Publications

Last updated: March 17, 2025

Our lab's research appears in diverse journals covering ecological, evolutionary, and computational topics. Below are our publications organized by research themes, followed by a chronological list of all publications.

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Recent Publications

2025

  • Dinnage, R. and Kleineberg, M. (2025). Generative AI helps extract ecological meaning from the complex three dimensional shapes of bird bills. PLoS Computational Biology. In Press.
  • Simonsen, A., and Dinnage, R. (2025). Rhizobia mutualists contribute to phylogenetic clustering and legume community assembly globally. Journal of Ecology. 00:1–14.

2024

  • Galán-Acedo, C., Verde Arregoitia, L.D., Arasa-Gisbert, R., Auliz-Ortiz, D., Saldivar-Burrola, L.L., Gouveia, S.F., Correia, I., Rosete-Vergés, F.A., Dinnage, R. and Villalobos, F. (2024). Global primary predictors of extinction risk in primates. Proceedings of the Royal Society B. 291, no. 2032: 20241905.
  • Dinnage, R., Sarre, S.D., Duncan, R.P., Dickman, C.R., Edwards, S.V., Greenville, A.C., Wardle, G.M. and Gruber, B. (2024). slimr: An R package for tailor‐made integrations of data in population genomic simulations over space and time. Molecular Ecology Resources, 24(3), e13916.

Publications by Research Theme

Foundation Models & Biological Understanding

  • Dinnage, R. (2024). NicheFlow: Towards a foundation model for Species Distribution Modelling. bioRxiv, 2024-10. doi: https://doi.org/10.1101/2024.10.15.618541 (Revising for special issue of Methods in Ecology and Evolution)
  • Dinnage, R. (2023). How many variables does Wordclim have, really? Generative AI unravels the intrinsic dimension of bioclimatic variables. bioRxiv, doi: https://doi.org/10.1101/2023.06.12.544623. (Revising for Ecology)
  • Dinnage, R. and Kleineberg, M. (2025). Generative AI helps extract ecological meaning from the complex three dimensional shapes of bird bills. PLoS Computational Biology. In Press.

High-Throughput Phenomics & Digital Specimens

  • Dinnage, R., Grady, E., Neal, N., Deck, J., Denny, E., Walls, R., Seltzer, C., Guralnick, R. and Li, D. (2024). PhenoVision: A framework for automating and delivering research-ready plant phenology data from field images. bioRxiv, 2024-10. doi: https://doi.org/10.1101/2024.10.10.617505 (Under review at Methods in Ecology and Evolution)

Phylogenetic Comparative Methods

  • Dinnage, R., Skeels, A., & Cardillo, M. (2020). Spatiophylogenetic modelling of extinction risk reveals evolutionary distinctiveness and brief flowering period as threats in a hotspot plant genus. Proceedings of the Royal Society B, 287(1926), 20192817.
  • Cardillo, M., Skeels, A., & Dinnage, R. (2023). Priorities for conserving the world's terrestrial mammals based on over-the-horizon extinction risk. Current Biology, 33(7), 1381-1388.
  • Machado, F. F., Jardim, L., Dinnage, R., Brito, D., & Cardillo, M. (2023). Diet disparity and diversity predict extinction risk in primates. Animal Conservation, 26(3), 331-339.

Phylogenetic Community Ecology

  • Cadotte, M.W., Dinnage, R. and Tilman, D. (2012). Phylogenetic diversity promotes ecosystem stability. Ecology, 93: S223-S233.
  • Dinnage, R., Cadotte, M. W., Haddad, N. M., Crutsinger, G. M., & Tilman, D. (2012). Diversity of plant evolutionary lineages promotes arthropod diversity. Ecology Letters, 15(11), 1308-1317.
  • Dinnage R. (2009). Disturbance alters the phylogenetic composition and structure of plant communities in an old field system. PLoS ONE 4(9): e7071.
  • Simonsen, A., and Dinnage, R. (2025). Rhizobia mutualists contribute to phylogenetic clustering and legume community assembly globally. Journal of Ecology. 00:1–14.

