Computational protocol: A Global Population Genetic Study of Pantala flavescens

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[…] For each sample, forward and reverse sequences were assembled into a consensus sequence, or contig, using Geneious software version 8.1.2 []. These sequences were then combined with all available P. flavescens CO1 gene sequences from both NCBI GenBank and BOLD Systems for analysis. All sequences were initially aligned using ClustalX 2.1 [], followed by manual alignment in Mesquite v.3.02 []. Trithemis festiva was chosen as the outgroup based on Ware et al. [] and Pilgrim and von Dohlen [].As determined by jModelTest 2.1.6 [], the best nucleotide substitution model was found to be TPM2uf+I+G. We thus implemented the GTR+I+G model, which is the closest model to TPM2uf that can be implemented in Mr. Bayes. The parameters of this model were used for both Bayesian and maximum likelihood analysis. Bayesian analysis was performed using MrBayes v3.2.3 x64 [,] running on CIPRES [] to determine a posterior probability distribution. Two Markov chain Monte Carlo (MCMC) runs were performed; each run consisted of 4 chains running over the course of 10,000,000 generations with sampling occurring every 1,000 generations. Run convergence and a 10% burn-in value were confirmed using Tracer 1.6 []. Likelihood analysis was carried out using GARLI 2.01 [] to reconstruct both a best likelihood tree () and a 50% majority rule, 1,000 repetition bootstrap consensus tree (). These trees were summarized and posterior probability support was applied using SumTrees 3.3.0 distributed through the DendroPy 3.12.0 package []. Both trees were visualized using FigTree v1.4.2 (available at analysis of molecular variance was performed using Arlequin [] and GenAlEx 6.5 [,]. A haplotype network () was constructed using DnaSP [] and PopART 1.7 [,]. […]

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