Geographic patterns of genetic distribution within Calochortus Gunnisonii in the central and southern Rocky Mountains

Organismal population ranges and genetic architecture have largely been shaped by climatic events. The Quaternary Period (2.6 million years to present) has been characterized by a series of climatic events manifested as Ice Ages. During glacial periods, plants and animals in temperate and arctic regions were restricted to small patches of suitable habitat less affected by expanding glaciers and extreme cooling. These refugia held importance for the persistence of organisms through glacier interphases. Mountain system vegetation in temperate latitudes was affected by patchy glacier patterns that separated some species into multiple refugia. The isolation of such populations has had a profound effect on genetic architecture across the globe. Glacial induced reproductive isolation causes genetic differences to arise and may result in the genesis of new species. Peripatric speciation is a species concept that seeks to explain these geneses and states that species arise when climatic or tectonic events isolate small populations from an ancestral population that differentiate due to no or limited gene flow. Isolation of populations to distinct geographic areas via peripatry exposes populations to local genetic drift and/or selection pressures and the resulting genetic architecture should reflect in a geographically concordant manner. Within the southern Rocky Mountains of North America, recent glacial patterns were patchy and plant populations were highly fragmented. Calochortus gunnisonii S. Watson (Liliaceae) is a common lily with a large range spanning Arizona, Utah, Colorado, Wyoming, Montana, and southwestern South Dakota. Herbarium records indicated disjunctions stemming from intermontane basins where suitable habitat is either too patchy or absent in the current climate conditions. The highly dissected range contains populations restricted to high elevation, “island-like” mountain ranges in the southern Rocky Mountains. Using microsatellite data, this research investigated the role of glacial oscillatory demographic changes in the central and southern Rocky Mountains in shaping genetic structure of populations across multiple montane disjunctions. Previous genetic studies of Calochortus are limited to AFLP and chloroplast DNA analyses. Neutral, codominant markers, such as microsatellites, are lacking for the genus. Here, 13 novel species-specific microsatellites were designed for analysis of C. gunnisonii populations within mountain ranges from Colorado, Wyoming, and South Dakota. All thirteen microsatellite loci were polymorphic for Calochortus gunnisonii and used to analyze 616 individuals spanning seven mountain ranges and 25 populations in the southern Rocky Mountain cordillera. Genetic analyses displayed large amounts of diversity and structure for each population and region. Patterns of relatedness between regions indicated recent colonization and diversification. Furthermore, genetic clustering of populations suggested that multiple areas within the region have served as macro and microrefugia for C. gunnisonii during Pleistocene glacial events. Calochortus gunnisonii appears to have resided in multiple montane refugia in the southern Rocky Mountains during warm interphases of the Earth’s glacier cycles. Here, four refugia were proposed including the Laramie Complex, Sierra Madre/Medicine Bow Complex, Central Colorado Complex, and the Absaroka region. Long-term isolation results in divergence patterns between refugia and complex patterns of admixture during cooling phases are evident from the genetic data. This lily also inhabits elevations beyond the border of boreal forests on the periphery of mountain ranges. It is this pattern that may be of value as an indicator for recolonization routes of the region for higher alpine floras in future genetic studies