Genomic Analysis of the Evolutionary History of the Baobabs (Adansonia)

Baobabs, comprising the genus Adansonia, are iconic trees native to deserts, savannahs, and dry forests of Africa, Madagascar, and northwestern Australia. Until recently, eight species were recognized: the tetraploid A. digitata from continental Africa, the diploid A. gregorii in Australia, and six diploid species forming a clade that is restricted to Madagascar. However, in 2012 a new, putatively diploid species, A. kilima, was recognized with a broad distribution in southern and eastern Africa. The genus Adansonia is a well-supported clade embedded in the otherwise mainly Neotropical Bombacoideae clade of Malvaceae. Using a combination of transciptome sequencing and target-enriched genome sequencing of a few hundred nuclear loci, this study aims to (a) resolve the phylogeny of the African, Australian, and Malagasy taxa and their relationships to other Bombacoideae, (b) clarify whether A. digitata is more likely to be an allo- or autopolyploid and whether A. kilima is best interpreted as a parental species, (c) assess the history of whole genome duplication in diploid baobabs, and (d) use new statistical methods to evaluate the extent of reticulate evolution in Madagascar and to guide species delimitations.  Analyses of pairwise synonymous distances and gene tree topologies support the existence of a whole genome duplication that is shared between Adansonia and Gossypium, but not Theobroma. Similar, analyses also suggests that tetraploidy in A. digitata is quite recent, but do not distinguish auto- vs. allopolyploidy.