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Table S1 Specimens used and locations sampled for the microsatellite marker development and cross-species amplification study.

Table S2 Species included for the determination of sequence divergence between sparid taxa based on mitochondrial DNA 16S rRNA sequences.

Table S3 Selected sequences containing repeats (SCR) with sufficient flanking region for primer design and meeting the criterion of a minimum of five repeat units from 454 sequences generated for Lithognathus lithognathus (WS) and Pachymetopon blochii (HS).

Table S4 Sequences of homozygotes for selected alleles.

Table S5 Summary of recent studies using GS-FLX to indicate the efficiency of identifying sequences containing repeats (SCR) when using 454 sequencing directly vs. repeat enrichment.

Fig. S1 (A) Size distributions of the fragments obtained from 454 lifeSciences/Roche GS-FLX sequencing for P. blochii (blue) and L. lithognathus (red) after repeat enrichment. (B) Number for each repeat type (di-, tri-, tetra- and pentanucleotides) for P. blochii (blue) and L. lithognathus (red).

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