DOI: 10.5061/dryad.k3j9kd59h
title: Data from: Shoaling guppies evade predation but have deadlier parasites

description: We collected data on coinfection rates, infection prevalence, and
 infection intensity for Gyrodactylus spp. on wild Trinidadian guppies
 (Poecilia reticulata). We also collected data on the shoaling preference
 of wild-caught guppy hosts. Further, we collected data on transmission
 rates, infection intensity, and infected host mortality rates of lines of
 these parasites on guppies in the laboratory. We fouind that wild guppy
 populations with stronger shoaling preferences had higher infection
 prevalence and coinfection rates. Further, we found a transmission
 rate-virulence tradeoff among parasite lines mediated by infection
 intensity. Lastly, parasite lines from populations with stronger shoaling
 preferences were found to attain higher infection intensity and impose
 higher mortality on infected hosts. These data may be re-used with
 citation of the corresponding manuscript, "Shoaling guppies evade
 predation but have deadlier parasites." For more information, see
 that corresponding manuscript.
description: See the corresponding manuscript, "Shoaling guppies evade
 predation but have deadlier parasites"
description: See the README file or these instructions.<br><br>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 our previously unpublished data uses different lines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.