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Mimulus gemmiparus is a rare, Colorado endemic plant which possesses a limited range, strict habitat requirement, and unique life history. Most peculiarly, Mimulus gemmiparus seemingly relies entirely on clonal spread using vegetative propagules known as brood bulbils to persist year to year. This inconspicuous annual is only found within a narrow range of Colorado’s Rocky Mountains, possessing a total known range of about 2500 km2. There are currently 11 known natural populations of Mimulus gemmiparus spread across three general regions: North (Larimer, Boulder, and Grand Counties), Central (Clear Creek and Jefferson Counties), and South (Jefferson County). Lack of sexual reproduction, disjunct populations, and threats such as recreation and climate change have raised conservation concern for Mimulus gemmiparus. Genetic analysis using a Next Generation Sequencing technique, double digest RADseq, was employed in this study to assess if Mimulus gemmiparus is genetically imperiled. To assess the full range of diversity for the species, all 11 known populations of Mimulus gemmiparus were sampled resulting in a genome wide data set consisting of 278 individuals and 8,011 single nucleotide polymorphisms. When allowing for slight variance (242 mutational steps) of ramets belonging to the same genet which are accrued via technical error and somatic mutation, all 278 sampled individuals in the dataset were assigned to 33 clones. Strong regional structure was found with the North region comprised of two clones, the Central region comprised of two clones, and the South region comprised of 29 clones. No clones were shared among regions and only three populations were found to possess more than a single clone. Two populations from the South region possessed the vast majority of the species’ clonal diversity while essentially all other populations were monoclonal. Ultimately, genetic analysis revealed that Mimulus gemmiparus possesses an extremely low genetic breadth and an incredibly uneven distribution of genetic diversity. The patterns observed in this study suggest that there should be four management units: the North region, the Central region split into population pairs, and the South region. The South region should be the highest conservation priority considering the greatest amount of genetic diversity is located there. Based on the genetic data, Mimulus gemmiparus should also be reevaluated for listing under the Endangered Species Act of 1973 as the total reliance on clonality, limited genetic diversity, and uneven genetic structuring imply the species is genetically imperiled.