Computational protocol: Population structure of elephant foot yams (Amorphophallus paeoniifolius (Dennst.) Nicolson) in Asia

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Protocol publication

[…] Multilocus genotypes were identified using CERVUS 3.0 [–]. The probability (PSIB<0.001) is the likelihood that the genotype of one individual will have the same ramet as that of a second individual; the ramet from one population was excluded. Thus, plants with the same SSR profile were considered one individual.The number of alleles (Na) and the observed (HO) and expected heterozygosity (HE) were calculated. The allelic diversity, frequency of null alleles and Hardy-Weinberg equilibrium (HWE) tests were estimated using CERVUS 3.0 and GENALEX softwares []. GENEPOP software [] was used to test the HWE for all loci and its linkage disequilibrium (LDE) using Fisher’s method. Pairwise FST (fixation index) and FIS (inbreeding coefficient) for each allele and subpopulation HE were estimated using GENALEX []. A pairwise genetic distance matrix using unbiased Nei's distance was also created []. FST was estimated using the program FSTAT 2.9.3 []. Population bottleneck was estimated based on 1000 replications using BOTTLENECK software []. A phylogenetic tree was constructed based on genetic distance matrices from allele frequencies using POPTREE with 1000 bootstrap replications [].AMOVA was conducted to examine genetic variation among regions, among populations, and among individuals. Genotypic differentiation was evaluated for each population by calculating the P value of the FST estimate. Values of FIS and FST were estimated based on the formula of Weir and Cockerham []. The likely area of origin might be inferred from geographic distributions by counting the gene flow. The amount of gene flow (Nm) was estimated from the FST estimates using 9,999 permutations in GENALEX []. Genetic distance was defined as FST/(1 − FST) []. Isolation by distance was performed []. FST was classified as low (<0.05), moderate (0.05–0.15), high (0.15–0.25) and very high (>0.25) genetic differentiation []. The FST value ‘0’ indicates no population structuring or panmixia, while ‘1’ indicates the existence of perfect barriers of gene flow. Inbreeding was concluded in a particular population based on FIS estimate [].Population structure was examined using STRUCTURE ver 2.3.4 [], followed by the admixture model and option of independent allele frequency between populations. A burn-in length of 50,000 iterations was followed by 100,000 Markov Chain Monte Carlo (MCMC) iterations. The pre-evaluation population number (cluster), K, was set from 1 to 15, and the model was run for 10 independent simulations for each K. True K was selected according to the assignment of Evanno et al. []. […]

Pipeline specifications

Software tools Cervus, GenAlEx, Genepop, POPTREEW
Applications Phylogenetics, Population genetic analysis
Organisms Loxodonta cyclotis