Shared Evolutionary History Shapes Skeletal Shape in Flatfishes

Black and Berendzen 20##

---

This code completes PCA and ANOVA analyses and generated publication figures.

Required R packages

geomorph , StereoMorph , phytools , ape , dplyr , vegan , devtools , and ggbiplot

Load data

Landmarks are in the form of a TPS file. Use readland.tps to load data into R environment.

Averaged individuals by species

Use aggregate to find the average landmark coordinates per species.

Phylomorphospace

Use read.tree to read tree file, and drop.tip to remove species from the tree that are not in the landmarked file. Code will produce figures 3, S4, S5, and S6 (interactive).

Chronophylomorphospace

Produces figures 4 and S7 (interactive).

Phylogenetic Signal

Use physignal in Geomorph to generate the phylogenetic signal and produces Figure S8.

Backtransformation Flatfishes

Use btShapes.R (https://aaronolsen.github.io/tutorials/morphometrics/backtransform.html) to generate figures 2, and S3.

Input Ecological Data and Procrusties ANOVA and Pairwise

Generate ANOVA in a phylogenetic context for shape and ecological data using procD.pgls and pairwise.

Plot ecological preferences to phylomorphospace

Produces single figure (figure S9) with 4 plots for each significant ecological type.