Dated Plant Phylogenies Resolve Neogene Climate and Landscape Evolution in the Cape Floristic Region

In the context of molecularly-dated phylogenies, inferences informed by ancestral habitat reconstruction can yield valuable insights into the origins of biomes, palaeoenvironments and landforms. In this paper, we use dated phylogenies of 12 plant clades from the Cape Floristic Region (CFR) in southern Africa to test hypotheses of Neogene climatic and geomorphic evolution. Our combined dataset for the CFR strengthens and refines previous palaeoenvironmental reconstructions based on a sparse, mostly offshore fossil record. Our reconstructions show remarkable consistency across all 12 clades with regard to both the types of environments identified as ancestral, and the timing of shifts to alternative conditions. They reveal that Early Miocene land surfaces of the CFR were wetter than at present and were dominated by quartzitic substrata. These conditions continue to characterize the higher-elevation settings of the Cape Fold Belt, where they have fostered the persistence of ancient fynbos lineages. The Middle Miocene (13-17 Ma) saw the development of perennial to weakly-seasonal arid conditions, with the strongly seasonal rainfall regime of the west coast arising ~6.5-8 Ma. Although the Late Miocene may have seen some exposure of the underlying shale substrata, the present-day substrate diversity of the CFR lowlands was shaped by Pliocene-Pleistocene events. Particularly important was renewed erosion, following the post-African II uplift episode, and the reworking of sediments on the coastal platform as a consequence of marine transgressions and tectonic uplift. These changes facilitated adaptive radiations in some, but not all, lineages studied

Consistent phenological shifts in the making of a biodiversity hotspot: the Cape flora

Background The best documented survival responses of organisms to past climate change on short (glacial-interglacial) timescales are distributional shifts. Despite ample evidence on such timescales for local adaptations of populations at specific sites, the long-term impacts of such changes on evolutionary significant units in response to past climatic change have been little documented. Here we use phylogenies to reconstruct changes in distribution and flowering ecology of the Cape flora - South Africa's biodiversity hotspot - through a period of past (Neogene and Quaternary) changes in the seasonality of rainfall over a timescale of several million years. Results Forty-three distributional and phenological shifts consistent with past climatic change occur across the flora, and a comparable number of clades underwent adaptive changes in their flowering phenology (9 clades; half of the clades investigated) as underwent distributional shifts (12 clades; two thirds of the clades investigated). Of extant Cape angiosperm species, 14-41% have been contributed by lineages that show distributional shifts consistent with past climate change, yet a similar proportion (14-55%) arose from lineages that shifted flowering phenology. Conclusions Adaptive changes in ecology at the scale we uncover in the Cape and consistent with past climatic change have not been documented for other floras. Shifts in climate tolerance appear to have been more important in this flora than is currently appreciated, and lineages that underwent such shifts went on to contribute a high proportion of the flora's extant species diversity. That shifts in phenology, on an evolutionary timescale and on such a scale, have not yet been detected for other floras is likely a result of the method used; shifts in flowering phenology cannot be detected in the fossil record

Data from: Measures of biologically relevant environmental heterogeneity improve prediction of regional plant species richness

Aim:Relatively few models of species richness explicitly consider aspects of environmental heterogeneity, other than topographic heterogeneity. We hypothesized that environmental heterogeneity is an important determinant of species richness, especially in ancient climatically stable environments. Location: South Africa, which accommodates a range of biomes that differ strongly in species richness.Methods: We included measures of climatic, edaphic and biotic variables and their spatial heterogeneities in boosted regression tree models of vascular plant species richness. Species richness was assessed using herbarium records per quarter degree square (QDS). To avoid autocorrelation and problems of variable collection rates we iteratively randomly subsampled 20% of the available QDS. We also verified estimates of species richness using an independent data source. Results: The models predicted 68% of QDS species richness and 95% of biome richness. Spatial variability in diurnal temperature range was the strongest predictor of species richness, and inclusion of edaphic and biotic terms as well as spatial heterogeneities increased the explanatory power of the model considerably. Heterogeneity variables featured strongly (8 of 13) as predictors of species richness, but several resource variables (e.g. precipitation, seasonality and evapotranspiration) were also important. The spatial heterogeneities of some variables (e.g. water availability, fire) were related to their mean values, possibly explaining why some global models that have not explicitly included heterogeneity (other than topographic) perform well. Main conclusions: Environmental heterogeneities are important predictors of species richness, yielding accurate predictions even in the absence of any consideration of diversification rates or environmental stability. Greater heterogeneity of some resource variables when limiting, contributed to modelled species richness, adding to understanding of why species richness of some resource-poor Mediterranean-ecosystems is high. We suggest that species richness in ancient, climatically stable Mediterranean-ecosystems is contingent on resource and environmental heterogeneity that has enabled both the diversification and maintenance of regional species richness