David M. Kingsley, Ph.D.
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Genetic Control of Vertebrate Evolution

Sticklebacks offer a powerful new system for studying the molecular basis of evolutionary change in many different natural populations (Kingsley and Peichel 2007). These fish have undergone one of the most recent and dramatic evolutionary radiations on earth, colonizing countless new freshwater lake and stream environments generated at the end of the last Ice Age approximately 10,000 years ago. Many recently evolved freshwater populations show dramatic differences in morphology, physiology, and behavior. Although often reproductively isolated in nature, different stickleback species can still be crossed using artificial fertilization in the laboratory. This provides a unique opportunity to identify the key chromosome regions, genes, and mutations that control repeated evolution of new traits and new species under a full range of fitness constraints in the wild.

Thousands of papers and several full-length textbooks have been written on the ecology, morphology, paleontology, and adaptive significance of stickleback traits. We have developed a complete set of genetic and genomic resources for this classic system, including the first genome-wide linkage maps, transgenic methods, expressed sequence tag (EST) collections, large-insert BAC (bacterial artificial chromosome) libraries, and physical maps useful for positional cloning (genetic work done in collaboration with Dolph Schluter [University of British Columbia–Vancouver]; molecular work done in collaboration with Jane Grimwood, Jeremy Schmutz, and Richard Myers [Hudson Alpha Institute]; Chris Amemiya [Benaroya Research Institute at Virginia Mason, Seattle]; Pieter de Jong [BACPAC Resources, Oakland, California]; and Marco Marra and Jacqueline Schein [University of British Columbia]). We also nominated threespine sticklebacks for complete genome sequencing to the National Institute of Human Genome Research (Kingsley 2003). We have worked with the Broad Institute and Ensembl to develop, assemble, and annotate the first whole-genome sequence assembly for Gasterosteus aculeatus, and to resequence additional stickleback genomes from many interesting populations around the world (Jones et al. 2012). The high-quality reference genome can be browsed using the UC-Santa Cruz and ENSEMBL genome browsers, and comparative results based on re-sequencing 21 other stickleback genomes can also be explored and downloaded at "sticklebrowser" (Jones et al. 2012).

We are using these new tools to identify the number, location, and type of genes and mutations that control major evolutionary differences in body size and color, skeletal armor, feeding modifications, fin development, behavioral characteristics, and physiological traits such as temperature preference and salinity tolerance. Our studies have focused on a number of populations that have been particularly well studied from a morphological and ecological perspective, including fish from lakes near Vancouver (in collaboration with Dolph Schluter, University of British Columbia, Vancouver); in Alaska (with Michael Bell, Stony Brook); the Haida Gwaii Islands (with Thomas Reimchen, University of British Columbia–Victoria); Iceland (with Bjarni Jónsson, Institute of Freshwater Fisheries, Iceland); and other populations in California, Washington State, Nova Scotia, and Scotland.

Charles Darwin and later population geneticists have predicted that most interesting evolutionary adaptations in nature will be controlled by large number of genetic changes with infinitesimally small effects. In contrast, our linkage studies have shown that large evolutionary changes in sticklebacks often map to some chromosomes with surprisingly large effects (Colosimo et al. 2004; Shapiro et al. 2004; Miller et al. 2007; Albert et al. 2008; Kitano et al. 2009; Chan et al. 2010; Greenwood et al. 2011; Wark et al. 2012; Cleves et al. 2014; Miller et al. 2014; Indjeian et al. 2016). Using positional cloning methods, we have now identified the genes responsible for some of the dramatic morphological changes between populations. For example, loss of the entire pelvic apparatus in some populations is controlled by changes in a master regulatory homeodomain transcription factor (Pitx1) that is normally expressed in hindlimbs but not forelimbs of most vertebrates (the homeodomain protein Pitx1; Shapiro et al. 2004; Chan et al. 2010). Similarly, large differences in armor plate patterning are controlled by changes in the developmental signaling gene Ectodysplasin (EDA) (Colosimo et al. 2005); and changes in body pigmentation are controlled by changes in the major stem cell factor signaling gene Kitlg (Miller et al. 2007). In all three of these cases, null mutations of the corresponding genes in mice or humans cause major developmental defects or lethality. However, evolution has been able to use these genes to induce major morphological changes in wild animals, using regulatory changes rather than coding region mutations to confine dramatic differences to particular body regions (Shapiro et al. 2004; Miller et al. 2007; Chan et al. 2010; O'Brown et al. 2015).

Our work on stickleback evolution began with genome-wide linkage mapping, followed by detailed case studies of a handful of major genes controlling large morphological changes. Using the lessons learned from these initial examples, we have recently been able to identify a large genome-wide set of loci that are repeatedly selected when marine fish colonize and adapt to new environments (Jones et al. 2012). With hundreds of adaptive loci now in hand from genome-wide re-sequencing studies we can now begin to address quite general questions about the genomic mechanisms contributing to evolutionary change (Jones et al. 2012). Our genome-wide studies show that chromosome inversions can play an important role in maintaining suites of differences between marine and freshwater fish. And, based on a large number of examples, we find that both protein-coding (Marques et al. 2017) and regulatory changes contribute to adaptive evolution, with regulatory changes predominating by about 4 to 1 during evolution of natural stickleback populations (Jones et al. 2012).

Finally, the widespread evolution of sticklebacks offers a unique opportunity to test whether the same or different genes are used when the same traits evolve in widely separated locations. Genetic mapping, complementation tests, gene expression studies, and genome-wide re-sequencing studies all show that similar genetic mechanisms are used when similar traits are selected in multiple populations around the world (Colosimo et al. 2005; Shapiro et al. 2006; Miller et al. 2007; Chan et al. 2010; Jones et al. 2012; O'Brown et al. 2015; Indjeian et al. 2016; Marques et al. 2017). How far might such reuse of particular genes extend? Our recent studies suggest that the genes underlying major morphological change in sticklebacks are also reused when similar morphological changes evolve even in distantly related animals, including loss of hindlimbs in marine mammals (Shapiro et al. 2006), changes in bone size in humans (Indjeian et al. 2016), and recent changes in skin and hair color in humans that have colonized new environments around the world (Miller et al. 2007; Guenther et al. 2014). We also find that the same type of regulatory changes that appear particularly important during stickleback evolution have also contributed to both loss and gain traits in the human lineage (McLean et al. 2011; Capellini et al. 2017). Further studies of sticklebacks may thus reveal general features of evolutionary change, with broad implications for our understanding of evolution in many other vertebrates, including humans.

More information on research projects in mice, human evolution, and human disease.

Stickleback Adaptive Genome Browser
Stanford University School of Medicine,  Department of Developmental Biology,  279 Capus Drive,  Beckman Center B300,  Stanford, CA,  94305-5329