Community richness and structure at multiple thresholds of genetic
similarity
Superficial layers tend to have higher richness than their corresponding
deep soil layers across all four habitats, with significant richness
differences between soil layers found for thermophilous woodland and
pine forest (Fig. S1). After combining superficial and deep soil layers
for all 52 sites, mean site richness (α diversity) within habitats
ranged 55 - 73.5 for haplotypes, 38.5 - 49 for 3% clusters and 34.5 -
43 for 15% clusters (Fig. 2A). Differences in richness by sample among
habitats were small and maintained across different clustering
thresholds, and pointed to dry scrubland community samples as poorer
(lower richness by site) compared to the other habitats (Fig. 2A).
Mean endemicity by site (proportion of lineages that occur exclusively
in that site) ranged from 24.0% to 48.8% at the haplotype level, from
13.5% to 22.7% for 3% clusters, and from 6.8% to 15.4% for 15%
clusters (Fig. 2B). Comparisons among habitats revealed that endemicity
was significantly higher for dry scrubland communities than for laurel
forest communities (Fig. 2B). Compositional dissimilarity among
communities (β diversity, βsor) was high and was dominated by lineage
turnover (βsim), rather than nestedness (βsne), with βsor values ranging
0.87-0.96 across all clustering levels and habitats. Dry scrubland
communities showed the highest levels of compositional dissimilarity
across the different clustering thresholds (Fig. 2C).
Total observed richness at the island scale (ɣ diversity) by habitat
ranged from 534 - 588 haplotypes, 278 - 316 lineages at 3% and 194 -
255 lineages at 15% (Fig. 2C), while extrapolated values (Chao index)
nearly doubled observed values (Fig. 2D). Differences in ɣ diversity
among habitats were not consistent across different clustering
thresholds, with thermophilous woodland showing the lowest number of
haplotypes but the highest number of lineages at the 15% clustering
threshold (Fig. 2C). Accumulation curves reveal no plateau in the
accumulation of entities across samples for any habitat or genetic
threshold, with the laurel forest showing the lowest rates of
accumulation (Fig. 2D).
Comparisons with biodiversity measures obtained by Arribas et al.(2020) in forest and grassland sites in a continental setting revealed
that richness by sample (α diversity) was lower in the samples of
Tenerife compared with continental soils (Kruskal p < 0.001;
Fig. S2). Comparisons of β diversity values restricted to a comparable
spatial scale of 15 km resulted in significantly lower β diversity
values in Tenerife for haplotypes (p < 0.001) but not for 3%
OTUs (Fig. S2). Finally, ɣ diversity by sampling region, as estimated by
the total number of haplotypes and OTUs recorded, was similar for the
different habitats of Tenerife (534 – 588 haplotypes and from 278 - 316
3% OTUs) and the six continental settings in Arribas et al. (2020) (558
- 623 haplotypes, and 276 – 319 OTUs) (Fig. S2).
NMDS for the compositional dissimilarity of the communities of Tenerife
soils showed habitat as a major driver of the ordination of samples, and
accordingly, for all clustering levels, a significant proportion of
variance (0.18 < r2 < 0.28; p < 0.001) was
explained by the habitat factor (Fig. 3A). In addition, dry scrubland
communities showed the highest dispersal, while the laurel forest
communities were the least scattered (Fig. 3A).
Analyses of community similarity (1-pairwise β diversity) with spatial
distance within each habitat revealed significant distance decay for all
clustering levels in all habitats, except for dry scrubland (Fig. 3B).
For laurel forest, pine forest, and thermophilous woodland, slopes of
the exponential decay curves were very similar at all threshold levels,
and assemblage similarity increased with each level (Fig. 3B). Genetic
similarity showed a high and significant log-log correlation with the
number of lineages (0.97 < r2 < 0.99, p <
0.001), initial similarity (0.92 < r2 < 0.99; p
< 0.001), and mean similarity of communities (0.97 <
r2 < 0.99; p < 0.001) (Table S5), as expected if
community variation across hierarchical levels of similarity is
described by a fractal geometry (Baselga et al., 2013, 2015).
A decrease in community similarity with environmental distance (Fig. S3)
was only significant for the laurel forest and some clustering levels in
the pine forest (Table S6). However, variance partitioning showed that
variance uniquely explained by environmental distance (i.e.
independently of the spatial distance) was lower (3.2% - 9.0% of
explained variation at all levels) than the uniquely explained variance
by the spatial distance (6.9% - 45.0% of explained variation).