Phylogénie Et Evolution Du Comportement Social Chez Les Blattes ...

Ev o l u t i o n d u c o m p o r t e m e n t s o c i a l16S, 18S, and 28S) were preliminarily aligned with Muscle (Edgar, 2004) and then 16S, 18S,28SA and 28SDEF were partitioned according to highly conserved regions in order to speedup phylogenetic analyses and to avoid misleading alignments when portions of genes werelacking. The portion of Leu tRNA was neither prealigned nor partitioned.The POY search parameters were:‘-fitchtrees -numslaveprocesses 50 -onan -onannum 1 -parallel -noleading-norandomizeoutgroup -sprmaxtrees 1 -impliedalignment -tbrmaxtrees 1 -maxtrees 5-holdmaxtrees 25 -slop 25 -checkslop 10 -buildspr -buildmaxtrees 2 -replicates 100 -stopat50 -multirandom -treefuse -fuselimit 10 -fusemingroup 5 -fusemaxtrees 50 -ratchetspr 2-ratchettbr 2 -checkslop 10 -repintermediate -terminalsfile taxa.txt -minterminals 10 -time-indices -stats -molecularmatrix 111.txt -seed -1 -phastwincladfile termites111.wcl’A sensitivity analysis was conducted in order to test the robustness of the phylogeneticconclusions to different costs of insertion, transversion and transition events. Ten sets ofparameters (gap: transversions: transitions) were tested this way: 111, 222 (with an extensiongap cost of 1), 211, 221, 421 and [16]41 with an extension gap cost equal to and half of theopening gap cost for these four last parameters sets (called hereafter 211x, 221x, 421x and[16]41x). The results are shown using stability plots or “navajo rugs” to summarize whether amonophyletic group was recovered or not at a node over the parameter space (Wheeler, 1995).Parsimony bootstrap values for 1000 replicates (Felsenstein, 1985), and Bremer andpartitioned Bremer support values (Bremer, 1988, 1994; Baker and DeSalle, 1997) werecalculated in PAUP 4.0b10 (Swofford, 1998) and TreeRot.v2b (Sorenson, 1999), respectively,using the implied alignment provided by POY in the analysis 111. The default parameterswere used in TreeRot.v2b.Additional analyses based on a static alignment were done in a Bayesian frameworkwith MrBayes v3.0b4 (Huelsenbeck and Ronquist, 2001), under the likelihood criterion withPHYML v2.4.4 (Guindon and Gascuel, 2003) and under parsimony with PAUP 4.0b10. Inall the cases Muscle v3.6 (Edgar, 2004) was used to generate alignments of the ribosomalsequences. For the probabilistic analyses, Modeltest v3-06 (Posada and Crandall, 1998) wasused to determine the model which best fit the data. A General Time Reversible model witha proportion of invariant sites and a gamma distributed rate variation among sites (GTR+ I + G) was selected as the best fit of the models investigated. In the likelihood analysis,bootstrap values were computed for 1000 replicates with PHYML v2.4.4. In the Bayesiananalysis, the parameters of the model GTR + I + G were estimated independently during thetree reconstruction for the different partitions, i.e. the genes, using the command ‘unlink’.Commands for these 3 analyses are provided in the Appendix I.346