Supplementary Information

Supplementary Figure 1: Marker placement across LOD scores for all chromosomes during the SeparateChromosomes2 function of Lep-MAP3. The red dashed line represents the number of unplaced markers, and the vertical dashed line shows the pairwise LOD = 28.

Supplementary Table 1: the mean distance between marker loci on each chromosome for the male and female maps.

Supplementary Figure 2: The female-only (top) and male-only (bottom) genetic linkage maps. These maps were created using the full 9 family dataset. Each point represents a marker locus. Chromosome numbering follows the current genome assembly, where chromosome 7 was split into two linkage groups (7.1 and 7.2), and chromosomes 16 and 22 were merged into a single linkage group (ASB_LG16_LG22). As a result, the map contains 24 linkage groups, but the numbering includes 71 and 72 and no 22 to reflect these assembly changes.

Supplementary Figure 3: The two different consensus maps created from this dataset: the additive map (top) and the mean averaged map (bottom). The additive map was created by adding the male and female marker positions together as regions of recombination are non-overlapping while the sex average map was created by finding the mean between the male and female marker positions. Chromosome numbering follows the current genome assembly, where chromosome 7 was split into two linkage groups (7.1 and 7.2), and chromosomes 16 and 22 were merged into a single linkage group (ASB_LG16_LG22). As a result, the map contains 24 linkage groups, but the numbering includes 71 and 72 and no 22 to reflect these assembly changes.

Supplementary Figure 4: The male position (y-axis) and female position (x-axis) recombination patterns of linkage group 14 in one full-sib family (A) and all families (B) without the use of the hyperPhaser parameter in OrderMarkers2.

Supplementary Figure 5: An example of 5 independent repetitions of the hyperPhaser parameter in the OrderMarkers2 function of Lep-MAP3 on chromosome 14. The y-axis depicts the cM of each marker (dot) for the males and the x-axis depicts the cM for the females. The likelihood score for each sex is displayed below each plot with the best likelihood for each sex being highlighted in green. In this example repetition 5 was chosen for the linkage map.

Supplementary Table 2: The length (cM) and number of informative markers of every chromosome in the male, female, average (mean), and average (additive) maps. The mean averaged maps were calculated by taking the mean distance for each marker between the male and female maps while the additive maps were created by adding the male and female distances together as there male and female recombination regions do not overlap and the additive method captures the entire length of the chromosome.

Supplementary Table 3: The average linkage disequilibrium (r2) between the misplaced marker and every other marker on chromosome 12 and 9 respectively.

Supplementary Figure 6: Two chromosomes that exhibited gap patterns (chromosomes 6 and 5). Regions of interest are highlighted in yellow and are connected to the sex of interest (x axis for the female and y axis for the male). SNP markers that were found to be homozygous in the sex of interest (females for chromosome 6 and males for chromosome 5) were marked with an “x”. Created using ggplot (R) and Microsoft PowerPoint.