Adaptation-to-climate-change-of-alfalfa

This is the script used for analysis the population data of alfalfa

step1, snp, indel and SV calling pipeline, including tetraploid variants calling

you can see the detail information from here:

snp_and_indel_calling.sh
freebayes_variants_calling.sh
SV_calling.sh

step2, population genetic analysis

This part includes all related content of population genetic-related analysis, including phylogenetic tree, admixture, PCA, IBD, introgression

phylogenetic tree: phylogenetic_tree.sh, phylogenetic_tree_plot.R, vcf2other.py
PCA and IBD: PCA_and_IBD.sh, PCA.R, IBD.R, lecture06_07_add_id.pl
admixture: admixture.sh, admixture.R
introgression: introgression.sh, F4-ratio.R, introgression_ABBA_R_plot.R

step3, population dynamics analysis

This part includes all related content of population dynamics analysis, including fastsimcoal, candidate gene analysis, MDS, deleterious variance and nucleotide diversity

fastsimcoal: fastsimcoal.sh, 2psfs.py
fst candidate gene analysis: fst_candidate_gene.R, candidate_gene.sh, candidate_gene_filter.R
MYB5 gene analysis: MYB5_gene.sh, MYB5_analysis.R, local_manhattan.sh
MDS analysis: MDS_analysis.R
Deleterious variance: deleterious_variance.sh, deleterious_variance_figure.R, change_vcf_format_genotype.pl
nucleotide diversity analysis: nucleotide_diversity.sh

step4, genotype and environmental factors association analysis

This part includes all related content of population dynamics analysis, including fastsimcoal, candidate gene analysis, MDS, deleterious variance and nucleotide diversity

LFMM (latent factor mixed model ) analysis: LFMM_analysis.R, LFMM_results_figure.R, match_indel_position.pl
PBS (population branch statistic ) analysis: PBS_analysis.R

step5, genetic offset analysis

This part includes offset estimation command and plot offset in map

step5.1 prepare_maf_matrix.R
step5.2 evaluate_representative_biofactor.R
step5.3 offset_estimation.R
step5.4 future_forward_offset_by_migration.R, local_forward_reverse_offset.R
species distribution region based on bioclimate variables: species_distribution.R

Publication:

Fan Zhang, et al. Evolutionary genomics of climatic adaptation and resilience to climate change in alfalfa. DOI:https://doi.org/10.1016/j.molp.2024.04.013

yunmika/Adaptation-to-climate-change-of-alfalfa