#NEXUS
[written Sat Jun 07 11:25:37 PDT 2008 by Mesquite  version 2.5 BETA 2 (build j76) at Thrandina.local/192.168.0.136 (Wayne Maddison)]

BEGIN TAXA;
	TITLE population;
	DIMENSIONS NTAX=1;
	TAXLABELS
		population 
	;
	BLOCKID WM1148e54189c37;

END;



BEGIN TAXA;
	TITLE genes;
	DIMENSIONS NTAX=8;
	TAXLABELS
		g_1 g_2 g_3 g_4 g_5 g_6 g_7 g_8 
	;
	BLOCKID WM1148e5418b238;

END;


BEGIN TaxaAssociation;
TITLE Untitled;
TAXA population ,  genes;
ASSOCIATES 

	population /  g_1 g_2 g_3 g_4 g_5 g_6 g_7 g_8

;

END;


BEGIN TREES;
	Title 'Trees block 2 from 08-fluctuating.nex';
	LINK Taxa = population;
	TRANSLATE
		1 population;
	TREE three_segments = (((1:100.0[%width = 10.0 ]):100.0[%width = 10.0 ]):100.0[%width = 10.0 ]):100.0[%width = 1.0 ];
	TREE oneBottleneck = (((1:100.0[%width = 10.0 ]):100.0[%width = 1.0 ]):100.0[%width = 10.0 ]):100.0[%width = 1.0 ];
	TREE twoBottlenecks = (((((1:100.0[%width = 10.0 ]):100.0[%width = 1.0 ]):100.0[%width = 10.0 ]):100.0[%width = 1.0 ]):100.0[%width = 10.0 ]):100.0[%width = 1.0 ];

END;


Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			setID 0 8262476367526418552 WM1148e54189c37;
			setID 1 5229699258384705612 WM1148e5418b238;
		endTell;
		getWindow;
		tell It;
			setResourcesState false false 72;
			setPopoutState 400;
			setExplanationSize 0;
			setAnnotationSize 0;
			setFontIncAnnot 0;
			setFontIncExp 0;
			setSize 475 460;
			setLocation 9 30;
			setFont SanSerif;
			setFontSize 10;
		endTell;
		getEmployee  #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
		tell It;
			makeTreeWindow #8262476367526418552  #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
			tell It;
				suppressEPCResponse;
				setTreeSource  #mesquite.trees.StoredTrees.StoredTrees;
				tell It;
					setTaxa #8262476367526418552;
					setTreeBlock 1;
					toggleUseWeights off;
				endTell;
				setAssignedID 1678.971300678609.5190757585608322126;
				getTreeWindow;
				tell It;
					popAsTile false;
					popOut;
					setExplanationSize 20;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 686 424;
					setLocation 532 35;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
						setTool mesquite.coalesce.LineageWidth.WidthsToolExtra.LineageWidth;
					endTell;
					getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
				tell It;
					suppress;
					setTreeDrawer  #mesquite.assoc.ContainedAssociates.ContainedAssociates;
					tell It;
						suppress ;
						getAssociationSource  #mesquite.assoc.StoredAssociations.StoredAssociations;
						tell It;
							setCurrentAssociation 0;
						endTell;
						getReconstructor  #mesquite.coalesce.RecCoalescenceHistory.RecCoalescenceHistory;
						tell It;
							toggleUnrooted off;
							toggleResolve on;
							toggleUseLengths on;
						endTell;
						setEdgeWidth 128;
						setTreeSource  #mesquite.trees.SimulateTree.SimulateTree;
						tell It;
							setTreeSimulator  #mesquite.coalesce.ContainedCoalescence.ContainedCoalescence;
							tell It;
								getAssociationTask  #mesquite.assoc.StoredAssociations.StoredAssociations;
								tell It;
									setCurrentAssociation 0;
								endTell;
								getTreeSource  #mesquite.trees.TreeOfContext.TreeOfContext;
								tell It;
									setContextID 1678.971300678609.5190757585608322126;
								endTell;
								setSimulator  #mesquite.coalesce.ContainedCoalescSim.ContainedCoalescSim;
								tell It;
									getEmployee #mesquite.coalesce.NeutralCoalescence.NeutralCoalescence;
									tell It;
										setEffective 100;
										toggleExponential on;
									endTell;
								endTell;
								forgetAssociation ;
							endTell;
							setSeed 984411941782;
						endTell;
						setContained 1;
						toggleScale on;
						setInitialOffsetX -142;
						setInitialOffsetY -160;
						desuppress ;
						getEmployee #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
						tell It;
							stretchToggle off;
							branchLengthsToggle on;
							toggleScale on;
							toggleBroadScale off;
							toggleCenter on;
							toggleEven on;
						endTell;
					endTell;
					setBackground White;
					setBranchColor Blue;
					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;
						setFont SanSerif;
						setFontSize 10;
						setColor Black;
						toggleColorPartition on;
						toggleShadePartition off;
						toggleNodeLabels on;
						toggleCenterNodeNames off;
						toggleShowNames on;
						namesAngle ?;
					endTell;
				endTell;
					setTreeNumber 2;
					useSuggestedSize off;
					toggleSizeToFit on;
					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;
					toggleHorizontal on;
					setFontSize 10;
					setOffset 0  0;
				endTell;
				getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues;
				tell It;
					panelOpen false;
				endTell;
			endTell;
		endTell;
		newAssistant  #mesquite.charts.TreeValuesChart.TreeValuesChart;
		tell It;
			suspendCalculations;
			setTaxa #5229699258384705612;
			setTreeSource  #mesquite.trees.SimulateTree.SimulateTree;
			tell It;
				setTreeSimulator  #mesquite.coalesce.ContainedCoalescence.ContainedCoalescence;
				tell It;
					getAssociationTask  #mesquite.assoc.StoredAssociations.StoredAssociations;
					tell It;
						setCurrentAssociation 0;
					endTell;
					getTreeSource  #mesquite.trees.TreeOfContext.TreeOfContext;
					tell It;
						setContextID 1678.971300678609.5190757585608322126;
					endTell;
					setSimulator  #mesquite.coalesce.ContainedCoalescSim.ContainedCoalescSim;
					tell It;
						getEmployee #mesquite.coalesce.NeutralCoalescence.NeutralCoalescence;
						tell It;
							setEffective 100;
							toggleExponential on;
						endTell;
					endTell;
					forgetAssociation ;
				endTell;
				setSeed 984411942829;
			endTell;
			setCalculator  #mesquite.coalesce.TreeDepth.TreeDepth;
			getCharter #mesquite.charts.ItemValuesChart.ItemValuesChart;
			tell It;
				getWindow;
				tell It;
					popAsTile false;
					popOut;
					setExplanationSize 20;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 561 268;
					setLocation 231 550;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
					endTell;
					itemsByValues;
					setChartType  #mesquite.charts.Histogram.Histogram;
				tell It;
					suspend;
					showAverageToggle on;
					showPercentToggle off;
					setCumulativeMode 0;
					showAsBarChartToggle on;
					showRawToggle off;
					setNumberIntervals 50;
					setIntervalSize 1.0;
					setMovingWindowSize 5.0 1.0;
					setMode 4;
					resume;
				endTell;
					toggleColorItems off;
					setNumberItems 500;
				endTell;
				enableCalculations;
			endTell;
			setChartVisible;
			doCounts;
			resumeCalculations;
			showWindow;
		endTell;
		newAssistant  #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
		tell It;
			setNextFileName '09-genesInSpecies.nex';
			setPrevFileName '06-twoPopulations2.nex';
			getWindow;
			tell It;
					setExplanationSize 0;
					setAnnotationSize 0;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 403 443;
					setLocation 9 30;
					setFont SanSerif;
					setFontSize 10;
					setActive;
				setExplanation 'This file shows the effects of fluctuating population size on coalescent gene tree depth.  There are two sets of taxa, the genes and the populations.  But there is only a single population, and so the population tree containing the gene tree consists of a single population descending through time.  By placing unbranched nodes (using the Insert Node tool) the population history has been broken into segments, each of which has its own length (time) and width (population size).   The branch lengths and widths are drawn in proportion in the "Tree window" above; to see their quantitative values, select the "Branch Info" tool ("?") and touch on the branch of interest.^n^nThe coalescence modules currently use the following rule: the lengths of branches are numbers of generations, while the widths of branches are used as multipliers of the current base effective population size (to see or change the base Ne select "Set Ne..." from the Coalescent Simulation submenu of the Contained menu of the population tree window above).  Thus if the base Ne is 100 and the branch width is 10, the actual Ne along that branch will be 100x10.0 = 1000 (haploid) individuals.  In the first of the three population histories ("trees") stored, these are the values for the three segments of the history.  Thus, in the first history the population size begins at 100, expands to 1000 and remains there for 300 generations.  Note that the average depth to the last coalescence of gene trees simulated in such a population is about 450 as shown in the chart at left (primarily because not a lot happens in the terminal 300 generations, and once in the original segment of Ne=100, it takes on average a bit less than 2Ne generations to complete coalescence).^n^nThere are two other population histories stored, that can be found by scrolling the "Tree #" scroll in the tree window above.  The first history keeps uniform population size after an initial expansion.  The second history has a single bottleneck to Ne=100 after the initial expansion, and shows a bimodal distribution of gene tree depths (because many gene trees coalesce completely in the bottleneck, but if they don''t, they are unlikely to complete coalescence until much deeper).  The third history shows two bottlenecks, and a trimodal distribution of gene tree depths.';
				setTitle Fluctuating_Ne;
				toggleFileNames off;
				setPrevButtonName Previous;
				setNextButtonName Next;
			endTell;
			showWindow;
		endTell;
		endTell;
end;