A project undertaken at La Trobe University, and supervised by Charles Feigin
Populations of many Australian animals are declining rapidly due to habitat destruction, climate change and invasive pests. As their populations decrease in size, animals are forced to find mates who are more closely related to them, leading to inbreeding. Inbred offspring tend to have poorer health and less reproductive success than their parents. This phenomenon, called Inbreeding Depression, can inhibit a population’s recovery or in extreme cases may cause a population to die out. Accurately assessing the risk of inbreeding depression is therefore essential for conservationists to set priorities when managing threatened species.
Inbreeding Depression is ultimately a consequence of genetics. All populations harbor rare, harmful genetic variants. Most of these harmful variants are recessive, meaning they can “skip generations” when offspring inherit them from just one of their parents. They only cause health problems when both parents pass them on. Unsurprisingly though, this happens much more frequently in inbred populations, where parents have similar genetics.
Naturally, researchers increasingly turn to new DNA sequencing technologies to improve the management of threatened species. However, many harmful genetic variants are difficult to distinguish from neutral or beneficial variants. Moreover, the specific consequences of genetics variants on traits like health and reproductive success are even harder to predict. Together, this makes assessing the risk Inbreeding Depression from the sequence of DNA alone challenging.
Epigenetic phenomena, such as DNA methylation, are important biological mechanisms that help to transform the instructions encoded in an animal’s DNA into the molecular and cellular behaviours that underpin that animal’s traits, and affect their health and reproduction. Recent work suggests that Inbreeding Depression produces characteristic epigenetic signatures.
The goal of our project is to better characterise these epigenetic signatures and use them as the basis for new approaches to predict Inbreeding Depression in threatened Australian mammals. We will conduct large studies linking DNA methylation to fitness-related traits in a model marsupial, the fat-tailed dunnart (Sminthopsis crassicaudata). This species is closely related to many threatened or endangered marsupials like the Tasmanian devil, quolls and numbats and shares many important features of their biology. These studies will allow us to develop predictive models and affordable biomarker tests that can be re-deployed in numerous conservation management efforts across Australia. Ultimately, we aim to use this science to expand the toolkit available to field biologists, captive breeding programs and to provide a general framework for developing similar tools across even more diverse threatened species around the world.