Computational protocol: Replicate Phylogenies and Post-Glacial Range Expansion of the Pitcher-Plant Mosquito, Wyeomyia smithii, in North America

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Protocol publication

[…] In parallel with our previous RAD-seq study , we inferred phylogenies using maximum parsimony (MP) with bootstrap support and maximum likelihood (ML) with approximate likelihood ratio (aLRT-SH). MP trees were found using PAUP* with a standard heuristic search. Support for branches on the MP tree was estimated using a bootstrap with 200 samples. ML trees were developed in three steps: model selection, model optimization, and branch support estimation. We first found the best-fitting nucleotide model using a hierarchical likelihood ratio test (hLRT) and the Akaike information criterion (AIC) as implemented in jModelTest and ModelTest . For the initial and new data set, the hLRT and AIC agreed that the best-fitting model was the transversion model (TVM) with variable base frequencies, variable transversion rates, and transition rates equal. We next found ML trees by optimizing the parameter values and branch lengths of the best-fitting models using PhyML version 3.0 . Finally, we estimated support values on the ML trees using a non-parametric Shimodaira–Hasegawa-like approximate likelihood ratio test (SH-like aLRT) scaled from 0 to 100. SH-like aLRTs were used in order to make parallel comparisons with the previously-published ML tree . […]

Pipeline specifications

Software tools PAUP*, jModelTest, PhyML
Application Phylogenetics