This repository contains the data and code for Coblentz, K.E., L. Yang, A. Dalal, M. Incarnato, D. Thilakarathne, C. Shaw, R. Wilson, F. Biagioli, K.L. Montooth, and J.P. DeLong. 2024. Heritable intraspecific variation among prey in size and movement interact to shape predation risk and potential natural selection. Functional Ecology.
The repository contains the following .csv files containing the raw data from the experiment:
CopepodForagingLengths_Clean.csv -- This file contains three columns: Copepod.ID which contains the label for each copepod, Length which gives each copepods length in mm, and Width which gives the width of each copepod in mm.
Paramecium_Phenotype_Data.csv -- This file contains the morphological and movement data for each cell maeasured across the 126 outcrossed Paramecium lines in the experiment. The final column contains a variable id that has a string for each row, and the component of the string consisting of "G_[Number]" gives the name of the outcrossed line that the cell belongs to. For explanations of the morphological and movement variables, see the supplementary material of the published manuscript.
Foraging trial data.csv -- This file contains the data from foraging trials of copepods consuming Parmamecium. The file contains information on the date on which the foraging trial was performed (Date), the ID of the of individual copepod used in the trial (Copepod ID), the ID number of the outcrossed line used in the foraging trial (Prey type, note that this corresponds to the number in the G_[Number] string in the id column of the phenotype data), the time at which the trial was started and ended (Time strarted and Time ended), the prey offered at the beginning of the trial and the prey remaining at the end of the trial (Prey offered and Prey remaining), a column for notes (Notes), and a column designating the copepod that died during the experiment (Dead).
The repository contains the two following .R files that were used to analyze the data:
QuantitativeGeneticsAnalysis_Clean.R -- This R file contains the code to quantify the heritability of the Paramecium traits from the Paramecium_Phenotype_Data.csv file.
CopepodForagingAnalysis_Clean.R -- This R file contains the code to perform a princpal components analysis on the Paramecium phenotype data, perform the regression analysis on the proportion of Paramecium consumed during the foraging trials, and generates all of the figures within the the manuscript and supplementary material.