3.1. Phylogenetic reconstructions
The ML topologies inferred from both the concatenated RAD-Seq data and the SNP data recovered identical, well-supported topologies (Fig 2). Major clades recovered here coincided with the production of distinct secondary metabolites, although specimens producing depsides of either sekikaic acid or divaricatic acid were each recovered in two polyphyletic clades (Fig. 2) with a much larger divaricatic acid clade sister to the depsidone (nonterpenoid) clade, or a clade divided into sekikaic acid and depsidone subclades. Phenotypically circumscribed species represented by multiple samples were not recovered as monophyletic except those identified as N. cornea ; they were collected from the Channel Islands, California, USA and from near San Quintín, Baja California, Mexico (Appendix 1; Fig. 2). Additionally, specimens collected in close proximity having the same chemotype—but differentiated morphologically as distinct species or varieties—occurred in different clades (Fig. 2); examples are divaricatic acid specimens that include saxicolous sl-16775 (N.aff. isidiosa ) and sl-16778 (N. laminaria ), sl-16705 (N. juncosa var. juncosa ) and sl-16706 (N. juncosa var. spinulifera ), sl-16707 (N. juncosa var. juncosa ) and sl-16708 (N. undulata ). Those specimens evidently growing in close proximity differentiated as species more by their secondary metabolites—obviously in different clades—include, for example, terricolous sl-161004 (N. palmeri , sekikaic acid), sl-161005 (N. arenaria , salazinic acid), and saxicolous sl-161006 (N rugosa , divaricatic acid). As many as eight species have been recognized at a location (Spjut et al., 2020). SVDQuartets+PAUP* resulted in a generally well-supported topology, although in some cases backbone relationships differ strikingly from the ML reconstruction (Fig. 2; Dryad file S55).