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TRACER version 1.5 (tree.bio.ed.ac.uk/software/tracer) was used to inspect posterior distributions and to estimate the relevant evolutionary parameters.
Therefore, logfiles of triplicates of the 50 million generation runs were combined into a single logfile by hand and the results were viewed in Tracer version v1.4.1 [53].
We did two independent runs of BEAST (chain length of 10,000,000; sampled every 1000; Yule speciation process; 10% burn in) and combined the results with Tracer version 1.4 [70] to calculate the time to most recent common ancestor (tmrca) for two nodes, Typhlatya/Stygiocaris spp. and S. lancifera/stylifera/sp.
The burn-in parameter was estimated empirically by plotting −ln L against the generation number using Tracer version 1.4 [59]; the trees corresponding to the first 10% of the generations were discarded, and the posterior probabilities were obtained by summarizing the remaining trees.
Log files were evaluated in TRACER version 1.5 [ 48].
The output was examined with Tracer version 1.5 (A.
Tracer version 1.4 [ 67] was used to determine the performance of the BEAST output.
This was evaluated by the Bayesian skyline plot [ 107] as calculated in Tracer, version 1.4 [ 106].
The program TRACER (version 1.3; [ 75]) was used to assess tree and parameter convergence.
Tracer version 1.5 (http://tree.bio.ed.ac.uk/software/tracer/) was used to monitor stationarity and efficient mixing.
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Murazaki and Hess (2006), using the SRES A1 scenario and a global chemical transport model [MOZART-2 [MOZART-2 OZone And Related cheModel Tracers, versiof 2 (gctm.acd.ucar.edu/MOZone)], projected thAndby the end of the twenty-fiRelatedtury anthropogenichemicale change alone would decrease background ozone concenTracerss oversion United States, while ozone produced internally would increase.
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