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Pipeline publication

[…] sets were compared with the subset comprised of the seven most diverged Schiedea species to minimize differences in interspecific divergence and species numbers per data set., Alignments of obtained sequences were created manually or using ClustalW with default parameter values (). All alignments were unambiguous, which is not surprising given the low divergence between Schiedea species as well as within the groups of mainland plants. Coding region assignment, intron splicing, and gene concatenation were performed in ProSeq3 (). Average pairwise divergence per nucleotide for silent and nonsilent sites as well as preliminary gene trees using the neighbor-joining algorithm were obtained using Mega v.4 (). The fully resolved phylogenies of Schiedea and mainland groups were reconstructed using silent mutations (noncoding and the third positions of exons) and indels manually recoded as single mutations in a concatenated data set of all sequenced genes. The statistical selection of best-fit models of nucleotide substitution was done using jModelTest (; ). The phylogenies were reconstructed by Bayesian analysis implemented in MrBayes 3.1.2 () using a GTR+Γ model of DNA sequence evolution. Potential topological conflicts between the phylogenetic trees obtained using concatenated data sets and individual genes were assessed with approximately unbiased (AU) and weighted Shimodaira–Hasegawa (WSH) tests performed in the Treefinder package (). The fully resolved phylogenies of Schiedea and the mainland groups obtained using concatenated data sets were in agreement with previously published ones () and showed no significant topological conflict with individual genes at the 5% level or below in AU and WSH tests. These fully resolved phylogenies of Schiedea and the mainland groups were used as input trees for analyses of […]

Pipeline specifications

Software tools MEGA-V, jModelTest, MrBayes