Adaptive genomics and phylogeography of Guazuma ulmifolia (Malvaceae)

Abstract

Guazuma is a member of the Malvaceae family and is a wild relative of Theobroma cacao. Guazuma ulmifolia is a species that is widespread both geographically and ecologically in tropical America, found from Mexico to the Caribbean and right through South America, in both dry (savanna and dry forest) and wet (rain forest) biomes. This geographical and ecological amplitude is unusual and makes G. ulmifolia an interesting case study in both biogeography and the evolution of drought tolerance. In order to investigate both the phylogeography and nature of drought tolerance in G. ulmifolia, a transcriptomics approach was used to generate a coding sequence collection, using tissues from plants exposed to different drought treatments in a glasshouse experiment. The transcriptome was used to identify candidate genes that may be involved in drought response, as well as other genes useful for phylogenetic reconstruction that are likely to be selectively neutral. This information was used to identify a panel of target loci that could be used in a hybrid capture experiment to capture target sequences in 55 accessions covering the geographic and ecological range of G. ulmifolia. Phylogenetic trees were generated from the resulting DNA sequence data using concatenated (maximum likelihood) and multi-species coalescent (ASTRAL) approaches.

Selectively neutral and drought genes were analysed separately, and resulting phylogenies showed differences. A combined dataset was used to examine patterns of phylogeography within G. ulmifolia, which revealed that the species has achieved its wide range by multiple long distance dispersal events across the Americas (for example, two colonisations of the Antilles), and multiple shifts between wet and dry ecologies.