******************************** GENERAL INFORMATION *************************** Date of compiling: January 19, 2018 THESE DATE ACCOMPANY: Can social partnerships influence the microbiome? Insights from ant farmers and their trophobiont mutualists. Ivens, Aniek; Gadau, Alice; Kiers, Toby; Kronauer, Daniel Molecular Ecology, in press 2018 ********************************** CONTENTS *********************************** This data package includes data and scripts underlying all results presented in figures and text of the publication. All field - and laboratory methods as well as the analyses and sample information are described in detail in the publication and its supplements. DNA sequences will be submitted to NCBI GenBank as well. Data is given in four categories: - Data underlying figure 2 - Data underlying figure 3 - Illumina MiSeq microbiome analyses - Network specificity analyses Data underlying figure 2: These data consist of six datasets obtained using Sanger sequencing and then manually curated in the software Geneouis 7.1. For each dataset are given: - the full alignment: .fasta files - the Neighbour Joining Tree: NJtree.newick - the raxML tree: raxmltree.newick - the Geneious archive containing the curated sequences The six datasets are: aphidCOI: COI mtDNA sequences of Prociphilus aphids mealybugCOI: COI mtDNA sequences of Rhizoecus mealybugs Buchnera16S: 16S rRNA sequences of Buchnera aphidocola from Prociphilus aphids Serratia16S: 16S rRNA sequences of Serratia symbiotica from Prociphilus aphids and Rhizoecus mealybugs Sodalis16S: 16S rRNA sequences of Sodalis endosymbionts from Rhizoecus mealybugs Tremblaya16S: 16S rRNA sequences of Tremblaya endosymbionts from Rhizoecus mealybugs files: aphidCOI_alignment.fasta AphidCOI_curatedSequences.geneious aphidCOI_NJtree.newick aphidCOI_raxmltree.newick Buchnera16S_alignment.fasta Buchnera16S_NJtree.newick Buchnera16S_raxmltree.newick Buchnera_16S_curatedSequences.geneious mealybugCOI_alignment.fasta mealybugCOI_curatedSequences.geneious mealybugCOI_NJtree.newick mealybugCOI_raxmltree.newick Serratia16S_alignment.fasta Serratia16S_curatedSequences.geneious Serratia16S_NJtree.newick Serratia16S_raxmltree.newick Sodalis16S_alignment.fasta Sodalis16S_curatedSequences.geneious Sodalis16S_NJtree.newick Sodalis16S_raxmltree.newick Tremblaya16S_alignment.fasta Tremblaya16S_curatedSequences.geneious Tremblaya16S_NJtree.newick Tremblaya16S_raxmltree.newick Data underlying figure 3: These data consist of two datasets of Sanger sequenced ant mtDNA (antCOI) and Illumina MiSeq sequences of ant-associated Acetobacteraceae (acetobacter16S). Sequences were manually curated in the software Geneouis 7.1. For both datasets are given: - the full alignment: .fasta files - the Neighbour Joining Tree: NJtree.newick - the raxML tree: raxmltree.newick - the Geneious archive containing the curated sequences files: acetobacter16S_alignment.fasta acetobacter16S_curatedSequences.geneious acetobacter16S_NJtree.newick acetobacter16S_raxmltree.newick antCOI_alignment.fasta antCOI_curatedSequences.geneious antCOI_NJtree antCOI_raxmltree Illumina MiSeq microbiome analyses: The publication presents results of five MiSeq runs: MS1, MS2 and MS3 (analyzed together as MS2MS3), MS4, MS5. All raw data can be found on NCBI's SRA and the files in this package can be used to re-run analyses in software package MOTHUR. To this end the included script can be run together with the stability file ('stab') and the raw sequence files from SRA. In addition, result files generated by MOTHUR are given for each run (taxonomy, fasta (sequences) and shared (read counts per sample). SRA download links to raw data: https://www.ncbi.nlm.nih.gov/sra/SRP128691 MS1: libraries MS1_L1 - MS1_L96 MS2: libraries MS2_L1 - MS2_L96 MS3: libraries MS3_L1 - MS3_L96 MS4: libraries MS4_L1 - MS4_L96 MS5: libraries MS5_L1 - MS5_L96 Files included: MS1: ABF_stab_MS1_0817.txt MS1.an.unique_list.0.03.cons.taxonomy MS1.an.unique_list.0.03.fasta MS1.an.unique_list.0.03.shared MS1_used_script_MS1_082017.txt MS2MS3: ABFI_stab_comb_MS2.txt ABFI_stab_comb_MS3.txt MS2MS3.an.unique_list.0.03.cons.taxonomy MS2MS3.an.unique_list.0.03.fasta MS2MS3.an.unique_list.0.03.shared script_comb_ms2ms3.rtf MS:4 MS4_script_032116.txt MS4_stab.txt NB: to read the result files, sample IDs need to be swapped according to data given in MS4_ID_Swap.txt MS4.an.unique_list.0.03.cons.taxonomy MS4.an.unique_list.0.03.fasta MS4.an.unique_list.0.03.shared MS5: MS5.an.unique_list.0.03.cons.taxonomy MS5.an.unique_list.0.03.fasta MS5.an.unique_list.0.03.shared MS5_scriptlog_021017.txt MS5_stab.txt Network specificity analyses Script and data are given for network specificity analyses on aphid COI - Buchnera association and ant - microbiome association. For both analyses, the .R script file can be ran in software package R, using the dataset in the .txt file files: ant_MB_networkanalysis_082017.txt antMB_network_Rscript082117.R BuchCOI-script.R COI-Buch.txt ***************************CONTACT INFORMATION****************************************** For questions or comments, please contact: Aniek Ivens, PhD Postdoctoral Fellow Animal Ecology Vrije Universiteit Amsterdam De Boelelaan 1085 1081 HV Amsterdam (e) a.b.f.ivens@vu.nl (t)+31 20 59 87077 (w) www.aniek.nyc (twitter) @AniekIvens ***************************ACKNOWLEDGEMENTS ************************************ The authors thank Christoph von Beeren, Leonora Olivos-Cisneros, Sean McKenzie, Piotr Lukasik, Marten van de Sanden and Stephanie Weldon for providing advice and support on laboratory procedures and data analysis to generate this data package; Tim Gale, Mark Wolek and Kate Leitch for providing help in the field, and the Rockefeller University Center for Field Research in Ethology and Ecology and the Cary Institute of Ecosystem Studies for granting access to their grounds for field sampling. We also thank the Rockefeller Genomics Resource Center and Connie Zhao for providing advice and logistic support. The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under Grant Agreement 624145, a Niels Stensen Fellowship, and a Rubicon Fellowship from the Netherlands Organisation for Scientific Research (all three to A.B.F.I). The project was further sponsored by the Iris and Junming Le Foundation and the Rockefeller University Center for Clinical and Translational Science grant #UL1 TR000043 from the National Center for Advancing Translational Sciences, National Institutes of Health Clinical and Translational Science Award Program and by the Sackler Center for Biomedicine and Nutrition Research, through the generosity of the Sackler Foundation (both to A.B.F.I) and a Rockefeller University Summer Undergraduate Research Fellowship (to A.G.).