Nuclear phylogenomics of alooids (subfam. Alooideae) and Asphodelaceae

With &gt;700 species, <i>Aloe</i> 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 <i>Aloe vera</i> and <i>A. ferox</i> are cultivated at scale for natural products, whole foods, and cosmetics. Despite substantial α-taxonomy contributions, infrageneric classification of <i>Aloe</i> 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. &gt;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 <i>Aloe</i> and 11 closely related genera in Asphodelaceae subfam. Alooideae. Available taxonomic classifications for <i>Aloe</i> 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 (<i>Aloidendron</i>, <i>Aloiampelos</i>, <i>Aristaloe</i>, <i>Gonialoe</i>, and <i>Kumara</i>) are separated. The topology for <i>Aloe</i> 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 <i>Aloe</i>. 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.