Computational protocol: Genome Size Diversity in Lilium (Liliaceae) Is Correlated with Karyotype and Environmental Traits

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Protocol publication

[…] To control for statistical non-independence, we accounted for phylogeny of Lilium previously generated by Du et al. () in our statistical analysis. All sequence data were derived from analysis of the nuclear rDNA internal transcribed spacer (ITS) region (Du et al., ). Phylogenetic analyses were conducted using MP and ML. An MP tree was constructed using PAUP* 4.0b10 (Swofford, ). An ML phylogenetic analysis was performed using RAxML 7.0.4 with unique model parameters (Stamatakis, ). A general time-reversible model was applied with a discrete gamma distribution. Bootstrap pseudo replicates were performed 1,000 times using the fast bootstrapping option and the best scoring ML tree. Phylogenetic trees were visualized using Treeview (Page, ). The best scoring tree was visualized with FigTree 1.3.1 (http://tree.bio.ed.ac.uk/). Species of Notholirion and Cardiocrinum were used as outgroup (Figure ).We first employed Pagel's λ (Pagel, ) implemented in the phylosig function in the phytools package (Revell, ) of R version 3.0.2 (Team, ) to test whether the data exhibited a significant phylogenetic signal. This package (Ågren et al., ) assesses the significance of phylogenetic signals by performing a likelihood ratio test against the null hypothesis that λ = 0. Next, we performed PGLS (Butler and King, ) regression between GS and karyological and ecological data, using the ape (Paradis et al., ) and geiger (Harmon et al., ) packages in R. We carried out the PGLS tests under both neutral (Brownian motion) and stabilizing selection (Ornstein–Uhlenbeck) models of trait evolution. AIC was employed to determine which model best described the data.Evaluation of the significance of differences between groups/sections was based on calculation of the ANOVA and Tukey-HSD tests. […]

Pipeline specifications

Software tools RAxML, TreeViewX, FigTree, Phytools, APE, GEIGER
Application Phylogenetics