Phylogenetics within Camassia (Asparagaceae): examining difficult taxonomy and unusual variation using genomic...

Diversification of Camassia (Asparagaceae) in North America has shaped variety in morphological, ecological, and reproductive traits, and resulted in a classification with ambiguity in taxon boundaries, including numerous putative subspecies. Phylogenetic analyses of restriction-site-associated DNA sequences (RADseq) allowed new insights into its evolution and taxonomy, enhancing understanding of basal relationships, geographic patterns, taxonomic boundaries, and potential new species.

A total of 157 individuals in 71 populations across all 15 putative taxa of Camassia and 42 outgroup individuals in 21 populations from Hastingsia and Chlorogalum were sampled and genomic libraries were generated using the modified single-digest RADseq method known as multiplexed shotgun genotyping. Assembly in ipyrad included targeted comparisons across a range of parameters that influence homology assessment and amount of missing data, with analysis of the set of resulting datasets in RAxML and SVDquartets followed by comparison and summary across the sets of trees.

Increasing the number of sampled loci improved phylogenetic signal despite concurrent increases in missing data. Each taxon was generally cohesive on the phylogenies, but some species and subspecies were not monophyletic. Results suggest that there was an early separation of C. howellii and C. leichtlinii from the rest of the genus during diversification. Different analysis parameters supported either a clade of both species as sister to the remainder of the genus, or C. howellii alone as sister. Relationships among all relatively deep clades within the genus were well supported. Within species, C. leichtlinii had particularly robust support for relationships compared to others in Camassia, and geographic patterns corresponding to the diversification of some subclades were resolved. The eight subspecies of C. quamash largely formed two main clades. Although most subspecies showed sufficient phylogenetic, morphological, or ecological distinctiveness to maintain recognition, we recommend synonymizing C. quamash ssp. intermedia into C. quamash ssp. maxima. Some outlier individuals of C. quamash were resolved with other species. For example, the status of C. quamash ssp. utahensis was called into question by a well-supported division placing two populations with C. cusickii. In the disjunct species complex distributed further east in North America (C. scilloides+), results confirmed at least one progenitor-derivative species pair (C. angusta arising from C. scilloides) and some evidence for a potential new taxon closely related to C. angusta. Overall, these taxa have diversified in traits that can result in genetic isolation, such as differences in flowering seasons and ecological preferences, but there also are indications of some continued gene flow among both subspecies and species.