Supporting Information

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Fig. 4. The gcm haplotype alignment. A PAIRCOMP analysis (window = 20 bp; similarity = 95%) of the SpBAC sequence and a contig obtained from the WGS assembly displayed in the region of the two cis-regulatory modules D and E shown in green. In addition to a surprising lack of sequence similarity in the region between the modules, there is a graphic example of either an insertion in the contig or a deletion in the BAC (asterisk).

Figs. 5-10. Sequence alignments. The pairwise sequence alignments used to calculate the proportion of base changes and gaps between either S. purpuratus and S. franciscanus or among a group of S. purpuratus individuals. The alignments are reformatted from a CLUSTALW output. In the interspecific comparisons, the S. purpuratus BAC sequence is the upper sequence; the lower sequence is the S. fransciscanus one. The intraspecific comparisons for the endo16 gene use the originally published sequence as reference.

Table 2. Ordered and oriented BAC sequences for Sp and Lv BAC clones

Table 3. S. franciscanus sequence within and contiguous to cis-regulatory modules