Additional files for Drivers of the temporal dynamics of social bee viromes

This folder contains:
the plant-insect interactions recorded for the three time points of April (1), June (2) and August (3) 2016, from which we calculated the Horn-Morisita niche dissimilarity indices.the insect virus normalized read numbers matrices between our focal 5 bee species (Apis mellifera, Bombus terrestris, Bombus lapidarius, Bombus hortorum and Bombus pascuorum), from which we calculated the virome dissimilarity indices for the three time points. VirINS files for insect viruses, number 1 for April, 2 for June, 3 for August.the plant virus normalized read numbers matrices between our focal 5 bee species (Apis mellifera, Bombus terrestris, Bombus lapidarius, Bombus hortorum and Bombus pascuorum), from which we calculated the virome dissimilarity indices for the three time points. VirPLANT files for insect viruses, number 1 for April, 2 for June, 3 for August.the mitochondrial gene COI sequence alignment for the 5 bee species.the R script used to test the effect of host ecological niche dissimilarity (Horn-Morisita), the host phylogenetic distance (using DNADist method to calculate the nucleotide distance between aligned sequences) and phenology (time points) on virome dissimilarity.Data (files 'ApisFromsiRNA', 'ApisMetaTrans', 'BombusFromsiRNA', and 'BombusMetaTrans'), and scripts to generate the Venn diagram showing overlap in virus composition between honeybees and bumblebees, and between meta-transcriptomes and small-RNA sequencing.Output files of small RNA sequences screen for viral reads, using CoverM and the same viral assembly targets as for meta-transcriptomes (text file names starting with 'covread_small*). Number 1 for April, 2 for June, 3 for August.17 individual meta-transcriptome library output files from virus screening with CoverM (text files with libary names). Number 1 for April, 2 for June, 3 for August.One table that provides the final names of viral assemblies used in the article (file named 'reference names viruses').The list of viral assemblies in FAS format (file named 'Viral assemblies for mapping').One data table with compiled and normalized (by viral target sequence length and transcriptome depth) read numbers for each viral target and libraries (file named 'Normalized Log Viromes').A text file (named 'BeeViromeRscript') shows the R script used to perform the analyses, including heat maps, PERMANOVA and NMDS plots.The datasets for both meta-transcriptomes (names 'NormalizedNumberReadsMetaTrans') and small RNA sequences (named 'NormalizedNumberReadssiRNA'), including for both normalized read numbers for each viral targets and libraries, including taxonomic classification of viruses (named 'NormalizedNumberReadsMetaTrans_withTAXA'), A text file with the R scripts to generate the bipartite networks, perform network modularity analyses and calculate diversity metrics (named 'BeeViromeBipartiteNetworks').