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.

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.