Data and Code Archive for Bolnick et al Indirect Genetic Effects Dominance

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: [e-mail] 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.

本数据集与代码存档配套的README文件，关联论文：Bolnick、Arruda、Polania、Simonse、Padhiar、Roth与Rodgers，2023年，《共感染寄生虫间接效应对宿主性状的主导作用》。
联系方式：美国康涅狄格大学生态与进化生物学系Daniel Bolnick博士，地址：斯托尔斯 CT 06269，电子邮箱：[e-mail]

研究概要：寄生虫可产生间接遗传效应（Indirect Genetic Effects, IGE）以修饰宿主性状。当两种寄生虫共感染同一宿主时，二者的间接遗传效应可能相互冲突。哪一种间接遗传效应占据主导？我们构建了包含数值模拟的数学模型，证明间接遗传效应的主导作用对演化动力学具有关键影响。随后我们呈现了三项抗原注射实验的结果，证实了感染棘鱼的绦虫存在间接遗传效应，且共感染过程中存在超显性现象。

资助信息：本研究由美国国立卫生研究院（NIH）1R01AI123659-01A1项目（DIB）以及康涅狄格大学资助。

存档文件内容：
### 代码（CODE）
代码文件的运行顺序无特定要求。论文中首先展示了模拟结果。所有代码分析由D. Bolnick编写并执行。
1. Simulations.R：该R脚本可运行数值模拟，复现论文中数学模型的相关结果，运行该脚本无需依赖任何数据文件。
2. Experiment Analyses and Graphs.Rmd：该R标记文档可生成论文中实证结果的全部统计结果与图表（含补充附图）。该文件需使用下述4个数据文件运行。
代码编写与运行环境如下：R version 4.1.0 (2021-05-18)，平台：x86_64-apple-darwin17.0 (64-bit)，运行系统：macOS 12.6.2。各代码文件顶部已列出所需依赖的R包（libraries）。

### 数据（DATA）
以下为各数据文件的名称与内容说明：
1. LakeSurvey2009.csv：该数据集此前已公开发表（Bolnick et al 2020 Ecography），包含2009年对46个棘鱼种群的调查所得的寄生虫负荷数据，由D. Bolnick、Kim Ballare与Julia Day采集。本存档仅复现与翘鼻棘头绦虫（Schistocephalus solidus）感染强度相关的数据。数据按个体鱼为行、变量为列排布，列标题如下：
A) site_name：鱼类采样地点
B) habitat_type：生境类型（河口、溪流或湖泊）
C) sex：鱼类性别
D) mass：鱼类体重（克）
E) std_length：鱼类标准体长（毫米）
F) Schisto_totalMass：宿主体内所有翘鼻棘头绦虫的总重量（克）
G) Schistocephalus：宿主体内翘鼻棘头绦虫的数量
2. PolaniaExperiment.csv：本数据集对应论文中的实验1。本实验向罗塞尔湖棘鱼注射源自4个湖泊的绦虫蛋白提取物，并在10天后评估纤维化程度，由Christian Polania开展实验并采集数据。数据按个体鱼为行、变量为列排布，列标题如下：
A) lake：用于提取绦虫蛋白的湖泊来源，包括Roselle、Boot、Cheney与Gosling湖
B) ID：鱼类编号
C) sex：鱼类性别（m为雄性，f为雌性）
D) fibrosis：纤维化评分，采用0至4的有序尺度
E) lakeBin：湖泊的数值分类变量
F) sexBin：性别的数值评分，雌性记为1，雄性记为0
3. ArrudaExperiment.csv：本数据集对应论文中的实验2。本实验向罗塞尔湖棘鱼注射生理盐水（对照组）、单一绦虫蛋白或两种绦虫蛋白的混合物（设置两种浓度），随后评估纤维化程度。实验由Sophia Arruda、Lauren Simonse开展，Maria Rodgers、Andrea Roth与Dan Bolnick提供协助并完成数据采集。数据按个体鱼为行、变量为列排布，列标题如下：
A) Fish_ID：鱼类编号
B) Treatment：处理组，其中Control为仅注射生理盐水，Boot为仅注射Boot湖绦虫蛋白，Cheney为仅注射Cheney湖绦虫蛋白，Roselle为仅注射Roselle湖绦虫蛋白，RCLow为低浓度共注射Roselle与Cheney湖蛋白，RCHigh为高浓度共注射Roselle与Cheney湖蛋白，RBLow为低浓度共注射Roselle与Boot湖蛋白，RBHigh为高浓度共注射Roselle与Boot湖蛋白
C) Roselle：是否注射Roselle湖绦虫蛋白（T/F，即是/否）
D) Boot：是否注射Boot湖绦虫蛋白（T/F）
E) Cheney：是否注射Cheney湖绦虫蛋白（T/F）
F) Concentration：浓度，共注射组设为Low（替代设计）与High（累加设计），非共注射组记为NA
G) Fibrosis_score：主观察者评分（通过显微镜与手剖）
H, I, J, K)：其他观察者通过屏幕/录像进行的评分
L) Mass_g：鱼类体重（克）
M) Sex：鱼类性别
N) Group：处理批次，鱼类按时间批次进行注射
O) Discard_data：因弹性染料标记模糊（部分染料颜色难以区分或已脱落）导致处理组信息不确定时，标记为需舍弃的数据
4. Arshad.csv：对应补充图3的数据集。本实验注射不同浓度的绦虫蛋白，以重新验证浓度效应不存在（证实未检测到浓度的显著影响），实验由Arshad Padhiar开展。该文件包含两列：
A) Treatment：处理组，包括阴性对照（生理盐水）、稀释蛋白组、全浓度蛋白组与阳性对照（明矾）
B) Fibrosis：纤维化评分，采用0至4的有序尺度

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