#nexus BEGIN Taxa; DIMENSIONS ntax=5; TAXLABELS [1] 'apo2915' [2] 'apo3528' [3] 'carpat' [4] 'cassub' [5] 'notabilis' ; END; [Taxa] BEGIN Characters; DIMENSIONS nchar=1677; FORMAT datatype=STANDARD missing=? gap=- symbols="atcgywmkrsdvb1234" labels=left transpose=no interleave=no ; MATRIX 'apo2915' yyyyyyyyyyyyyyyyyyyyyyyyywwwwwwwwwwwwvttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttsssssssssssssssssrrrrrrrrrrrrrrrrrrrrrrrrrmmmmmmmmmmmmmmmmmmmmmmmmmmmkkkkkkkkkkkkkkkkkkkkggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------222221111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111 'apo3528' yyyyyyyyttttttscccccccc--wtaaaaaa----vyyyyyyyywwwwwwttttttttttttttttttttttttttttttttttttttttttttttttkkkggggggggccccccccccaaaaaaaaaaaaaaaaaaaa---------------------------------------------------------------------ssskggggggcc-----wrrrrrrgggggggaaa--------mmmmmmmmmgcccccccaaaaaa----tttttttkkkkggggg----tttttttttttttsssrrrrrrrrrrrkkkkggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggcccccaaaaaaaaa-----------------------------------------------------yyyyyyyyyyyytttttttsssssssmmmmmmmmmmmmmmmmgggggggggcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccaaaaaaaaaaaa----------------------------------------------wwwwwwwtttttttttttttttttttttrrrrrmmmggggggccccccccccaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa---------------------------------------yyyyyyyyyywwwwwwwwwwttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttsssssssssrrrrrrrmmkkkkkgggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggdcccccccccccccccccccccccccccccccccccccccccccccccccccccaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------211111111111111111111111111111111111111111111111111111111111--211--------------------------------------22222222222222222222222222222222222222222222222222222111111111111111111111111111111111111111111111111111111111 'carpat' tt------tcc----ccc---------aaa---a----tta-----t-----yttttttttkggggccaaaa----------------------------tg-gg------cc--------ttaa----------------tttttgggggcaaaaa---------------------------------------------------------ggc-----gc----ggaa--ggaa---ga-ggga----cc--------ccca---a-----cc---------tt--tg---tgg-tt-----------g--gggggg-----g---ttttrrkgggggggggggggggggccccaaaaaaaaa-----------------------cccc-a--------trggggggggccccaaaaaa---------------------------------tccc--------c------ccc----ccccc-----------c--------yyttttttsgggcccccccccccccccaaaaaaa---------------------------------a-----------ttmgccccccaa----------------------------------a------ttaaaa---------------aaa--a--g-----ccccaa----wttrrmmgggcccccaaaaaaaaa--------------------wttttggcaaaa---------------------------ttcccc----taaaa-----wwwwttttttgggggcccccccccaaaaaaaaaaaaaa----------------------------------ggcca----gggaa--c-ttgg-ttttttttkgggggcccccccccccaaaa-------------------------------------------ttttsggggggggccaaaaaaaa------------------------------ttttttttttttttrggggggggccccccaa------------------------------------------yywwtttttttttttttttttttttttttttttttttttttttttttttttttttttttttttsrmmmkkkkggggggggggggggggggggggggggggggggggggggggggggggggggggggccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa---------------------------------------------------------------------------------11111111111111111111111111111111111111111111111--------------------------222222222222222222222222222221111-1321--------------------------322222222221---------------------------------------33332222111111----------------------22222222222222222222222211111111111 