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Independent runs were carried out to check congruence in likelihood scores [ 49].
We used a multi-gene approach to check congruence of phylogenetic and phylogeographic patterns inferred from independent genes.
In BEAST analyses, only a single MCMC explores the data; thus several independent analyses were performed to check congruence of results and likelihood scores.
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A maximum likelihood analysis using RaxML v7.0.3 [42], [42] with 1000 bootstrap replicates under the GTRCAT approximation was run on the combined dataset to check for congruence with the Bayesian analysis.
We are thus able to check the congruence of results consisting of the test statistic, df and a precise P value.
This will allow us to check for congruence among markers and for the possibility of combining them in a joint dataset.
We did not check the congruence of confidence intervals and other statistics because it would be generally impossible without access to the raw data.
For the divergence hotspot regions, the maximum parsimony method was used to construct the phylogenetic trees with PAUP4.0b10 to check the congruence of evolution and life history of the species.
The phylogenies of single-gene families were reconstructed based on nucleotide and amino acid sequence alignments (to check for congruence) in a Bayesian Markov chain Monte Carlo (MCMC) statistical framework using MrBayes 3.2 (Ronquist et al. 2012), as well as a maximum likelihood (ML) method implemented in RAxML 7.7 (Stamatakis 2006).
In absence of significant difference, we further checked the congruence of each node by visual inspection.
Other kinds of markers have thus to be checked for congruence.
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