Computational protocol: Laboratory Selection Quickly Erases Historical Differentiation

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Protocol publication

[…] Global genetic differentiation among the three foundations (Adraga, Montpellier and Groningen) was measured at generation 2 using haploid data from chromosomal inversion polymorphisms. Differentiation through FST was obtained with Arlequin v3.5 . [...] Nested Analyses of Variance (ANOVA) were performed at each generation to test for differences among foundations in all traits. The linear model used was:where Y refers to the trait analysed, Found refers to the fixed factor Foundations (with three categories, Adraga, Montpellier and Groningen), and Pop{Found} refers to the random factor Populations nested in each Foundation (i.e, the three replicate populations). Analyses including TA controls were also performed. A type III sum of squares was used in all tests, with the error being the population term. Pairwise comparisons between foundations were performed, with adjustment for multiple testing following the false discovery rate (FDR) procedure of Benjamini and Yekutieli (2001, theorem 1.3 ).The evolutionary trajectory of each trait and foundation was estimated using in each generation the three average values of the replicate populations (as differences from to the average control values); the best linear model being calculated by Type I least-squares linear regression. To test for significance of the overall response across foundations as well as differences in evolutionary rate between them ANCOVA analyses were performed using the linear model:where Y refers to the different traits analysed, Gen to the generations assayed (as covariate) and the other factors as mentioned above. Analyses using body size as a covariate were also done to account for its effects on other traits.All data analyses described above were performed using STATISTICA 10 and EXCEL. […]

Pipeline specifications

Software tools Arlequin, Statistica
Applications Miscellaneous, Population genetic analysis
Organisms Drosophila melanogaster