Computational protocol: Phylogenetic and Taxonomic Status Analyses of the Abaso Section from Multiple Nuclear Genes and Plastid Fragments Reveal New Insights into the North America Origin of Populus (Salicaceae)

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Protocol publication

[…] Both the nuclear and chloroplast sequences were aligned using the program ClustalX () and were refined manually in BioEdit (). For all loci, regions with more than five mononucleotide or microsatellite repeats were excluded because of the uncertainty of homology that could be exacerbated by potential inaccuracies of the enzymatic process during PCR and sequencing (; ). Some loci or regions that failed to amplify and were treated as missing data in the subsequent phylogenetic analyses. Phylogenetic relationships were reconstructed with maximum parsimony (MP), maximum likelihood (ML), and Bayesian inference (BI) using PAUP/4.0b10 (), PhyML-v2.4.4 () and MrBayes 3.1.2 (), respectively, with S. triandra, S. arbutifolia, Idesia polycarpa, Itoa orientalis, and Poliothyrsis sinensis as outgroups.For the MP analysis, all characters were treated as unordered and equally weighted. A heuristic search was performed with 1000 replicates of random stepwise addition of sequences and the number of trees held in RAM was set to be 100000, with tree-bisection–reconnection (TBR) branch swapping and MULTREES on. The bootstrap analysis was conducted with 1000 replicates using simple taxon addition ().The evolutionary models for the ML and BI phylogenetic analyses were determined by jModelTest 2.1.1 () with an Aikaike Information Criterion (AICc). The variability of alleles from each individual and the sequence characteristics of each nuclear gene and plastid gene as well as the most appropriate models fitting each locus are shown in Supplementary Table . ML analyses for heuristic tree searches were carried out with the selected substitution model, random taxon addition of 1000 replicates, TBR branch swapping, the MULPARS option on, 100000 trees held in RAM and 100 replications of the bootstrap analysis. For BI, we conducted two independent Markov Chain Monte Carlo (MCMC) runs, each consisting of one cold and three heated MCMC chains that were run for 1000,000 generations and sampled every 100 generations; all other parameters were set to default. The first 25% of the sampled trees were discarded as burn-in to ensure that the chains had become stationary, and the posterior probabilities were calculated from the remaining trees. The statistical support values were presented on the phylogenetic trees. All the phylogenetic trees were viewed in the program FigTree v 1.4.2 (). […]

Pipeline specifications

Software tools Clustal W, BioEdit, PAUP*, PhyML, MrBayes, jModelTest, FigTree
Application Phylogenetics
Organisms Poecilia mexicana