Nuclear phylogenomics of Aloe and related genera (alooids) and Asphodelaceae

With >700 species, Aloe and its generic kin (alooids) are a morphologically diverse group of leaf succulents with a wide range across Africa, Madagascar and the Arabian Peninsula. Species such as Aloe vera and A. ferox are cultivated at scale for natural products, whole foods, and cosmetics. Despite substantial α-taxonomy contributions, infrageneric classification of Aloe has remained unresolved. Molecular systematics has been compromised by the lack of informative characters in standard markers and high costs of obtaining informative nuclear loci from large genomes (e.g. >15 Gbp); and the difficulty of obtaining quality DNA extractions from plant material of known provenance. Here these constraints are overcome with target capture sequencing that allows cost-effective sequencing of informative low-copy nuclear loci; and unlocks genetic resources from preserved specimens in herbaria as well as silica-dried plant tissues. Using a custom kit for alooids, 189 nuclear loci in 295 species, including 50 herbarium specimens, were sequenced to build a new phylogenomic framework for the big genus Aloe and 11 closely related genera in Asphodelaceae subfam. Alooideae. Available taxonomic classifications for Aloe sensu stricto were contrasted against the obtained topology in an effort to stabilise the taxonomy. Genus-level representations of the family Asphodelaceae were sequenced with the same tool. The new phylogenomic framework demonstrates the monophyly of the alooids and confirms recent classifications in which smaller genera (Aloidendron, Aloiampelos, Aristaloe, Gonialoe, and Kumara) are separated. The topology for Aloe is strongly correlated with geographic patterns, and to a much lesser extent with habit (growth form), and vegetative or reproductive morphology that are mainstays of α-taxonomy. Repeated incidents of adaptive radiation and niche specialisation appear to underlie species diversity in Aloe. This study illustrates the power of combined (nuclear) phylogenomic and taxonomic (morphological) inference, including the utility of herbarium genomics, in resolving the systematics of big genera.