Computational protocol: Range expansion of the Bluetongue vector, Culicoides imicola, in continental France likely due to rare wind-transport events

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Protocol publication

[…] All the sequences were edited and aligned with ClustalW algorithm implemented in the software GENEIOUS v.6.0.5 (Biomatters, www.geneious.com). COI and CytB data sets were analysed separately and showed the same pattern but with a lower resolution. We thus combined COI and CytB data for all analyses.The genetic diversity was estimated by computing the number of haplotypes (H), haplotype diversity (Hd) and nucleotide diversity (π) using DNASP v.5. The relationships and the geographical distribution of genetic variation among sites were explored with a median-joining network conducted in Network v.4.6.1.2 (www.fluxus-engineering.com) on the concatenated COI and CytB dataset. Genealogical relationships were further investigated by a Bayesian phylogenetic inference as implemented in MRBAYES v.3.2.2. The software JMODELTEST v.2.1.3 was used to assess the best-fit substitution model based on the Akaike Information Criterion (AIC). The phylogenetic tree was estimated after 1 million generations of four Markov chains ran twice and sampled every 100 generations. Chain convergence was checked with Tracer v.1.6 software and the first 2,500 generations were discarded as burn-in phase. Finally, population structure was assessed by computing pairwise FST values between populations. […]

Pipeline specifications

Software tools Clustal W, Geneious, DnaSP, MrBayes, jModelTest
Application Phylogenetics