Phylogenomic analysis of Madagascar's baobabs reveals admixed populations and supports resurrection of a previously described species

Baobab trees ( Adansonia ) are iconic members of Madagascar's biota that serve as emblems for the island's unique biodiversity. Despite this recognition, many questions remain regarding evolutionary relationships and species limits within the genus. We used custom‐designed targeted sequence capture data to obtain phased allelic sequences for hundreds of nuclear loci and plastomes. Using broad geographic sampling, representing all species in the genus, and including a few possible hybrid individuals, we reconstructed the population history of Malagasy baobabs using network inference methods to detect reticulation. We obtained a species tree that is well supported, but with clear cases of reticulation, most notably admixture between Adansonia rubrostipa and A. madagascariensis in northwestern Madagascar, and instances of introgression involving the widespread species, A. za . Analysis of exclusivity factors suggests elevating one variety of A. za to the species rank, and also raises the possibility, pending additional sampling, of splitting A. rubrostipa into two species. We discuss the implications of gene flow on species delimitation and diversification in the context of conservation efforts for these iconic and threatened trees. Given our results, we formally resurrect the species A. bozy from A. za var. bozy , thus raising the number of endemic Malagasy baobab species from six to seven.