Computational protocol: Historical domestication-driven population expansion of the dung beetle Gymnopleurus mopsus (Coleoptera: Scarabaeidae) from its last refuge in Mongolia

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[…] The COI sequences were aligned using Clustal W in BioEdit v.7.0.1 and checked manually, and the haplotypes of the 418 individuals were determined using Neighbor-Joining algorithms in MEGA 7.0. A haplotype network was then inferred using HAPSTAR v0.7.The total and population genetic diversity indices, including the number of haplotypes (HN), haplotype diversity (h), and nucleotide diversity (π), were estimated using ARLEQUIN v3.5, and Tajima’s D and Fu’s Fs statistics were also analyzed to test for neutrality. Ten populations that had insufficient sample sizes (N < 10) were excluded from all subsequent analyses, except the AMOVA. Haplotype richness was calculated using a rarefaction method in CONTRIB v1.02 that corrects for unequal sample sizes among populations. [...] The fixation index (Fst) was calculated for population pairs using ARLEQUIN v3.5, and the geographical distance between sampling localities was measured in decimal degrees using ArcGIS Desktop 10.5 (ESRI, USA). The correlation between genetic distance (Fst) and geographic distance (decimal degrees), i.e., the Mantel test (spatial autocorrelation multivariate approach), was used to test for isolation by distance (IBD) in GenAlEx v6.502. [...] The expansion of G. mopsus populations was tested using mismatch distribution analysis and both Tajima’s D and Fu’s Fs neutrality tests in ARLEQUIN v3.5. Meanwhile, the demographic history of G. mopsus in Mongolia was determined using Bayesian Skyline Plot (BSP) analysis in BEAST v2.4.5. The GTR + G + I model of evolution was selected as the best model by jModeltest. MCMC run was performed with 300 M iterations, with sampling every 1000 iterations, the first 10% of generations discarded as “burn-in”, a constant skyline model, and Bayesian skyline tree priors. The molecular clock rate and substitution rates were estimated as a default function. The run was examined using Tracer v.1.6, and all the parameters were analyzed to confirm that the effective sample sizes were sufficient (ESS > 200). […]

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