The genomic basis of parallel evolution in three-spined stickleback (Gasterosteus aculeatus)

Adaptation is a critical process in evolution and much remains unknown regarding some of the most fundamental aspects of how adaptation occurs. This Dissertation uses an array of genetic and genomic resources in an emerging evolutionary model system, three-spined sticklebacks (Gasterosteus aculeatus) to understand the following questions: the molecular basis of an adaptive mutation underlying major morphological adaptation; whether molecular signatures of selection can help identifying loci underlying evolutionary change; the genomic architecture of parallel evolution; the role of chromosomal rearrangements in adaptation; and the birth of a neo sex chromosome during an incipient speciation event. In this Dissertation, I have shown results that speak to each of the above aspects. Certain notable results include the identification of the exact molecular lesion for a naturally occurring cis-regulatory mutation underlying adaptive pelvic reduction; the identification of more than twenty additional loci likely underlying parallel adaptation using novel association methods; the characterization of several inversion polymorphisms with likely adaptive consequences; and the finding that adaptive parallel evolution in sticklebacks has occurred via reuse of standing variation as well as by de novo mutations. In the process, I have helped develop new genetic tools for transgenic assays, genome-wide bioinformatic resources, various different lists of candidate genes for future in-depth studies, as well as population genetic methods to assist future attempts to detect molecular signatures of selection. This Dissertation demonstrates how by employing a multi-disciplinary approach, some longstanding problems in evolutionary biology are now eminently tractable, and can lend themselves to logical, yet surprising insights.