Figure 1 . Typic coastal fog desert community in Punta Mazo Nature Reserve, near San Quintín, Baja California, supporting diverseNiebla communities. A. Niebla communities on volcanic slopes on Volcán Sudoeste, Punta Mazo. B. soil dwelling Niebla arenaria near Bahía Falsa, San Quintín. C. Niebla communities on West-facing slopes of Monte Ceniza, Punta Mazo. D. Niebla flagelliforma (Leavitt 16856BF ). E. Niebla aff. isidiosa ; this specimen was identified as N. aff. isidiaescens and differs from N. aff. isidiosa in key morphological traits by the branches curved downwards near apex in contrast to the rigid terminal divaricate to reflex segments shown in panel ‘K’ (Leavitt 16775 ), which closely resembles the type from Isla Guadalpe. F.Niebla flabellata (Leavitt 16713 ). G. Niebla “sp. nov”. (Leavitt 16849BF ). H. Niebla juncosa var.juncosa (Leavitt 16707 ). I. Niebla undulata(Leavitt 16708 ). J. Niebla flagelliforma (Leavitt 16731 ). K. Niebla aff. isidiosa ; (Leavitt 16853 ). L.Niebla marinii (Leavitt 16763 ). M. Niebla lobulata(Leavitt 16859BF ). N. Niebla juncosa var.spinulifera (Leavitt 16719 ). O. Niebla cornea(Leavitt 16863BF ). All specimens identified by R. Spjut.
Figure 2 . ML topology inferred from 298,000 variable sites distributed across over 25,000 RADseq loci. Pink “shadow” tree is the species tree inferred under the multispecies coalescent model in PAUP+SVDquartets. Colors at tips correspond to sampling sites in map in bottom-left panel. Chemical clades are indicated with colored branches on the ML topology: black branches indicate lichens producing divaricatic acid (two clades), dark-blue branches indicate lichens producing sekikaic acid (two clades); and light blue branches indicate lichens producing salazinic acid. Grey boxes correspond to ASAP partitions from analyses of the standard DNA barcoding marker for fungi (ITS), with double shaded tips representing separate ASAP partitions that were combined for all subsequent analyses. Outgroup –Vermalicinia specimens – not shown.
Figure 3 . Candidate species and species delimitation analyses using BPP+gdi . A. Clades labeled ‘A’ through ‘Q’, and highlighted in pink boxes, represent candidate species defined based on phylogenetic subdivision inferred from the ML and SVDquartets+PAUP tree inferences (Pink “shadow” tree is the species tree inferred under the multispecies coalescent model in SVDquartets+PAUP); tips collapsed in the “tip-down” BPP+gdi approach are highlighted with purple boxes. B. Heuristic gdi values inferred from different candidate species comparisons – see candidate species in panel ‘A’ – and using different subsampled RADseq datasets (5649 variable RADseq loci; three random subsets of 1000 variable loci; three random subsets of 500 variable loci; the 500 most variable loci; the 163 most variable loci; three random subsets of 100 variable loci; and the ten most variable loci); following Jackson et al. 2017, gdi scores ≤ 0.2 indicate a single species (highlighted in blue), gdi scores ≥ 0.7 indicate distinct species highlighted in yellow, and status for comparisons withgdi scores between 0.2 and 0.7 are ambiguous (highlighted in grey).
Figure 4 . Probability of different species delimitation models – species ‘A’ – ‘Q’, Fig. 3 – inferred using the ‘A10’ species delimitation model in the program BPP. The results are summarized from all analyses of RADseq data subsets, with the Y-axis shows the probability, in aggregate, for the inferred number of species.
Figure 5 . Distribution of gdi scores estimated from different subsets of RADseq loci (143 bp each).