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).