'cassub' t-ttt---ty-t---cc-yc---tca-aaaa---t--gytctttt-tta----yyttkgaa-t---c-tta-ywwwttttttkgcccaaaaaaa------tt-t-tg----c-yttc----tat-taa-------------ta---tk----t----ytttkkkgggggga---------------------------------------gc--gggs--c--cc--arggargg-a-g---a-g---ga--c-mmcaaa--c---c---tmm----a-ttkg---tkt-g----tg-t--ttt---------g-gggggggg---gkggtgg-g--ttssrkkggggggcc--r---gggaa----ttttssrrkkgggggcc------gcc-caa-------tgtttrg---g---ggaa--tttttttttkkggggca-----------------ccctccccc--ac--------cc--ccc--ccccca------cc--------ccc----cccyttmgccccca----ccc----yyyytmmmmggcccccccccccaaa--------cccaa-------tc--yy----m-yyttttttmmggcccccccca--------------aaa-----ta--ttt------------aa-a--maggaa--cc----m---ataaaa----ccaa-trrmcaaa-wwtrmmmggccaa--------ta--g-am---wttttttgcccaa--------------------tc--ta---t----ta--ytkg--k----tt-------ttaa----------ywtttttkgggccc--------------------g---gcc--r----gac---g--tt-------tsg--c--------------tttttsssrrrrrrkkggggccccccaa---------------c------------a-c-------yssmmmmgggccccca--------------aa-------------ga------mca---rmwwwwtttttrrrggcccccccccca-----------------yt--ywttkkkgggggggggcccaaaaaaaaaaa-----------------------------a-c--tg--tttttttssrkgggcccccccaaaaaaaaa------------------------yyytttttttmmggggggccccaaaaaaa---------------------------------ytttttttttttrmgggggggcccccc-----------------------------------------yyywwttttttttttttttttrmkkkggggggggggggggggggccccccccccccccccccaaaaaaaaa1111111111------------------------2222222222222222222111----------------22222222222----------------------211111122111--1------------------2222222213------3222-----------------------33222222221111111--32-221-----1------2222222222111111--------3221111111111111----2221111 'notabilis' t----c--ty--t--c--ctcc-cta-t---a-ataa-ctcytt-t-ttt---ttkg----t----------ttt-ywkccc-----ttaaa--yykcaatg---t-----tcyt-ytt--ta-----ta-----------atkaa--tgcc-tttatyaag--------awwwrgggggggggcccccccccaaaaaaaaaaaaaaaaa-c-bgg-cg-ccgccgca-gaaggggggg---a--gga-aga--macma-accc---mca-m---caaatkg----ttt--kg--t-g-g-gg-gg------gg-ggggg-g----g-g--g-------gcgk-trrkkag-rr-g--gg-rgg---tg--gg--g-tskaagcttrcca-c-c---ggg-----gg---tttc-ggg----ggtt---------tkcabatttttsrccccccccacy---c----c-act----cc-ccgcmc-cccc---a------ccg-----c-cc-cc--c--cc-ccyymmgctggacc-----c---cc-----ytssgggggga---ytmaaaaacc---c--------gc--ttaa-cc-c-------g-yyttgaaaaysssggggaaaaa-a-----a--a--ta-a-----------aar-aa-agaaag---c---a---a--aa-----c-a--aa-a-rrmra-t----g-c-tgwtttttta-ata-a-cwwg--------c--wtwwwtttrrggcccct-c-----cc-a----wtta-t---gtgaagg---tc-------taa-ttt-------t-ggaaa-------wggggccccaaaaaaaaaaag------gcg-------tg-k-gt-g--------rrk---------------g----g--ggg-----ttkcg-----a-tttttrrrkkcccatc----c--------acc---------c---gg-tgaaa-ytttttggggaaaa--a---------------------c----a-----t---------aaa-------ttttttttttttgggccct-tt-taa---g----------------------ykkkkgggggggcccccccccaaaaaaaa-acca--tgt------s---tsa-------gaa------ttttttttttsrrkcccaaaaaaa---tt-------g-----ytaa-------yytttttttttsmmgggggggaaaaaaaaaaaa-t------------g------------ywwwtttttttttttttttttttrrmmggggccccccccccttctaykggggccccaaaaaaaattgttttttsskccaaaaaaayytsrgggaaaaaaaaaawwwttttcc2222222222222222222222222222222222------------------3222-222222222222222--------222--------------------21------1-1222242122222222222222222------1124211111----2------------333211111133---32221----111--4-2222----11322222-------211222222-----2111-2-----3111111122221112222 ; END; [Characters] BEGIN Distances; DIMENSIONS ntax=5; FORMAT labels=left diagonal triangle=both; MATRIX [1] 'apo2915' 0.0 0.5224111 0.63037246 0.5893224 0.6770073 [2] 'apo3528' 0.5224111 0.0 0.7258427 0.63320464 0.7235294 [3] 'carpat' 0.63037246 0.7258427 0.0 0.6860759 0.7665904 [4] 'cassub' 0.5893224 0.63320464 0.6860759 0.0 0.6522727 [5] 'notabilis' 0.6770073 0.7235294 0.7665904 0.6522727 0.0 ; END; [Distances] BEGIN Splits; DIMENSIONS ntax=5 nsplits=10; FORMAT labels=no weights=yes confidences=yes intervals=no; PROPERTIES fit=100.0 cyclic; CYCLE 1 2 4 5 3; MATRIX [1, size=1] 0.28314668 1.0 1 3 4 5, [2, size=2] 0.0013199307 0.352 1 3 5, [3, size=2] 0.024474045 0.874 1 3, [4, size=1] 0.21347046 1.0 1, [5, size=1] 0.28097397 1.0 1 2 3 5, [6, size=2] 0.01574497 0.902 1 2 3, [7, size=2] 0.053339 0.997 1 2, [8, size=1] 0.3663936 1.0 1 2 3 4, [9, size=2] 0.003585239 0.471 1 2 4, [10, size=1] 0.35997778 1.0 1 2 4 5, ; END; [Splits] BEGIN Network; DIMENSIONS ntax=5 nvertices=13 nedges=14; DRAW to_scale; TRANSLATE 2 'notabilis', 3 'carpat', 4 'apo2915', 5 'apo3528', 6 'cassub', ; VERTICES 1 0.0 0.0 w=2 h=2 s=n, 2 -0.22653441 -0.30661255 w=2 h=2 s=n, 3 -0.124943905 -0.4285114 w=2 h=2 s=n, 4 0.008664195 -0.3596111 w=2 h=2 s=n, 5 0.110415906 -0.38925236 w=2 h=2 s=n, 6 0.1849184 -0.27014643 w=2 h=2 s=n, 7 0.012914069 -0.12203842 w=2 h=2 s=n, 8 -0.0018242485 -0.09024296 w=2 h=2 s=n, 9 0.004311814 -0.054907877 w=2 h=2 s=n, 10 0.0 -0.03663936 w=2 h=2 s=n, 11 0.010789133 -0.24082476 w=2 h=2 s=n, 12 0.0064570345 -0.079338886 w=2 h=2 s=n, 13 0.061664987 -0.2556454 w=2 h=2 s=n, ; VLABELS 1 'root' x=-9 y=23 f='Dialog-PLAIN-10', 2 'notabilis' x=-28 y=-13, 3 'carpat' x=-19 y=-15, 4 'apo2915' x=-21 y=-16, 5 'apo3528' x=-17 y=-15, 6 'cassub' x=-8 y=-13, ; EDGES 1 8 3 s=10 w=0.35997778, 2 9 6 s=5 w=0.28097397, 3 10 1 w=0.03663936, 4 10 2 w=0.35242498, 5 11 8 s=-1 fg=0 0 255, 6 12 8 s=-1 fg=0 0 255, 7 12 9 s=-1 fg=0 0 255, 8 7 13, 9 13 9 s=-1 fg=0 0 255, 10 13 5, 11 10 12, 12 12 7 s=8, 13 7 11, 14 11 4, ; ELABELS 1 '100' ll=11 f='Dialog-PLAIN-10', 2 '100' ll=11, 12 '100' ll=11, ; END; [Network] BEGIN st_bootstrap; DIMENSIONS ntax=5 nchar=1677 nsplits=15; FORMAT labels=no splits=yes all=yes; RUNS=1000; LENGTH=1677; MATRIX [1] 100.0 1 3 4 5, [2] 35.2 1 3 5, [3] 87.4 1 3, [4] 100.0 1, [5] 100.0 1 2 3 5, [6] 90.2 1 2 3, [7] 99.7 1 2, [8] 100.0 1 2 3 4, [9] 47.1 1 2 4, [10] 100.0 1 2 4 5, [--------------------------------------------------] [11] 27.8 1 2 5, [12] 25.4 1 3 4, [13] 3.0 1 4, [14] 3.6 1 4 5, [15] 2.6 1 5, ; END; [st_Bootstrap] BEGIN st_Assumptions; uptodate; chartransform=Uncorrected_P; disttransform=NeighborNet Variance = OrdinaryLeastSquares; splitstransform=HybridizationNetwork ShowSplits = false MaxReticulationsPerTangle = 4 Which = 1 Method = RECOMB2007 OutGroup = notabilis Layout = EqualAngle120 PercentOffset = 10; SplitsPostProcess filter=dimension value=4; autolayoutnodelabels; END; [st_Assumptions]