Speciation, the process by which new species arise, is associated not only with the accumulation of molecular changes in DNA composition but often also with physical rearrangements in chromosome structure. Chromosome inversions, one common type of chromosomal rearrangement that occurs when a chromosome breaks at two points and the area between those breakpoints is repaired in the opposite orientation, are regularly observed as fixed differences between species and as polymorphisms segregating within species. Inversions were first discovered by Alfred Sturtevant in 1921 and have since been found to propel the evolution of sex chromosomes, supergene formation, local adaptation, and reproductive isolation. Despite their evolutionary significance, the widespread presence of inversions is in some ways puzzling, as new rearrangements may be initially disfavored due to structural underdominance in heterokaryotypes, if crossing over within the inverted region during meiosis results in the production of aneuploid gametes. Reconciling the widespread presence of chromosome inversions with possible selective disadvantages that a new inversion faces remains an unsolved problem and largely motivated this dissertation. Birds have long been used as models of speciation and are perhaps the best-studied group with respect to how behavior and ecology contribute to population divergence but little attention has been given to the role of chromosome rearrangements to bird speciation. Indeed, the gross physical structure of the avian genome is highly conserved with the most easily observed types of macro-rearrangements (fusions, fissions, translocations, etc.), which so often distinguish the karyotypes of species in other taxonomic groups, are relatively rare in birds. As such, karyotype evolution has generally been considered to be an unrelated and unimportant aspect of avian diversification. Chromosome inversions, however, appear to occur regularly in birds. Comparative cytological investigations of avian karyotypes regularly detect chromosome inversion differences between and within species based on rearrangement to chromosome banding patterns and/or centromere movement. Recent comparative genomic analyses of both distantly and closely related avian taxa support the findings of earlier cytological studies in detecting large numbers of inversions differences both pericentric, inversions that include the centromere, and paracentric, inversions that do not include the centromere, in nature. Here, I have made efforts in the course of this dissertation in order to better understand the evolutionary dynamics underlying chromosome inversion evolution in birds through i) a synthesis of classic cytological data placed in a phylogenetic context in order to evaluate support for alternative theoretical models of inversion evolution (Chapters 1 and 2) and ii) a genomic assessment of an avian hybrid zone where inversion polymorphism on the Z chromosome may underlie the maintenance of reproductive isolation between hybridizing taxa (Chapter 3).




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