Projects
Polyphenolic Inhibition of Nanopore Sequencing
During my PhD I struggled with Nanopore sequencing of seaweeds - an issue that turned out to be widespread in macroalgal genomics. Working with Nick Green in Chemistry at Otago, we used LC-MS on our DNA extracts and found strong evidence for polyphenol-DNA adducts causing rapid pore blocking and reduced sequencing yield, particularly in dried tissue. The findings have implications for genomic resource generation from macroalgae, including long-read sequencing of herbarium specimens.
Published as: A cry for kelp: Evidence for polyphenolic inhibition of Oxford Nanopore sequencing of brown algae, Journal of Phycology (2024).
Seaweed Microbiome Biogeography
Work on the structure and biogeography of macroalgal (seaweed) microbiomes - looking at how host population dynamics, dispersal, and environmental drivers shape the microbial communities associated with kelp and other macroalgae across their range.
Published as: Macroalgal microbiome biogeography is shaped by environmental drivers rather than geographical distance, Annals of Botany (2024), and related work on host dispersal and rafting microbiomes in Nature Communications (2024).
Hardy-Weinberg Equilibrium Filtering for RADseq Data
A methods project investigating how commonly used Hardy-Weinberg equilibrium filtering schemes affect population structure inferences drawn from RADseq (reduced-representation sequencing) data - relevant to anyone using these filters as a standard QC step in population genomics pipelines.
Published as: Commonly used Hardy-Weinberg equilibrium filtering schemes impact population structure inferences using RADseq data, Molecular Ecology Resources (2022).
Mitogenomics and Biogeography of Isocladus armatus
The bulk of my Master’s research, on the New Zealand endemic marine isopod Isocladus armatus. First, I generated a mitogenome for this colour-polymorphic isopod and found it had a bizarre structure - an inverted, duplicated arrangement rather than the typical small circular mitogenome. Alongside this, I used genotyping-by-sequencing to study the species’ biogeography, finding strong population structure and isolation-by-distance, with the geographic arrangement of populations concordant with the genetic PCA space.
Published as: Long-read sequencing reveals atypical mitochondrial genome structure in a New Zealand marine isopod, Royal Society Open Science (2022), and Concordant geographic and genetic structure revealed by genotyping-by-sequencing in a New Zealand marine isopod, Ecology and Evolution (2020).
Holobiont Eco-Evolutionary Simulations
Ongoing work developing eco-evolutionary simulations of microbial communities within hosts, to build and test hypotheses about holobiont (host-microbiome unit) evolution - in particular, how environmental variability shapes selection for microbiome-mediated host adaptation. This modelling work pairs with experimental work in Daphnia to test microbial contributions to host fitness under environmental change.
Published as: Within-host microbial selection and multiple microbial generations buffer the loss of host fitness under environmental change, FEMS Microbiology Ecology (2025).
See the Research page for the full publication list.