Bootstrap analyses with 100 pseudoreplicates were performed in both methods.
Non-parametric bootstrapping with 1000 pseudoreplicates was performed to assess the nodal support.
A maximum likelihood phylogenetic analysis of T. urticae, D. melanogaster and human ABC protein NBDs, bootstrapping with 1000 pseudoreplicates, was performed using Treefinder [ 124] to confirm the position of T. urticae ABCs within ABC classes (A-G).
Bootstrap analysis with 1,000 pseudoreplicates was performed by using the program Seqboot (28 ).
A maximum likelihood analysis was performed using RaxML v8 [ 117] and a bootstrap analysis with 1000 pseudoreplicates was performed to evaluate the branch strength of each tree.
To assess the stability of the tree branching patterns in rpoB, cpn60 and 16S rRNA gene trees bootstrap analysis with 100 pseudoreplicates was performed using evolutionary models and tree building as described above.
Decay indices (=Bremer support values) were calculated and a bootstrap resampling analysis, using 10,000 pseudoreplicates, was performed reporting both absolute and GC (i.e. difference between the frequencies of recovery in pseudoreplicates of the original group and the most frequently recovered contradictory group) frequencies.
Unweighted maximum-parsimony analyses using heuristic searches with 100 random-taxon-addition replicates, and non-parametric bootstrapping [36] based on 1000 pseudoreplicates and 10 random taxon-addition-replicates per pseudoreplicate, were performed in PAUP* v. 4.0b10 [37].
For both methods of ML analysis, 1,000 bootstrap pseudoreplicates were used to assess the support for the ML topology.
To assess nodal support, nonparametric bootstrap analyses were performed [200 pseudoreplicates and 10 random sequence additions; [ 63]].
