The role of genome reorganisation in adaptation and speciation

Adaptation and speciation are fundamental evolutionary processes that rely on changes to the genome. However, the role of genome architecture (e.g. chromosomal rearrangements, gene duplications) in driving these processes is poorly understood. This project will use advanced comparative genomics and bioinformatics to examine the role of chromosome rearrangements in driving adaptation and speciation, and evaluate rates of molecular evolution between the X-chromosome and autosomes. Utilising Australia’s endemic mammalian fauna as a tractable model system, this project will link population processes with macro-evolutionary outcomes to show how genome architecture underpins biodiversity. This project focuses of four mammalian genera: Petrogale, Pseudomys, Rattus and Sminthopsis to compare and contrast chromosomally diverse and chromosomally conserved groups to understand how structural variation drives divergence.

Do chromosomal rearrangements drive genomic evolution and speciation?

Australian rock-wallabies (genus Petrogale) are chromosomally diverse and provide an amazing natural system to explore the process of chromosomal speciation. Chromosomal rearrangements in this group range from simple to complex and include fusions, fissions and inversions. We are focusing on five recently diverged species from north-east Australia to disentangle the role of chromosome structure and genome evolution in driving reproductive isolation. I am applying population and comparative genomics to understand the mechanisms driving diversification between these species. This project is in collaboration with Prof Craig Moritz, Prof Janine Deakin, Dr Mark Eldridge, Dr Jason Bragg and Prof Mark Kirkpatrick. We are also applying cytogenetics and epigenetic approaches in an integrative framework to disentangle the role of chromosome rearrangements on genomic divergence. In particular, we are interested in how genetic variation within chromosomal rearrangements compares to outside rearrangements to determine if recombination suppression is causing selection and driving adaptation in this group. 

Molecular evolution in marsupials (X vs autosome divergence)

Understanding the variation in processes driving molecular evolution is crucial to understanding how biodiversity forms and persists. Rates and patterns of molecular evolution vary across even closely related groups of species. A better knowledge of how such changes evolve is important to our understanding of how species adapt and form, but also to our broader understanding of genome function. Here we aim to understand the processes driving molecular evolution, particularly differences between sex chromosome and autosome evolution across marsupials (e.g., faster X evolution with associated effects on speciation). Comparative research across diverse biological systems is critical to gain a better understanding of how mutation, selection, recombination, genetic drift influence molecular evolution and speciation. This project uses comparative genomics within the Australian marsupials (Australidelphia) to understand the consequences of diverse biology in driving molecular evolutionary processes. This research is part of the BioPlatforms Australia “Oz Mammal Genomics” initiative.

Macroevolution of skinks (family Scincidae)

Here we focus on the Australian skink family Scincidae to obtain a higher resolution understanding of speciation processes, and how different speciation dynamics translate to macroevolutionary outcomes. With dense sampling of intraspecific (phylogeographic) lineages through to large clades of species we identify cryptic diversification, as well as evidence of lineage fusion and/or introgression. These observations have several implications for macroevolutionary analyses, which we are exploring. This is collaborative work led by Dr Jason Bragg, in collaboration Prof Craig Moritz, Dr Huw Ogilvie, Dr Mozes Blom, Dr Ana Afonso Silva and Dr Eric Rittmeyer.

Understanding the diversity and connectivity of populations of Lampropholis skinks from the east coast of Australia

Understanding population structure, diversity and gene flow amongst east coast Australian fauna is critical, especially as events such as the 2019-20 bushfires wipe out entire populations or fragment current distributions of species. This project builds on the mitochondrial data for three closely related skinks in the genus Lampropholis to understand species boundaries, hybridisation, population structure, diversity and history. Using population genomics and a ddRAD approach we will resolve the evolutionary history of populations and species in this group. This project is in collaboration with Callum McDiarmid, Prof David Chapple and Dr Oliver Griffith. This project is funded as part of the BioPlatforms Australia AusARG (Australian Amphibian and Reptile Genomics) initiative.

Using museumomics to disentangling mito-nuclear discordance in rock-wallabies across northern Australia

This research uses museum specimens to better understand the complex evolutionary history of rock-wallabies from northern Australia. Resolving the evolutionary relationships amongst the four species of rock-wallabies in the brachyotis group, and evaluating their demographic and divergence histories, we aim to understand the causes of milo-nuclear discordance in this group. These species are of conservation concern and currently the taxonomy is still unresolved for parts of this group. Using targeted capture sequencing of exons, we are able to use museum specimens to increase our geographic and sampling size to address outstanding questions about the population structure and divergence histories within this group which has both chromosomal variation and size variation. This is a collaboration including Dr Maxine Piggott, Dr Jason Bragg, Dr Mark Eldridge and Prof Craig Moritz. This research involves broader collaborations with museums across Australian (Australian Museum Research Institute in particular), Western Australian government and the Australian Wildlife Conservancy.

Taxonomy and evolutionary history of tree-kangaroos

This research aims to build upon our understanding of the phylogenetic relationships of tree-kangaroos from Australia and Papua New Guinea. This project uses museum skins to evaluate the phylogenetic relationships and taxonomy of tree-kangaroos. The use of museum specimens provides a valuable contribution to evaluating the taxonomy within this genus and understanding how this diversity has formed and persisted across these landscapes.