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Table S1. Taxa included in this study and accession numbers of sequences in GenBank.

Table S2. PCR/Sequencing primer information.

Figures S1–S5. Best scoring maximum-likelihood tree of Teleostei obtained from the partitioned RAxML analysis of the five nuclear gene dataset from the matrix “123ry” partitioned in 5 (Fig. S2) or 3 (Fig. S4), and the matrix “123” partitioned in 15 (Fig. S1), 5 (Fig. S3), and 3 (Fig. S5).

Figure S6. Phylogenetic chronogram of the Teleostei based on a Bayesian relaxed clock approach and calibrated with 30 fossil-based constraints following uniform distributions.

Figure S7. Reconstruction of the evolution of the ecological character within the Ostariophysi using likelihood optimization on the Bayesian topology (Fig. 3). “Freshwater” is indicated in white and “marine” in black. At each node, the relative probabilities of each state (sum = 1) are drawn using pie charts.

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