Computational protocol: A new species of blunt-headed vine snake (Colubridae,Imantodes) from the Chocó region of Ecuador

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Protocol publication

[…] Editing, assembly, and alignment of sequences were performed with Geneious ProTM 5.3 (Drummond et al., 2010). Phylogenetic relationships were assessed under a Bayesian approach in MrBayes 3.2.0 (Ronquist and Huelsenbeck, 2003). The model of character evolution for each gene was obtained in JModeltest (Posada, 2008) under the Akaike information criterion. Genes were combined into a single dataset with two partitions, one per gene. Four independent analyses were performed to reduce the chance of converging on a local optimum. Each analysis consisted of five million generations and four Markov chains with default heating values. Trees were sampled every 1000 generations resulting in 5000 saved trees per analysis. Stationarity was confirmed by plotting the log-likelihood scores per generation in the program Tracer 1.2 (Rambaut and Drummond, 2003). Additionally, the standard deviation of the partition frequencies and the potential scale reduction factor (Gelman and Rubin, 1992) were used as convergence diagnostics for the posterior probabilities of bipartitions and branch lengths, respectively. Adequacy of mixing was assessed by examining the acceptance rates for the parameters in MrBayes and the effective sample sizes (ESS) in Tracer. After analyzing convergence and mixing, 500 trees were discarded as “burn-in” from each run. We then confirmed that the four analyses reached stationarity at a similar likelihood score and that the topologies were similar, and used the resultant 18,000 trees to calculate posterior probabilities (PP) for each bipartition on a 50% majority rule consensus tree. […]

Pipeline specifications

Software tools Geneious, MrBayes, jModelTest
Application Phylogenetics