Fremontodendron (Flannelbush, Fremontia, Malvaceae) is a genus of shrubs native to California, Arizona, and Baja California Norte. There are three species in the genus: Fremontodendron californicum is widespread throughout the range and is highly variable in its appearance, F. mexicanum is endemic to Otay mountain in Southern California, and F. decumbens is endemic to gabbro soils in the Sierra Nevada foothills. Fremontodendron decumbens is currently only known from the Pine Hill Preserve and adjacent areas in El Dorado County and was listed as endangered in 1996. Fremontodendron decumbens is mainly distinguished from F. californicum by its orange or reddish flowers and decumbent habit. Many plants with a decumbent habit but lacking the floral characters to be placed in F. decumbens have been collected over the years, primarily in the Northern Sierra Nevada/Cascade foothills and there has long been speculation as to whether these could be hybrids between F. californicum and F. decumbens. Here we investigated the potential hybrid origin of morphologically intermediate individuals using full genome resequencing data from 99 individuals of F. californicum, F. decumbens and potential hybrids, mapped to a F. californicum reference genome. We investigated population structure and potential admixture using principal components analysis, model-based evolutionary clustering, and D-statistics, as well as additional analyses. We also systematically investigated the morphology of F. californicum, F. decumbens, and potentially intermediate individuals, by measuring a suite of 10 characters in the field on 68 individuals. We found no evidence that the morphologically intermediate forms are of hybrid origin; rather, they generally group genetically with F. californicum. We also found that specimens from populations noted to be morphologically intermediate showed considerable overlap with F. californicum, but not F. decumbens, based on a morphological principal components analysis. The results lead us to conclude that F. decumbens is indeed a genetically distinct taxon, and that individuals of F. californicum with a decumbent habit, but lacking the distinct floral characters of F. decumbens, are not the results of hybridization. This dataset archives the VCF used for performing all analyses as well as the morphological data.

We investigated species boundaries between Juncus ensifolius, J. saximontanus, and their putative closest relative [or sister taxon] J. macrandrus, three members of a group of seven species of Juncus that are native to North America and have iris-like leaves. Juncus ensifolius and J. saximontanus have overlapping ranges in the central portion of Western North America, but J. ensifolius has a more northerly distribution, while J. saximontanus has a more southerly distribution. The distinctions between the two species have long been unclear, primarily due to the presence of individuals with a variable number of stamens, which is the primary character used to differentiate them. J. macrandrus is distinguished from our focal species by the length of its anthers, and is found only in the California floristic province, where the ranges of J. ensifolius and J. saximontanus overlap. We generated genotyping by sequencing data for 95 individuals of our two focal species and one individual from J. macrandrus, our putative outgroup. We used phylogenetic inference, evolutionary clustering, principal components analyses of morphological measurements, and other methods to investigate species boundaries in this group. We found that introgression with closely related species in the group such as J. macrandrus, but not between J. ensifolius and J. saximontanus, is a primary driver of uncertainty about species distinctions. We also found evidence for an independently evolving lineage in J. saximontanus that may deserve recognition at the species level. We determined that J. saximontanus and J. ensifolius are distinct species and can be recognized based on stamen number as well as number of heads per inflorescence. We propose that individuals with intermediate characters are most likely the result of hybridization with J. macrandrus or another closely related species.