#NEXUS [ **partial output for r8s analysis of Pinusaug07PLTS156max308age.out]** Reading tree PAUP_1 Executing blformat command... Branch lengths assumed to be in units of numbers of substitutions per site Number of sites in sequences set to 2708 All branch lengths multipled by the 2708 sites in the sequence Branch lengths rounded to nearest integer (This may not be a good idea when using CALIBRATE on ultrametric user supplied input trees. Use ROUND=NO then) Pruning taxon Sciadopit Pruning taxon Cryptomer Pruning taxon Amentotax Pruning taxon Podocarpu Pruning taxon Ginbiloba 2 zero-length branches collapsed Defining clade name: ABKE Defining clade name: PLTS Defining clade name: ABCE Defining clade name: ABPL Defining clade name: PSLA Defining clade name: PINS Defining clade name: PINC Defining clade name: PARR Defining clade name: ARPI Fixing age of PLTS at 156.000000 (The age of this node will no longer be estimated.) (This command overides any previous age constraints for this node.) (The total number of fixed ages is now 1) Setting minimum age constraint for taxon PINS to 108.400000 Setting maximum age constraint for taxon ARPI to 308.500000 Setting minimum age constraint for taxon PSLA to 45.500000 Setting minimum age constraint for taxon ABKE to 45.500000 Setting minimum age constraint for taxon PARR to 27.200000 ********************* WARNING ********************** You are trying to estimate the age of the root but with the given constraints it is possible that a range of solutions exist **************************************************** ---------------------------------------- LINEAGE RATE/TIME ANALYSIS FOR TREE PAUP_1 Method = Penalized Likelihood Smoothing factor = 251.188643 Penalty function = Ancestor-Descendant Scale for rate penalty = ADDITIVE Minimum allowed rate = 0.050000 of initial average rate estimate Minimum allowed duration on 0-length terminal branches = 0.001000 of root's age Optimization via Truncated-Newton (TN) method with bound constraints ---------------------------------------- Substitution Model Rates are equal across sites Global/Local Search Parameters Number of searches from random starts = 5 Number of restarts after each search = 3 Local perturbation on restarts = 0.05 Local fractional tolerance after restarts = 0.01 Optimization parameters set automatically by TN routine Length of tree input = 1205 Number of taxa = 44 Number of sites in sequences = 2708 ---------------------------------------- Starting optimization (random starting point 1) ...Checking the starting point...(for some barrier constant)... ...Passed...now optimizing... ...Initial solution=259.908707 ] begin trees; tree PAUP_1 = (((((Abhidalge:105.733405,KetdavidD:105.733405)ABKE:53.888645,((Notholong:78.382903,Tcanadens:78.382903):77.617097,Pseudamab:156.000000)PLTS:3.622050)ABPL:12.420742,Cedeodara:172.042792)ABCE:11.823143,((Lgmelinii:86.989239,Pmenziesi:86.989239)PSLA:80.939408,((Cathaya22:142.226789,Pichihuah:142.226789):12.837342,(((((johannis8:8.059594,pinceana8:8.059594,rzedowski:8.059594):2.542546,cembroide:10.602140,monophy23:10.602140):16.597860,(((aristata3:8.695036,longae309:8.695036):1.468033,balfouria:10.163069):11.677404,nelsonii3:21.840473):5.359527)PARR:10.032130,(((bungeana2:5.481436,gerardi12:5.481436):1.518480,squamata0:6.999916):13.162562,(((monticola:4.303221,cembra106:4.303221):4.383519,strobus50:8.686739):3.777489,peuce0427:12.464228):7.698250,krempfiiL:20.162478):17.069652):49.507618,((((pondRMP04:2.225050,montezuma:2.225050):9.617996,((leiophyll:4.643855,radiata37:4.643855):1.714454,pungeGret:6.358309,palustris:6.358309):5.484737):8.389527,(contorta4:6.100086,BANKListo:6.100086):14.132487):10.311541,(((roxburg06:9.609803,halepGret:9.609803,pineaKew3:9.609803):1.981933,heldListo:11.591737):4.633749,(((nigraGret:5.339004,sylvestri:5.339004):0.883975,thunbergi:6.222979):1.628849,resinosa:7.851829):8.373658):14.318628):56.195633)PINC:68.324384)PINS:12.864515):15.937288):124.634065,Araraucan:308.500000)ARPI; end;