Résumé
Here is a brief description of the files present in each folder: List of genes: List Immunity genes: Description and references for the immunity genes. list_Sma3s: List of genes identified by Sma3s program list_database: List of genes identified Immunome Knowledge Base, InnateDB and gene annotation. Polymorphism analysis : README: help to run seq_stat_coding seq_stat_coding: Executable C++ file and source file (.cpp) to estimate synonymous nucleotide genetic diversity (Ps) and non-synonymous nucleotide diversity (Pn) removeStopCodon: Executable C++ file and source file (.cpp) to remove the stop codon from the alignments Clean_Alignment : Executable C++ fileand source file (.cpp) to exclude the site with less than a define number of individuals TLR7_Pmajor_XP_015492521.1: Input file example Scripts and dataset : Simulations with SliM: SliM__immunity.slim: Script used to simulate sequences under balancing selection using codon format and exon-intron format Formating dataset: out_Seq_stat_*: Output of Seq_stat_coding according to our differents gene categories and selection pressure Formating_dataframe_script: Script to calculate Pn/Ps ratio and make a dataframe ready to plot. Plots and models : Dataframe_ready_to_plot.csv: Output from Formating_dataframe_script. Table containing : Species, PNPS, PN, PS, D_Taj, GC, S, category, Origin, family and selection regime. Plot_and_models_script: Script to plot results, and make differents models data_from_Leroy_etal_2021.csv : Informations and statistics about dataset from Leroy et al., 2021. Mitochondrial_phylogeny.treefile: Phylogeny based on mitochondrial genes of species from the dataset reconstructed by maximum likelihood method (IQTREE model GTR+Gamma and ultrafast bootstrap). Simulation analysis Tab_h_overdominance : Effect of parameters h (dominance coefficient) on Pn/Ps for sequences simulated under overdominace. Tab_m3_freq_dep : Effect of parameters S (selection coefficient) on Pn/Ps for sequences simulated under frequency dependent. Tab_Ne_overdominance : Effect of population size on Pn/Ps for sequences simulated under overdominance Tab_Ne_freq_dep : Effect of population size on Pn/Ps for sequences simulated under frequency dependent. Plot_simulated_results: Script to plot the effect of parameters on Pn/Ps from simulations. Supplementary table and figures : Figure S1 : Distribution of the percentage of contaminating contigs. The red line represents the 80% quantile. Figure S2: PCA of Cyanistes species Figure S3: PCA of Cyanomitra and Turdus species Figure S4: PCA of Ploceus species Figure S5: Fis ~Nucleotide diversity Figure S6: Correlation between Pn/Ps (a) and Ps (b) calculated on the control genes in this study's dataset and those calculated by Leroy et al. (2021). Figure S7 - Missing_data_ps_Phylloscopus.pdf : Relationship between the maximum number of missing individuals allowed and synonymous nucleotide diversity (Ps) Phylloscopus trochilus and Fringilla coelebs. Figure S8: Effect of sub-sampling size on PN/PS Figure S9: Pn/PS according to Ps for sub-sampling control, TLR and BD genes. Figure S10: Boxplot of Pn/Ps according to population size for simulated sequences under overdomiance via SLiM Figure S11: Boxplot of Pn/Ps according to population size for simulated sequences under frequency dependence via SLiM Figure S12: Boxplot of Pn/Ps according to a) initial selection coefficient of the mutation under frequency dependence b) dominance coefficient (h) for simulated sequences under overdominance via SLiM Table S1 - Model comparison using reduce number of families : Model selection of all genes categories using reduce number of families (we grouped Turdidae within Muscicapidae, Nectariniidae, and Estrildidae within Ploceidae and Fringillidae within Thraupidae). Table S2 - Lm & PGLS on dPn/Ps : Alternative models (Lm for linear models and PGLS for Phylogenetic Generalized Least Squares) using the difference between Pn/Ps of immunity genes and control genes (Pn/Ps) as dependent variable, and species origin as explanatory variable. Table S3 - Samples & sequencing information : Table with sampling and sequencing information regarding the samples newly-sequenced in this study, and those obtained from Leroy et al. 2021 Table S4 - Quality of sequences per individual : Table with sequencing quality information ( number of genes analysed, proportion of available positions, depth coverage) regarding the samples newly-sequenced in this study, and those obtained from Leroy et al. 2021 Table S5 to S14 : Model selection by AICc criterion and ANOVA test. Summary of the best models. Mitochondrial phylogeny: AllSp_ultrafastaboot.treefile: The species phylogeny was estimated using mitochondrial genes and a maximum likelihood method implemented in IQTREE (model GTR+Gamma and ultrafast bootstrap AllSp_mito.fst : Alignment of the mitochondrial genes in fasta format. Table and figure of the main text: Figure 1: Phylogeny based on mitochondrial genes of species from the dataset Figure 2 : Conceptual diagram showing the expected results Figure 3 : Boxplot of Pn/Ps according to species origin for different gene categories under purifying selection. Figure 4 : Boxplot of Pn/Ps according to species origin for different gene categories under purifying selection. Figure 5 : Effect of mutation type on Pn/Ps acording to Ne Figure 6 : Boxplot of Pn/Ps according to species origin (mainland in green and insular in orange) for different gene categories under balancing selection. Table 1: List of species and sampling localities, along with the type of data obtained and the number of individuals (N). Table 2 : Statistical model explaining Pn/Ps variation of Toll-Like Receptors, Beta-Defensins genes, and control genes. The p-values of ANOVA test between simpler models are not reported if a more complex model explains a larger proportion of the variance. Table 3 : Summary of the best statistical model selected using AICc explaining variation in Pn/Ps in control genes, Toll-Like receptors and Beta-Defensins genes under purifying selection with origin, gene category parameters.* indicates significances : * < 0.05; ** < 0.01; *** < 0.001. Table 4 : Statistical model explaining Pn/Ps variation of genes under balancing selection (i.e MHC class I and II), and simulated sequences under frequency dependence.