Supplemental Material for Picq et al., 2018

<u>File S1</u> details the experimental design used to generate spruce budworm families for the linkage map. <u>File S2</u> summarizes linkage map information i.e. number of marker and size in cM, for each linkage group. <u>File S2</u> also provides details on position, errors and sequence for each marker included in the linkage map, and the significant hits in tblastx searches against the <i>Bombyx mori</i> and the <i>Melitaea cinxia</i> genomes. <u>File S3</u> details assignment of the <i>Choristoneura fumiferana </i> linkage groups to <i>B. mori</i> and the <i>M.a cinxia</i> chromosomes. The file named <u>Picq_et_al_SBW_linkage_map_filtered_SNP_20180403.txt </u>contains genotypes of the 4 families used to generate the linkage map (8 parents and 109 descendants) for the 13,900 filtered SNPs (see main manuscript for details). The SNP data for individuals are in columns and loci are in rows; the first column provides loci name. The individuals names contains the following informations: family number, individual number and sex (<u>F</u>emale or <u>M</u>ale). For example, the individual Fm10I01F is the descendant number 1 of the family 10 and this is a female. The individuals which names begins with P are parents. For example PFm10 means parents of the family 10. The file named <u>Picq_et_al_SBW_linkage_map_filtered_SNP_20180403.linkage</u> presents the same data as the file above but in format ready-to-use in Lep-MAP (pre-makeped linkage format).