Dr Maddie James
Research Fellow
School of the Environment
Researcher biography
I am a population geneticist specialising in natural plant systems. I explore systems of parallel evolution, where similar phenotypes have evolved independently in response to similar environmental pressures, to understand how repeatable and predictable evolutionary outcomes are. My research integrates large-scale genomic data with extensive field experiments and phenotypic measurements to uncover the genetic architectures underlying plant adaptation.
Areas of interest: - Adaptation and specition - Chromosomal inversions and recombination rate evolution - Pangenomics - Linking genotype-phenotype-fitness - Applying evolutionary genomics to crop breeding systems
Book Chapter
James, Maddie E. and Ortiz-Barrientos, Daniel (2025). Genetic Basis of Adaptation. Reference Module in Life Sciences. (pp. 1-1) Amsterdam, Netherlands: Elsevier. doi: 10.1016/b978-0-443-15750-9.00112-9
Journal Articles
Zhou, Meikun, James, Maddie E., Engelstädter, Jan and Ortiz-Barrientos, Daniel (2026). Chimeric reference panels for genomic imputation. Genetics, 232 (1) iyaf212, 1-16. doi: 10.1093/genetics/iyaf212
James, Maddie E. (2025). Pangenomics in the
Mimulus guttatus
Species Complex. Molecular Ecology Resources, 26 (1) e70087, e70087. doi: 10.1111/1755-0998.70087
James, Maddie E., Melo, Maria C., Roda, Federico, Bernal‐Franco, Diana, Wilkinson, Melanie J., Walter, Gregory M., Liu, Huanle, Engelstädter, Jan and Ortiz‐Barrientos, Daniel (2025). Ecological and mutation‐order speciation in Senecio. Molecular Ecology, 34 (22) e70090, e70090. doi: 10.1111/mec.70090
Macdonald, Arlie R., James, Maddie E., Mitchell, Jonathan D. and Holland, Barbara R. (2025). From trees to traits: a review of advances in PhyloG2P methods and future directions. Genome Biology and Evolution, 17 (9) evaf150, 1-18. doi: 10.1093/gbe/evaf150
James, Maddie E. and Ortiz‐Barrientos, Daniel (2024). The genomic consequences of selection across development. Molecular Ecology, 33 (4) e17280, e17280. doi: 10.1111/mec.17280
James, Maddie E., Allsopp, Robin N., Groh, Jeffrey S., Kaur, Avneet, Wilkinson, Melanie J. and Ortiz‐Barrientos, Daniel (2023). Uncovering the genetic architecture of parallel evolution. Molecular Ecology, 32 (20), 5575-5589. doi: 10.1111/mec.17134
James, Maddie E., Brodribb, Tim, Wright, Ian J., Rieseberg, Loren H. and Ortiz-Barrientos, Daniel (2023). Replicated evolution in plants. Annual Review of Plant Biology, 74 (1), 697-725. doi: 10.1146/annurev-arplant-071221-090809
Wilkinson, Melanie J., Yamashita, Risa, James, Maddie E., Bally, Ian S. E., Dillon, Natalie L., Ali, Asjad, Hardner, Craig M. and Ortiz-Barrientos, Daniel (2022). The influence of genetic structure on phenotypic diversity in the Australian mango (Mangifera indica) gene pool. Scientific Reports, 12 (1) 20614, 1-13. doi: 10.1038/s41598-022-24800-7
James, Maddie E., O'Brien, Nicholas L. V. and Bukkuri, Anuraag (2022). Digest: Stable phenotypes, fluid genotypes: how stochasticity impacts network evolution and speciation. Evolution, 76 (4), 821-823. doi: 10.1111/evo.14452
Wilkinson, Melanie J., Roda, Federico, Walter, Greg M., James, Maddie E., Nipper, Rick, Walsh, Jessica, Allen, Scott L., North, Henry L., Beveridge, Christine A. and Ortiz-Barrientos, Daniel (2021). Adaptive divergence in shoot gravitropism creates hybrid sterility in an Australian wildflower. Proceedings of the National Academy of Sciences, 118 (47) e2004901118, e2004901118. doi: 10.1073/pnas.2004901118
James, Maddie E., Wilkinson, Melanie J., Bernal, Diana M., Liu, Huanle, North, Henry L., Engelstädter, Jan and Ortiz‐Barrientos, Daniel (2021). Phenotypic and genotypic parallel evolution in parapatric ecotypes of Senecio. Evolution, 75 (12), 3115-3131. doi: 10.1111/evo.14387
Parry, Rhys, James, Maddie E. and Asgari, Sassan (2021). Uncovering the worldwide diversity and evolution of the virome of the mosquitoes Aedes aegypti and Aedes albopictus. Microorganisms, 9 (8) 1653, 1653. doi: 10.3390/microorganisms9081653
James, Maddie E., Arenas-Castro, Henry, Groh, Jeffrey S., Allen, Scott L., Engelstädter, Jan and Ortiz-Barrientos, Daniel (2021). Highly replicated evolution of parapatric ecotypes. Molecular Biology and Evolution, 38 (11), 4805-4821. doi: 10.1093/molbev/msab207
Ortiz-Barrientos, D. and James, M. E. (2017). Evolution of recombination rates and the genomic landscape of speciation. Journal of Evolutionary Biology, 30 (8), 1519-1521. doi: 10.1111/jeb.13116
Walter, Greg M., Wilkinson, Melanie J., James, Maddie E., Richards, Thomas J., Aguirre, J. David and Ortiz-Barrientos, Daniel (2016). Diversification across a heterogeneous landscape. Evolution, 70 (9), 1979-1992. doi: 10.1111/evo.13009
Roda, Federico, Liu, Huanle, Wilkinson, Melanie J., Walter, Gregory M., James, Maddie E., Bernal, Diana M., Melo, Maria C., Lowe, Andrew, Rieseberg, Loren H., Prentis, Peter and Ortiz-Barrientos, Daniel (2013). Convergence and divergence during the adaptation to similar environments by an Australian groundsel. Evolution, 67 (9), 2515-2529. doi: 10.1111/evo.12136
Thesis
James, Maddie (2021). The nature of parallel evolution. PhD Thesis, School of Biological Sciences, The University of Queensland. doi: 10.14264/f9e2a5c
Data Collections
Allsopp, Robin, James, Maddie, Ortiz-Barrientos, Daniel, Wilkinson, Melanie, Groh, Jeffrey and Kaur, Avneet (2023). Data associated with publication: James et al. "Uncovering the genetic architecture of parallel evolution". The University of Queensland. (Dataset) doi: 10.48610/40dec7a
Wilkinson, Melanie J., Roda, Federico, Walter, Greg M., James, Maddie E., Nipper, Rick, Walsh, Jessica, Allen, Scott L., North, Henry L., Beveridge, Christine A. and Ortiz-Barrientos, Daniel (2021). Data associated with forthcoming publication - Wilkinson et al. 2021 - "Adaptive divergence in shoot gravitropism creates hybrid sterility in an Australian wildflower". The University of Queensland. (Dataset) doi: 10.48610/2c603c6