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Robustness of lineages was tested by bootstrap analyses based on 1000 rounds of bootstrap resampling.
Cluster stabilities were assessed by bootstrap analyses based on 1,000 replicates.
We evaluated the support for the nodes of the resultant tree clusters by bootstrap analyses based on 100 replicates.
We performed the alignments with Clustal W and constructed evolutionary trees using the neighbor-joining algorithm [ 38] with the Kimura transformation for protein sequences [ 39], and with bootstrap analyses based on 1000 samples.
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Therefore, a sensitivity analysis of the models is paramount, for example through stochastic simulation (e.g. Monte Carlo simulation analyses based on bootstrap sampling) [ 18, 44, 46].
Genetic relationships were inferred by TREECON software using unweighted paired group method with arithmetic averages (UPGMA) cluster analysis evaluated by bootstrapping and compared with previous analyses based on ITS and 5S IGS.
All results were confirmed by analyses based on the bootstrap sample.
Separate parsimony analyses of the ITS (175 taxa, 799 nucleotides) and plastid (231 taxa, 5933 nucleotides) datasets were undertaken with the parsimony ratchet implemented in PAUPRat [ 26], to check for strongly supported phylogenetic conflicts (bootstrap percentages >75), before proceeding with analyses based on a total evidence approach using all characters.
These procedures included multi-way analyses based on trimmed means and winsorised variances as well as bootstrapping.
The monophyly of Nepomorpha (including both Helotrephidae and Pleidae) received strong support in Bayesian analyses (based on posterior probabilities: PP) but with relatively weak support in ML analyses (based on bootstrap proportions: BP).
Phylogenetic analyses based on amino acid sequences of 42 proteins place Zinderia and Nasuia as sister lineages with high bootstrap support (BS = 100; fig. 6).
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