Project highlights

  1. New research aimed at uncovering the genomic adaptations driving the shift between annual and perennial growth. 
  2. A collaborative supervisory network across multiple institutes, offering access to cutting-edge technology and fostering broader collaboration opportunities. 
  3. An integration of diverse skills, including laboratory work, computational analysis, and field-based methodologies. 

Overview

Biological invasions pose a significant threat to global biodiversity, with profound impacts on ecosystems. However, invasions also offer unique opportunities for large-scale natural experiments to investigate ecological and evolutionary processes in real-world settings. While there is an extensive body of ecological research and an increasing number of evolutionary studies on invasive species, functional genetic and genomic approaches have been less commonly applied in this field until recently. Beyond the use of neutral markers to analyze population structure, there is still relatively little known about the genomic innovations that contribute to the success of invasive plant species. To address this gap, this project will focus on Alliaria petiolata, an invasive herbaceous plant capable of shifting between annual and perennial growth. This species has also been the subject of studies on secondary metabolite production and its impact on soil microbiota, particularly in suppressing mycorrhizal fungi in plant roots. Despite these studies, the genomic basis for the species’ developmental plasticity and its ecological impacts remains largely unexplored. The aim of this research is to integrate ecological and population-level analyses with advanced genomic tools to uncover the molecular mechanisms underlying the adaptive success of Alliaria petiolata. By investigating the interplay between ecological dynamics and genomic adaptations, this study will provide new insights into the developmental flexibility and invasive potential of the species. This integrated approach will contribute to a more comprehensive understanding of the factors driving biological invasions, bridging the gap between population ecology and functional genomics. 

Host

University of Warwick

Theme

  • Organisms and Ecosystems

Supervisors

Project investigator

Co-investigators

How to apply

Methodology

We will use a multi-step methodology to investigate the genetic and molecular mechanisms associated with growth behaviour in Alliaria petiolata. First, they will perform genomic analysis by collecting plant samples from both native (EU) and invasive (USA) populations. DNA will be extracted, and sequencing libraries will be prepared for high-throughput sequencing. The resulting data will undergo bioinformatic analysis to assemble their genomes, and identify genomic variations, followed by model generation to understand evolutionary patterns, Next, the student will conduct field studies to collect data on various Alliaria petiolata populations. Using molecular markers such as SSRs or SNPs, they will analyse genetic diversity, population structure, and population dynamics. This molecular data will be critical for understanding the spread and adaptation of the species. In controlled growth conditions, the student will study the plant’s reproductive behaviour under different environmental scenarios. They will use genome-wide association studies (GWAS) and epigenome analysis to identify the molecular mechanisms driving the transition from annual to perennial growth. This integrated approach will reveal the genetic and epigenetic factors influencing life cycle variation in this species. 

Training and skills

DRs will be awarded CENTA Training Credits (CTCs) for participation in CENTA-provided and ‘free choice’ external training. One CTC can be earned per 3 hours training, and DRs must accrue 100 CTCs across the three and a half years of their PhD.  

Training during this fellowship includes a wide range of molecular techniques and analyses (DNA extraction, genomic library construction and sequencing, and bioinformatics) as well as population analyses (Genetic diversity, population structure and dynamics). Field-based sampling and measurements from different ecosystems will also be emphasized with additional training opportunities through collaboration with CEH scientists.  

Partners and collaboration

Prof. Jose Gutierrez-Marcos leads a research team interested in the genomic and epigenomic analysis of acquired adaptations in plants. Dr. Stephen Caverns leads a team interested in the study of genetic diversity, gene flow and adaptation in plants. Prof. Robin Allaby leads a team interested in understanding the evolution of domestication in plants, working with archaeologists, developing and using archaeogenomic techniques and connecting archaeological data with genetics through computational models. 

Further details

For any enquiries related to this project please contact Prof. Jose Gutierrez-Marcos, University of Warwick, [email protected].  

To apply to this project:  

  • You must include a CV with the names of at least two referees (preferably three) who can comment on your academic abilities.  

 Applications must be submitted by 23:59 GMT on Wednesday 8th January 2025.  

Possible timeline

Year 1

Genomic analysis of Alliaria petiolate collected from native (EU) and invasive (USA). Sample, collection, preparation of sequencing libraries, bioinformatic analysis and generation of models.

Year 2

Seasonal field measurements from different Alliaria petiolate populations. Collection of samples for molecular analysis using molecular markers for the determination of genetic diversity, population structure and dynamics.

Year 3

Evaluation of Alliaria petiolate reproductive behaviour under different environments using controlled growth conditions. Use genome/epigenome-association analysis to determine the molecular bases underpinning the conversion of annual to perennial growth in this species.

Further reading

  1. Catford, J. A., Jansson, R., & Nilsson, C. (2009) ‘Reducing redundancy in invasion ecology by integrating hypotheses into a single theoretical framework’, Diversity and Distributions, 15(1), pp. 22-40. 
  2. Liao, C., Peng, R., Luo, Y., Zhou, X., Wu, X., Fang, C., … & Li, B. (2008) ‘Altered ecosystem carbon and nitrogen cycles by plant invasion: A meta‐analysis’, New Phytologist, 177(3), pp. 706-714. 
  3. Matheson, P. and McGaughran, A. (2022) ‘Genomic data is missing for many highly invasive species, restricting our preparedness for escalating incursion rates’, Scientific Reports, 12, 13987. 
  4. McGaughran, A., Dhami, M.K., Parvizi, E., Vaughan, A.L., Gleeson, D.M., Hodgins, K.A., Rollins, L.A., Tepolt, C.K., Turner, K.G., Atsawawaranunt, K., Battlay, P., Congrains, C., … and Wilson, J. (2024) ‘Genomic tools in biological invasions: Current state and future frontiers’, Genome Biology and Evolution, 16(1), evad230. 
  5. Mounger, J., Ainouche, M.L., Bossdorf, O., Cavé-Radet, A., Li, B., Parepa, M., Salmon, A., Yang, J. and Richards, C.L. (2021) ‘Epigenetics and the success of invasive plants’, Philosophical Transactions of the Royal Society B: Biological Sciences, 376, 20200117. 
  6. Pyšek, P., Jarošík, V., Hulme, P.E., Pergl, J., Hejda, M., Schaffner, U. and Vilà, M. (2012) ‘A global assessment of invasive plant impacts on resident species, communities, and ecosystems: the interaction of impact measures, invading species’ traits, and environment’, Global Change Biology, 18(5), pp. 1725-1737. 
  7. van Kleunen, M., Dawson, W., Schlaepfer, D., Jeschke, J. M., & Fischer, M. (2010) ‘Are invaders different? A conceptual framework of comparative approaches for assessing determinants of invasiveness’, Ecology Letters, 13(8), pp. 947-958. 
  8. Vilà, M., Espinar, J.L., Hejda, M., Hulme, P.E., Jarošík, V., Maron, J.L., … and Pyšek, P. (2011) ‘Ecological impacts of invasive alien plants: a meta‐analysis of their effects on species, communities, and ecosystems’, Ecology Letters, 14(7), pp 702-708.