Abstract
The dispersal and subsequent proliferation of mammalian invasive species in new environments has significant impacts on food security, disease, and conservation worldwide, particularly in island nations where they have disproportionately large consequences in these unique insular ecosystems. Traditional control techniques such as kill trapping, and poison control strategies have served well in the past for controlling problem species. However, concerns for animal welfare, off-target effects and limits to long-term efficiency have fuelled a search for novel, highly effective control techniques. Harnessing the power of “super Mendelian inheritance”, gene drive technology can propagate a particular gene through a population, even if it is deleterious to the organism. By targeting key genes associated with reproductive processes, gene drives can be used to control a species by inducing infertility in one sex, while the other sex continues to propagate the impaired fertility phenotype through the population. Despite established theory and empirical experiments using gene drives in insects, there is, as yet, no gene drive fertility control system established for mammals. A major current limitation is the lack of validated candidate genes for mammalian gene drive systems.
My research establishes the first systematic review framework for identifying candidate genes for a range of invasive species. Using this framework, I have subsequently identified a list of 17 genes that could be targeted in a rodent gene drive system. Remarkably, results are significantly biased towards genes with male-specific fertility phenotypes, as those with female fertility phenotypes demonstrate additional pleiotropic attributes. I also provide a foundational bioinformatics pipeline to characterise these loci across populations of target invasive species, applying this to whole genome sequences from 42 ship rat (Rattus rattus) samples representative of the Aotearoa New Zealand (NZ) population. Subsequently, highly conserved sequences were used to inform potential gRNA design and parameters in a computational model exploring the dynamics of a CRISPR-Cas9 homing gene drive in the NZ ship rat population. Results from the model are consistent with previous findings that suggest targeting female fertility more reliably results in successful eradication, compared with targeting male fertility. However, the evident disparity between optimal theoretical parameters (i.e., targeting female fertility), and biological feasibility (i.e., candidate gene bias towards the male reproductive system) presents an important technical challenge for the design and development of mammalian gene drives.
To investigate the feasibility of utilising the same gene drive targets across a cohort of species, I further employed comparative genomics to evaluate sequence conservation of my candidate genes across nine invasive species in NZ - house mouse (Mus musculus), Norway rat (Rattus norvegicus), ship rat (Rattus rattus), European rabbit (Oryctolagus cuniculus), European hedgehog (Erinaceus europaeus), domestic cat (Felis catus), domestic ferret (Mustela putorius furo), stoat (Mustela erminea), and brushtail possum (Trichosurus vulpecula). Although no target loci that met my criteria were conserved across my evaluated list of invasive species, it is evident that several candidate genes have highly conserved sequences between distantly related groups of invasive species, implying that the molecular co-design of mammalian gene drives across several invasive species may be feasible.
Gene drive technology is still in its infancy, and many questions regarding the risks and benefits of its applications are yet to be resolved. However, in an era of global biodiversity crisis, it is necessary to thoroughly assess promising new avenues for the control of invasive species. My research contributes a list of strong candidate genes that could be targeted in a rodent gene drive for population suppression, and I further refined that list by identifying genes that may have strong multi-species utility. Such results progress research in a highly economically, socially, and environmentally significant area for international conservation.