I am undertaking my PhD research in the Avian Ecology Lab with Prof. Simon Griffith at Macquarie University. My project is co-supervised by Dr. Daniel Hooper, formerly of the American Museum of Natural History. My work focuses on using genomic techniques to understand species divergence and adaptation. A large part of my project is focused on the black-throated finch and the long-tailed finch in the genus Poephila, a recently-diverged clade in northern Australia which our lab has been developing as a model system for studying speciation in birds. I also work on related taxa in the subfamily Poephilinae, a group of fourteen species known for their ecomorphological diversity and complex chromosomal evolution.
My work is supported by an Australian Research Council Discovery Project grant, the BioPlatforms Australia Avian Genomics Initiative, and the Australian-American Fulbright Commission.Â
Using RNAseq data from liver and gonad in both sexes, we are investigating how gene expression has evolved in three recently diverged finch taxa. The study uses "pure" individuals and experimentally-generated F1 hybrids from our captive colony at Macquarie university. We find that regulatory incompatibilities between taxa are likely due to compensatory evolution of cis and trans elements under stabilising selection. We also find strong evidence for a "fast-Z" effect driven by relaxed constraint on the evolution of gene expression in males (the homogametic sex). We formulate several new approaches for quantifying regulatory divergence in hybrid studies.
This project formed the basis of my Masters thesis (2024) and will be published soon.
Although the importance of structural variants (SVs) in the evolution of reproductive isolation and adaptation is increasingly recognised, limitations in sequencing technology and computational methods have prevented us from studying how they evolve - until now. In this project, we are building new chromosome-level reference genomes for all named genera in the subfamily Poephilinae and generating population-level linked-read genomic data for all fourteen species. This will allow us to identify SVs both between and within species and model their evolution using a cross-species pangenomic approach.
The Australian Zebra Finch, Taeniopygia castanotis, is a globally important model organism and has been central to genetic and genomic research in birds for decades. However, very little is known about the population structure of this species in the wild as genetic work has focused on domesticated lab birds. Fascinatingly, previous research has found that multiple chromosomal inversion polymorphisms segregate at high frequency in this species within the same population. In this project, we aim to construct a new high-quality reference genome of the Australian Zebra Finch from a wild bird, with a focus on improving the sex chromosome assemblies. We will generate linked-read genomic data for hundreds of birds across the Australian continent to construct the first pangenome of this species, and we will use this data to understand how SVs contribute to ecological adaptation.
These projects are collaborations with Oli Griffith and Sally Potter at MQU, Irby Lovette, Nina Therkildsen and Jen Genier at Cornell University, and Frank Chan at the University of Groningen.
Incompatibility between the nuclear and mitochondrial genomes is thought to be a potential driver of hybrid incompatibility, especially in birds. In this project, we are using high-resolution respirometry (Oroboros O2K) and genomic sequence data to assess mitochondrial performance in pure Poephila finches and their F1 hybrids. Previous work by our lab has found some evidence for mitonuclear incompatibility in subspecies of the long-tailed finch, both in the wild and under experimental conditions. This study is the largest of its kind and will give us direct insight into how divergence in mitonuclear genes can affect fitness in interspecific hybrids.
Part of this project is being led by Yun Shan Sua, a Masters student in our lab, who I am co-supervising.
Recently published work by our lab has shown that bill colour, the most striking morphological difference between Poephila taxa, is controlled by a handful of loci under strong selection. Building on these results, we are characterising bill-colour variation in experimentally-generated later generation (F2+) hybrids between long-tailed and black-throated finches to understand dominance and epistasis between these genes. We are combining this with gene expression data from bill integument in the different species to gain insight into the functional pathways underpinning colouration.
Our team has identified a rare Z-chromosome inversion in the long-tailed finch with a striking effect on sperm morphology, presumed to be deleterious. Despite this, we have also detected this inversion in the black-throated finch, sister species to the long-tail. This suggests that the inversion has either persisted at low frequency for at least two million years or has crossed species boundaries despite its negative fitness consequences. How can this be? We are now investigating this inversion to understand its effects in females, possible meiotic drive dynamics, and whether it is present in the related masked finch, P. personata.
This project builds on currently unpublished work by Callum McDiarmid, a recent PhD graduate from our lab.
As lineages diverge, they become more different from each other - but the rates of genetic, morphological and ecological divergence are not always the same, and depend heavily on eco-evolutionary context. In this project (recently published in Evolution), we formulate a new method to find and categorise speciation modes across a phylogeny. We apply this to a continent-wide radiation of lizards in Australia, the tribe Eugongylini.
This project formed the basis of my Honours thesis (2021) and was supervised by Dr. Xia Hua, Prof. Lindell Bromham, and Prof. Craig Moritz. Our manuscript has just been selected as the Editor's Choice in the next edition of Evolution.
Anepischetosia maccoyi, also known as Maccoy's Skink or the Salamander Skink, is an unusual lizard from southeastern Australia: it is adapted to cool, wet habitats, is strongly desiccation and heat sensitive, and rarely emerges from the leaf litter as it does not bask. It has been presumed to be a single species based on morphology. However, using genome-wide SNPs and mitochondrial sequence data, we show that this genus contains three deeply divergent lineages that have been genetically isolated for 7-9 million years. These candidate species are range-restricted and inherently vulnerable to extinction from the effects of climate change.
This project was done in collaboration with Dr. Paul Oliver and was recently published in Conservation Genetics).
In this project, we are using genome-wide SNP data to untangle the evolutionary history of the Brown Antechinus complex. This group includes Antechinus stuartii, A. agilis, and A. subtropicus, three largely indistinguishable species found throughout southeastern Australia. We are working to understand how to reliably delimit morphologically cryptic parapatric species in contexts with low levels of divergence, strong genetic drift, and limited sampling (all classic hallmarks of short-range endemic taxa) using demographic modelling.
This project is a collaboration with Dr. Mark Eldridge and A/Prof. Andrew Baker.
I am developing a new R package implementing the "Peter & Slatkin" method for detecting demographic expansions from SNP data, and then calculating the geographic origin of those expansions. This project builds on recently-published work showing that the P&S method can be biased by edge effects, necessitating a correction for population structure. Importantly, it will also resolve major bugs in the existing R package commonly used in popgen studies, and won't bring on dependency hell.
Led by Jarrod Sopniewski and Renee Catullo (UWA)
Led by Lindell Bromham (ANU)
Led by Stephen Zozaya (ANU)
Led by Sergio Gonzalez Mollinedo (MQU)