Computational protocol: The Temporal and Spatial Invasion Genetics of the Western Corn Rootworm (Coleoptera: Chrysomelidae) in Southern Europe

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Protocol publication

[…] Estimates of genetic diversity (i.e., mean number of alleles per locus (A), expected (HE) and observed (HO) heterozygosity, FIS (inbreeding co-efficient)) per locus and population per phase of invasion, including tests of fit to Hardy-Weinberg equilibrium (HWE) and genotypic linkage equilibrium were estimated using GENEPOP on the Web v3.4 [,]. We compared A values between population samples by estimating allelic richness (AR) based on the smallest sample size using the rarefaction method in HP-RARE []. [...] The genetic clustering of individuals based on Bayesian methods was undertaken using the program STRUCTURE v2.3.3 []. Genetic clusters (K) were either set between one and seventeen (one more than the total number of populations for the complete data set) and a series of 10 replicate runs for each prior value of K were analysed. The parameter set for each run consisted of a burn-in of 10, 000 iterations followed by 1, 000, 000 MCMC iterations. The first inference performed, combined the admixture model of ancestry with the correlated allele frequency model of Falush et al. [] and the sampling information. The second inference performed combined the admixture model of ancestry with the correlated allele frequency model without the sampling information []. For both inferences, the default parameters in STRUCTURE were maintained. To estimate K the Evanno et al. [] method implemented in STRUCTURE HARVESTER v0.6.93 [] was used, where the highest ΔK value was indicative of the number of genetic clusters. In addition, when estimating K, the proportion of the sample assigned to a population was checked for asymmetry (indicates population genetic structure) or symmetry (1/K = indicates no population genetic structure) []. The graphical program DISTRUCT v1.1 [] was used to display the STRUCTURE output. [...] Identification of the most likely geographic source of populations was performed by calculating the mean individual assignment likelihood (L) for each individual (i) to the possible source population(s), referred to as Li→s [,], using GENECLASS v2.0 []. Li→s values were calculated using the Rannala and Mountain []) criterion, Paetkau et al. [] simulation algorithm and 1,000,000 simulated individuals. The evaluation of the most likely geographic source population was determined in each sample based on the combined lowest FST and the highest Li→s value []. […]

Pipeline specifications

Software tools Genepop, Structure Harvester, DISTRUCT, GeneClass
Application Population genetic analysis
Organisms Zea mays subsp. mays