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For each phenotype, 10000 bootstrap replicates are performed using the statistical programming language R. Our second analysis uses single locus MK tests to evaluate individual gene alignments for signatures of positive natural selection.
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Ten thousand bootstrap replicates were performed.
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).
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 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.
One thousand nonparametric bootstrap replicates were performed in RAxML using the same partitions and models of sequence evolution with one search replicate per bootstrap replicate and a random starting tree; branch lengths and model parameters were optimized during the bootstrap analysis.
100 bootstrap replicates were performed.
1000 bootstrap replicates were performed.
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