Defensive symbiont genotype distributions are linked to parasitoid attack networks - Dataset and scripts

This R project includes data and scripts for paper - Defensive symbiont genotype distributions are linked to parasitoid attack networks

Script for analysis:

    Run all the scripts in order, to get all analyses and results in this paper. 

    Script_0_package_install_load.R:         Installs and loads the necessary R packages required for all subsequent scripts.        This R project

    Script_1_Extract_from_Table_S2.R        Extracts information from:            Table_S2.csv (located in /Rawdata/)    Data_4_Aphid_sequences.fas        Generates 10 files for further analyses:            Aphid relatedness distance:              Aphid_phylogenetic_relatedness_16species.csv              Aphid_phylogenetic_relatedness_22species.csv              Aphid_phylogenetic_relatedness_31species.csv            Hamiltonella - Aphid Matrices:              Hamiltonella_Aphid_matrix_16species.csv              Hamiltonella_Aphid_matrix_22species.csv              Hamiltonella_Aphid_matrix_31species.csv            Parasitoid - Aphid Matrices:              Para_Aphid_matrix_16species.csv              Para_Aphid_matrix_22species.csv            Plant - Aphid Matrices:              Plant_Aphid_matrix_16species.csv              Plant_Aphid_matrix_31species.csv

    Script_2_BarPlot_Fig1.R:         Generates Fig. 1 using:             Data_11_Parasitoid_genus_aphid_22_species_Fig.1.csv  Data_12_Plant_genus_aphid_31_species_Fig.1.csv        The bar order in Fig. 1 is arranged by proportion, which is not directly supported in the ggplot2 package in R. Therefore, we need manually reordered if using the first plot code; or, manually colour it using the second plot code. 

    Script_3_MMRR_analysis.R        Uses 10 distance/distribution matrices of Parasitoid, Plant, Hamiltonella, and Aphid relationships to compute matrix correlations with the MMRR (Multiple Matrix Regression with Randomization) model.

    Script_4_Species_linkage_Fig2_FigS4.R        Uses 7 distribution matrices of Parasitoid, Plant, and Hamiltonella relationships with Aphids (excluding Aphid genetic distance matrices) to generate the species linkage diagrams for Fig. 2 and Fig. S4, For aesthetic purposes, unconnected sample points have been moved.

    Script_5_MMRR_Fig3_FigS5.R        Plots the MMRR correlations using the 10 distance/distribution matrices for Parasitoid, Plant, Hamiltonella, and Aphid relationships (Fig. 3 & Fig. S5). 

    Script_6_parasitoid_specialization_Fig4.R        Computes specialization levels using the H2 Index for:            Parasitoid-Aphid            Aphid-Hamiltonella            Parasitoid-Hamiltonella relationships         Generates Figure 4.

    Script_7_Ecologicial_indices&plots_Table1_FigS3.R        Uses 7 distribution matrices of Parasitoid, Plant, and Hamiltonella relationships with Aphids (excluding Aphid genetic distance matrices) to:            Calculate ecological indices (Richness, Shannon Index, Simpson Index).            Use linear models to analyze the relationships between Parasitoid/Plant-Aphid and Aphid-Hamiltonella communities.           Outputs results for Table 1 and Figure S3.

    Script_8_Bubble_plot_FigS2.R        This script using             Hamiltonella_Aphid_matrix_31species.csv         and two phylogeny trees             Data_8_Aphid_species_phylogeny.txt &             Data_9_Hamiltonella_phylogeny.txt        To create a Cophylogeny tree of Hamiltonella strains and aphid species that we identified in this study and previously known strains.        (Fig. S2)

    Script_9_DADA2_pipeline_(Optional).R         Implements the DADA2 pipeline to generate:             Data_1_Deep_sequencing_data_block_1.xlsx &             Data_2_Deep_sequencing_data_block_2.xlsx        Requirements:            Download raw sequencing data from GenBank (BioProject PRJNA1139364) before running this script.         Download the Fastq file to /Rawdata/Illumina_Block1/ and /Rawdata/Illumina_Block2/

        Raw FASTQ files Genbank inofrmation:            The 370 samples of Block1 are SRX25431825 to SRX25432194            The 738 samples of Block2 are SRX25431012 to SRX25431744

Raw data and inofrmation:

    Data_1_Deep_sequencing_data_block_1.xlsx & Data_2_Deep_sequencing_data_block_2.xlsx         Sample: The sample name from Illumina sequencing, which can later be found on GenBank (BioProject PRJNA1139364).        Aphid: The detected aphid species for each sample.        Parasitoid: The detected parasitoid species.        The remaining columns contain ASV (Amplicon Sequence Variant) data derived from high-throughput barcoding sequencing.

