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bioRxiv · 10.64898/2025.12.31.697164

Stabilising selection and ecological trade-offs underpin coexistence in a tropical flora

Niissalo, M. A.·Lim, J. Y.·Ngiam, J. J.·Rajaraman, S.·Choo, L. M.·Jong, J. J. Y.·Ngo, K. M.·Leong, F. W. S.·Lum, S. K. Y.·Beentje, H. J.·Buerki, S.·Callmander, M. W.·Chen, J.·Chua, M. S. E.·De Kok, R. P. J.·De Wilde-Duyfjes, B. E. E.·Duistermaat, H.·Esser, H.-J.·Fleck, S.·Ganesan, S. K.·Gardner, E. M.·Hughes, M.·Koh, S. L.·Leong, P. K. F.·Leong-Skornickova, J.·Lindsay, S.·Low, Y. W.·Lua, H. K.·Neo, L.·Pannell, C. M.·Puglisi, C.·Rodda, M. L.·Savinov, I. A.·Seah, W. W.·Simpson, D. A.·Strijk, J. S.·Thomas, D. C.·Turner, I. M.·van Welzen, P. C.·Wilkie, P.·Wo
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Abstract

Tropical forests harbour the majority of global plant biodiversity1,2, yet the genomic mechanisms governing the assembly and maintenance of these communities remain poorly understood. Here, we assembled draft genomes for 499 angiosperm species from a lowland rainforest in Singapore, representing 67% of its flora, and integrated these with plant traits and comprehensive forest census data. Across the community, most gene families evolve under stabilising selection, with copy numbers maintained near long-term optima that differ among ecological strategies. These niche-associated genomic attractor states provide a mechanism for convergent adaptation and species coexistence. Modelling stabilising selection also identified a strong trade-off between defence and growth, indicating that pathogen pressure constrains developmental diversification. Consistent with this, species-specific genome space was enriched for resistance genes and transposable elements. In contrast, genomic processes structuring present-day plant community composition differ from those driving deep-time convergence. Genomic comparisons across forest types revealed stronger selection on defence-related pathways in old-growth primary forests and on growth-related processes in regenerating secondary forests, while community-level genomic profiles showed expansions in gene families associated with rapid responses to environmental fluctuations. Stabilising selection therefore links population-level adaptation3,4 with long-term species diversification in the tropics. Niche similarity promotes long-term coexistence, whereas local community structure is shaped by more rapid ecological filtering driven by environmental change. Taken together, these two distinct evolutionary layers provide a genomic framework for understanding how hyperdiverse rainforest floras arise and persist.

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Niissalo, M. A., Lim, J. Y., Ngiam, J. J., Rajaraman, S., Choo, L. M., Jong, J. J. Y., Ngo, K. M., Leong, F. W. S., Lum, S. K. Y., Beentje, H. J., Buerki, S., Callmander, M. W., Chen, J., Chua, M. S. E., De Kok, R. P. J., De Wilde-Duyfjes, B. E. E., Duistermaat, H., Esser, H.-J., Fleck, S., Ganesan, S. K., Gardner, E. M., Hughes, M., Koh, S. L., Leong, P. K. F., Leong-Skornickova, J., Lindsay, S., Low, Y. W., Lua, H. K., Neo, L., Pannell, C. M., Puglisi, C., Rodda, M. L., Savinov, I. A., Seah, W. W., Simpson, D. A., Strijk, J. S., Thomas, D. C., Turner, I. M., van Welzen, P. C., Wilkie, P., Wo. 2025-12-31. Stabilising selection and ecological trade-offs underpin coexistence in a tropical flora. https://doi.org/10.64898/2025.12.31.697164

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