Below, you'll find a description of the main projects I am currently working on, from understanding rapid evolution using >100 year old pinned moths, to looking at genomic diversity in Australian and Antarctic species, to looking at the accuracy of multiple sequence alignment software methods, to working on a model for understanding and predicting which species live where on Earth.
Understanding rapid evolution using antique dna
As a DECRA fellow at ANU, my main focus is a project entitled, Historical pest genomes inform debate about how rapid evolution proceeds.
This project focuses on Helicoverpa armigera, an Australian pest moth that causes billions of dollars of damage globally in pest management and crop losses.
It's global success relies on inherent 'pesty' characteristics that make it a successful and highly adaptive species:
High migratory capacity;
Wide host plant range;
Ability to enter diapause to avoid adverse environmental conditions.
This makes H. armigera an ideal species for studying the effects of insecticide resistance on driving rapid evolution.
Populations can adapt to new environments in two distinct ways:
They can wait for the appearance of an advantageous novel mutation, which will become quickly established in the population; or
They can evolve immediately by co-opting standing (i.e. pre-existing) genetic variation.
However, determining whether adaptive mutations pre-date environmental change is difficult. To discriminate between the two possibilities in natural populations requires samples that have not been exposed to the selection pressure, i.e., insecticides.
My research addresses this by comparing DNA sequences from historical, insecticide-free pest genomes (using pinned specimens from several Australian Museums and the Australian National Insect Collection) to contemporary populations of H. armigera that are currently exposed to insecticides.
My work examines the genetic make-up of a fast adaptive response to environmental change, providing a template for testing questions about the presence or absence of pre-adapted resistance genes, and for understanding the mechanisms behind successful pest status.
Understanding biological invasions: the biosecurity threat of the pink bollworm to Northern Australia
Making the most of degraded DNA: optimising wet-lab protocols to improve genome data quality
The technological innovations underlying next generation sequencing (NGS) have resulted in an unprecedented ability to obtain DNA sequence data from specimens encompassing the vast diversity of biological life. In recent times, NGS has opened up possibilities not just for recovering DNA data from extant species, but from historical samples and even extinct species. However, historical DNA has proven difficult to work with because of its fragmented nature – after the death of an organism, DNA is degraded by endogenous nucleases, as well as damaged by chemical and physical events. Thus, even the most successful NGS methods for degradation-vulnerable samples result in the loss of a substantial percentage of DNA, with conversion efficiencies in the range of 30-70%.
However, degraded DNA is usually an indicator of precious samples that hold important information. Therefore, maximising the efficiency of NGS methods with respect to such samples is of vital importance. In this project, Dr. Kerensa McElroy and I are developing a revised laboratory protocol for NGS of degraded DNA samples that maximises the quality of the resulting genomic data. We are testing the effects of different clean-up methods, PCR enzymes, and the USER enzyme, on the quality of genomic data in finches.
Biological invasions are rapid evolutionary events that dramatically affect global ecosystems and can result in high economic and environmental costs. The pink bollworm (Pectinophora gossypiella) is one of the most destructive global pests of cotton and its spread has largely resulted from human activities around cotton production.
This species is now established throughout nearly all cotton-growing countries. It is controlled with transgenic cotton that contains genes from the bacteria, Bacillus thuringiensis (Bt), which produce proteins toxic to most caterpillars following ingestion. However, in some parts of the world (e.g., India), the pink bollworm has become resistant to Bt-cotton crops.
Together with my collaborators, Dr. Rob Lanfear and Dr. Tom Walsh, I am working on an exciting new project focused on creating a draft assembly of the genome of the pink bollworm. In a pilot study using samples collected from NW Australia, our project will initially aim to assess the biosecurity risk of P. gossypiella, identifying the source population of Australian individuals, and assessing whether the Australian population has connectivity to the Indian (Bt-resistant) population.
mind the gap: multiple sequence alignment methods are too generous with alignment gaps
biodiversity dynamics: developing a model for an integrated and predictive theoretical framework
Biodiversity is the variety and variability of all life-forms on Earth. While we understand the value of biodiversity, we lack unified answers to questions such as: How does biodiversity form? How does it change over time?
Biodiversity patterns generally arise through a combination of short-term ecological and long-term evolutionary processes. We can observe and test the short-term phenomena, but can usually only indirectly infer their longer-term outcomes. What we need is a way to examine the interaction between these patterns and processes.
This sDIV project involves a team of international researchers with expertise in ecology and evolutionary biology. Working together, the sEcoEvo group aims to produce a working model of species diversity patterns to enable testable predictions about species abundances and genetic diversity over time.
This project is a collaboration involving Dr. Lars Jermiin. Multiple sequence alignments (MSAs) play a pivotal role in phylogenetic analysis because the accuracy of phylogenetic estimates relies on that of the MSAs.
Many methods have been proposed for inferring MSAs, but their results often differ, implying that most MSAs must have errors and that alignment gaps are incorrectly inserted in the MSAs.
To explore this problem, we are examining the performance of several MSA methods.
We are finding that the different methods insert alignment gaps into inferred MSAs when they should not.
Currently, we are quantifying the amount and distribution of these alignment gaps to provide a guideline for the use of specific MSA methods for different alignment problems.
Mitochondrial and nuclear discordance in Heteronotia binoei
evaluating genomic diversity in antarctic springtails
In collaboration with Dr. Crid Fraser, I am re-visiting my MSc and PhD roots, to look at genomic diversity in Antarctic springtails.
We have GBS data from ~400 springtail samples distributed widely across continental Antarctica.
We aim to examine questions around population connectivity and are particularly interested in whether genomic diversity co-distributes with the dynamic environments associated with Antarctic volcanoes.
The Moritz Lab have a range of Heteronotia (gecko) samples collected throughout Northern Australia.
In most cases, mitochondrial lineages identified across samples correspond well with nuclear (exon capture) data. However, in Heteronotia binoei, there is discordance between mitochondrial and nuclear phylogenies.a.
Dr. Craig Moritz and I are examining the possible causes of this discordance in a population demographic framework.