Fig 1.
LD patterns observed in Crotalaria SNP data.
a) LD box plot showing ranges of r2 values in the different populations, b) LD decay (in kb) in the SNP data set of 80 Crotalaria samples.
Fig 2.
SFS bar plots based on the SNP data of 80 Kenyan Crotalaria samples.
Fig 3.
Putatively adaptive and neutral SNPs separation based on the FST OutFLANK and PCadapt techniques.
From the 9820 SNP loci, PCadapt identified 649 SNPs (red circles) while FST OutFLANK did not identify any outlier SNPs. The remaining SNPs (black dots) were considered as putatively neutral loci.
Table 1.
Population differentiation represented by different fixation index (Fst) estimates on Kenyan Crotalaria species.
Fig 4.
Population structure analyses of 80 Crotalaria accessions based on the GBS-SNP genotyping.
(a) The stacked bar plot generated for the K values = 2–10. (b) The number of cluster (K) values as plotted using the Bayesian information criterion (BIC). (c) Cross-entropy plot with clusters (K) = 1 to 10.
Fig 5.
Principal component analysis (PCA) bi plot based on SNP data of 80 Kenyan Crotalaria accessions.
Fig 6.
Phylogenetic analysis of 80 Kenyan Crotalaria accessions.
(a) Phylogenetic tree generated using the Maximum Likelihood method and Tamura-Nei model using MEGA 11. (b) Consensus based phylogenetic tree generated using BEAST.