Data from: Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics

High-throughput DNA methods hold great promise for the study of
taxonomically intractable mesofauna of the soil. Here, we assess species
diversity and community structure in a phylogenetic framework, by
sequencing total DNA from bulk specimen samples and assembly of
mitochondrial genomes. The combination of mitochondrial metagenomics and
DNA barcode sequencing of 1494 specimens in 69 soil samples from three
geographic regions in southern Iberia revealed >300 species of soil
Coleoptera (beetles) from a broad spectrum of phylogenetic lineages. A set
of 214 mitochondrial sequences longer than 3000 bp was generated and used
to estimate a well-supported phylogenetic tree of the order Coleoptera.
Shorter sequences, including cox1 barcodes, were placed on this
mitogenomic tree. Raw Illumina reads were mapped against all available
sequences to test for species present in local samples. This approach
simultaneously established the species richness, phylogenetic composition
and community turnover at species and phylogenetic levels. We find a
strong signature of vertical structuring in soil fauna that shows high
local community differentiation between deep soil and superficial horizons
at phylogenetic levels. Within the two vertical layers, turnover among
regions was primarily at the tip (species) level and was stronger in the
deep soil than leaf litter communities, pointing to layer-mediated drivers
determining species diversification, spatial structure and evolutionary
assembly of soil communities. This integrated phylogenetic framework opens
the application of phylogenetic community ecology to the mesofauna of the
soil, among the most diverse and least well-understood ecosystems, and
will propel both theoretical and applied soil science.