Computational protocol: Relevant genetic differentiation among Brazilian populations of Anastrephafraterculus (Diptera, Tephritidae)

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Protocol publication

[…] The mean number of alleles (na) and mean null allele frequency (An) (non-amplifying alleles due to changes in the primer binding regions), expected and observed heterozygosity were estimated using GENEPOP version 4.0.7 () for each population. Deviation from the Hardy-Weinberg equilibrium and linkage disequilibrium, together with their critical levels after the sequential Bonferroni test (), were tested using GENEPOP version 4.0.7 (). The allelic Polymorphic Information Content (PIC) was derived using CERVUS ().Polymorphic Information Content Microsatellite Analyzer (MSA) () was applied to estimate the pairwise Fst values among populations (). The statistical significance of each Fst value was assessed by comparing the observed values with the values obtained in 10,000 matrix permutations. Spatial analyses of molecular variance were investigated using SAMOVA 2.0 (). This approach identifies groups of populations that are genetically homogeneous and maximally differentiated from each other without the constraint of being geographically close. The method requires the a priori definition of the number of groups (K) of populations that exist and generates F-statistics (FSC, FST and FCT) using an AMOVA approach. Different numbers of groups (K) were tested, and a simulated annealing procedure permitted the identification of the composition of each of the K groups that maximizes the FCT index (proportion of total genetic variance due to differences between groups). The program was run for two to five groups (K = 2 to K = 5) each time with the simulated annealing process repeated 100 times, starting each time with a different partition of the population samples into the K groups. The analysis of molecular variance (AMOVA) was carried out using ARLEQUIN software version 3.11 (Excoffier et al. 2006). Principal Coordinate Analysis (PCoA) in the program GenAIEx 6.5 () was applied to identify the relationships among populations on the basis of their allele frequencies.Microsatellite Analyzer […]

Pipeline specifications

Software tools Genepop, Cervus, SAMOVA, Arlequin
Application Population genetic analysis