Landscape Genomics Pipeline - Version 2
These suit of scripts were developed based on LanGen_pipeline from @rojaff/LanGen_pipeline
These scripts perform the following analysis:
1. SNPs dataset filtering using PCadapt, sNMF, and TESS3 to outlier detection.
2. Assessment of population genetic structure using sNMF, DAPC, TESS3, and PCA.
3. Creating maps for ancestry coefficients from step 2.
4. Estimate Tajima's D, genetic diversity and genetic distance inter and intra populations.
5. Assessment of fine-scale spatial genetic structure using LOESS.
6. Assessment of fine-scale spatial genetic structure using Spatial Principal Components (sPCA).
7. Isolation by Distance (IBD) using Mantel Tests.
8. Isolation by Distance (IBD) using Procrustes Analysis.
9. Selection of environmental data
10. Isolation by Resistance (IBR) using Partial Mantel Tests and distance-based Redundancy Analyses (dbRDA).
11. Identification of outlier (adaptive) loci using PCadapt.
12. Identification of genotype-environment associations (GEA) using Redundancy Analyses (RDA) & Mahalanobis distances.
13. Identification of genotype-environment associations (GEA) using Latent Factor Mixed Models (LFMM2).
14. Plotting detections with a Venn Diagram.
15. Visual assessment of genotype-environment associations using Redundancy Analyses (RDA) on the candidate loci.
16. Mapping adaptive genetic variation using Spatial Principal Components (sPCA).
17. Predicting adaptive genotypes from RDA models and environmental data.