Data and code from: Extremely fine-scale soil heterogeneity in a rare serpentine endemic plant shapes patterns of genetic diversity

Studies of population genetic structure are typically conducted at the
scale of species distributions and encompass large distances and
substantial environmental variation. However, population genetic structure
could also be present in species with highly restricted global
distributions, such as habitat specialists with threatened or vulnerable
conservation status. For these organisms, low dispersal distances coupled
with fine-scale environmental heterogeneity could influence population
genetic composition, potentially creating spatial genetic structure and
genotype by environment associations. Here we use the serpentine endemic
plant Calochortus tiburonensis, with a global distribution of 160 ha, to
evaluate whether fine-scale structure in soil composition and low seed
dispersal distances result in the development of population genetic
structure. We paired soil elemental analysis with a RAD-seq SNP dataset
for 24 C. tiburonensis individuals. Although no population structure was
detected between C. tiburonensis sampling locations, multiple analyses
identified associations between soil composition and genetic distance
between individuals. This included associations with nickel and magnesium,
two elements that were expected a priori to impact plant fitness in
serpentine landscapes. However, redundancy analyses and a generalized
dissimilarity model both suggest that total soil variation better explains
differences in genetic composition between individuals, implying that
selection from the holistic soil environment has a role in matching plant
genotypes to the microenvironment. Our results indicate that fine-scale
environmental heterogeneity could influence genetic differences between
individuals in plant populations, even in the absence of population
genetic structure. Additionally, these associations between genetic
composition and fine-scale environmental heterogeneity implicate extremely
fine-scale environmental heterogeneity as an essential mechanism for
preserving genetic variation, particularly within range-limited species.