Computational protocol: Molecular Phylogeny of Asian Meconopsis Based on Nuclear Ribosomal and Chloroplast DNA Sequence Data

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Protocol publication

[…] The DNA sequences were aligned using the default parameters in Clustal X , and then refined manually in BioEdit. To reconstruct the phylogeny of Meconopsis and its close relatives, Maximum parsimony (MP) and Bayesian inference (BI) analyses for the nrDNA ITS and cpDNA trnL-F regions were implemented in software packages PAUP* 4.0b10 and MrBayes version 3.1.2 , respectively. For the MP analysis, all characters were weighted equally and treated as unordered, with gaps considered as missing. Heuristic searches were conducted using 1,000 replicates of random addition, tree-bisection-reconnection branch swapping, the MULTREES option, and a maximum of 1,000 trees saved per round. The confidence of clades in the MP trees was estimated by performing bootstrap analysis with 1,000 replicates by using the heuristic search. Before performing the BI analysis, the best evolutionary models of the two regions were determined using the Akaike Information Criteria implemented in MrModeltest 2.3 . The GTR+I+G model was chosen for the nrDNA ITS and trnL-F regions. Two separate runs of four Markov chains for 10,000,000 generations were applied for each data set, sampling one tree per 1000 generations. The 50% majority-rule consensus tree was constructed after removing the first 2,000 trees. MCMC convergence was explored by examining the Potential Scale Reduction Factor (PSRF) convergence diagnostics for all parameters in the model. Posterior probabilities were calculated for sampled trees. […]

Pipeline specifications

Software tools Clustal W, BioEdit, PAUP*, MrBayes, MrModelTest
Application Phylogenetics