The Frequency and Importance of Polyploidy in Tropical Rainforest Tree Radiations

Abstract

[Abstract] The presence of more than two copies of the genome in an organism, termed ‘polyploidy’, is a crucial force in plant evolution, generating genetic, phenotypic and ecological diversity. [Correction added on 22 January 2026, after first online publication: the preceding sentence has been corrected.] The Amazonian tree flora is the most species-rich on Earth and largely arose as a result of rapid evolutionary radiations. While polyploidy is an important catalyst of rapid radiations, it remains poorly studied in tropical tree radiations. We examined ploidy variation across Inga (Fabaceae), a characteristic Amazonian tree radiation, using DNA-sequence data from 1305 loci for 189/282 Inga species. We then tested whether polyploid species experience more positive selection than diploids, particularly in loci underlying chemical defence against herbivory, which is a key ecological pressure affecting rainforest tree diversification. We show that tetraploidy occurs in 15% (n = 29) of the Inga species we studied, with several widespread species showing geographical ploidy variation, alongside minimal phylogenetic signal in ploidy which suggests recurrent polyploidisation. Interestingly, we found more loci under selection in polyploids than in diploids, most notably in chemical defence loci. Our results show that polyploidy has arisen independently in several Inga species, and that polyploidisation can lead to elevated selection in chemical defence, helping to shape ecological interactions and influence diversification in Inga.