Welcome to the Standing genetic variation and introgression shape the cryptic radiation of Aquilegia in the mountains of Southwest China project. This repository contains the scripts and workflows used to explore the genomic mechanisms underlying the rapid formation of cryptic diversity in Aquilegia species from the Southwest China (Peng et al., 2025, Communications Biology, accepted).
(1) 1-fastp.sh: Cleans raw sequencing reads using the fastp tool. The output files are appended with a .clean suffix.
(2) 2-bwa.sh: Maps cleaned reads (.fastq.gz files) to the reference genome using BWA.
(3) 3-picard.sh: Uses MarkDuplicates from Picard to identify and remove duplicate reads from the aligned BAM files.
(4) 4-gvcf.sh: Executes GATK's HaplotypeCaller on the input BAM files to generate GVCF files.
(5) 5-merge.sh: Merges individual GVCF files into a single VCF file.
(6) 6-filtering.sh: Filters the merged VCF file using GATK and VCFtools to obtain high-quality variant calls.
(7) 1.ASTRAL_100kb.sh: Constructs the species tree using IQ-TREE and ASTRAL based on 100kb windows.
(8) 2.tsne.py: Python script for t-SNE analysis on unlinked SNPs to visualize population structure.
(9) 1-smcpp.sh: Estimates the demographic history using smc++.
(10) 2-QUIBL.sh: Estimates introgression and incomplete lineage sorting (ILS) among lineages using QUIBL.
(11) 3-Dsuite.sh: Quantifies the proportions of introgression among lineages with Dsuite.
(12) 1.PBS_deltaFST.R: a R script to screen and plot the outliers based on population branch statistics and deltaFst
(13) 2.convert_to_outlier_detection.sh and 2.NAMESTOCHANGE_outlier_IBD_IBE.R: to calculate the IBD and IBE effect of each outlier based on GLMM.
(14) 3.Balancing_selection.sh: Screens loci under balancing selection using the betascan tool.
(15) 4.cor_among_all.R: Explores correlations among genomic divergence, diversity, genetic architecture, and introgressions.
(16) 5.cor_fst_pi_GN_RR_da.R: Investigates the link between genomic diversity and selection by analyzing correlations between diversity metrics and genomic architecture over time, proxied by da.
(17) 6.FST_dxy_outliers_poplevel.R: Compares genomic islands between sympatric and allopatric population pairs, focusing on Fst and dxy metrics.
(18) 1.vcftools_mac.sh: Uses VCFtools to identify fixed divergent SNPs between morphological species.
(19) 2.da_ILS_introgression.R: Generates density plots of da values in Aquilegia kansuensis and Aquilegia rockii using 5-kb windows to distinguish the introgression and ILS scenario.