Heterogeneous genomic architecture of skeletal armour traits in sticklebacks

Whether populations adapt to similar selection pressures using the same underlying genetic variants depends on population history and the distribution of standing genetic variation at the metapopulation level. Studies of sticklebacks provide a case in point: when colonising and adapting to freshwater habitats, three-spined sticklebacks (Gasterosteus aculeatus; TSSs) with high gene flow tend to fix the same adaptive alleles in the same major loci, whereas nine-spined sticklebacks (Pungitius pungitius; NPSs) with limited gene flow tend to utilize a more heterogeneous set of loci. In accordance with this, we report results of quantitative trait locus (QTL) analyses using a F2 back-cross design showing that lateral plate number variation in the western European lineage of NPSs mapped to three moderate-effect QTL, contrary to one major QTL in TSSs and these QTL were different from the four previously identified QTL in the eastern European lineage of NPSs. Furthermore, several QTL were identified associated with variation in lateral plate size, and three moderate-effect QTL with body size. Together, these findings indicate that genetic underpinnings of skeletal armour variation in Pungitius sticklebacks are more polygenic and heterogenous than those in three-spined sticklebacks, indicating limited genetic parallelism underlying armour trait evolution in the family Gasterostidae.