Widespread-linked-selection

Scripts for Wang et al (2020) Evidence for widespread selection in shaping the genomic landscape during speciation of Populus. Molecular Ecology, accepted

Documentation of Scripts

1. Read alignment, SNP and genotype calling

    1-runBWA_mem.sh - Use bwa-mem to do read alignment
    2-realign.sh - Use GATK to do read realignment near indels
    3-picard_markduplicates.sh - Use Picard to correct for artifacts of PCR duplication
    4-haplotypecaller.sh - Use HaplotypeCaller of GATK to do SNP calling
    5-genotypeGVCFs.sh - Use GenotypeGVCFs of GATK to do genotype calling among multiple individuals
    6-vcf_geno_dep.filtering.4species.sh - Use multiple commands of BEDtools and VCFtools to do SNP filtering

2. Phylogenetic relationships and population structure analysis

    1-UnifiedGenotyper.chloroplast.sh - Use UnifiedGenotyper of GATK to call chloroplast SNPs
    2-chloroplast_vcf_filtering.sh - Use a set of VCFtools commands to filter chloroplast SNPs
    3-SNPhylo-chloroplast.sh - Use SNPhylo to construct a consensus tree based on chloroplast SNPs
    4-SNPhylo-chloroplast.tree.R - Use R to plot the chloroplast phylogenetic tree
    5-angsd_PCA.4species.sh - Use ANGSD to perform principal component analysis
    6-pca.plot.R - Use R to plot PCA results
    7-beagle_phasing.sh - Use BEAGLE to impute and phase SNPs and perform identity-by-descent block analysis
    8-beagle_ibd.plot.R - Use R to plot the IBD and haplotype sharing between individuals of species

3. Demographic history reconstruction

 fastsimcal
    1-angsd_2dsfs.chr.sh - Use ANGSD to construct two-dimensional joint site frequency spectrum (2d-sfs) 
    2-angsd_2dsfs.matrix.R - Use R to transfer the output from angsd to the input format of fastsimcoal2
    3-aspen.3species.model26.sh - One example showing the script running the fastsimcoal for one model
    4-model26_bootstrap.sh - Script to running bootstrap analysis for the best model (model26) inferred
 msmc
    1-msmc2.4species.input.sh- Shell script to generate the input file format for msmc 
    2-msmc2.4species.run.sh - Script for running msmc on different combinations of haplotypes
    3-msmc2.4species.submit.sh - Because there are many individual configurations and we use this script to submit these jobs respectively
    4-msmc2.4species.results_merge.sh - Script to merging the msmc results for different haplotype configuration
    5-msmc2.plot.R  - Use R to plot the msmc results for the four Populus species

4. Intra- and inter- species summary statistics

    1-angsd_SFS_davidiana.sh - Use ANGSD to estimate the genetic diversity at each site of P. davidiana
    1-angsd_SFS_tremula.sh - Use ANGSD to estimate the genetic diversity at each site of P. tremula
    1-angsd_SFS_tremuloides.sh - Use ANGSD to estimate the genetic diversity at each site of P. tremuloides
    1-angsd_SFS_trichocarpa.sh - Use ANGSD to estimate the genetic diversity at each site of P. trichocarpa
    2-thetas_table.R - Use R to summarize the genetic diversity along the windows
    3-angsd_FST.6species_pair.sh - Use ANGSD to estimate genetic divergence, Fst, at each site between pairs of species
    4-angsd_dxy.6species_pair.sh - Use ANGSD to estimate genetic divergence, dxy, at each site between pairs of species
    5-angsd_fst_stat_win.noChr.R - Use R to summarize the genetic divergence (Fst and dxy) along the windows
    5-fst.dxy.6species_pair.sh - Script to summarize the fst and dxy estimates from ANGSD to 10Kbp and 100Kbp non-overlapping windows
    6-ldhelmet.4species.sh - Use Ldhelmet to estimate the population-scaled recombination rate of the four species
    6-ldhelmet.window.summary.R - Use R to summarize the population-scaled recombination rate from Ldhelmet into windows
    7-diversity_divergence_rho.4species.10kb.R - Summary analysis of genetic diversity, divergence and population-scaled recombination rate in 10kbp windows
    7-Figure2_diversity_divergence_rho.4species.100kb.R - Summary analysis of genetic diversity, divergence and population-scaled recombination rate in 100kbp windows and also include scripts for plotting Figure 2
    8-linked_selection.correlation.R - Use R to integrate the analysis of genetic diversity, divergence, recombination rate, coding density, incomplete lineage sorting, phylogenetic topologies and introgression proportion (fd)
    9-Figure4.R - Use R script to make analysis and plot the figure4

5-phylogenomic_introgression_analyses

    1-twisst.ABBABABA.sh - Use twisst and ABBABABA to perform topology weighting and gene flow analysis (D statistics and fd)
    2-ILS.allele_freq.sh - Calculate incomplete lineage sorting (ILS) from allele frequencies of the four species
    3-ILS_gene.sh - Use script to calculate the distance to genes, exons and coding sequences and make the output files
    3-vcf2bed.awk - Awk script to transfer the vcf file into bed file format
    4-ILS.R - Use R script to estimate the level of incomplete linage sorting and plot the level of ILS with increasing distance of coding density
    5-Figure3_FigureS10S11.R - Use R script to plot Figure3 and Figure S10 and Figure S11
    6-angsd_abbababa2.sh - Use the abbababa2 option in ANGSD to perform the D statistics

6-positive_balancing_selection

    1-xpclr_convert_rho_to_cM.R - Use R script to convert recombination rate estimates from Ldhelmet to centi-Morgan (cM) for P.tremula
    1-interpolate_map_to_snp.R - Use R script to interpolate genetic distance between adjacent SNPs according to the centimorgan values
    1-xpclr.aspen_species.rec_cM.sh - pipeline to run XPCLR
    1-Figure5.R - R script to plot the Figure5
    1-manhanttan_plot.R - Function to make the manhanttan plot
    2-betascan.sh - Script to run BetaScan analysis
    2-Figure6.R - R script to plot the Figure6