Data from: Isolation by distance and isolation by environment contribute to population differentiation in Protea repens (Proteaceae L.), a widespread South African species

Premise — The Cape Floristic Region (CFR) of South Africa is renowned for its botanical diversity, but the evolutionary origins of this diversity remain controversial. Both neutral and adaptive processes have been implicated in driving diversification, but population-level studies of plants in the CFR are rare. Here, we investigate the limits to gene flow and potential environmental drivers of selection in Protea repens L. (Proteaceae L.), a widespread CFR species. Methods — We sampled nineteen populations across the range of Protea repens and used genotyping by sequencing (GBS) to identify 2066 polymorphic loci in 663 individuals. We used a Bayesian FST-outlier analysis to identify SNPs marking genomic regions that may be under selection and used those SNPs to identify potential drivers of selection but excluded them from analyses of gene flow and genetic structure. Results — A pattern of isolation by distance suggested limited gene flow between nearby populations. The populations of Protea repens fell naturally into two or three groupings, which corresponded to an east-west split. Differences in rainfall seasonality contributed to diversification in highly divergent loci as do barriers to gene flow that have been identified in other species. Conclusions — The strong pattern of isolation by distance is in contrast to the findings in the only other widespread species in the CFR that has been similarly studied, while the effects of rainfall seasonality are consistent with well-known patterns. Assessing the generality of these results will require investigations of other CFR species.