DOI: 10.6084/m9.figshare.22083230.v2
title: Data and Code Archive for Bolnick et al Indirect Genetic Effects Dominance

description: README file for the data and code archive to accompany:
Bolnick, Arruda, Polania, Simonse, Padhiar, Roth, and Rodgers. 2023. The dominance of coinfecting parasites’ indirect effects on host traits.
Contact:  
Dr. Daniel Bolnick
Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs CT 06269, USA. 
email: daniel.bolnick@uconn.edu
Summary of the research: Parasites can generate Indirect Genetic Effects that modify host traits. When two parasites coinfect a single host, their IGEs may conflict. Which IGE is dominant? We present a mathematical model with numerical simulations to show that IGE dominance is important in dictating evolutionary dynamics. Then we present results from three antigen injection experiments showing that IGEs exist for tapeworms infecting stickleback, and that there is overdominance during coinfection.
Funding: NIH grant 1R01AI123659-01A1 to DIB, and by the University of Connecticut 
Archive file contents:
CODE: The order that the code files are run is not important. Simulation results are presented first in the paper. Code analyses were written and executed by D. Bolnick.
Simulations.R  This R script runs the numerical simulations needed to recreate the results of the mathematical model presented in the paper. No data files are required to run this code.
Experiment Analyses and Graphs.Rmd This R markdown script produces all statistical results and graphics for the empirical results in the paper (including supplemental figures). This file uses four data files, listed below.
Code was written and analyzed in the following versions:
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS 12.6.2
Code dependencies (libraries) are listed at the top of each code file.
DATA: Here each data file is named, and its contents described.
LakeSurvey2009.csv  This data file is originally published elsewhere (Bolnick et al 2020 Ecography). It contains parasite load data from a survey of 46 stickleback populations, done in 2009. These data were collected by D. Bolnick, Kim Ballare, and Julia Day. Here we only reproduce the data specifically pertinent to Schistocephalus solidus intensity. Data are arranged as individual fish (rows) and variables (columns), with the following column headers:
A) site_name: the location where fish were sampled
B) habitat_type: estuary, stream, or lake
C) sex: sex of the fish
D) mass: fish mass (grams)
E) std_length; fish standard length (mm)
F) Schisto_totalMass: total mass (g) of all Ssolidus in the fish
G) Schistocepahlus: the number of S.solidus in the fish.
PolaniaExperiment.csv This data file is for Experiment 1 in the paper. We injected Roselle Lake stickleback with tapeworm protein extract from one of four source lakes, and scored fibrosis 10 days later. This study was conducted and data collected by Christian Polania. Data are arranged as individual fish (rows) and variables (columns) with the following column headers:
A) lake: the lake from which the tapeworm was collected to obtain protein extract. Roselle, Boot, Cheney, and Gosling Lakes.
B) ID: fish ID
C) sex: fish sex (m for male, f for female)
D) fibrosis: fibrosis score on an ordinal scale of 0 to 4
E) lakeBin: a numerical category for lake
F) sexBin: a numerical scoring for sex, 1 for females 0 for males
ArrudaExperiment.csv This data file is for Experiment 2 in the paper. We injected Roselle Lake stickleback with either saline (control), one tapeworm protein, or a mix of two tapeworm proteins (at two concentrations), then scored fibrosis. This study was conducted and data collected by Sophia Arruda, Lauren Simonse, with help from Maria Rodgers and Andrea Roth and Dan Bolnick. Data are arranged as individual fish (rows) and variables (columns) with the following column headers:
A) Fish_ID: fish ID
B) Treatment: 
Control = saline only
Boot = Boot Lake protein only
Cheney = Cheney Lake protein only
Roselle = Roselle Lake protein only
RCLow = Roselle + Cheney coinjection at low concentration
RCHigh = Roselle + Cheney coinjection at high concentration
RBLow = Roselle + Boot coinjection at low concentration
RBHigh = Roselle + Boot coinjection at high concentration
C) Roselle: presence/absence (T/F) of Roselle Lake protein injection
D) Boot: presence/absence (T/F) of Boot Lake protein injection
E) Cheney: presence/absence (T/F) of cheney Lake protein injection
F) Concentration: Low (substitutive design), High (additive design), only for coinjected fish, NA otherwise
G) Fibrosis_score: Primary observer (through microscope and hands-on dissection)
H, I, J,K) - scores by other observers using video screen / video recording
L) Mass_g: fish mass in grams
M) Sex: fish sex
N) Group: treatment batch; fish were injected in temporal blocks
O) Discard_data: when Treatment assignment is not confident due to ambiguous elastomer color dye marks (some colors were harder to distinguish in small quantities or were lost)
Arshad.csv: Data for Supplementary Figure 3. We injected tapeworm protein at very different concentrations to re-evaluate the lack of concentration effect (confirming there is no detectable effect of concentration). The experiment was conducted by Arshad Padhiar. The file contains two columns:
A) Treatment: Negative control (saline), Protein diluted, Protein full concentration, and positive control (alum).
B) Fibrosis: fibrosis score on an ordinal 0 - 4 scale.
Copyright information: MIT License:
Copyright (c) 2023, Daniel I. Bolnick
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.