Computational protocol: Are humans the initial source of canine mange?

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Protocol publication

[…] The PCR-amplified products of 400 bp were purified and directly sequenced. The Otodectes cynotis cox1 sequence (KF891933) was retrieved from GenBank. Multiple sequence alignments of nucleotide sequences in this study and sequences available from GenBank (n = 81) were generated using MAFFT v.6.951. The dataset was analyzed with Maximum Likelihood using MEGA5 and RAxML-HPC v7.0.4 under General Time-Reversible (GTR + G) model and Bayesian Inference analysis. Support of internal branches was evaluated by non-parametric bootstrapping with 500 replicates. Bayesian Inference analysis was performed with MrBayes v.3.2.1 conducting in two simultaneous runs with four parallel Markov chains (one cold and three heated) for 1 million generations, sampling every 1000 generations and discarding the first 25 % of samples as burn-in. Potential Scale Reduction Factor approached 1.0 and average of split frequencies under 0.01 were used for examining convergence. All trees were visualized using FigTree with Otodectes cynotis as outgroup (http://tree.bio.ed.ac.uk/software/figtree). To visualize the relationships between haplotypes, a median joining haplotype network of cox1 sequence was constructed using Network v4.6 according to host. […]

Pipeline specifications

Software tools MAFFT, MEGA, RAxML, MrBayes, FigTree
Application Phylogenetics
Organisms Sarcoptes scabiei, Canis lupus familiaris, Homo sapiens, Nyctereutes procyonoides
Diseases Scabies, Tick Infestations