Lineages characterisation and meta-phylogeographical patterns
Across all 52 samples across Tenerife island, a total of 813 OTUs (3%
clustering) and 533 15% lineages (15% clustering) were found, with a
mean of 2.2 haplotypes by OTU and a mean of 1.5 OTUs by 15% lineage.
Table 2 shows the number of OTUs and 15% lineages obtained and
extrapolated values (Chao index) for Acari, Collembola, and Coleoptera
across the 52 sites. Among OTUs, 488 (60%) included a single haplotype
(single-haplotype OTUs), and 325 (40%) were classified asmulti-haplotype OTUs (Fig. 4). The most diverse OTU included 40
haplotypes and corresponded to a species of Acari from the order
Sarcoptiformes, not represented in public sequence repositories. Among
the 533 15% lineages, 413 (77%) included a single OTU
(non-diversified lineages ), and 122 (23%) included 2 or more
OTUs and were classified as diversified lineages . (Fig. 4). The
most diverse 15% lineage included 21 OTUs (77 haplotypes),
corresponding to the weevil genus Laparocerus Schoenherr, 1834,
the most diverse beetle genus in Tenerife (Machado, Rodríguez-Expósito,
López, & Hernández, 2017). Among the 813 OTUs, 135 (16.6%) were
classified as non-endemic OTUs because they have a similarity
≥97% with sequences of external (non-Canarian) databases. Of these, 115
OTUs (14.1%) showed a similarity ≥99% and so were additionally
categorised as likely introduced OTUs (Table S7).
Each OTUs was found on average on 2.9 sampling sites and each 15%
lineage on 3.9 sites. Four hundred and five OTUs (49.8%) were detected
in a single site, and the remaining 408 (50.2%) in two or more sites
(Fig. 4). Two-hundred 15% lineages (37.5%) were detected in a single
site, and the remaining 333 (63.5%) were found in two or more sites.
The most widespread 15% lineage, including a single OTU, was found in
37 sites and corresponded to a likely introduced species identified asCeratophysella gibbosa (Bagnall, 1940), having similarity
>99% with specimens from France and Australia (Table S7).
Regarding the distributions of OTUs and 15% lineages across the
habitats, habitat specificity was estimated for those entities sampled
in n or more sites, with n = 3, 4, 5, and 6. The
percentage of OTUs considered OTUs with high habitat specificity ,
with at least 80% of occurrences within the same habitat, ranged from
31% to 29% (Fig. 5A). Similarly, lineages with high habitat
specificity ranged from 30% to 26% (Fig. 5B). Patterns of shared OTUs
and 15% lineages among habitats revealed that spatially (and
climatically) adjacent habitats presented higher numbers of shared OTUs
and lineages (e.g., laurel forest and thermophilous woodland; 102 shared
15% lineages), compared to spatially disconnected habitats (e.g. laurel
forest and dry scrubland; 50 shared 15% lineages, of which 45 are also
shared with the thermophilous woodland typically located in between)
(Fig. 5). Individual Venn diagrams for Acari, Collembola, and Coleoptera
were highly consistent with this general pattern (Fig. S4).
Regarding the structure of the genetic diversity within OTUs and 15%
lineages, the analyses were restricted to those entities showing a
product of the number of sites by the number of haplotypes ≥ 15; n = 107
OTUs and 128 15% lineages. The proportion of these entities with a
significant geographical structure of genetic diversity constituted
29.0% of the OTUs and 30.5% of the 15% lineages (Fig. 6). The
proportion of entities with a significant structure of genetic diversity
associated with the factor habitat was lower and represented 8.4% of
OTUs and 16.4% of 15% lineages (Fig. 6). The overlap between the
entities structured by spatial distance and habitat revealed that 13 of
the 21 entities structured by habitat were also structured by spatial
distance (Fig. 6).
Discussion
Using the recently developed metaMATE pipeline (Andújar et al., 2021),
we have generated a stringently filtered dataset of amplicon sequence
variants (ASVs) for mesofaunal soil communities sampled across an
oceanic island. By achieving a level of spurious sequences estimated to
be no more than 5% of ASVs in the final dataset, we have been able to
undertake both phylogeographic and community ecological analyses at
different hierarchical levels of relatedness. These data reveal both
ecological patterns and evolutionary processes, providing novel insights
into community assembly within soil mesofauna at an unprecedented
taxonomic scale. In doing so, we demonstrate wocDNA metabarcoding to be
a powerful tool for understanding ecological and evolutionary processes
within dark taxa – highly diversified lineages for which described
species are estimated to be only a limited proportion of true species
richness (Hartop, Srivathsan, Ronquist, & Meier, 2021).