Dr Melanie Wilkinson
Affiliate of ARC COE for Plant Success in Nature and Agriculture
ARC COE for Plant Success in Nature and Agriculture
Senior Research Fellow
Queensland Alliance for Agriculture and Food Innovation
Researcher biography
Plant geneticist specialising in predictive breeding and evolutionary genetics, Melanie's research focuses on accelerating crop improvement by integrating genomics and predictive modelling across both horticultural and field crops.
Her recent work includes uncovering the role of chromosomal inversions in driving variation in mango breeding traits, the ensemble of genomic prediction methods through the EasiGP framework, and integrating APSIM crop growth models with genomic prediction for soybean and sorghum.
Melanie leads interdisciplinary collaborations combining quantitative genetics, machine learning, and crop modelling, with active partnerships across industry and international research institutions.
Journal Articles
Tomura, Shunichiro, Powell, Owen, Wilkinson, Melanie J and Cooper, Mark (2026). Ensembles of Graph Attention Networks Supervised by Genotype-to-Phenotype Structures Improved Genomic Prediction Performance. in silico Plants, 8 (1) diag014, 1. doi: 10.1093/insilicoplants/diag014
Tomura, Shunichiro, Powell, Owen, Wilkinson, Melanie J, Lefvre, James and Cooper, Mark (2026). Optimisation of Weighted Ensembles of Genomic Prediction Models in Maize. in silico Plants, 8 (1) diag010. doi: 10.1093/insilicoplants/diag010
Tomura, Shunichiro, Powell, Owen, Wilkinson, Melanie J and Cooper, Mark (2026). Ensemble-based genomic prediction for maize flowering-time improves prediction accuracy and reveals novel insights into trait genetic variation. G3: Genes, Genomes, Genetics, 16 (6) jkag090. doi: 10.1093/g3journal/jkag090
Ahmad, Bilal, Su, Ying, Arshad, Rida, Razzaq, Tayyaba, Zhang, Yi, Hou, Ting, Li, Chaochao, Jin, Zhongxin, Chen, Chengjie, Wang, Peng, Wilkinson, Melanie J., Bai, Yibo, Chen, Yeyuan, Zhang, Yu, Dang, Zhiguo, Zhou, Yongfeng, Tian, Xinmin and Huang, Jianfeng (2026). Integrative genomics for mango genetics and breeding. Horticulture Research, 13 (1) uhaf260. doi: 10.1093/hr/uhaf260
Tomura, Shunichiro, Wilkinson, Melanie J., Powell, Owen and Cooper, Mark (2025). Ensemble AnalySis with Interpretable Genomic Prediction (EasiGP): Computational tool for interpreting ensembles of genomic prediction models. The Plant Genome, 18 (4) e70138, 1-16. doi: 10.1002/tpg2.70138
Munyengwa, Norman, Wilkinson, Melanie J., Ortiz-Barrientos, Daniel, Dillon, Natalie L., Webb, Matthew, Ali, Asjad, Bally, Ian S. E., Myburg, Alexander A. and Hardner, Craig M. (2025). Increased genomic predictive ability in mango using GWAS-preselected variants and fixed-effect SNPs. Frontiers in Plant Science, 16 1664012, 1-21. doi: 10.3389/fpls.2025.1664012
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
Broad, Zoe, Lefreve, James, Wilkinson, Melanie J., Barton, Samuel, Barbier, Francois, Jung, Hyungtaek, Donovan, Diane and Ortiz‐Barrientos, Daniel (2025). Gravitropic gene expression divergence associated with adaptation to contrasting environments in an Australian wildflower. Molecular Ecology, 34 (15) e17543, 1-18. doi: 10.1111/mec.17543
Cooper, Mark, Tomura, Shunichiro, Wilkinson, Melanie J., Powell, Owen and Messina, Carlos D. (2025). Breeding perspectives on tackling trait genome-to-phenome (G2P) dimensionality using ensemble-based genomic prediction. Theoretical and Applied Genetics, 138 (7) 172, 1-24. doi: 10.1007/s00122-025-04960-6
Tomura, Shunichiro, Wilkinson, Melanie J., Cooper, Mark and Powell, Owen (2025). Improved Genomic Prediction Performance with Ensembles of Diverse Models. G3: Genes, Genomes, Genetics, 15 (5) jkaf048, 1-15. doi: 10.1093/g3journal/jkaf048
Wilkinson, Melanie J., McLay, Kathleen, Kainer, David, Elphinstone, Cassandra, Dillon, Natalie L., Webb, Matthew, Wijesundara, Upendra K., Ali, Asjad, Bally, Ian S. E., Munyengwa, Norman, Furtado, Agnelo, Henry, Robert J., Hardner, Craig M. and Ortiz‐Barrientos, Daniel (2025). Centromeres are hotspots for chromosomal inversions and breeding traits in mango. New Phytologist, 245 (2), 899-913. doi: 10.1111/nph.20252
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
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
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
Walter, Greg M., Richards, Thomas J., Wilkinson, Melanie J, Blows, Mark W., Aguirre, J. David and Ortiz‐Barrientos, Daniel (2020). Loss of ecologically important genetic variation in late generation hybrids reveals links between adaptation and speciation. Evolution Letters, 4 (4) evl3.187, 302-316. doi: 10.1002/evl3.187
Walter, Greg M., Wilkinson, Melanie J., Aguirre, J. David, Blows, Mark W. and Ortiz-Barrientos, Daniel (2018). Environmentally induced development costs underlie fitness tradeoffs. Ecology, 99 (6), 1391-1401. doi: 10.1002/ecy.2234
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
Conference Paper
Takagi, T., Hong, H. T., Dillon, N., Wilkinson, M. J. and O’Hare, T. J. (2025). Identifying key genes controlling flesh colour in mangoes using genome-wide association studies (GWAS). XIII International Mango Symposium, Malaga, Spain, 29 September - 3 October 2023. Leuven, Belgium: International Society for Horticultural Science. doi: 10.17660/ActaHortic.2025.1415.28
Thesis
Wilkinson, Melanie (2019). The genetic basis of adaptive evolution and divergence in an Australian wildflower. PhD Thesis, School of Biological Sciences, The University of Queensland. doi: 10.14264/uql.2019.338
Data Collections
Wilkinson, Melanie (2024). Centromeres are hotspots for chromosomal inversions and breeding traits in mango. The University of Queensland. (Dataset) doi: 10.48610/1819a7b
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