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| Gillespie LE, Ruffley M, Exposito-Alonso M. (2024) Deep learning models map rapid plant species changes from citizen science and remote sensing data. Proceedings of the National Academy of Sciences of the United States of America. 121: e2318296121 |
| Luiselli J, Overcast I, Rominger A, et al. (2024) Detecting the ecological footprint of selection. Plos One. 19: e0302794 |
| Exposito-Alonso M, Booker TR, Czech L, et al. (2022) Genetic diversity loss in the Anthropocene. Science (New York, N.Y.). 377: 1431-1435 |
| Lagerstrom KM, Vance S, Cornwell BH, et al. (2022) From coral reefs to Joshua trees: What ecological interactions teach us about the adaptive capacity of biodiversity in the Anthropocene. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 377: 20210389 |
| Ruffley M, Smith ML, Espíndola A, et al. (2022) Genomic evidence of an ancient Inland Temperate Rainforest in the Pacific Northwest of North America. Molecular Ecology |
| Peterson K, Ruffley M, Parent CE. (2021) Phylogenetic diversity and community assembly in a naturally fragmented system. Ecology and Evolution. 11: 18066-18080 |
| Overcast I, Ruffley M, Rosindell J, et al. (2021) A unified model of species abundance, genetic diversity, and functional diversity reveals the mechanisms structuring ecological communities. Molecular Ecology Resources |
| Ruffley M, Peterson K, Week B, et al. (2019) Identifying models of trait-mediated community assembly using random forests and approximate Bayesian computation. Ecology and Evolution. 9: 13218-13230 |
| Sullivan J, Smith ML, Espíndola A, et al. (2019) Integrating life history traits into predictive phylogeography. Molecular Ecology |
| Ruffley M, Smith ML, Espíndola A, et al. (2018) Combining allele frequency and tree-based approaches improves phylogeographic inference from natural history collections. Molecular Ecology |