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).