Roycroft Honours Projects

Phylogeography of northern Australian mammals

Background: Phylogeography provides a window into the past, allowing us to reconstruct the evolutionary history of species, and of the environments in which they live. Past environmental change leaves signatures in the genomes of individuals and populations, which enable high-resolution insight into past and ongoing patterns of isolation, connectivity, introgression, range shifts, and speciation across taxa.
During the Pleistocene period, repeated climate cycles have driven expansions and contractions of suitable habitat for species across Australia. These patterns have been especially pronounced across northern Australia (the region spanning from the Pilbara, through the Top End and into the Wet Tropics). Our recent work has described new species of delicate mice in northern Australia, but the phylogeography and diversification of a number of other similarly distributed small mammals has not yet been investigated. Understanding the past demographic responses of species to changing environments is crucial to understanding their current distributions, genetic health, and their susceptibility to future environmental change. This is especially important for Australia’s native rodents, which have the highest rate of recent extinction of any mammal group.

Project Aims: This project will investigate the 1) comparative phylogeography, 2) genetic diversity/genetic health, and 3) demographic history of multiple co-distributed small mammals across northern Australia, and compare this to the patterns observed in other taxonomic groups.

Techniques: This project will involve bioinformatics, phylogenetics, population genomics and statistical analysis in Linux command line/Python/R, and would suit a student who is motivated to develop these skills. The project may also involve molecular laboratory work (DNA extraction and genomic library preparation), depending on the interests of the student.

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Genetic health of Australia’s island mammals

Background: Australia has the highest rate of recent mammal extinction in the world, with 46 mammals lost since European colonisation in 1788, and over 30% of surviving species at risk. If not for offshore islands, this world-leading rate of mammal extinction would be even higher. Largely free from feral-predators and other threats prevalent on mainland Australia, islands protect 29 nationally threatened mammal species from extinction. These very small populations, isolated from the mainland for at least ~8,000 years, are now crucial sources for conservation translocations and genetic rescue, but little is known about their genetic health.
Population genetic theory predicts that small populations rapidly lose genetic diversity and potentially accumulate harmful mutations ‘genetic load’, increasing their risk of extinction. Island populations maintained at small size for thousands of years are expected to be more susceptible to extinction than their mainland counterparts, but our recent work has shown lower genetic load than expected on islands. This points to genetic purging, where deleterious mutations are exposed by increased homozygosity in small populations and removed from the population by selection.

Project Aims: This project will investigate 1) genetic diversity, 2) isolation time, and 3) harmful mutations in island populations compared to mainland populations of a chosen focal species. The focal species is flexible and can be selected based on the interests of the student.

Techniques: The core component of this project involves bioinformatic analysis of whole-genome sequencing data and population genomics, using Linux command line, high-powered computational analysis, and data visualisation/statistics in Python/R. This project would suit a student that has some experience with Linux command line or coding, or is very motivated to learn these skills. The project may also involve molecular laboratory work (DNA extraction and genomic library preparation), depending on the interests of the student.

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