Estimation of Morphological and Molecular Diversity of Seventy-Two Advanced Pakistani Cotton Genotypes Using Simple Sequence Repeats

Probiotic Characterization and Population Diversity Analysis of Gut-Associated Pediococcus acidilactici for Its Potential Use in the Dairy Industry

“…Three genotypic diversity measures were employed by poppr; comparing the results of these populations, the H (Shannon-Wiener Index) was lower for the populations and the G (aka inverse Simpson's index) was greater, which shows that diversity is higher in the populations with higher MLGs. Note that lower H (Shannon-Wiener Index) values indicate more diversity [20]. Keeping in mind that the overall MLG count was lower, the diversity pattern indicated a slow evolution rate that can be an indicator for the stability of this strain.…”

“…Different indices of diversity were applied using R software on the randomly selected strains from around the world. Among different indices of diversity, AMOVA revealed significant population differentiation at one out of all three levels because the observed data did not fall inside the expected distribution from the permutation [20]. The hue and thickness of the edges were proportional to Bruvo's distance in the minimal spanning network (MSN), which used a distance matrix for the selected populations representing various multilocus genotypes at each node [32].…”

“…For cluster analysis, the Minitab 16 (Minitab Ltd., Coventry, UK) was used to create a dendrogram. The expected/observed heterozygosity, number of alleles per locus, and subpopulation statistics were computed by R language citations (locus_table, mlg, nei.dist, and plot_poppr_msn) using poppr package [20]. The strain and their accession numbers were used as a template/sample hence they are not present in final graphs; however, they form a baseline if added.…”

“…The hue and thickness of the edges were proportional to Bruvo's distance in the minimal spanning network (MSN), which used a distance matrix for the selected populations representing various multilocus genotypes at each node [32]. Nei's genetic distance, which assumes that mutation and genetic drift cause the genetic differences if the rate of amino acid substitution is constant per year or generation, was used to create the rooted UPGMA bottom-up hierarchical cluster diagram [20].…”