Predator-induced shape plasticity in D. pulex

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 differen..., The data from this study was collected by analysing photographs taken by Dennis et al., 2011. This included three Daphnia pulex clones which had been exposed to six levels of predation risk from their larval midge predator, Chaoborus flavicans. We used the geomorph package in R to digitise these images of D. pulex 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., 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; geomorph v4.0.5 and RRPP v1.3.1. Figures were produced using Rmarkdown v2.20., # 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
* Mo...