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A single gene with pleiotropic effects accounts for the Scottish endemic taxon Athyrium distentifolium var. flexile.

•  Experiments were conducted to determine the genetic relationship between the alpine fern Athyrium distentifolium and the Scottish endemic taxon A. distentifolium var. flexile. •  Segregation of the taxa was studied after growing sporophytes from spore families, and after selfing and crossing gametophytes. The growth of both gametophytes and sporophytes was measured under a range of nutrient regimes. •  The distinction between the two taxa is due to variation at a single gene with pleiotropic effects expressed at both the sporophyte and gametophyte stages. A. distentifolium sporophytes (genotypes AD /AD or AD /AF ) are taller, have fewer fronds, and produce fewer spores than A. distentifolium var. flexile sporophytes (genotype AF /AF ). Gametophytes containing the AF allele have a 50% higher growth rate than those with the AD allele on a range of media. •  The polymorphism may be maintained by a balance between selection for and against the AF allele at the gametophyte and sporophyte stages of the life cycle, respectively. Implications for the conservation of the A. distentifolium var. flexile taxon are discussed.