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Background  This study investigates orbitally-forced range dynamics at a regional scale by exploring the evolutionary history of  Nymania capensis  (Meliaceae) across the deeply incised landscapes of the subescarpment coastal lowlands of South Africa; a region that is home to three biodiversity hotspots (Succulent Karoo, Fynbos, and Maputaland-Pondoland-Albany hotspots).    Methods  A range of methods are used including: multilocus phylogeography (chloroplast and high- and low-copy nuclear DNA), molecular dating and species distribution modelling (SDM).    Results  The results support an ‘evolutionarily distinct catchment’ hypothesis where: (1) different catchments contain genetically distinct lineages, (2) limited genetic structuring was detected within basins whilst high structuring was detected between basins, and (3) within primary catchment populations display a high degree of genealogical lineage sorting. In addition, the results support a glacial refugia hypothesis as: (a) the timing of chloroplast lineage diversification is restricted to the Pleistocene in a landscape that has been relatively unchanged since the late Pliocene, and (b) the projected LGM distribution of suitable climate for  N. capensis  suggest fragmentation into refugia that correspond to the current phylogeographic populations.    Discussion  This study highlights the interaction of topography and subtle Pleistocene climate variations as drivers limiting both seed and pollen flow along these lowlands. This lends support to the region’s large-scale conservation planning efforts, which used catchments as foundational units for conservation as these are likely to be evolutionarily significant units.

peerj

Catchments catch all in South African coastal lowlands: topography and palaeoclimate restricted gene flow in<i>Nymania capensis</i>(Meliaceae)—a multilocus phylogeographic and distribution modelling approach

Catchments catch all in South African coastal lowlands: topography and palaeoclimate restricted gene flow inNymania capensis(Meliaceae)—a multilocus phylogeographic and distribution modelling approach