#NEXUS [written Sun May 04 15:25:54 PDT 2008 by Mesquite version 2.01+ (build j65) at Thrandina.local/10.0.1.8 (Wayne Maddison)] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=48; TAXLABELS nig1 nig2 nig3 nig4 nig5 nig6 nig7 nig8 nig9 nig10 nig11 nig12 met1 met2 met3 met4 met5 met6 met7 met8 met9 met10 met11 met12 moj1 moj2 moj3 moj4 moj5 moj6 moj7 moj8 moj9 moj10 moj11 moj12 pac1 pac2 pac3 pac4 pac5 pac6 pac7 pac8 pac9 pac10 pac11 pac12 ; BLOCKID WM114cbd3ad085; END; BEGIN CHARACTERS; TITLE 'Matrix in file "01-wingsPlot.nex"'; DIMENSIONS NCHAR=4; FORMAT DATATYPE = CONTINUOUS; CHARSTATELABELS 1 V1, 2 V2, 3 ACV, 4 PCV ; MATRIX nig1 1.784 1.994 0.1007 0.2488 nig2 1.662 1.946 0.0882 0.2503 nig3 1.92 2.244 0.0678 0.2707 nig4 1.838 2.107 0.0678 0.2653 nig5 1.843 2.111 0.0784 0.2791 nig6 1.953 2.194 0.0671 0.2696 nig7 1.782 2.03 0.0795 0.2678 nig8 1.792 2.137 0.0852 0.2694 nig9 1.889 2.203 0.0746 0.2575 nig10 1.836 2.092 0.0925 0.2592 nig11 1.877 2.13 0.0941 0.2696 nig12 1.826 2.133 0.0741 0.2751 met1 1.451 1.659 0.0805 0.2425 met2 1.672 1.949 0.0754 0.2687 met3 1.67 1.943 0.0745 0.2862 met4 1.783 2.037 0.1074 0.2612 met5 1.734 2.048 0.0814 0.2503 met6 1.624 1.858 0.0736 0.2555 met7 1.697 1.939 0.0871 0.2728 met8 1.695 1.979 0.0923 0.2748 met9 1.552 1.835 0.0674 0.2417 met10 1.7 1.994 0.0875 0.2781 met11 1.723 1.945 0.0808 0.2705 met12 1.688 1.987 0.0875 0.2847 moj1 1.19 1.298 0.0667 0.1871 moj2 1.209 1.336 0.06 0.1962 moj3 1.255 1.387 0.0806 0.2011 moj4 1.224 1.351 0.0666 0.1847 moj5 1.196 1.318 0.0596 0.176 moj6 1.188 1.345 0.074 0.1991 moj7 1.187 1.314 0.0696 0.1745 moj8 1.235 1.371 0.06 0.1877 moj9 1.153 1.29 0.0471 0.1688 moj10 1.208 1.352 0.0731 0.1818 moj11 1.177 1.29 0.0679 0.1777 moj12 1.226 1.363 0.06 0.1909 pac1 1.343 1.479 0.0821 0.1719 pac2 1.429 1.56 0.0731 0.2052 pac3 1.391 1.537 0.0731 0.2192 pac4 1.496 1.673 0.093 0.2283 pac5 1.347 1.514 0.0795 0.1978 pac6 1.311 1.449 0.062 0.1795 pac7 1.424 1.62 0.0682 0.21 pac8 1.411 1.596 0.0787 0.2128 pac9 1.338 1.502 0.0653 0.2077 pac10 1.449 1.618 0.0745 0.231 pac11 1.447 1.603 0.0787 0.2346 pac12 1.465 1.621 0.0765 0.214 ; BLOCKID WM114cbd3ad1e0; END; BEGIN TREES; Title 'Trees from "01-wingsPlot.nex"'; LINK Taxa = Taxa; TRANSLATE 1 nig1, 2 nig2, 3 nig3, 4 nig4, 5 nig5, 6 nig6, 7 nig7, 8 nig8, 9 nig9, 10 nig10, 11 nig11, 12 nig12, 13 met1, 14 met2, 15 met3, 16 met4, 17 met5, 18 met6, 19 met7, 20 met8, 21 met9, 22 met10, 23 met11, 24 met12, 25 moj1, 26 moj2, 27 moj3, 28 moj4, 29 moj5, 30 moj6, 31 moj7, 32 moj8, 33 moj9, 34 moj10, 35 moj11, 36 moj12, 37 pac1, 38 pac2, 39 pac3, 40 pac4, 41 pac5, 42 pac6, 43 pac7, 44 pac8, 45 pac9, 46 pac10, 47 pac11, 48 pac12; TREE colored = (((1[%color = 5 ],(2[%color = 5 ],(3[%color = 5 ],(4[%color = 5 ],(5[%color = 5 ],(6[%color = 5 ],(7[%color = 5 ],(8[%color = 5 ],(9[%color = 5 ],(10[%color = 5 ],(11[%color = 5 ],12[%color = 5 ])[%color = 5 ])[%color = 5 ])[%color = 5 ])[%color = 5 ])[%color = 5 ])[%color = 5 ])[%color = 5 ])[%color = 5 ])[%color = 5 ])[%color = 5 ])[%color = 5 ],(13[%color = 8 ],(14[%color = 8 ],(15[%color = 8 ],(16[%color = 8 ],(17[%color = 8 ],(18[%color = 8 ],(19[%color = 8 ],(20[%color = 8 ],(21[%color = 8 ],(22[%color = 8 ],(23[%color = 8 ],24[%color = 8 ])[%color = 8 ])[%color = 8 ])[%color = 8 ])[%color = 8 ])[%color = 8 ])[%color = 8 ])[%color = 8 ])[%color = 8 ])[%color = 8 ])[%color = 8 ])[%color = 8 ]),((25[%color = 10 ],(26[%color = 10 ],(27[%color = 10 ],(28[%color = 10 ],(29[%color = 10 ],(30[%color = 10 ],(31[%color = 10 ],(32[%color = 10 ],(33[%color = 10 ],(34[%color = 10 ],(35[%color = 10 ],36[%color = 10 ])[%color = 10 ])[%color = 10 ])[%color = 10 ])[%color = 10 ])[%color = 10 ])[%color = 10 ])[%color = 10 ])[%color = 10 ])[%color = 10 ])[%color = 10 ])[%color = 10 ],(37[%color = 11 ],(38[%color = 11 ],(39[%color = 11 ],(40[%color = 11 ],(42[%color = 11 ],(41[%color = 11 ],(43[%color = 11 ],(44[%color = 11 ],(45[%color = 11 ],(46[%color = 11 ],(47[%color = 11 ],48[%color = 11 ])[%color = 11 ])[%color = 11 ])[%color = 11 ])[%color = 11 ])[%color = 11 ])[%color = 11 ])[%color = 11 ])[%color = 11 ])[%color = 11 ])[%color = 11 ])[%color = 11 ])); END; BEGIN LABELS; TAXAGROUPLABEL nig COLOR = (RGB 1.0 0.03137255 