Pre‐Pleistocene origin of an endangered habitat: links between vernal pools and aquatic Oxalis in the Greater Cape Floristic Region of South Africa

AIM: Vernal pools constitute a minute and under‐studied habitat type scattered across the species‐rich Greater Cape Floristic Region (GCFR), and harbour a number of endemic species from a wide variety of phylogenetic backgrounds. The unique species complements, restricted habitat size and high levels of anthropogenic threat to these ecosystems merit more intensive research focus. In this study, we explore the history of vernal pool habitat through the lens of a major component of the vernal pool flora, Oxalis L. LOCATION: Greater Cape Floristic Region of South Africa. METHODS: We reconstructed phylogenies of southern African Oxalis using two plastid markers, including all vernal pool inhabitants, in a Bayesian Markov chain Monte Carlo context. We conducted Shimodaira–Hasegawa and Bayes factor tests of topology to assess the number of independent invasions of vernal pool habitat. We used ancestral state reconstruction across a range of probable trees to find the oldest nodes that could be convincingly reconstructed as vernal pool inhabitants. Divergence time estimation of these nodes used two different approaches to account for a lack of fossil data in the Oxalidaceae. RESULTS: Phylogenetic analyses of DNA sequence data show conclusively that Oxalis has invaded this habitat type multiple times. Ancestral state reconstruction and divergence time estimation suggest an extreme minimum age for this habitat type of 2.3 million years, with more credible estimates suggesting origins deep in the Pliocene or latest Miocene. MAIN CONCLUSIONS: These data suggest that, despite their insignificant total surface areas, vernal pools are a surprisingly ancient and persistent feature of the GCFR landscape.