000000000001??0000000110000000110001000001000000100001100000000000100101?001?1?000001001000000110100101001?0000001?0010000011?00001100110000000000001000110101?10101001 Pseudotropheus_sp._acei 000000000001??0000000110000000110001000001000000100001100000000000100101?001?1?000001001000000110100101001?0000001?0010000011?00001100110000000000000000110101100101001 Cynotilapia_pulpican 000000000001??0000000110000000110001000001000000100001100000000000100101?001?1?000001001000000110100101001?0000001?0010000011?00001100110000000000000000110101?10101001 Rhamphochromis_esox 000000000001??00000001100000001100010000010000001000011000000000000000000001?1?000001001000000110100101001?0000001?0010000011?00001100110000000000000000000000000101001 Tilapia_sparrmanii 001000000000010000000110000000010001000001000000100001100000000000010?01?0010000000010010000001101001000000000000000010000010100000100110000000000000000000000000100000 ; END; BEGIN TREES; Title 'GAPS_garli'; LINK Taxa = Taxa; TRANSLATE [0] 1 Astatotilapia_burtoni, [1] 2 Aulonocranus_dewindti, [2] 3 Callochromis_macrops, [3] 4 Grammatotria_lemairii, [4] 5 Ophthalmotilapia_ventralis, [5] 6 Xenotilapia_spiloptera, [6] 7 Cyprichromis_leptosoma, [7] 8 Neolamprologus_caudopunctatus, [8] 9 Lamprologus_callipterus, [9] 10 Lepidiolamprologus_elongatus, [10] 11 Neolamprologus_modestus, [11] 12 Neolamprologus_tetracanthus, [12] 13 Neolamprologus_pulcher, [13] 14 Variabilichromis_moorii, [14] 15 Boulengerochromis_microlepis, [15] 16 Oreochromis_tanganicae, [16] 17 Trematocara_nigrifrons, [17] 18 Bathybates_graueri, [18] 19 Eretmodus_cyanostictus, [19] 20 Pseudocrenilabrus_philander, [20] 21 Ctenochromis_benthicola, [21] 22 Neolamprologus_prochilus, [22] 23 Ctenochromis_horei, [23] 24 exGnathochromis_pfefferi, [24] 25 Lobochilotes_labiatus, [25] 26 Tropheus_moorii, [26] 27 Cyphotilapia_gibberosa, [27] 28 Limnochromis_abeelei, [28] 29 Tylochromis_polylepis, [29] 47 Gnathochromis_permaxillaris, [30] 31 Haplotaxodon_microlepis, [31] 32 Perissodus_microlepis, [32] 33 Serranochromis_macrocephalus, [33] 34 Altolamprologus_compressiceps, [34] 35 Julidochromis_ornatus, [35] 36 Labrochromis_stone, [36] 37 Neochromis_rufocaudalis, [37] 38 Pundamilia_nyererei, [38] 39 Paralabidochromis_sp._rockkribensis, [39] 40 Haplochromis_cf.stappersii, [40] 41 Labidochromis_caeruleus, [41] 42 Pseudotropheus_sp._acei, [42] 43 Cynotilapia_pulpican, [43] 44 Rhamphochromis_esox, [44] 45 Tilapia_sparrmanii; TREE 'bestREP39+' = (29:0.05158452,(16:0.03986505,(45:0.01130603,((15:0.01005282,(17:0.03325957,18:0.02850954):0.01706482):0.00950916,(28:0.00657713,47:0.00659893,(31:0.00000001,32:0.00000001):0.00989975,(7:0.02024639,(21:0.00000001,27:0.00989872):0.00666778):0.00323134,(4:0.00818741,((2:0.01009486,5:0.00332562):0.00433582,(3:0.01942923,6:0.00466386):0.00859238):0.00717343):0.00513395,(13:0.00660029,(14:0.01344518,35:0.01007774):0.00662037,(11:0.01680474,(12:0.0132906,22:0.00329515,(8:0.00329415,34:0.00659372,(9:0.00663722,10:0.00330525):0.0066434):0.00660311):0.00667872):0.00325041):0.00990573,(19:0.02402432,(33:0.02630524,(20:0.01604291,(((1:0.02340336,25:0.00659183,44:0.01339128):0.00327779,(23:0.0095022,(24:0.00950261,26:0.00373988):0.00328738):0.00374393):0.00326362,((42:0.00000001,(41:0.00333233,43:0.00000001):0.00333255):0.00314561,(36:0.00000001,(37:0.00000001,39:0.00000001):0.00662107,(38:0.00000001,40:0.01666693):0.00328901):0.01696031):0.01710908):0.00737687):0.00304766):0.0108552):0.00329379):0.0077066):0.0099652):0.01572543):0.05158452); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 167; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 167; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1415718074388; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 1410263258693600441; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 6679744976993449704; mqVersion 301; checksumv 0 3 172141945 null getNumChars 167 numChars 167 getNumTaxa 45 numTaxa 45 short true bits 3 states 3 sumSquaresStatesOnly 12021.0 sumSquares 12021.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 312; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1201 692; setLocation -1473 -243; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #1410263258693600441 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 4217.1415718043297.8512134680514875089; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 889 620; setLocation -1473 -243; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareLineTree.SquareLineTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle on; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; setFixedTaxonDistance 0; endTell; setEdgeWidth 4; showEdgeLines on; orientRight; endTell; setBackground White; setBranchColor Black; showNodeNumbers off; showBranchColors on; labelBranchLengths off; centerBrLenLabels on; showBrLensUnspecified on; showBrLenLabelsOnTerminals on; setBrLenLabelColor 0 0 255; setNumBrLenDecimals 6; desuppress; getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames; tell It; setColor Black; toggleColorPartition off; toggleColorAssigned on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; showWindow; endTell; desuppressEPCResponse; getEmployee #mesquite.trees.ColorBranches.ColorBranches; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.ornamental.BranchNotes.BranchNotes; tell It; setAlwaysOn off; endTell; getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition; tell It; colorByPartition off; endTell; getEmployee #mesquite.ornamental.DrawTreeAssocDoubles.DrawTreeAssocDoubles; tell It; setOn on; setDigits 4; writeAsPercentage off; toggleCentred off; toggleHorizontal on; toggleWhiteEdges on; setFontSize 10; setOffset 0 0; endTell; getEmployee #mesquite.ornamental.DrawTreeAssocStrings.DrawTreeAssocStrings; tell It; setOn on; toggleCentred on; toggleHorizontal on; setFontSize 10; setOffset 0 0; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; endTell; end;