DOI: 10.5281/zenodo.13886167
title: Defensive symbiont genotype distributions are linked to parasitoid attack networks - Dataset and scripts

description: The data and scripts for paper - Defensive symbiont genotype distributions are linked to parasitoid attack networks

    In the Data_1_Deep_sequencing_data_block_1.xlsx & Data_2_Deep_sequencing_data_block_2.xlsx files, "Sample" was the sample name from Illumina sequencing that can be found on Genbank later on, "Aphid" was the detected aphid species, "Parasitoid" are the detected parasitoid sepceies.

    Data_3_Parasitoid sequences.fas & Data_4_Aphid sequences.fas & Data_5_Hamiltonella sequences.fas are the fasta file of Parasitoids species/ Aphid species/ Hamiltonella strains that used for phylogeny reconstruction and following analysis.

    Data_6_Parasitoid_Aphid_pooled_table.xlsx contains the Parasitoid/Aphid OTU pooling based on 99%(4 base pair) similarity. "Parasitoid pooling together group" and "Aphid pooling together group" were the original name out of Illumina sequencing. "Original name" was the sequences represent the corresponding name. "Pooled species name" was the final name used in all analyses, while the "Pooled sequences" was the final sequence used in all analyses.

    Data_7_Parasitoid_species_phylogeny.txt & Data_8_Aphid_species_phylogeny.txt & Data_9_Hamiltonella_phylogeny.txt were the three phylogeny out of the analysis.

    Hamiltonella_Aphid_matrix_16species.csv & Hamiltonella_Aphid_matrix_22species.csv & Hamiltonella_Aphid_matrix_31species.csv & Para_Aphid_matrix_16species.csv & Para_Aphid_matrix_22species.csv & Plant_Aphid_matrix_16species.csv & Plant_Aphid_matrix_22species.csv & Plant_Aphid_matrix_31species.csv were the matrixes derived from Table_S2, The Row of them reprensent the Aphid species, the Column represent the Hamiltonella strains/Parasitoid species/Host plant species linked to each aphid species. They were used to generated the Figure 2, Figure 3 as well as Mantel's test/ MMRR test in Script_2_Tripartite_analysis_and_network_constraction.R & Script_7_MMRR_analysis.R. 

    Aphid_phylogenetic_relatedness_31species.csv & Aphid_phylogenetic_relatedness_22species.csv are two phylogenetic_relatedness used in plant-aphid analysis model and parasitoid-aphid analysis model, respectively. 

    Data_17_Parasitoid_genus_aphid_22_species_Fig.1.csv & Data_18_Plant_genus_aphid_31_species_Fig.1.csv were the reduced matrix only for generating Fig. 1.

    Script_1_Barplot_for_Fig.1.R: This script generates Figure 1.    Script_2_Tripartite_analysis_and_network_construction.R: This script performs the Mantel test analysis and generates Figures 2 and 3.    Script_3_Linking_parasitoids_and_Hamiltonella.R: This script analyzes the specialized parasitoid-aphid-Hamiltonella associations and generates Figure 4.    Script_4_Bubble_plot.R: This script generates Figure S2.    Script_5_Ecological_indexes_and_plot.R: This script calculates ecological indexes and produces Table 1.    Script_6_Dada2.R: This script provides the analysis pipeline for high-throughput Illumina sequencing data.    Script_7_MMRR_analysis.R: This script reanalyzed the correlation of  community similarity of plant/parasitoid/Hamiltonella and phlogenetic distance of aphid species, to compensate Mantel's test.