Computational protocol: Phylogeographic Analysis Elucidates the Influence of the Ice Ages on the Disjunct Distribution of Relict Dragonflies in Asia

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Protocol publication

[…] Sequences were compiled and aligned using MEGA version 5 . Ribosomal DNA sequences were aligned automatically with the clustalW algorithm and standard parameters. Protein coding mitochondrial sequences were aligned manually via the corresponding amino acid sequences. For alignment of ITS sequences the online version of MAFFT , was used.The most appropriate models of DNA substitution for bayesian and maximum likelihood tree searches were selected with MrModeltest 2.3 and PAUP*4.0 b10 separately for each sequence alignment and for a combined dataset containing all sequences except CO1, which was not used in the analysis since it was not possible to obtain sequences of this gene from E. laidlawi or E. sinensis specimens. The complete dataset contained 17 taxa, including a representative of Zygentoma as outgroup, and 4799 positions. Taxa from Odonata were chosen to represent all major clades as present in the phylogeny of . A Nexus file of the alignments are provided as .To find the most probable phylogenetic relationships of the Epiophlebia species the aligned sequences were combined into a mixed dataset for analysis with MrBayes 3.1.2 , . MrBayes offers the unique possibility to reconstruct a phylogeny based on information form several different genes in a single analysis, while applying the most appropriate model to each gene sequence. Additional tree searches were done for the combined dataset with global parameters with the maximum likelihood (ML) algorithm in PAUP* and for each gene individually with MrBayes and with ML in PAUP*. To check node stability for ML a bootstrap analysis with 1000 replicates was done with the same parameters as for the original analysis. […]

Pipeline specifications

Software tools MEGA, Clustal W, MAFFT, MrModelTest, MrBayes
Application Phylogenetics