Summary Marine stickleback fish have colonized and adapted to innumerable streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of 20 additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine-freshwater divergence. Our results suggest that reuse of globally-shared standing genetic variation, including chromosomal inversions, plays an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine-freshwater evolution, with regulatory changes likely predominating in this classic example of repeated adaptive evolution in nature.

The distribution of effect sizes of genes underlying adaptation is unknown (Orr 2005)

Understanding the genetic architecture of evolutionary change remains a long-standing goal in biology. In vertebrates, skeletal evolution has contributed greatly to adaptation in body form and function in response to changing ecological variables like diet and predation. Here we use genome-wide linkage mapping in threespine stickleback fish to investigate the genetic architecture of evolved changes in many armor and trophic traits. We identify .100 quantitative trait loci (QTL) controlling the pattern of serially repeating skeletal elements, including gill rakers, teeth, branchial bones, jaws, median fin spines, and vertebrae. We use this large collection of QTL to address long-standing questions about the anatomical specificity, genetic dominance, and genomic clustering of loci controlling skeletal differences in evolving populations. We find that most QTL (76%) that influence serially repeating skeletal elements have anatomically regional effects. In addition, most QTL (71%) have at least partially additive effects, regardless of whether the QTL controls evolved loss or gain of skeletal elements. Finally, many QTL with high LOD scores cluster on chromosomes 4, 20, and 21. These results identify a modular system that can control highly specific aspects of skeletal form. Because of the general additivity and genomic clustering of major QTL, concerted changes in both protective armor and trophic traits may occur when sticklebacks inherit either marine or freshwater alleles at linked or possible "supergene" regions of the stickleback genome. Further study of these regions will help identify the molecular basis of both modular and coordinated changes in the vertebrate skeleton. U NDERSTANDING the quantitative genetic architecture underlying evolutionary change in nature remains a major goal in genetics. The past two decades have seen a rapid increase in experimental data from various model systems, generating vigorous debate over the relative importance of coding vs. regulatory alleles, the prevalence of pleiotropy, and the role of large-effect mutations during adaptation to new environments (Stern and Orgogozo 2008;Streisfeld and Rausher 2011;Rockman 2012).One particularly interesting genetic architecture found in several natural systems is close linkage of loci controlling multiple, often coadaptive, phenotypes. Such trait clusters, sometimes called "supergenes," have been observed in primroses (Darwin 1877;Mather 1950;Li et al. 2011), butterflies (Clarke et al. 1968Mallet 1989;Joron et al. 2006), snails (Murray and Clarke 1976), and fish (Winge 1927;Protas et al. 2008;Roberts et al. 2009;Tripathi et al. 2009). Trait clusters could result from recombination suppression (Noor et al. 2001), for example through chromosomal inversions (Lowry and Willis 2010;Joron et al. 2011;Fishman et al. 2013). Alternatively, trait clusters could result from tightly linked loci or pleiotropic effects of individual genes (Mallet 1989;Studer and Doebley 2011 Cis-regulatory changes may predominate during morphological evoluti...

Armor plate changes in sticklebacks are a classic example of repeated adaptive evolution. Previous studies identified ectodysplasin (EDA) gene as the major locus controlling recurrent plate loss in freshwater fish, though the causative DNA alterations were not known. Here we show that freshwater EDA alleles have cis-acting regulatory changes that reduce expression in developing plates and spines. An identical T → G base pair change is found in EDA enhancers of divergent low-plated fish. Recreation of the T → G change in a marine enhancer strongly reduces expression in posterior armor plates. Bead implantation and cell culture experiments show that Wnt signaling strongly activates the marine EDA enhancer, and the freshwater T → G change reduces Wnt responsiveness. Thus parallel evolution of low-plated sticklebacks has occurred through a shared DNA regulatory change, which reduces the sensitivity of an EDA enhancer to Wnt signaling, and alters expression in developing armor plates while preserving expression in other tissues.DOI: http://dx.doi.org/10.7554/eLife.05290.001