Species Distribution Modelling

  • Li, D, Dinnage, R, Nell, LR, Helmus, MR, Ives, AR. (2020). phyr: An r package for phylogenetic species-distribution modelling in ecological communities. Methods in Ecology and Evolution. 11: 1455–1463.
  • Warren, D.L., Matzke, N.J., Cardillo, M., Baumgartner, J.B., Beaumont, L.J., Turelli, M., Glor, R.E., Huron, N.A., Simões, M., Iglesias, T.L., Piquet, J.C. and Dinnage, R. (2021). ENMTools 1.0: an R package for comparative ecological biogeography. Ecography, 44: 504-511.
  • Cardillo, M, Dinnage, R., McAlister, W. (2019). The relationship between environmental niche breadth and geographic range size across plant species. Journal of Biogeography. 46: 97–109.
  • Dinnage, R., Simonsen, A. K., Barrett, L. G., Cardillo, M., Raisbeck‐Brown, N., Thrall, P. H., & Prober, S. M. (2019). Larger plants promote a greater diversity of symbiotic nitrogen‐fixing soil bacteria associated with an Australian endemic legume. Journal of Ecology, 107(2), 977-991.

Cultural Comparative Analysis

  • Bromham, L., Dinnage, R., Skirgård, H. et al. (2022). Global predictors of language endangerment and the future of linguistic diversity. Nature Ecology & Evolution. 6, 163–173.
  • Bromham, L., Skeels, A., Schneemann, H., Dinnage, R., & Hua, X. (2021). There is little evidence that spicy food in hot countries is an adaptation to reducing infection risk. Nature Human Behaviour, 5(7), 878-891.
  • Bromham, L., Dinnage, R. & Hua, X. (2016). Interdisciplinary research has consistently lower funding success. Nature 534, 684–687.
  • Skirgård, H., Haynie, H.J., Blasi, D.E., Hammarström, H., Collins, J., Latarche, J.J., Lesage, J., Weber, T., Witzlack-Makarevich, A., Passmore, S., Chira, A., Maurits, L., Dinnage, R., et al. (2023). Grambank reveals the importance of genealogical constraints on linguistic diversity and highlights the impact of language loss. Science Advances, 9(16), eadg6175.

Simulation and Theoretical EEB

  • Dinnage, R., Sarre, S.D., Duncan, R.P., Dickman, C.R., Edwards, S.V., Greenville, A.C., Wardle, G.M. and Gruber, B. (2024). slimr: An R package for tailor‐made integrations of data in population genomic simulations over space and time. Molecular Ecology Resources, 24(3), e13916.
  • Hill, P., Dickman, C.R., Dinnage, R., Duncan, R.P., Edwards, S.V., Greenville, A., Sarre, S.D., Stringer, E.J., Wardle, G.M., & Gruber, B. (2023). Episodic population fragmentation and gene flow reveal a trade-off between heterozygosity and allelic richness. Molecular Ecology, 32(24), 6766-6776.
  • Abrams, P. A., Rueffler, C., & Dinnage, R. (2008). Competition-similarity relationships and the nonlinearity of competitive effects in consumer-resource systems. The American Naturalist, 172(4), 463-474.

Citations and Impact

Total Citation Count: 2893
H-index: 19
i10-index: 22
Mean Citations per Article: ~103

Preprints

  • Dinnage, R. (2024). NicheFlow: Towards a foundation model for Species Distribution Modelling. bioRxiv, 2024-10. doi: https://doi.org/10.1101/2024.10.15.618541
  • Dinnage, R., Grady, E., Neal, N., Deck, J., Denny, E., Walls, R., Seltzer, C., Guralnick, R. and Li, D. (2024). PhenoVision: A framework for automating and delivering research-ready plant phenology data from field images. bioRxiv, 2024-10. doi: https://doi.org/10.1101/2024.10.10.617505
  • Dinnage, R. (2023). How many variables does Wordclim have, really? Generative AI unravels the intrinsic dimension of bioclimatic variables. bioRxiv, doi: https://doi.org/10.1101/2023.06.12.544623