Genomic conflict is pervasive in nature and affects a number of fundamental evolutionary processes. Genomic conflict occurs when different genetic entities within a species have different interests in terms of the optimal transmission strategy to future generations, resulting in antagonistic interactions between these elements. When this conflict is over the reproduction strategy within an individual, it can result in sex ratio biases in an individual’s offspring. For instance, genomic conflict occurs between maternally transmitted genetic elements (such as female limited chromosomes or cytoplasmic elements) and nuclear elements over the optimal sex ratio of an individual’s offspring due to the fact that maternally transmitted elements benefit from a female biased sex ratio (as they are transmitted through the matriline) while nuclear elements benefit from an equal sex ratio. I am investigating a maternally transmitted genetic element in a sexual booklouse, Lipsocelis nr. bostrychophila (Insecta; Psocodea) that manipulates reproduction such that all females carrying it produce exclusively female offspring. This is expected to affect L. nr. bostrychophila evolution in a number of ways. I investigated the ecology of L. nr. bostrychophila to gain a better understanding of whether and how the selfish reproductive manipulator (designated the distorting element) persists over time. I found that the distorting element is able to persist in L. nr. bostrychophila populations, both in the wild and in the laboratory, and this is partially due to the fact that females that carry the distorting element have a shorter lifespan and do not produce as many offspring as females that do not carry the element. This helps to counteract the advantage that females carrying the distorting element would otherwise have due to the fact that they do not produce male offspring. Additionally, I found that females that do not carry the distorting element also produce a female biased sex ratio. This also likely mediates the persistence of the distorting element in wild and laboratory L. nr. bostrychophila populations, and is particularly interesting in that I found that other wild Liposcelis species also exhibit female biased sex ratios. This suggests that L. nr. bostrychophila populations likely exhibited female bias sex ratios before the distorting element arose in this species. I also assessed the effect that the distorting element has had on the genomic evolution of L. nr. bostrychophila. I found that females that carry the distorting element have radically different mitochondria from females that do not carry it, leading me to speculate that the reduced longevity in females that carry the distorting element may be a consequence of impaired mitochondrial function. Finally, I found that all L. nr. bostrychophila individuals have unusual mitochondria, with females that carry the distorting element having five mitochondrial minichromosomes and females that do not carry the distorting element having seven (rather than the single chromosome typical in animals). These findings contribute to the growing body of evidence suggesting that genomic conflict is an important force shaping species’ evolution, supporting the importance of investigating the evolutionary forces at play within as well as between individuals. / Graduate / 2018-12-16 / 0329 / 0369 / 0353

Genomes usually work together to promote the fitness of the organism, but sometimes parts of the genome cause intragenomic conflict, and act selfishly in order to promote their transmission. An example of this conflict is a selfish B chromosome known as paternal sex ratio (PSR) in the jewel wasp Nasonia vitripennis. Transmitted solely to new progeny with the sperms hereditary material, PSR completely destroys the paternal genome during the first mitotic division of the newly fertilized embryo. This effect enhances transmission of the PSR chromosome because of the unique haplodiploid reproductive mode of Nasonia and other members of the hymenopteran insect group. Through transcriptomic analyses, our group recently discovered that the PSR chromosome expresses eleven transcripts in the wasp testis. A plausible hypothesis is that one or more of these transcripts play some role in paternal genome elimination. In this study I have begun to test this hypothesis by screening through a set of previously produced truncated versions of the PSR chromosome. Specifically, I used PCR in order to screen these truncated chromosomes for the presence of each of these PSR-specific transcripts. I could then correlate the level of genome elimination induced by each truncated PSR chromosome with the presence or absence of the expressed transcripts. My work has established that (i) three of the eleven transcripts are likely not involved in genome elimination; (ii) no single transcript alone causes genome elimination; (iii) the remaining eight of eleven transcripts are viable candidates for causing genome elimination; and (iv) it is likely that a sub-group of these transcripts may operate together to induce this effect. I discuss several models in which PSR-expressed RNA molecules could operate to cause genome elimination.

A genome is shaped by many different forces. Recombination can for instance both create and maintain genetic diversity, but the need to locally reduce recombination rates will also leave specific signatures. Genetic elements can act selfishly and spreading at the expense of the rest of the genome can leave marks of their activity, as can mechanisms that suppresses them, in a phenomenon known as genomic conflict. In this thesis, I have studied the forces driving genome evolution, using modern genome sequencing techniques and with a special focus on a class of selfish genetic elements known as Spore killers found in the fungus Neurospora. First, we show novel findings on large-scale suppression of recombination by non-structural means in the N. tetrasperma genomes. In contrary, in the genomic region harbouring the spore killer elements Sk-2 and Sk-3 of N. intermedia, a dense set of inversions that are interspersed with transposable elements have accumulated. The inversions are unique for each killer type, showing that they have a long separated evolutionary history and likely have established themselves independently. For the Sk-2 haplotype, where we have polymorphism data, we see signs of relaxed selection, which is consistent with the hypothesis that recombination suppression reduces the efficacy of selection in this region. These results show the strong effects the divergent selective forces of genomic conflicts can have on chromosome architecture. Furthermore, we investigate the hypothesis that spore killing can drive reproductive isolation, by comparing the fertility of crosses between N. metzenbergii and either killer or non-killer N. intermedia strains. We show that crosses with spore killer strains have lower fertility, which cannot be explained by the killing itself, but is potentially caused by an incompatibility gene captured in the non-recombining region. Finally, we identified the genetic element responsible for causing spore killing in the Sk-1 spore killer strains found in N. sitophila. Unlike the Sk-2 and Sk-3 elements, Sk-1 is not connected to a large, non-recombining region, but is caused by a single locus, and we also find indications that this locus was introgressed from N. hispaniola.