Computational protocol: Genetic evidence of multiple invasions and a small number of founders of Asian Palmyra palm (Borassus flabellifer) in Thailand

Similar protocols

Protocol publication

[…] All loci were tested for linkage disequilibrium (LD) using PowerMarker version 3.25 []. The sequential Bonferroni correction [] was performed according to the multiple tests. The Hardy-Weinberg equilibrium (HWE) was conducted using POPGENE version 1.31 []. PowerMarker V3.25 was used to determine polymorphism information content (PIC) based on Botstein et al. (1980) [].EST-SSR and gSSR data were used to infer the most likely number of population genetic clusters (K), based on a Bayesian approach implemented in STRUCTURE version 2.3.4 []. Each of individual B. flabellifer was initially grouped according to the sampling locations: provinces and geographical parts of Thailand. Assuming a population admixture model, 100,000 burn-ins and 100,000 Markov chain Monte Carlo (MCMC) replicates for K varied from 1 to 10 were performed. Twenty independent runs were performed for each K. The best K was then inferred based on lnP(D) and delta K []. A hierarchical analysis of molecular variance (AMOVA) was performed using Arlequin version 3.1 [] to test for significance of grouping based on provinces and regional parts of Thailand and that of genetic clustering using STRUCTURE. The level of polymorphism was determined by using all 29 polymorphic loci. The observed (H o) and expected (H E) heterozygosity, the number of observed alleles and the number of effective alleles were calculated using POPGEN version 1.31. Allelic richness (Ar) and pairwise F ST among groups were calculated using FSTAT version 2.9.3.2 []. The number of migrants (N M) was estimated using an equation according to Wright []: N M = 1(1/F ST-1)/4. […]

Pipeline specifications