Fig. S1 The entire WR × Sw (WS) genetic map.

Appendix S1 DNA sequences of the 40649 RAD tag loci. Sequences include the 8 bp SbfI site plus 60 bp of flanking sequence. Each locus is either not polymorphic or has a SNP allele shared by Cl and Sw (Cl/SW), Cl and WR (Cl/WR), or Sw and WR (Sw/WR).

Appendix S2 Genotypes and phenotypes of the doubled haploid progeny.

Appendix S3 Genetic map positions of the 4563 mapped RAD tag markers.

Appendix S4 Genetic map positions of the 63 PCR-based markers.

Appendix S5 Genomic distribution of the Cl/Sw and Cl/WR SNPs.

Protocol S1 RAD library construction protocol.

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