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Data from: Shoaling guppies evade predation but have deadlier parasites

Citation

Walsman, Jason et al. (2022), Data from: Shoaling guppies evade predation but have deadlier parasites, Dryad, Dataset, https://doi.org/10.5061/dryad.k3j9kd59h

Abstract

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.

Methods

See the corresponding manuscript, "Shoaling guppies evade predation but have deadlier parasites"

Usage Notes

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previously unpublished data uses different lines such as “GyTu_CA_L3”, which means Gyrodactylus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

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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

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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.

Funding