Fine-scale patterns of genetic variation indicate non-equilibrium gene frequency divergence in the stream lily, Helmholtzia glaberrima

1. Helmholtzia glaberrima (Philydraceae) is a rare plant, endemic to streams of the border ranges of Queensland and New South Wales, Australia.
2. We used AFLP markers to investigate genetic diversity and patterns of differentiation among 19 populations of H. glaberrima (24 for demographic analyses), and also collected data on the size, distribution and altitude of populations.
3. Based on the distribution of populations, altitude significantly influenced the spatial arrangement of H. glaberrima along stream systems, with population size and frequency greatest in upstream habitat.
4. Patterns of genetic diversity within populations were not related to population size or distribution. Altitude and genetic diversity were related, with upstream and downstream populations having higher genetic diversity than mid-stream populations. Differentiation among populations was pronounced at all spatial scales and did not conform to a hierarchical model of gene flow.
5. Both genetic diversity and differentiation data sets indicated that strong non-equilibrium conditions associated with persistent founder effects, and not landscape characteristics, have shaped patterns of genetic diversity and differentiation in H. glaberrima . Patterns of distribution indicate that populations are distributed over a discontinuous ecological gradient, which becomes marginal at lower altitudes.