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Appendix S1 Additional methods

Fig. S1 Effect of restriction fragment length in three RAD-Seq data sets.

Fig. S2 Shearing of plasmids pOJ260 (3.5 kb, red) and pLUM (9 kb, blue).

Fig. S3 Read depth varies with modified shearing conditions.

Fig. S4 Heliconius allele counts cannot be separated by removing PCR duplicates.

Fig. S5 Additional RAD contig assembly comparisons.

Table S1 Caenorhabditis elegans PstI RAD library details.

Table S2 Restriction site-associated DNA contig assembly details.

Table S3 Restriction site-associated DNA adapter and primer sequences.

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