Armour plate diversity in Japanese freshwater threespine stickleback (Gasterosteus aculeatus)

Background: Independent colonization of freshwater habitats by threespine stickleback (Gasterosteus aculeatus) offers a great opportunity to investigate the repeatability of phenotypic evolution and the genetic mechanisms underlying parallel evolution. Armour plate reduction occurs repeatedly in North American and European freshwater populations of the threespine stickleback. The repeated fixation of the single-origin freshwater alleles at the Ectodysplasin (Eda) locus explains the parallel evolution of plate number reduction in these populations. In contrast, we know little about the patterns and genetic basis of armour plate diversification in Japanese freshwater populations. Questions: Do Japanese freshwater populations show similar patterns of armour plate reduction as the North American and European freshwater populations? Do the same freshwater alleles underlie plate number reduction in Japanese populations? Methods: We analysed the armour plate morphology of eleven freshwater populations and one anadromous population of threespine stickleback in Japan. We first classified each fish into one of the three morphs: completely-, partially-, and low-plated morphs. We next measured the heights of armour plates for the completely-plated morph. We also compared the genome sequences at the Eda locus among Japanese, North American, and European populations. Results: Only one Japanese freshwater population was exclusively low-plated. Two freshwater populations were a mixture of low- and partially-plated morphs. One freshwater population was a mixture of partially- and completely-plated morphs. Seven freshwater populations and one anadromous population were exclusively completely-plated, and in four of those freshwater populations, plate heights were reduced compared with those in the anadromous population. Genome sequences at the Eda locus of all Japanese freshwater populations were more similar to those of the Japanese, North American, and European anadromous and marine populations than the freshwater alleles of the North American and European populations. Conclusion: The parallel evolution of plate reduction occurs in some Japanese freshwater populations, but the genetic basis for this phenotypic change differs from that of the North American and European freshwater populations.