All minimum evolution analyses were performed using MEGA 2.1 [ 40] and PAUP [ 41], while likelihood and parsimony analyses, as well as the estimation of the specific gamma parameters for the minimum evolution analyses were carried out using PAUP.
Two runs of computations were done on the 251 proteins from Cluster 4, and evolution analyses were done through the same 19 species.
Minimum evolution analyses were performed using Kimura two-parameter distances with transversions-only, gamma corrected Kimura two-parameters distances with transversions-only, and paralinear distances.
The right sampling of homologous sequences for phylogenetic or molecular evolution analyses is a crucial step, the quality of which can have a significant impact on the final interpretation of the study.
Neighbor-joining (NJ) and minimum-evolution analyses were also performed in MEGA.
Due to structural constraints on integrin proteins during evolution, phylogenetic analyses are likely to be complicated by homoplasy effects.
Despite the fact that different partitions of the data may evolve under different models of evolution and partitioned analyses are therefore preferred [ 75 ], alternative Bayesian analyses that combined data for the nuclear and plastid DNA into a single partition were conducted, since by definition they permit phylogenetic reconstructions based on larger numbers of characters.
Since species may share character values as a result of a common ancestry rather than independent evolution, regression analyses were performed using a phylogenetic generalized least-squares (PGLS) approach [ 45].
However, the branches leading to both groups diverged very early in rodent evolution and transposon insertion analyses are inconclusive with regard to their monophyly [7], [8].
We also note that estimated absolute rates of sclerobunine COI evolution, as implied by relaxed clock analyses, are consistent with arthropod rates reported in the literature (Table S6).
