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Bootstrapping with 1000 subjects per each bootstrap run was conducted to provide estimates of the precision of fixed effects.
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The results of the single-gene analyses are summarized in Additional file 5. Partitioned ML analyses were carried out in GARLI-PART 0.97.r737 [ 66] using parallel processing; most ML bootstrap runs were conducted on the University of Maryland distributed-computing Lattice Project (http://boinc.umiacs.umd.edu/about.php; [ 67]).
A single run was conducted with 1000 bootstrap replicates followed by a full maximum likelihood search, using the partitioned data with the GTR+G+I model selected for each partition and the Oregon Cave sample selected as an out-group.
The bootstrap test was conducted by burning 10,000 trees.
All runs were conducted with 100 bootstrap replicates, and majority-rule consensus trees with bootstrap branch support were calculated by PHYML.
Multiple runs were conducted.
Twenty-five runs were conducted for each problem.
Four independent runs were conducted.
All runs were conducted at 4 °C.
lbIn total, 468 runs were conducted.
Three independent MCMC runs were conducted.
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