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

Andújar C, Arribas P, Ruzicka F, Crampton Platt A, Timmermans MJTN, Vogler AP

Date Published: April 9, 2015

DOI: http://dx.doi.org/10.5061/dryad.f61bp

 

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Title Cox1_barcode_Sanger_x813seqs_Andujar_et_al. 2015
Description 813 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.
Download Cox1_barcode_Sanger_x813seqs_Andujar_et_al...fasta (592.6 Kb)
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Title #2. DNA_BC_dataset_x13_protein_coding_genes_x264_contigs
Description DNA alignment of the mitogenome contigs included in the BC dataset in Andújar et al. 2015 Mol. Ecol.
Download #2. DNA_BC_dataset_x13_protein_coding_gene...fasta (2.998 Mb)
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Title #3. DNA_3KB_dataset_x13_protein_coding_genes_x214_contigs
Description Alignment of the mitogenome contigs included in the 3KB dataset in Andújar et al. 2015 Mol. Ecol.
Download #3. DNA_3KB_dataset_x13_protein_coding_gen...fasta (2.458 Mb)
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Title #4. DNA_3KB+REF_dataset_x13_protein_coding_genes_x214_contigs + 245_ref_mitogenomes
Description Alignment 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.
Download #4. DNA_3KB+REF_dataset_x13_protein_coding...fasta (5.268 Mb)
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Title #5. AminoAcid_3KB+REF_dataset_x13_protein_coding_genes_x214_contigs+245_ref_mitogenomes
Description Alignment 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.
Download #5. AminoAcid_3KB+REF_dataset_x13_protein_...fasta (1.761 Mb)
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Title #6. DNA_3KB+BC+REF_dataset_x13_protein_coding_genes_x214_contigs+264contigs+245_ref_mitogenomes
Description DNA 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.
Download #6. DNA_3KB+BC+REF_dataset_x13_protein_cod...fasta (8.280 Mb)
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Title #7. Phylogenetic_tree_in Figure_1_Andujar_et_al. 2015
Description Phylogenetic 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).
Download #7. Phylogenetic_tree_in Figure_1_Andujar...15.con (336.0 Kb)
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Title #8. Phylogenetic_tree_in Figure_S2_Andujar_et_al. 2015
Description Phylogenetic 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.
Download #8. Phylogenetic_tree_in Figure_S3_Andujar....tree (211.4 Kb)
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When using this data, please cite the original publication:

Andújar C, Arribas P, Ruzicka F, Crampton Platt A, Timmermans MJTN, Vogler AP (2015) Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics. Molecular Ecology 24(14): 3603–3617. http://dx.doi.org/10.1111/mec.13195

Additionally, please cite the Dryad data package:

Andújar C, Arribas P, Ruzicka F, Crampton Platt A, Timmermans MJTN, Vogler AP (2015) Data from: Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.f61bp
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