Does hybridisation promote tree species diversification in the Amazon?

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The Amazon rain forest holds the highest diversity of plant species on Earth, but the mechanisms which gave rise to this superlative diversity remain enigmatic. A long-held view, first proposed by Alfred Russell Wallace, was that this diversity reflected gradual accumulation of species over long geological periods due to minimal extinction. However, more recent studies point to a large contribution of rapid and recent formation of new species of some groups of trees. Inga, the focus of this proposal, is an exemplar for these recent evolutionary radiations, having evolved at least 300 species in the last 6 million years in the Amazon and other Latin American rain forests. Moreover, in Amazonia hundreds of tree species can coexist in a single hectare (up to 300), and this extremely high local diversity is largely accounted for by a few species-rich genera such as Inga. The high overall and local diversity of Amazonian forests suggests parallels with other species-rich systems where evolutionary radiation - the rapid rise of many species from one ancestor population - produced many new lineages. Here, we aim to develop Inga as a model for plant species radiation in Amazonia, building global examples beyond animals (e.g. Darwin's finches, rift lake cichlid fishes) and a few plant groups that are geographically restricted (e.g. Hawaiian silverswords), or non-tropical (e.g. Andean lupins).In particular, we will investigate the role of hybridization, the interbreeding between groups of species, as recent work shows it is a major cause of evolutionary radiations. Hybridization's effect on evolutionary radiation has not yet been studied within tropical trees, despite being widely acknowledged as a powerful creative force in plant evolution. Hybridization generates morphological and genetic novelty, impacting the rate of speciation in many groups and is evident in all major adaptive radiation events for which multiple sequenced genomes exist. In plants, one mechanism of speciation, polyploidy or the doubling of genome size, which is often linked with hybridisation, is known to be particularly important. While the prevailing view has been that hybridization between tropical tree species is exceptionally rare, this view is challenged by recent DNA sequence data. In Inga, hybridization has been recently demonstrated to occur, despite prior reports of species intersterility, and a few chromosome counts have demonstrated that unrelated species are polyploid. Here, using new genomic techniques for the first time in Amazonian trees, we aim to test the significance of hybridization and polyploidy in Inga diversification. We will use DNA sequences for 810 genes generated by the target capture technique to find signatures of hybridisation and polyploidy across all 300 Inga species. Because insect herbivore pressure demonstrably structures local Inga communities at fine spatial scales, we suspect that a powerful selective factor driving divergence among Inga species may be chemical defences. We will therefore search for signatures of selection among 113 chemical defence gene regions in our target capture gene set. We will then generate whole-genome data for multiple populations of a select number of widespread Inga species to determine whether groups of chemical defence genes are transferred together during hybridization in 'linkage blocks', thereby facilitating the movement of adaptive variation between species. Finally, we will use our target capture data to identify possible polyploid Inga species and use genome sequencing to discover if they are the result of hybridisation and genome doubling (allopolyploidy) or genome doubling without hybridisation (autopolyploidy).This project will improve our understanding of the evolution of a large portion of Amazonian tree diversity, because Inga is an exemplar for other species-rich tree genera that have high local species diversity and underwent similar recent evolution.