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Parsimony analyses of the individual genes and concatenated matrices were conducted with the program TNT v. 1.0 [ 95].
Mantel tests between the geographical distances and the Slatkin linearized Фst (Rst) matrices were conducted in Arlequin 3.1 with 10,000 permutations.
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First, an iterative approach using DOE screening and space filling experimental matrices is conducted.
The Box's test of equality of covariance matrices is conducted to validate the assumption of homogeneity before proceeding further.
One-way ANOSIM with pair-wise comparisons (which is an approximate analogue of standard analysis of variance based on similarity matrices) was conducted to formally test the factors.
Principal component analyses using correlation matrix were conducted using Paleontological Statistics Software package for education and data analysis, version 2.17c [ 30].
Maximum likelihood analyses of the concatenated data matrix were conducted with the software program RAxML v. 7.0.4 [ 104] and run remotely at the CIPRES portal [ 105].
Protein alignments using MAFFT and Maximum Likelihood analyses using RAxML Black Box and the JTT substitution matrix were conducted through the CIPRES portal (http://www.phylo.org/).
The alignment (of translated nucleotides) is presented in Figure 2. Maximum likelihood analyses, nucleotide substitution model selection and bootstrap resampling of the nucleotide distance matrix were conducted as above.
A compliant modeling and a symbolic expression of the stiffness matrix are conducted.
By creation of a conjugate-symmetric series, the summing operation of the decomposed lagged coherence matrix is conducted in the frequency-domain, which decreased the executions of IFFT.
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