Data from: Brood ball-mediated transmission of microbiome members in the dung beetle, Onthophagus taurus (Coleoptera: Scarabaeidae)

Estes AM, Hearn DJ, Snell-Rood EC, Feindler M, Feeser K, Abebe T, Dunning Hotopp JC, Moczek AP

Date Published: November 5, 2013

DOI: http://dx.doi.org/10.5061/dryad.266qs

 

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Title README
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Description This file describes the contents of all the files submitted to Dryad.
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Title BacterialGenomesConcatenated.ConstraintTree
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Description This NEXUS formatted file provides two items. It provides the masked alignment of 264 loci for the 1095 taxa used to construct the constraint tree used later for the phylotyping analysis. It also provides the single maximum likelihood estimate of the bacterial phylogenetic relationships, as estimated by RAxML-Light (http://bioinformatics.oxfordjournals.org/content/early/2012/05/24/bioinformatics.bts309.abstract). This NEXUS file can be read by the program Mesquite (http://mesquiteproject.org/mesquite/mesquite.html).
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Title ConcatenatedAlignmentPositions
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Description This file provides the positions in the alignment in the file ‘BacterialGenomesConcatenated.ConstraintTree.nex’ for each of the 264 loci used for the constraint tree phylogenetic analyses.
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Title Concatenated_gyrB_lepA_PhylotypingTree
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Description This NEXUS formatted file provides two items. It provides the masked alignment of gyrB and lepA for the 1095 taxa and cultured isolates, and it provides the single maximum likelihood phylogeny that includes the cultured dung beetle microbiota samples and the 1095 reference bacteria. The RAxML analysis was topologically constrained by the phylogeny resulting from the full analysis of the 1095 bacterial genomes and 264 loci.
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Title ConcatenatedAlignmentPositions_gyrB_lepA
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Description This file provides locus positions in the alignment in the file ‘Concatenated_gyrB_lepA_PhylotypingTree.nex’ for the gyrB and lepA loci used by the phylotyping analysis. This file includes the gyrB and lepA sequences of the cultured microbiota samples from Othnophagus taurus.
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Title Analysis
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Description This text file contains commands to carry out the RaxML analyses of the matrices contained in BacterialGenomesConcatenated.ConstraintTree.nex and Concatenated_gyrB_lepA_PhylotypingTree.nex. Please note that the data matrices of the NEXUS files must be converted to the Phylip format for use with RAxML. The matrices can be exported using the program Mesquite.
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When using this data, please cite the original publication:

Estes AM, Hearn DJ, Snell-Rood EC, Feindler M, Feeser K, Abebe T, Dunning Hotopp JC, Moczek AP (2013) Brood ball-mediated transmission of microbiome members in the dung beetle, Onthophagus taurus (Coleoptera: Scarabaeidae). PLoS ONE 8(11): e79061. http://dx.doi.org/10.1371/journal.pone.0079061

Additionally, please cite the Dryad data package:

Estes AM, Hearn DJ, Snell-Rood EC, Feindler M, Feeser K, Abebe T, Dunning Hotopp JC, Moczek AP (2013) Data from: Brood ball-mediated transmission of microbiome members in the dung beetle, Onthophagus taurus (Coleoptera: Scarabaeidae). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.266qs
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