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RAD-seq-based phylogeny of the 12 Drosophila species, based on 100-bp-long RAD-seq reads, inferred by maximum likelihood using PhyML 3.0. under a GTR+ G substitution model, using the concatenated alignments from orthologous-only clusters containing at least four sequences. Bootstrap values (100 replicates) were equal to 100% on every node. We indicate the number of informative loci at each node (shared by at least one species on each side of the bifurcation and at least one outgroup).