0.25882353) ; TAXAGROUPLABEL met COLOR = (RGB 0.25882353 1.0 0.08627451) ; TAXAGROUPLABEL moj COLOR = (RGB 1.0 0.62745098 0.05882353) ; TAXAGROUPLABEL pac COLOR = (RGB 0.02745098 0.58431373 1.0) ; END; BEGIN SETS; TAXPARTITION * UNTITLED = nig : 1 - 12, met : 13 - 24, moj : 25 - 36, pac : 37 - 48; TAXPARTITION species = nig : 1 - 12, met : 13 - 24, moj : 25 - 36, pac : 37 - 48; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = Squared: 1 - 4; END; BEGIN NOTES; TEXT FILE TEXT = 'This file shows data of Eric Dyreson for wing characteristics measured for specimens of four species of Drosophila. The taxa are individual specimens, and they are grouped (by color) into four species. (The grouping is done by a taxa partition, which can be done via the List of Taxa window).^n^nAbove right is a plot of character 2 versus character 1, which are obviously highly correlated because of their correlation with size. This plot is phylogeny-free.'; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = Brownian_default: 1 - 4; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 208212565903807533 WM114cbd3ad085; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 124634251740354766 WM114cbd3ad1e0; checksum 0 578547273 WM114cbd3ad1e0; endTell; getWindow; tell It; setResourcesState false true 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 513 324; setLocation 6 22; setFont SanSerif; setFontSize 10; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #124634251740354766 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; popAsTile false; popOut; setExplanationSize 20; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 493 470; setLocation 18 371; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.ColorByState.ColorByState; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleShowChanges on; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames on; toggleShowDefaultCharNames off; toggleConstrainCW on; setColumnWidth 70; toggleBirdsEye off; toggleAllowAutosize on; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel; tell It; togglePanel off; endTell; getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.ColorCells.ColorCells; tell It; setColor Red; removeColor off; endTell; endTell; endTell; newAssistant #mesquite.charts.TaxaScattergram.TaxaScattergram; tell It; setTaxonSource #mesquite.minimal.StoredTaxa.StoredTaxa; tell It; setTaxa #208212565903807533; endTell; setTaxa #208212565903807533; axesSame; setValues #mesquite.cont.ContinuousStatesT.ContinuousStatesT; tell It; getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed; tell It; setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters; tell It; setDataSet #124634251740354766; endTell; endTell; setCharacter 2; setItem 0; endTell; showNamesToggle on; getCharter #mesquite.charts.ItemsBiplot.ItemsBiplot; tell It; getWindow; tell It; setX 1; setY 2; popAsTile false; popOut; setExplanationSize 20; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 493 470; setLocation 534 36; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; endTell; enableCalculations; getEmployee #mesquite.charts.Scattergram.Scattergram; tell It; markerSize 10; toggleJoin off; toggleShowDots on; movingWindowSize 1; sumByBlocks off; endTell; endTell; setChartVisible; doCounts; showWindow; endTell; newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator; tell It; setNextFileName '02-wingsPCA.nex'; setPrevFileName '00-introduction.nex'; getWindow; tell It; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 513 307; setLocation 6 22; setFont SanSerif; setFontSize 10; setActive; setExplanation 'This file shows data of Eric Dyreson for wing characteristics measured for specimens of four species of Drosophila. The taxa are individual specimens, and they are grouped (by color) into four species. (The grouping is done by a taxa partition, which can be done via the List of Taxa window).^n^nThe scattergram shows a plot of character 2 versus character 1, which are obviously highly correlated because of their correlation with size. This plot is phylogeny-free.'; setTitle Raw_data; toggleFileNames off; setPrevButtonName Previous; setNextButtonName Next; endTell; showWindow; endTell; endTell; end;