    Data_3_Parasitoid sequences.fas &     Data_4_Aphid sequences.fas &     Data_5_Hamiltonella sequences.fas,        FASTA files for:            Parasitoid species            Aphid species            Hamiltonella strains        These sequences were used for phylogenetic reconstruction and subsequent analyses.

    Data_6_Parasitoid_Aphid_pooled_table.xlsx         Contains the OTU (Operational Taxonomic Unit) pooling results for Parasitoid and Aphid species based on 99% (4 base pair) sequence similarity:            Parasitoid pooling together group & Aphid pooling together group: Original names from Illumina sequencing.            Original name: Representative sequences for each group.            Pooled species name: Final species names used in all analyses.            Pooled sequences: Final representative sequences used in all analyses.

    Data_7_Parasitoid_species_phylogeny.txt & Data_8_Aphid_species_phylogeny.txt & Data_9_Hamiltonella_phylogeny.txt         Phylogenetic trees for:            Parasitoid species            Aphid species            Hamiltonella strains        These trees were generated using the PhyML tool on the ATGC Montpellier platform, original fasta file was Data_3, 4 & 5.

    Data_10_aphid_host_info.csv         Provides aphid host information for generating Figure 2 and Figure S4:        Aphid: Names of aphid species included in this study.        Host: Host categories:            1: Herb aphids            2: Grass aphids            3: Tree aphids        Host_category: Detailed descriptions of host categories.

    Data_11_Parasitoid_genus_aphid_22_species_Fig.1.csv & Data_12_Plant_genus_aphid_31_species_Fig.1.csv         Reduced matrices used for Figure 1, created by merging data from:            OTUs associated with the same parasitoid species.            Plant species belonging to the same genus.

    7 Distribution Matrices (from Script_1_Extract_from_Table_S2.R)        Hamiltonella-Aphid Matrices:           Hamiltonella_Aphid_matrix_16species.csv            Hamiltonella_Aphid_matrix_22species.csv            Hamiltonella_Aphid_matrix_31species.csv        Parasitoid-Aphid Matrices:            Para_Aphid_matrix_16species.csv            Para_Aphid_matrix_22species.csv        Plant-Aphid Matrices:            Plant_Aphid_matrix_16species.csv            Plant_Aphid_matrix_31species.csv        Structure:            Rows represent aphid species.            Columns represent Hamiltonella strains, parasitoid species, or host plant species linked to each aphid species.        Usage: These matrices were used to generate Figures 2, 3, 4, Figures S2, S3, S4, S5, and for MMRR tests, ecological indices, and H2 index calculations.

    3 Aphid phylogenetic relatedness matrices derived from Script_1_Extract_from_Table_S2.R        Aphid_phylogenetic_relatedness_16species.csv        Aphid_phylogenetic_relatedness_22species.csv        Aphid_phylogenetic_relatedness_31species.csv        These matrices provide phylogenetic distance information, showing pairwise genetic distances between the 31 aphid species included in this study.

    Table_S2.csv        The Table S2 from supplementary Tables:             No: the number of this sample            City: The city that collected this sample            Location: the location of sample collection            Sample category: Aphid mummies or alive aphids            Sample code: the name of sample (self defined)            Collection year: when this sample was collected            Aphid taxa / Wasp taxa / Plant species /Hamiltonella strain: The Aphid/Parasitoid/Plant             Sequencing method: Illumina or Sanger sequencing               Sequencing date: the date of sending this sample to sequencing            Data source: From this study or from Wu et al. 2022: Local adaptation to hosts and parasitoids shape Hamiltonella defensa genotypes across aphid species

    SraRunTable.csv        The BioProject (PRJNA1139364) information downloaded directly from Genbank.