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).