The genetic and molecular basis of morphological evolution is poorly understood, particularly in vertebrates. Genetic studies of the differences between naturally occurring vertebrate species have been limited by the expense and difficulty of raising large numbers of animals and the absence of molecular linkage maps for all but a handful of laboratory and domesticated animals. We have developed a genome-wide linkage map for the threespine stickleback (Gasterosteus aculeatus), an extensively studied teleost fish that has undergone rapid divergence and speciation since the melting of glaciers 15,000 years ago 1 The benthic species feeds on invertebrates near shore and has a great reduction in the amount of body armor, increased body depth, and a decreased number of gill rakers for filtering ingested food. The limnetic species more closely resembles an ancestral marine fish, with more extensive body armor, a longer and more streamlined body, and an increased number of gill rakers. Despite reproductive isolation between the two species in the wild 3-6 , it is possible to establish productive matings between the two species under laboratory conditions 2 . The resulting F1 hybrids are viable and fertile, making it possible to carry out a formal genetic analysis of the number and location of loci responsible for the adaptive morphological differences between these naturally occurring vertebrate species.To develop resources for genome-wide linkage mapping in Gasterosteus aculeatus, we used large-scale library screening and sequencing to identify a collection of genomic and cDNA clones containing microsatellite repeat sequences. Initially, we sequenced of 192 kb of random genomic clones and showed that CA dinucleotides were the most common form of microsatellite in sticklebacks, occurring approximately once every 14 kb. We subsequently screened genomic and cDNA libraries with a (GT) 15 probe, sequenced 3560 clones, and identified 1176 new microsatellite loci. Primers flanking 410 new and 18 previously identified microsatellites 7-9 were designed and used to type a genetic cross between the benthic and limnetic species from Priest Lake, British Columbia (Figure 1). For this cross, an individual Priest benthic female was mated with a single Priest limnetic male, and a single F1 male (B 1 L 1 ) was crossed to a second Priest benthic female (B 2 B 3 ) to generate 103 progeny. Of the 281 markers that amplified robust bands from the F1 and benthic parent, 227 (81%) were polymorphic, and therefore informative, in one or both parents. Higher rates of polymorphism were seen in the F1 male than the benthic female parent (71% vs. 57% of 281 markers), consistent with a greater level of genetic diversity between the distinct populations of benthic and limnetic fish than within the benthic population.The segregation patterns of the 227 informative markers were scored on 92 progeny from the cross, and the 20,884 resulting genotypes were analyzed for linkage using JoinMap software 10 . The markers were ordered into 26 linkage groups co...

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...

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