Data from: Shoaling guppies evade predation but have deadlier parasites

See the README file or these instructions.In the .rmd file, we provide the code for replicating our results. Below is a data dictionary naming the code files and explaining their contents in order of appearance in this file; this file is in order of empirical data appearance in the main text, then in the supplementary information, then has modelling code at the end. Files, uses, and variable names: SI_transmission.csv contains the data from our Transmission Rate Experiment and the data from Stephenson et. al 2017 which we used in creating Figure 3A. The variables are full_dwormattrans: natural log of the number of parasites the donor had at the point of transmission full_rspeedtrans: the transmission rate, calculated following the details in the main text full_line: the identity of the isogenic line: Gt3 is the line used by Stephenson et. al 2017, while our previously unpublished data uses different lines such as “GyTu_CA_L3”, which means Gyrodactylus turnbulli line CA_L3; this also corresponds to the CA_L3 line in SI_parasitetraits.csv. NA in a row indicates that the donor fish did not transmit its infection in the 5 days of the experiment. SI_tradeoff.csv contains data averages and identifying information from 22 lines. This is a summary and subset of the data in SI_parasitetraits.csv. linename: the identifying name of the isogenic line meanintensity: the mean intensity recorded on fish infected with that line meandeath: the mean death rate of fish infected with that line, as explained in the main text. meantransmission: the mean transmission rate of each isogenic line, estimated from their individual measurements of intensity and the relationship in Fig. 3A origin: whether the isogenic line originated from a guppy collected in the wild (‘Wild’), or obtained from a commercial supplier (‘Domestic’) SI_Behav.csv contains data from our Field Survey of Shoaling Rate, which contains the following variables: Sex: sex of the fish River: the river of origin of the fish Course: the course of the river of origin - upper or lower Length: length of the fish (mm) Infec: whether or not the fish was infected Prop.Shoal200: the proportion of time the fish spent shoaling during a behavioral trial DOT: date the data were collected in YYYYMMDD format ShoalID: identity of the shoal used - each was used more than once ShoalSide: side of the enclosure that contained the shoal - to control for side bias enclosure: which enclosure was used for the trial Lighting: whether the trial was conducted in relatively light or dark lighting Lit_behavior.csv is data on shoaling rate taken from the literature, which contains: river: the river of origin of the fish course: the course of the river of origin - upper or lower value: the proportion of time the fish spent shoaling during a behavioral trial year: the year in which the data were collected source: the source of the data - either the paper from which they were extracted, or ‘Lab’, denoting that 2 we collected them ourselves during our Field Survey of Shoaling Rate in Trinidad in March 2020. Lit_prevalence.csv, which contains the following variables: river: the river of origin of the fish course: the course of the river of origin - upper or lower prev.yr: the year in which the data were collected prev.n: the number of fish sampled for that prevalence estimate prev: the proportion of hosts that were found infected with Gyrodactylus spp. source: the source of the data - either the paper from which they were extracted, or ‘Lab’, denoting that we collected them ourselves during our Field Survey of Prevalence in Trinidad in March 2020. Lit_density.csv is data from the literature on guppy density and contains the following variables: river: the river of origin of the fish course: the course of the river of origin - upper or lower year.collected: the year in which the data were collected value: the estimated number of fish per square meter paper.source: the source of the data SI_parasitetraits.csv, which gives data per individual fish per row, and includes the following variables: line: the identity of the isogenic line species: the species identity of the line with t for turnbulli, b for bullatarudis, and NA for unknown as not all lines had an individual checked for species ID by molecular methods date: the calendar date on which the observation was made in YYYYMMDD linf: the total number of days the worm line was maintained in the lab lineday: the number of days since the line was established in the lab lnldy: lineday nested in line: gives each line/lineday combination a unique label to control for psuedoreplication in our analysis gyro: the number of gyrodactylus found on the fish at that date. NA for fish that were dead. type: categorical variable describing whether the fish was dead, uninfected or infected course: whether the isogenic line was initiated from a worm wild-caught in the upper or lower courses of a Trinidadian river, or from a commercially available lab stock fish (‘Lab’) river: the river (or “Lab” meaning a domestic line) from which the worm line originated lagint: the mean intensity (total number of parasites/total number of infected fish) at the previous observation daysls: the number of days since the previous observation lagdeathinf: the number of dead fish at this observation/the number of infected fish at the previous observation [note this can theoretically be larger than 1 because new uninfected fish added at the previous timepoint would not be included in the denominator here, but may become infected and die by the subsequent timepoint] nfish: the number of fish in the tank at the observation (excluding newly added uninfected fish) SI_ParasiteCounts2020.csv holds counts of parasites in wild populations taken in 2020. These are used for comparing laboratory intensities to field intensities (Fig. S2) and for estimating the proportion of infected fish with just one worm to determine wild coinfection rates (Table S1). Each row is one fish. The relevant columns are Course2 This states whether a sample was from an upper coure or lower course population River The river that was sampled Gyro The number of Gyrodactylus spp. on that fish. SI_ParasiteCountsOther.csv holds data from Stephenson et. al 2015 to help establish what is a normal percentage of fish with more than one worm by providing additional power, thus contributing to Table S1. Each row is one fish. The relevant columns are 3 course This states whether a sample was from an upper coure or lower course population river The river that was sampled gyro The number of Gyrodactylus spp. on that fish. SI_coinfection.csv holds data from the Field Survey of Coinfection Rates. Each row is one fish. The columns are Fish.ID A unique ID for each fish. River The river the fish was sampled from. Course The course the fish was sampled from. Number.of.GB.genotyped The number of worms sampled from the fish that were found to be G.B. Number.of.GB.genotypes The number of different G.B. genotypes found on the fish. Number.of.GT.genotyped See corresponding column for G.B. Number.of.GT.genotypes See corresponding column for G.B.