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Premise of the Study Climate cycles of the Quaternary have impacted plants at a global scale, leaving behind a complex genetic legacy. Species of the northern Rocky Mountains of North America were exposed to more uniform glacial patterns than the central and southern ranges, where synergistic relationships between temperature and precipitation caused differences in the timing and extent of glacier onset. We examined the genetic impacts of climate oscillations on Calochortus gunnisonii (Liliaceae) in the central and southern Rocky Mountains. Methods Populations were sampled from disjunct mountain ranges across the basins of Wyoming and northern and central Colorado. Allelic data from nuclear microsatellites and plastid sequences (trnV‐ndhC, petA‐psbJ, and rpl16) were used to examine patterns of genetic structure between and among populations along the southern Rocky Mountain corridor. Key Results We infer considerable population structure concordant with mountain range of origin. Clustering analysis supports separate north and south genetic clusters on either side of major basins in Wyoming, suggesting that populations were maintained in two distinct refugia. Additionally, populations within the Sierra Madre Range of southern Wyoming show localized, divergent genetic signal indicative of a third potential glacial refugium. By contrast, recent genetic admixture is observed in the Laramie, Medicine Bow, and Front ranges, where population expansion from glacial refugia has likely occurred. Conclusions We conclude that during climate cycles of the Quaternary, C. gunnisonii experienced periods of population expansion and reduction, habitat fragmentation, isolation in three or more refugia, and admixture mirroring genetic impacts of other southern Rocky Mountains organisms.

Premise of the study:Microsatellite primers were designed for Calochortus gunnisonii (Liliaceae), a montane lily species of the central and southern Rocky Mountains, using next-generation DNA sequencing. The markers will be used to investigate population structure, genetic diversity, and demographic history.Methods and Results:Thirteen polymorphic microsatellite loci were isolated from C. gunnisonii using Illumina MiSeq next-generation DNA sequencing and bioinformatic screening. The mean number of alleles per locus ranged from 4.15 to 5.92 (avg. = 4.97). Observed and expected heterozygosity ranged from 0.077 to 0.871 and 0.213 to 0.782, respectively. The primers were also tested for cross-species amplification value with C. flexuosus, C. nuttallii, C. kennedyi var. kennedyi, and C. subalpinus.Conclusions:These primers will be useful for genetic and evolutionary studies across C. gunnisonii’s range within the southern and central Rocky Mountains. Furthermore, these markers have proven valuable for cross-species amplifications within Calochortus.

A RAD-seq phylogeny is presented for the genus Ulmus, and a revised infrageneric classification is given, with keys, descriptions, and range maps for the subgenera and sections. The previously accepted classification was based on a cpDNA phylogeny, but several well-marked clades in the chloroplast phylogeny are not recovered in the RAD-seq phylogeny and do not seem to represent valid clades in the organismal phylogeny. Ordination and STRUCTURE analysis support a broad species concept in Ulmus sect. Foliaceae and demonstrate interspecific hybridization in the section. Several sections of the genus are disjunct between Asia, Europe, and North America, indicating dispersals between the northern continents with inferred dates from ca. 20 Ma to ca. 3 Ma. Morphological variation is discussed, and some characterspreviously considered characteristic of Ulmus subg. Oreoptelea (narrowly winged achenes, ciliate achene margin) are shared with the unrelated U. villosa. A new subgenus, Ulmus subg. Indoptelea, is described. It can be recognized morphologically by its combination of compact inflorescences with very short pedicels, and samaras with narrow, strongly ciliate wings. It is sister to Ulmus subg. Ulmus, but has a smaller genome than either of the other subgenera.