Gasterosteus aculeatus Raw sequence reads

Marine populations of the threespine stickleback (Gasterosteus aculeatus) have repeatedy colonized and rapidly adapted to freshwater habitats, providing a powerful system to map the genetic architecture of evolved traits. Here we developed and applied a binned Genotyping-by-Sequencing (GBS) method to build dense genome-wide linkage maps of sticklebacks, using two large marine by freshwater F2 crosses of over 350 fish each. The resulting linkage maps significantly improve the genome assembly by anchoring 78 new scaffolds to chromosomes, reorienting 40 scaffolds, and rearranging scaffolds in 4 locations. In the revised genome assembly, 94.6% of the assembly was anchored to a chromosome. To assess linkage map quality, we mapped quantitative trait loci (QTL) controlling lateral plate number, which mapped as expected to a 200 kilobase genomic region containing Ectodysplasin, as well as a chromosome 7 QTL overlapping a previously identified modifier QTL. Finally, we mapped eight QTL controlling convergently evolved reductions in gill raker length in the two crosses, which revealed that this classic adaptive trait has a surprisingly modular and non-parallel genetic basis.