DOI: 10.5061/dryad.f61bp
title: Data from: Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics

description: 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 &gt;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.
description: Cox1_barcode_Sanger_x813seqs_Andujar_et_al. 2015813 cox1 gene DNA sequences obtained by PCR and Sanger sequencing of soil adult beetles and larvae. Name of sequences correspond to the voucher as indicated in table S5 of the supplementary materials in Andujar et al. 2015 Mol. Ecol.#2. DNA_BC_dataset_x13_protein_coding_genes_x264_contigsDNA alignment of the mitogenome contigs included in the BC dataset in Andújar et al. 2015 Mol. Ecol.#3. DNA_3KB_dataset_x13_protein_coding_genes_x214_contigsAlignment of the mitogenome contigs included in the 3KB dataset in Andújar et al. 2015 Mol. Ecol.#4. DNA_3KB+REF_dataset_x13_protein_coding_genes_x214_contigs + 245_ref_mitogenomesAlignment of the mitogenome contigs included in the 3KB dataset (214 contigs) and the reference coleoptera mitogenomes (245 sequences) used in Andújar et al. 2015 Mol. Ecol.#5. AminoAcid_3KB+REF_dataset_x13_protein_coding_genes_x214_contigs+245_ref_mitogenomesAlignment of the amino acidic sequences for the mitogenome contigs included in the 3kb dataset (214 contigs) and the reference mitogenome sequences (245 sequences) used in Andújar et al. 2015 Mol. Ecol.#6. DNA_3KB+BC+REF_dataset_x13_protein_coding_genes_x214_contigs+264contigs+245_ref_mitogenomesDNA alignment of the mitogenome contigs included in the BC dataset (264 contigs), the 3KB dataset (214 contigs) and the reference mitogenomes (245 sequences) used in Andújar et al. 2015 Mol. Ecol.#7. Phylogenetic_tree_in Figure_1_Andujar_et_al. 2015Phylogenetic tree in Figure 1 in Andújar et al. 2015 Mol. Ecol.: Ultrametric time-calibrated Bayesian tree obtained in Phylobayes and BEAST for the dataset including 214 contigs longer than 3,000bp and 245 reference mitogenomes for Coleoptera (3KB dataset).#8. Phylogenetic_tree_in Figure_S2_Andujar_et_al. 2015Phylogenetic tree in figure S3 in Andujar et al. 2015 Mol. Ecol.: Maximum likelihood phylogenetic tree including all reference mitogenomes (named in black), contigs in the 3KB dataset (green), contigs in BC dataset (blue) and Sanger cox1 barcodes (red). A backbone tree was obtained on the 3KB dataset including references using Phylobayes and BEAST software and subsequently metagenomic contigs from the BC dataset and the Sanger cox1 barcodes were added using a backbone tree approach in RAxML.#8. Phylogenetic_tree_in Figure_S3_Andujar_et_al. 2015.tree