Isolated populations have potential to become new species that should have less genetic variation than their ancestors. Small populations are more likely to lose genetic variation, which is, thus, expected to be greater in ancestors. Aliciella caespitosa and A. tenuis, two endemic species, may be derived from small populations of A. subnuda, a widespread species. Chloroplast DNA sequences were used to test this hypothesis. Allozyme data were used to compare genetic variation and numbers of alleles. Chloroplast data do not support the proposed relationships between A. subnuda and the other two species. Allozyme data were not more variable in A. subnuda. The data suggest that A. tenuis is derived from A. caespitosa, although the former did not show lower allozyme diversity. I detected fewer alleles in A. tenuis. These data suggest that the original population of A. tenuis was not small enough to lose genetic variation relative to its progenitor.

Phylogenetics is crucial in the study of evolutionary processes and the determination of appropriate conservation units, and often these efforts are complicated by hybridization and introgression. Aliciella subsection Subnuda consists of seven species of herbaceous plants occurring in Utah and the Four Corners region of North America. Previous molecular and morphological work left relationships in the subsection unresolved. Here, we use comparative DNA sequencing of ITS and cpDNA regions and RAD-seq data to clarify phylogenetic relationships and examine the role of hybridization in the subsection. We construct haplotype and nucleotype networks from the cpDNA and ITS sequence matrices and compare nuclear and chloroplast phylogenies to identify multiple putative chloroplast capture events. The RAD-seq maximum likelihood phylogeny robustly resolves relationships between six clades, supportive of merging of two species. We employ STRUCTURE and HyDe on the RAD-seq data to evaluate the influence of hybridization within the subsection. The HyDe results provide evidence of hybridization among and between all species in the subsection. Our study robustly resolves relationships in Aliciella subsection Subnuda and provides a framework for discussing its speciation despite a history of hybridization and introgression.