Background and Aims Adaptation to different pollinators has been hypothesized as one of the main factors promoting the formation of new species in the Cape region of South Africa. Other researchers favour alternative causes such as shifts in edaphic preferences. Using a phylogenetic framework and taking into consideration the biogeographical scenario explaining the distribution of the group as well as the distribution of pollinators, this study compares pollination strategies with substrate adaptations to develop hypotheses of the primary factors leading to speciation in Lapeirousia (Iridaceae), a genus of corm-bearing geophytes well represented in the Cape and presenting an important diversity of pollination syndromes and edaphic preferences. Methods Phylogenetic relationships are reconstructed within Lapeirousia using nuclear and plastid DNA sequence data. State-of-the-art methods in biogeography, divergence time estimation, character optimization and diversification rate assessments are used to examine the evolution of pollination syndromes and substrate shifts in the history of the group. Based on the phylogenetic results, ecological factors are compared for nine sister species pairs in Lapeirousia. Key Results Seventeen pollinator shifts and ten changes in substrate types were inferred during the evolution of the genus Lapeirousia. Of the nine species pairs examined, all show divergence in pollination syndromes, while only four pairs present different substrate types. Conclusions The available evidence points to a predominant influence of pollinator shifts over substrate types on the speciation process within Lapeirousia, contrary to previous studies that favoured a more important role for edaphic factors in these processes. This work also highlights the importance of biogeographical patterns in the study of pollination syndromes.

The southeastern Madagascan endemic and monotypic genus Eligmocarpus is highly threatened due to a combination of factors. Firstly, general human-induced habitat destruction and fragmentation has degraded the environment in which it occurs, leading to an increased threat of extinction for itself and other co-occurring species. Secondly, and more specifically to Eligmocarpus, the desirable properties of its timber, which is an excellent construction material, has led to over-collection beyond levels of sustainability. Thirdly, and with the highest relevance for this project, it is a combination of mode of dispersal, germination and seedling establishment. For all these reasons, its range has contracted and the only remaining population (21 trees) is located in Petriky, a future mining site. In this study we investigate the phylogeography and population dynamics of Eligmocarpus based on molecular tools (not only conducted on extant individuals but also using herbaria preserved DNA from individuals from neighbouring populations which are no longer alive, to give a glimpse of the past). Prior to human colonisation, the species was successful in using the river network to invade several biomes (most likely from the humid to subarid, where it is now constrained). Hence, due to its location, Petriky is a mosaic of the genetic variability from populations higher up in the river network, therefore, despite the low number of remaining individuals, all hope of restoration is not lost. Within this project we hope that a more complete understanding of the evolution of the flora will allow conservation, not only of current patterns of variation, but also the processes that gave rise to these patterns.

Madagascar is renowned for its unparalleled species richness and levels of endemism, which have led, in combination with species extinction caused by an unprecedented rate of anthropogenic deforestation, to its designation as one of the most important biodiversity hotspots. It is home to 10 650 species (84% endemic) of angiosperms in 1621 genera (19% endemic). During the last two centuries, botanists have focused their efforts on the provision of a taxonomic framework for the flora of the island, but much remains to be investigated regarding the evolutionary processes that have shaped Madagascan botanical diversity. In this article, we review the current state of phylogenetic and biogeographical knowledge of the endemic angiosperm genera. We also propose a new stratified biogeographical model, based on palaeogeographical evidence, allowing the inference of the spatio-temporal history of Madagascan taxa. The implications of past climate change and extinction events on the evolutionary history of the endemic genera are also discussed in depth. Phylogenetic information was available for 184 of the 310 endemic genera (59.3%) and divergence time estimates were available for 67 (21.6%). Based on this evidence, we show the importance of phylogenetic clustering in the assemblage of the current Madagascan diversity (26% of the genera have a sister lineage from Madagascar) and confirm the strong floristic affinities with Africa, South-East Asia and India (22%, 9.1% and 6.2% of the genera, respectively). The close links with the Comoros, Mascarenes and Seychelles are also discussed. These results also support an Eocene/Oligocene onset for the origin of the Madagascan generic endemic flora, with the majority arising in the Miocene or more recently. These results therefore de-emphasize the importance of the Gondwanan break-up on the evolution of the flora. There is, however, some fossil evidence suggesting that recent extinctions (e.g. Sarcolaenaceae, a current Madagascan endemic, in southern Africa) might blur vicariance patterns and favour dispersal explanations for current biodiversity patterns.