To estimate support for the nodes, 1000 bootstrap replicates were performed and we retained only the values supporting the nodes accounting for more than 50% of the bootstrap replicates.
Ten thousand bootstrap replicates were performed.
In addition, 1000 bootstrap replicates were performed using the maximum-parsimony (MP) method, based on a branch-and-bound search by PAUP 4.0b10 (Swofford 2002).
A total of 1,000 bootstrap replicates were performed using neighbor-joining, and clades having >60% bootstrap support were identified (Fritz-Laylin et al. 2005).
A total of 1000 bootstrap replicates were performed for each maximum parsimony analyses.
Five hundred bootstrap replicates were performed in each program for each dataset.
1000 bootstrap replicates were performed and phylogenetic trees were constructed for each genomic segment by the neighbor-joining method using the MEGA 4.0.2 program.
In order to assess topological support, 500 bootstrap replicates were performed with RAxML on each alignment with the parameters described above.
100 bootstrap replicates were performed.
1000 bootstrap replicates were performed.
Bootstrap replicates were performed using 1000 replicates.
