SUBSET_18_GENES

Nexus alignment file for the subset (37 taxa and 18 gene fragments; 17616 sites; no missing data). The alignment file is fully annotated for gene partitions, including the batch command in PAUP* to export individual gene files

Supplementary_Table_1

Supplementary Table 1. Material examined and GenBank Accession numbers

Supplementary_Table_2

Supplementary Table 2. Primers used and optimized PCR conditions

Supplementary Table4

Likelihood (ln) scores for gene trees and AU test P values comparing gene tree topologies estimated with RAxML against the concatenation topology (from Fig. 3, pruned to only include taxa in the subset), calculated under homogeneous (RAxML) and non-homogeneous (nhPhyML) optimization. The nhPhyML model used unlimited base equilibrium frequencies. Values in bold highlight cases in which the concatenation topology resulted in either better or non-significantly worse likelihood scores

Supplementary_Table_3

Supplementary Table 3. Characterization of molecular markers, variation, distribution of present/missing sequences and taxa, and GenBank accession numbers (see also Supplementary Table 1)

FIG_SUP_2_Subset_trees

Supplementary Figure 2. Four representative multi-locus phylogenies based on the subset. Color branches represent flatfish lineages (cyan, Pleuronectoidei; orange, Psettodoidei)

ALL_TAXA_20_GENES

Nexus dataset with the complete alignment (214 taxa and 20 gene fragments; 19461 sites). The alignment file is fully annotated for gene partitions, including the batch command in PAUP* to export individual gene files