Spine length association sequencing of threespine stickleback

Vertebrates have repeatedly modified skeletal structures to adapt to their environments. The threespine stickleback is an excellent system for studying skeletal modifications, as different wild populations have either increased or decreased the lengths of their prominent dorsal and pelvic spines in different environments. Here we identify a new regulatory locus that has a major morphological effect on the length of stickleback dorsal and pelvic spines, which we term Maser (MAjor Spine EnhanceR). Maser maps in a closely-linked supergene complex that controls multiple armor, feeding, and behavioral traits on chromosome IV. Natural alleles in Maser are differentiated between marine and freshwater sticklebacks; however, alleles found among freshwater populations are also differentiated, with distinct alleles found in short- and long-spined freshwater populations. This whole genome association mapping, with fish from Little Meadow Creek and Matanuska Lake, Alaska, supports Maser as the major locus controlling spine length in stickleback and helps offer insight into the genetic basis for variation in major skeletal structures.