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

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 generates Figures 2, 3 and S5. 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.本数据集及配套脚本对应论文《防御性共生菌基因型分布与寄生蜂攻击网络的关联》。 在Data_1_Deep_sequencing_data_block_1.xlsx与Data_2_Deep_sequencing_data_block_2.xlsx文件中，"Sample"为样本名称，该Illumina测序样本的相关数据后续可在GenBank获取；"Aphid"为检测到的蚜虫物种；"Parasitoid"为检测到的寄生蜂物种。 Data_3_Parasitoid sequences.fas、Data_4_Aphid sequences.fas与Data_5_Hamiltonella sequences.fas为用于系统发育重建及后续分析的寄生蜂物种、蚜虫物种及汉森菌（Hamiltonella）菌株的FASTA格式序列文件。 Data_6_Parasitoid_Aphid_pooled_table.xlsx包含基于99%序列相似性（4碱基差异阈值）聚类的寄生蜂/蚜虫操作分类单元（Operational Taxonomic Unit，OTU）聚类表。其中，"Parasitoid pooling together group"与"Aphid pooling together group"为Illumina测序得到的原始分组名称；"Original name"为代表对应类群的序列名称；"Pooled species name"为所有分析中最终采用的类群名称；"Pooled sequences"为所有分析中最终采用的序列。 Data_7_Parasitoid_species_phylogeny.txt、Data_8_Aphid_species_phylogeny.txt与Data_9_Hamiltonella_phylogeny.txt为本次分析得到的三类系统发育树文件。 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与Plant_Aphid_matrix_31species.csv为源自表S2的关联矩阵。其行代表蚜虫物种，列分别代表与各蚜虫物种关联的汉森菌菌株、寄生蜂物种及宿主植物物种。上述矩阵用于生成图2、图3，以及Script_2_Tripartite_analysis_and_network_construction.R与Script_7_MMRR_analysis.R中开展的曼特尔（Mantel）检验与MMRR检验。 Aphid_phylogenetic_relatedness_31species.csv与Aphid_phylogenetic_relatedness_22species.csv为分别用于蚜虫-植物关联分析模型与蚜虫-寄生蜂关联分析模型的两类蚜虫系统发育亲缘关系矩阵。 Data_17_Parasitoid_genus_aphid_22_species_Fig.1.csv与Data_18_Plant_genus_aphid_31_species_Fig.1.csv为仅用于生成图1的简化关联矩阵。 Script_1_Barplot_for_Fig.1.R：本脚本用于生成图1。 Script_2_Tripartite_analysis_and_network_construction.R：本脚本用于开展三方关联分析与网络构建，生成图2、图3及图S5。 Script_3_Linking_parasitoids_and_Hamiltonella.R：本脚本用于分析特化的寄生蜂-蚜虫-汉森菌关联关系，并生成图4。 Script_4_Bubble_plot.R：本脚本用于生成图S2。 Script_5_Ecological_indexes_and_plot.R：本脚本用于计算生态学指数并生成表1。 Script_6_Dada2.R：本脚本提供了Illumina高通量测序数据的标准化分析流程。 Script_7_MMRR_analysis.R：本脚本用于重新分析植物、寄生蜂及汉森菌的群落相似性与蚜虫物种系统发育距离之间的相关性。