Konstantinos Papachristos: Genomics of Neotropical Fruit Flies and Their Maternally Inherited Associates

Abstract

This thesis examines the evolutionary history of Neotropical Drosophila fruit flies and their maternally inherited associates, i.e., their mitochondria and their intracellular endosymbiont Wolbachia. Moreover, we study nuclear genomic features that have emerged from insertions of the mitochondrial genome into the nuclear genome, called Mega-NUMTs. 

In the four papers produced for this thesis, we find the following. First, the Wolbachia strain wPau that is obligate for its host, i.e., D. paulistorum, shows genomic differences in the number of pseudogenes, transposable elements and rearrangements compared to closely related facultative strains. Second, mitochondrial and Wolbachia phylogenies are almost perfectly congruent both between and within multiple host species of the willistoni and saltans groups of Drosophila, indicating co-speciation since their most recent common ancestor. However, divergence times of mitochondria and Wolbachia do not match, suggesting either unprecedentedly slow rates of evolution for a bacterial endosymbiont or horizontal transfer between hosts. Third, we find that wPau from different semispecies of D. paulistorum are overall congruent with the phylogeny of their hosts, suggesting co-divergence. These strains also differ in genomic features thought to be involved in host interaction, specifically in a handful of effector proteins, and the genomic arrangement of a genomic island known as the Undecim cluster. Fourth, we find multiple mitochondrial introgression events within the willistoni subgroup, and that one of the two mitotypes of D. paulistorum, the β mitotype, is likely introgressed, while the α mitotype may be native to the species. Despite this, we find limited evidence for nuclear compensation in D. paulistorum, as a response to the introgression of the β mitotype, indicating that mitochondrial introgression may not have caused deleterious effects. Lastly, we describe tandem insertions of complete “α-like” mitochondrial genomes in chromosome 3 of some lines of D. paulistorum, forming Mega-NUMTs. Phylogeny shows they have a common origin, but their genomic location, NUMT completeness and transposable element content supports lineage-specific amplification. 

In summary, this thesis contributes to the understanding of the evolutionary relationships between Neotropical Drosophila, their mitochondria and their Wolbachia endosymbionts.