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In order to access the statistical confidence in the estimated parameter values, we performed a non-parametric bootstrap test of the demographic history by resampling the SNPs to generate data sets of the same size with replacement.
Positivity of the individual IFN-γ response by ELISpot was determined by a one-sided bootstrap test of the null hypothesis that the responses in the experimental wells were twice those of the background (α = 0.05) [28].
The bootstrap test of the phylogeny was performed using 1,000 repetitions.
Ané et al. [ 33] recently describe a parametric bootstrap test of the covarion model that tests the degree of independence in the proportion of invariant sites in the two subgroups.
Tabled values are the magnitude of the difference between the SShD of each pair of species (in units of Procrustes distance, upper value in each table cell) and the P-value for the respective bootstrap test of the null hypothesis of no difference in SShD (lower value in each table cell).
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Phylogenetic analyses and statistical neighbour-joining bootstrap tests of the phylogenies were carried out using the Mega package [26].
Phylogenetic analysis and statistical Neighbor Joining (NJ) bootstrap tests of the phylogenies were done with the Mega package [ 85].
Phylogenetic analysis and statistical neighbor-joining bootstrap tests of the phylogenies were also done with the Mega3 package [ 166].
Phylogenetic analysis and statistical neighbour-joining (NJ) bootstrap tests of the phylogenies were done with the Mega package [ 165].
Phylogenetic analysis and statistical neighbor-joining bootstrap tests of the phylogenies were done with the Mega package [ 93].
Phylogenetic analysis and statistical neighbour-joining (NJ) bootstrap tests of the phylogenies were done using the Mega package [ 35] after sequence alignment was performed using ClustalX [ 36].
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