A study of X-chromosome meiotic drive in the Palearctic fly Drosophila subobscura

This thesis examines a particular selfish genetic element (SGE), X-chromosome meiotic drive (XCMD), in the species Drosophila subobscura. XCMD is a system where the X-chromosome kills or disables Y-chromosome sperm to enhance their own transmission to the next generation. This also results in those males producing female biased broods. This selfish enhancement of their own transmission results in conflict with the rest of the genome that can be a potent force in evolution. The first chapters deal with sex and mating behaviour and how XCMD and other SGEs are linked to it. Chapter three focusses on the marking techniques and mating behaviour in three species of Drosophila. This work was completed while establishing the XCMD system from wild populations Chapter four presents case studies of how SGEs are intrinsically linked to sex. Chapter five examines XCMD in D. subobscura and reveals that this species is completely monandrous. This shows that polyandry does not play a role in preventing the spread of XCMD in this species, unlike in a number of other taxa which have XCMD. I also demonstrate weak female choice against XCMD in this chapter. In chapter six and seven I examine the XCMD phenotype when it is expressed in different population genetic backgrounds. I test for evidence of suppression and incompatibilities, when XCMD is exposed in four different populations (Tunisia, Morocco, Spain, and UK). I find evidence of suppression in North Africa, but no suppression in Europe. I also find evidence for severe incompatibilities specific to XCMD on European genetic backgrounds, which are absent in North African backgrounds. These results are consistent with genetic conflict causing rapid evolution in North Africa between XCMD and suppressors, which results in XCMD specific hybrid incompatibilities in naïve European populations. My final chapter evaluates how the testes proteomes of two species, D. subobscura and D. pseudoobscura, differ between XCMD and non-XCMD individuals. This ongoing work identifies some putative candidate genes that could be involved in the network that results in XCDM in these species. Interestingly, very few strong candidate genes overlapped in the two species, supporting the idea that separate genes and mechanisms are responsible for the two XCMD systems

Selfish genetic elements and male fertility

This is the author accepted manuscript. The final version is available from the Royal Society via the DOI in this recordSelfish Genetic Elements (SGEs) are diverse and near ubiquitous in Eukaryotes and can be potent drivers of evolution. Here we discuss SGEs that specifically act on sperm to gain a transmission advantage to the next generation. The diverse SGEs that affect sperm often impose costs on carrier males, including damaging ejaculates, skewing offspring sex-ratios and in particular reducing sperm competitive success of SGE carrying males. How males and females tolerate and mitigate against these costs is a dynamic and expanding area of research. The intense intra-genomic conflict that these selfish elements generate could also have implications for male fertility and spermatogenesis more widely

A Synthesis of Tagging Studies Examining the Behaviour and Survival of Anadromous Salmonids in Marine Environments

This paper synthesizes tagging studies to highlight the current state of knowledge concerning the behaviour and survival of anadromous salmonids in the marine environment. Scientific literature was reviewed to quantify the number and type of studies that have investigated behaviour and survival of anadromous forms of Pacific salmon (Oncorhynchus spp.), Atlantic salmon (Salmo salar), brown trout (Salmo trutta), steelhead (Oncorhynchus mykiss), and cutthroat trout (Oncorhynchus clarkii). We examined three categories of tags including electronic (e.g. acoustic, radio, archival), passive (e.g. external marks, Carlin, coded wire, passive integrated transponder [PIT]), and biological (e.g. otolith, genetic, scale, parasites). Based on 207 papers, survival rates and behaviour in marine environments were found to be extremely variable spatially and temporally, with some of the most influential factors being temperature, population, physiological state, and fish size. Salmonids at all life stages were consistently found to swim at an average speed of approximately one body length per second, which likely corresponds with the speed at which transport costs are minimal. We found that there is relatively little research conducted on open-ocean migrating salmonids, and some species (e.g. masu [O. masou] and amago [O. rhodurus]) are underrepresented in the literature. The most common forms of tagging used across life stages were various forms of external tags, coded wire tags, and acoustic tags, however, the majority of studies did not measure tagging/handling effects on the fish, tag loss/failure, or tag detection probabilities when estimating survival. Through the interdisciplinary application of existing and novel technologies, future research examining the behaviour and survival of anadromous salmonids could incorporate important drivers such as oceanography, tagging/handling effects, predation, and physiology

Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster

Wolbachia are maternally-inherited symbiotic bacteria commonly found in arthropods, which are able to manipulate the reproduction of their host in order to maximise their transmission. Here we use whole genome resequencing data from 290 lines of Drosophila melanogaster from North America, Europe and Africa to predict Wolbachia infection status, estimate cytoplasmic genome copy number, and reconstruct Wolbachia and mtDNA genome sequences. Complete Wolbachia and mitochondrial genomes show congruent phylogenies, consistent with strict vertical transmission through the maternal cytoplasm and imperfect transmission of Wolbachia. Bayesian phylogenetic analysis reveals that the most recent common ancestor of all Wolbachia and mitochondrial genomes in D. melanogaster dates to around 8,000 years ago. We find evidence for a recent incomplete global replacement of ancestral Wolbachia and mtDNA lineages, which is likely to be one of several similar incomplete replacement events that have occurred since the out-of-Africa migration that allowed D. melanogaster to colonize worldwide habitats.Comment: 41 pages, 5 figure

The discovery, distribution, and evolution of viruses associated with drosophila melanogaster

Drosophila melanogaster is a valuable invertebrate model for viral infection and antiviral immunity, and is a focus for studies of insect-virus coevolution. Here we use a metagenomic approach to identify more than 20 previously undetected RNA viruses and a DNA virus associated with wild D. melanogaster. These viruses not only include distant relatives of known insect pathogens, but also novel groups of insect-infecting viruses. By sequencing virus-derived small RNAs we show that the viruses represent active infections of Drosophila. We find that the RNA viruses differ in the number and properties of their small RNAs, and we detect both siRNAs and a novel miRNA from the DNA virus. Analysis of small RNAs also allows us to identify putative viral sequences that lack detectable sequence similarity to known viruses. By surveying >2000 individually collected wild adult Drosophila we show that more than 30% of D. melanogaster carry a detectable virus, and more than 6% carry multiple viruses. However, despite a high prevalence of the Wolbachia endosymbiont—which is known to be protective against virus infections in Drosophila—we were unable to detect any relationship between the presence of Wolbachia and the presence of any virus. Using publicly available RNA-seq datasets we show that the community of viruses in Drosophila laboratories is very different from that seen in the wild, but that some of the newly discovered viruses are nevertheless widespread in laboratory lines and are ubiquitous in cell culture. By sequencing viruses from individual wild-collected flies we show that some viruses are shared between D. melanogaster and D. simulans. Our results provide an essential evolutionary and ecological context for host-virus interaction in Drosophila, and the newly reported viral sequences will help develop D. melanogaster further as a model for molecular and evolutionary virus research