DOI: 10.5061/dryad.zkh1893fx
title: Predator-induced shape plasticity in D. pulex

description: All animals and plants respond to changes in the environment during their
 life cycle. This flexibility is known as phenotypic plasticity and allows
 organisms to cope with variable environments. A common source of
 environmental variation is predation risk, which describes the likelihood
 of being attacked and killed by a predator. Some species can respond to
 the level of predation risk by producing morphological defences against
 predation. A classic example is the production of so-called ‘neckteeth’ in
 the water flea, Daphnia pulex, which defend against predation from
 Chaoborus midge larvae. Previous studies of this defence have focussed on
 changes in pedestal size and the number of spikes along a gradient of
 predation risk. Although these studies have provided a model for
 continuous phenotypic plasticity, they do not capture the whole-organism
 shape response to predation risk. In contrast, studies in fish and
 amphibians focus on shape as a complex, multi-faceted trait made up of
 different variables. In this study, we analyse how multiple aspects of
 shape change in D. pulex along a gradient of predation risk from C.
 flavicans. These changes are dominated by the neckteeth defence, but there
 are also changes in the size and shape of the head and the body. We
 detected change in specific modules of the body plan and a level of
 integration among modules. These results are indicative of a complex,
 multi-faceted response to predation and provide insight into how predation
 risk drives variation in shape and size at the level of the whole
 organism.
description: The data from this study was
 collected by analysing photographs taken by Dennis <em>et
 al.</em>, 2011. This included three <em>Daphnia
 pulex</em> clones which had been exposed to six levels of predation
 risk from their larval midge predator, <em>Chaoborus
 flavicans</em>. We used the <em>geomorph</em> package in
 R to digitise these images of <em>D. pulex</em> into sets of
 anatomical co-ordinates, called landmarks, to measure key aspects of
 shape. Principal component analysis was combined with phenotypic
 trajectories to measure how shape changed for each clone along the
 gradient of predation risk. Also, modularity and integration analysis was
 used to identify how shape was co-ordinated across different regions of
 the body plan.
description: All of the analyses from this study
 were performed in R v4.2.1. The following R packages were downloaded for
 use in the analysis; <em>geomorph </em>v4.0.5 and
 <em>RRPP </em>v1.3.1. Figures were produced using
 <em>Rmarkdown </em>v2.20.
description: # Guide to data from 'Predator-induced shape plasticity in D.
 pulex' ## List of filenames * Photos.zip * Analyses.R *
 Landmarks_1.tps * Landmarks_err.tps * Exp_design.csv * Code for
 figures.Rmd * Method_pic.tps ## Description of files * Photos.zip -
 Selected photos taken by Dennis et al. 2011, including: * Subfolders for
 each clone * Subfolders organised in order of the date photos were taken *
 Original - original version of the photos prior to editing in Microsoft
 Paint * Paint - edited version of the photos Note: photos are labelled
 with the date, level of predation risk, mother id (photos with the same
 letter share the same mother) and replicate number * Analyses.R - R code
 for running all of the analyses used in the publication, including: *
 Procrustes analysis * Procrustes ANOVA * Calculation of repeatability *
 Principle component analysis * Trajectory analysis * Modularity analysis *
 Integration analysis * Landmarks_1.tps - Landmark data for the all of the
 images from the main experiment * Landmarks_err.tps - Landmark data used
 to calculate repeatability * Exp_design.csv - Clone, instar and predation
 risk metadata for each animal * Code for figures.Rmd - R Markdown code for
 reproducing figures 2-6 * Method_pic.tps - Landmark data for the digitised
 image used in figure 2