Computational protocol: On the Diversity of Malaria Parasites in African Apes and the Origin of Plasmodium falciparum from Bonobos

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Protocol publication

[…] Initial Neighbor Joining (NJ) trees were inferred under Tamura-3P model of nucleotide substitution in Mega4 . Maximum likelihood (ML) search of a tree topology was implemented in PAML4 under a General Time Reversible (GTR) + I + Γ4 substitution model, chosen based on likelihood ratio tests , and employing the NJ method to generate an initial tree. Bayesian support for the nodes was inferred in MRBAYES , under a General Time Reversible (GTR) + I + Γ4 substitution model, using 4 Markov chains and 10,000,000 Markov Chain Monte Carlo (MCMC) steps, discarding the first 3,000,000 steps (30%) as a burn-in. Sampling was performed every 500 generations. Mixing of the chains and convergence was properly checked after runs. The recovered ML and Bayesian trees were identical.Although a total of eight distinct near-complete mitochondrial genomes were obtained from the parasites found in the bonobos, we stringently excluded any where the accuracy of the sequence obtained was not optimal, thus only 4 sequences were included in the phylogenetic and other analyses. […]

Pipeline specifications

Software tools MEGA, PAML, MrBayes
Application Phylogenetics
Organisms Pan paniscus, Plasmodium falciparum, Pan troglodytes, Homo sapiens, Plasmodium reichenowi, Plasmodium vivax, Plasmodium malariae
Diseases Malaria, Malaria, Falciparum