Research

Landscape genomics – Plants inevitably occur across environmental gradients. This distribution generally results in plant populations being more fit in their local environment compared to populations farther afield (local adaptation). I’m generally interested in understanding how plant species manage to adapt to different environments? Also, how species manage to adapt to similar environments using vastly different mechanisms? I believe that part of the answer to these questions lies in their genetic code. Considering how much has changed in the past few years in terms of sequencing technology, it is becoming possible to understand the rich evolutionary history of plant species. Therefore, I use many different types of genomic information (e.g. reduced representation, whole-genome sequencing, transcriptomics) to ask fundamental questions about adaptation. I collect data from naturally occurring populations, field experiments (i.e. common gardens or reciprocal transplants), and controlled experiments (i.e. glasshouse) to try to quantify local adaptation and adaptive capacity.

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Pathogen resistance – Over the past few centuries, humans have been traversing the world, bringing things with them, this includes pathogens. Homogenisation of plant pathogens around the world means that plant species are continuously being exposed to new pathogens. The result is that unadapted plant species are under threat of loss of fitness and even mortality in some respects from these novel pathogens. This scenario is particularly evident in Australia, where local and state government organisations are trying to protect their native ecosystems from devastating impacts. Things may not be so grim, because some current work suggests that there are some inherent pre-adaptations (exadaptation) available for some species that culminates in resistance or tolerance. While these exadaptations are not ubiquitous across a species range, resistance is generally genetically controlled. I am currently using whole-genome sequencing to understand the genetic basis for this resistance and identify causal genes. The hope is that this work can be used by organisations that are focused on on-ground management of plant species, they can genetically screen what individuals can be bred for future populations that are more pathogen resistant, resulting in populations that are somewhat protected.

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Local adaptation of traits – Local adaptation is polygenic. There are many genes that are involved in the adaptation of a population to its local environment, many of these genes are likely genes of small-effect. Meaning that it is difficult to identify, through genomics, all of the causal alleles associated with an environment or a trait. Therefore, some of my projects involve growing plants in common gardens or manipulative experiments (to reduce the environmental variable in the E + G = P equation to as close to zero as we can get it). This effectively means that G = P, so by measuring the phenotype (trait) we can get a good understanding of local adaptation within the species or at least between the populations. In manipulative experiments, we can also quantify the plasticity of a trait by growing plants from the same population in different environments.

Of foundational species – Often times we think conservation principals only apply to rare species. For the most part this is true, particularly from a genomics perspective. What happens to alleles in small populations? How do we increase effective population size? However, I think that in order to protect the rare species, we also have to ensure that the foundational species remain diverse and robust to ongoing environmental changes. Therefore, I spend time thinking about how we can better manage widespread species to protect biodiversity. By understanding adaptive potential from a genetics and trait perspective, we can identify the most vulnerable populations to future conditions and apply management strategies that improve long-term persistence.

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Of rare species – I believe that we should protect biodiversity for it’s own sake. Therefore, I study why rare species are rare. Generally, rare plant species have some odd trait that helps them survive but reduces their reproduction and persistence. Some examples include polyploidy, clonality, and environmental specificity. I use genomics to measure diversity, reproduction, migration, and gene flow. These measures can provide ways to improve management strategies.

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Comparative genomics – It is inherently difficult to measure the adaptive potential of rare species that have restricted distributions. I am currently developing methods that aim to compare conspecifics to identify adaptive variants and general patterns of adaptation.

Quantitative genetics – Estimating the heritability of quantitative traits has been a valuable asset of plant breeding for decades. I have been using these techniques for ecological purposes. It gives us an overview of what we can expect if we choose to move some populations to new places. If we have more than one common garden, we can estimate genotype by environment interactions. If we measure more than one trait we can estimate genetic and phenotypic correlations.

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Trait plasticity – Traits are funny things. They are difficult to completely quantify because of many types of error due to stochastic effects. While I spend a lot of time developing ways to understand the adaptability of traits through genetic mechanisms, this only partially accounts for the phenotypes measured. Trait values can inherently change within the lifespan of an individual, sometimes within hours or days. In order to capture this variation I employ manipulative experiments in controlled environments. Raising the temperature or lowering the water availabililty, we can see these changes in real time. Sometimes these changes happen within hours (metabolomics, photosynthesis response, or transcriptomics), other traits require long-term investment (leaf size, wood density, δ¹³C). Estimates of plasticity can provide important information on if a species or population can overcome the stress of novel environments or if that stress will test tolerance threshold limits.

Genomic determination of traits – I gather data on species in many different ways. I collect data from field collections, common gardens, reciprocal transplants, and manipulative experiments. By connecting the dots between these types of collections and combining phenotypic measurements with whole-genome sequencing we can identify causal variants of the trait, overall heritability of the trait, and complex interactions (epistasis and pleiotropy). Together, these outputs can provide incredible resolution, of not only one trait, but how the architecture of trait complexes behave. We can take this information a step further by using environmental data (e.g. edaphic features, climate variables, and biotic pressures) to understand the selection of a trait. Connecting all of these dots is difficult, therefore I have been developing new ways to analyse and visualise how these are all connected. These outputs are important for the fundamental understanding of adaptation, and can also inform applicable outcomes such as adaptive management strategies.

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Testing predictions – We use associative models to identify putative variants under selection. I often wonder how we can remove the word ‘putative’ from the previous sentence. I think one way is to test these variants in long-term manipulative experiments. We can use many different sequencing platforms to test the sorting of adaptive variants. In the future, I hope to be able to knock out some of these genes before manipulative experiments take place to quantify the possible effects of the gene and the effect of the variant.