Summary

• Crassulacean acid metabolism (

  CAM
  ) photosynthesis is an adaptation to water and atmospheric
  CO
  ₂ deficits that has been linked to diversification in dry‐adapted plants. We investigated whether
  CAM
  evolution can be associated with the availability of new or alternative niches, using Eulophiinae orchids as a case study.

• Carbon isotope ratios, geographical and climate data, fossil records and

  DNA
  sequences were used to: assess the prevalence of
  CAM
  in Eulophiinae orchids; characterize the ecological niche of extant taxa; infer divergence times; and estimate whether
  CAM
  is associated with niche shifts.

• CAM
  evolved in four terrestrial lineages during the late Miocene/Pliocene, which have uneven diversification patterns. These lineages originated in humid habitats and colonized dry/seasonally dry environments in Africa and Madagascar. Additional key features (variegation, heterophylly) evolved in the most species‐rich
  CAM
  lineages. Dry habitats were also colonized by a lineage that includes putative mycoheterotrophic taxa.

• These findings indicate that the switch to

  CAM
  is associated with environmental change. With its suite of adaptive traits, this group of orchids represents a unique opportunity to study the adaptations to dry environments, especially in the face of projected global aridification.

Eulophiinae comprise c. 270 species divided into nine genera, with the species-rich terrestrial genus Eulophia representing 60% of this diversity. Remarkable ecological and morphological variation, and an absence of clear diagnostic characters have led to uncertain generic delimitation in the subtribe. Using a combination of new and previously published DNA sequences, we created a dataset representing 122 taxa and all genera of Eulophiinae and inferred a complete generic-level phylogeny for the subtribe for the first time. Our sampling focused on analysing Afro-Madagascan taxa and therefore included representatives of the four mostly epiphytic Madagascan endemic genera, the near Madagascan endemic Oeceoclades and additional sampling of the predominantly African genera Eulophia and Orthochilus. In total, 104 new accessions were collected for this study in Zambia and Madagascar (88 of which represented 36 Eulophia spp. and 12 Oeceoclades spp.). Independent plastid and nuclear phylogenetic trees were inferred using Bayesian and maximum-likelihood algorithms, which recovered strong support for a monophyletic Eulophiinae, the first-branching position of the mostly epiphytic Madagascan endemic genera, and increased support for recognition of the terrestrial genera Oeceoclades and Orthochilus. Eulophia, the largest genus in the group, was recovered as polyphyletic, but with implications for its classification and that of Geodorum, that was nested in the main Eulophia clade. Although relationships among several genera were resolved with some confidence, the positions of the South African endemic genus Acrolophia and the epiphytic Madagascan endemic Paralophia require further work. Taxon sampling of Asian Eulophia is a priority for future work on the systematics of this group.

With 14 species, Badula (Primulaceae) is the most species-rich endemic angiosperm genus of the Mascarene Archipelago. The relationship between Badula and its ally Oncostemum (c. 100 spp; Madagascar and the Comoros Islands) is uncertain, with implications for the circumscription of Badula as a Mascarene endemic. Within Badula, species rarity (several being critically endangered) and a paucity of herbarium specimens hamper proper species delimitations. Here, we estimate the phylogenetic relationships of Badula based on DNA sequence data from the nuclear ribosomal internal transcribed spacer (ITS) and plastid trnS-trnG-trnG regions with complete taxon sampling of the genus and three samples or more of each taxon. The results strongly supported the monophyly of Badula. Paraphyly of Oncostemum was inferred with weak support; explicit hypothesis testing did not favour this hypothesis over one that forced the monophyly of Oncostemum. Monophyly of several Badula spp. was supported, particularly for taxa from the older islands of Mauritius and Rodrigues. Badula is inferred to have reached the Mascarene Archipelago through a single colonization event. The majority of species segregated into island clades, implying that few, rather than multiple, colonization events have occurred in Badula among the islands of the archipelago.