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Firescape genomics: predicting plant responses to changing fire regimes

Periodic Reporting for period 1 - FIRESCAPE (Firescape genomics: predicting plant responses to changing fire regimes)

Reporting period: 2018-01-01 to 2019-12-31

Fire has played a crucial role in plant evolution, exemplified by species in fire-prone ecosystems which rely on fire for reproduction and persistence. The fire landscape, or ‘firescape’, is undergoing rapid change worldwide, with increases in fire frequency being driven by invasive species, land use change and climate change. Plant species are now confronted with novel firescapes and we need to understand how, or if, species will adapt to these pressures to predict whether they will persist or decline across landscapes with changing fire regimes.

Most research on fire-driven evolution has focussed on macroevolutionary scales (among species), providing essential knowledge about how traits, such as seed dormancy and fire-stimulated germination, are shaped by the cumulative effects of historical fire regimes. However, studies of fire-driven adaptation within species are essential for understanding adaptive potential and predicting how fire will affect species under rapid global change. The handful of studies addressing this issue within species has been limited by a lack of spatially contrasting fire histories across species native ranges. However, many European plant species have been introduced into Australia where fire frequency exceeds levels found in their native range (i.e. 3 vs > 6 wildfires in the past 100 years). This presents a unique opportunity to predict how ecosystems will respond to increases in fire frequency that are occurring in Europe under climate change. My project, hosted by the School of Natural Sciences, Trinity College Dublin (TCD) and supervised by Professor Yvonne Buckley, capitalised on this opportunity to investigate the phenotypic and genomic basis underlying adaptation to changing fire regimes in European plant species.

This project used next-generation sequence data from two European species which are invasive in Australia: Ribwort plantain (Plantago lanceolata L., Plantaginaceae) and St John’s wort (Hypericum perforatum L., Clusiaceae)) to address four research objectives:

(i) Quantify the phenotypic distribution of fire-related seed traits in native and non-native ranges (WP1, WP2)
(ii) Quantify continental-scale genomic relationships among populations and identify the European sources of non-native samples (WP1, WP3)
(iii) Use landscape resistance models to analyse the influence of fire history, topography and climatic gradients on genomic structure in native and non-native ranges (WP1, WP3, WP4)
(iv) Integrate demographic population models into landscape resistance analysis to examine the relative contribution of environmental drivers and demography on genomic structure (WP1, WP3, WP5)
Strategic sampling (WP1): In 2018, I collected a total of 875 samples for DNA from six European species that are invasive in Australia, strategically across fire frequency gradients ranging from 0 to 5 fires in the last 50 years. Samples were also collected from Ireland, Spain and Romania as a baseline for genetic structure in the native range.

Seed trait experiments (WP2): In 2019, I conducted seed experiments using field-collected material from WP1 to quantify seed shape, seed weight and seed germination rate under different conditions. I wrote a preliminary report on the results to inform future seed germination work at TCD and the results are being used to interpret results being prepared for publication. Seeds from 520 individuals were weighed in the lab and seeds from 320 individuals were grown under different heat treatments in growth chambers at TCD.

Genotyping-by-sequencing (WP3): I produced genotypes for a total of 276 individuals from three species,from material collected during WP1: Plantago lanceolata, Cenchrus ciliaris and Hypericum perforatum. Samples were prepared by homogenising dried plant material in the lab at TCD. Sequencing was performed by Diversity Arrays Technology and data was analysed in WP4 and WP5.

Spatial genomics analysis (WP4): I developed an extensive library of scripts based on analysis of global genetic diversity in Plantago lanceolata at TCD (https://github.com/annabellisa/PLANTPOPNET_genetics). I used these scripts in the FIRESCAPE project to analyse spatial patterns of genetic diversity across fire frequency gradients using data collected in WP2 and WP3. These scripts have been archived in an open-access repository (PLANTPOPNET Genetics Release v1.1. Custom R scripts used in SNP filtering and analysis: DOI: stable Zenodo release).

Demographic landscape genomics (WP5): I developed a new analytical framework to analyse the influence of demographic parameters on genetic diversity (Smith et al. 2020, Proceedings of the National Academy of Sciences USA, accepted 10th Jan 2020). Specific data on fire related traits and genetic markers are currently being prepared for publication. I also published three papers during 2018 and 2019, related to the FIRESCAPE project (Smith, AL 2018, Fire 1: 42; Kelly, LT, et al. 2018, Fire 1: 29, Driscoll, DA, et al. 2019, Ecological Entomology doi.org/10.1111/een.12798).
Climate change and invasive species are driving shifts in fire regimes globally. These changes have already had profound changes on natural environments, leading to declines of plant and animal species and irreversible changes in ecosystem structure and function. In addition to these severe environmental costs, adapting policy and management to these fire regime changes comes at a huge public expense.

There is ample evidence that invasive species can undergo rapid evolution in new environments but no research had previously examined rapid evolution of fire-adaptive traits in invasive species. This is surprising considering that invasive species can alter fire regimes when they change fuel properties (e.g. increased connectivity among individual plants) and when fire promotes their establishment and growth. The result is a positive ecological feedback, whereby the invasion process accelerates and fire frequency and/or intensity increases, sometimes beyond the level where native vegetation can recover. Thus, it is has long been clear that invasive species can alter fire regimes by changing fuel properties but it has remained unknown whether adaptation of fire-related traits contributes to these changes.

Results from this project will ultimately inform fire management by revealing whether microevolution of fire adaptive traits contributes to fire regime shifts. This information will help to reduce the risk of fire management decision making. For example, the species examined in this study are not generally considered to contribute strongly to fire fuel loads. My project is helping to determine the likelihood that this kind of positive ecological feedback will occur in future. Fire might assist invasion by reducing competition, meaning that traits that promote fire spread (e.g. increased fine fuel flammability) and post-fire reproduction (e.g. heat resistant seed) will be selected for under a regime of frequent fire. If repeated burning promotes adaptations for species to survive or promote recurrent fire, reducing prescribed burning in areas where invasive species dominate will help to reduce the risk of further invasion while also saving management costs.
Dr Smith (right) at EU Researchers Night with a display about the influence of fire on plants