Mixed Mode Dynamics of Ecological and Geographic Speciation in the <em>Rhagoletis cingulata</em> Sibling Species Group and Associated <em>Wolbachia</em> Endosymbionts

<p>In sexual organisms, speciation occurs as genetically based barriers evolve between populations to cause them to become reproductively isolated. The types and chronology in which different reproductive isolating (RI) barriers arise may vary depending on the ecological and geographic context of divergence and may not necessarily remain constant throughout the divergence process. Thus, mixed modes of speciation may be common. Research has mainly focused on divergent ecological adaptation, sexual selection, and intrinsic nuclear genomic incompatibilities as the sources of RI brought about by ecological and geographic speciation, but recent work demonstrates that endosymbionts may also contribute RI. For example, one of the most common endosymbionts, <em>Wolbachia</em>, can induce cytoplasmic incompatibility (CI) that causes postmating reproductive isolation between populations infected with incompatible strains. Like other forms of RI barriers, <em>Wolbachia</em> induced RI is not constant through time as <em>Wolbachia </em>are continuously purged from and horizontally transferred into host lineages. Studies are needed that synthesize across both endosymbiont and non-endosymbiont related RI to understand how episodic RI provided by <em>Wolbachia</em> can contribute to host-related RI and influence the diversification process of its host.</p><p>To address this gap, the goal of my dissertation is to study how <em>Wolbachia</em> induced CI and other mixed modes of speciation influence host RI dynamics during speciation. To accomplish this objective, my research leveraged the biology and natural history of the <em>Rhagoletis</em> (Diptera: Tephritidae) <em>cingulata</em> sibling species group endemic to N. America. Chapters 2, 3, and 4 characterize forms of premating and postmating isolation between cherry flies, between olive flies, and between both clades respectively. Chapter 5 uses comparative genomics to study a case of putative <em>Wolbachia</em> strain introgression, and Chapter 6 uses comparative genomics to study the variation of the universal <em>Wolbachia </em>strain, <em>w</em>Cin2, from cherry flies across N. America. </p><p>In Chapter 2, I found a unique <em>Wolbachia</em> strain, <em>w</em>Cin3, that putatively causes CI in crosses to other cherry fly populations, and, when coupled with other strong ecological RI, may contribute meaningful RI to the speciation process. In Chapter 3, I identified strong ecological allochronic isolation between olive flies. In Chapter 4, I observed a mixed mode of speciation between olive and cherry flies in which ecological and allopatric divergence both contribute at differing times to the evolution of pre- and postmating reproductive isolation, including the observation of increased premating isolation potentially due to reinforcement or reproductive character displacement. In Chapter 5, despite near identical sequences for the multi locus sequencing markers, substantial sequence differences for other loci were found between <em>w</em>Cer2 and <em>w</em>Cin2, as well as structural rearrangements, and differences in prophage, repetitive element, gene content, and CI inducing genes. Finally in Chapter 6, I report that <em>w</em>Cin2 from the Southwest strain is highly diverged in gene content, structure, and <em>cif</em> genes from <em>w</em>Cin2 genomes from other regions. In contrast, the <em>w</em>Cin2 strains from these other regions are very near identical in sequence content and <em>cif</em> gene content, but possess unique structural rearrangements associated with mobile genetic elements, some of which impact <em>cif</em> gene function.</p><p>Overall, my Dissertation provides new evidence for the importance of geographic and biological context when studying speciation and how dynamics driving the evolution of RI barriers can potentially change over the course of speciation. My research also shows <em>Wolbachia</em> associated RI is likely transient on an evolutionary time scale due its dynamic genome. Taken together, these findings provide insight into how mixed modes of speciation, including any associated endosymbionts, may have impacted the chronology and strength of RI barriers in the <em>R. cingulata</em> sibling species group.</p>