DOI: 10.5061/dryad.tqjq2bw5m
title: How does parasite environmental transmission stage concentration change before, during, and after disease outbreaks?

description: Outbreaks of environmentally transmitted parasites require that
 susceptible hosts encounter transmission stages in the environment and
 become infected, but we also know that transmission stages can be in the
 environment without triggering disease outbreaks. One challenge for
 understanding the relationship between environmental transmission stages
 and disease outbreaks is that the distribution and abundance of
 transmission stages outside of their hosts have been difficult to
 quantify. Thus, we have limited data about how changes in transmission
 stage abundance influence disease dynamics; moreover, we do not know
 whether the relationship between transmission stages and outbreaks differs
 among parasite species. We used digital PCR to quantify environmental
 transmission stages of five parasites in six lakes in southeastern
 Michigan every two weeks from June to November 2021. At the same time, we
 quantified infection prevalence in hosts and host density. Our study
 focused on eight zooplankton host species (Daphnia spp. and Ceriodaphnia
 dubia) and five of their parasites from diverse taxonomic groups
 (bacteria, yeast, microsporidia, and oomycete) with different infection
 mechanisms. We found that parasite transmission stage concentration
 increased prior to disease outbreaks for all parasites. However, parasites
 differed significantly in the relative timing of peaks in transmission
 stage concentration and infection outbreaks. The ‘continuous shedder’
 parasites had transmission stage peaks at the same time as or slightly
 after the outbreak peaks. In contrast, parasites relying on host death for
 transmission (‘obligate killers’) had transmission stage peaks before
 outbreak peaks. For most parasites, lakes with outbreaks had higher spore
 concentrations than those without outbreaks, especially once an outbreak
 began; the exception was for a parasite, Pasteuria ramosa, with very
 strong genotypic specificity of infection. Overall, our results show that
 disease outbreaks are tightly linked to transmission stage concentration;
 outbreaks were preceded by increases in transmission stage concentration
 in the environment and then were fueled by the production of more
 transmission stages during the outbreak itself, with concentrations
 decreasing to pre-outbreak levels as outbreaks waned. Thus, tracking
 transmission stages in the environment improves our understanding of the
 drivers of disease outbreaks and reveals how parasite traits may affect
 these dynamics.
description: # Davenport et al. study on parasite environmental transmission stage
 concentration and disease outbreaks --- The files include all the data and
 code used to create the figures in the Davenport et al. manuscript. Data
 collection was led by Elizabeth Davenport and supported by Marcin Dziuba,
 Logan Jacobson, Siobhan Calhoun, and Kira Monell. Figures were created by
 Elizabeth Davenport and Meghan Duffy of the University of Michigan. ##
 Description of the data and file structure There are three main folders in
 the zip file: 1. scripts: this contains the code used to create figures.
 2. data: this contains the data collected during the study. 3. figures:
 this is the folder where plots will be saved from the output of the R
 markdown files. ## Sharing/Access information During the review process,
 data and code were posted at:
 # Spore
 Concentrations and Outbreak Data Data and code for 2021 field study led by
 Elizabeth Davenport Citation: How does parasite environmental transmission
 stage concentration before, during, and after outbreaks? Authors:
 Elizabeth S. Davenport 1*, Marcin K. Dziuba 1, Logan E. Jacobson 1,
 Siobhan C. Calhoun 1, Kira J. Monell 1, and Meghan A. Duffy 1 1 Department
 of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor,
 MI 48109, USA Contact: * Author responsible for writing code related to
 analyses and figures: Date: August 2023 --- DATA
 AvgDaysBetweenSporeIncreaseAndOutbreakStart.csv: this data file contains
 the number of days between the initial spore increase and the beginning of
 the disease outbreak (defined as the first sampling date when percent
 infection reached 1% or higher). Negative values describe spore
 concentrations increasing before outbreaks begin. Data are shown for the
 13 lake*parasite outbreaks described in the manuscript. Lake = name of the
 lake sampled. HostSpecies = name of the host species experiencing the
 outbreak. Parasite = name of the parasite species causing the outbreak.
 DaysBetweenSporeIncreaseAndOutbreakStart = number of days between the
 initial spore increase and the beginning of the outbreak.
 DaysBetweenPeaks.csv: this data file contains the number of days between
 the peaks in spore concentration and the peaks in disease outbreaks.
 Positive values describe spore concentration peaking after disease
 outbreaks peak. Negative values describe spore concentrations peaking
 before outbreaks peak. Parasite = name of the parasite species causing the
 outbreak. Lake = name of the lake sampled. DaysBetweenPeaks = the number
 of days between the peak in spore concentration and the peak in
 infections. Walsh_Mean_Metsch_PercentInfected.csv: this data file contains
 the mean spore concentration of Metschnikowia bicuspidata and percent
 infection of Daphnia dentifera by Metschnikowia bicuspidata in Walsh Lake
 from June 14, 2021 to November 12, 2021. datetime = sampling dates. Lake =
 name of lake sampled. Mean = mean spore concentration of Metschnikowia
 bicuspidata in spores per L. PercentInfected = percentage of the Daphnia
 dentifera host population infected with Metschnikowia bicuspidata.
 Metsch_Mean_Spores_Outbreak.csv: this data file contains the mean spore
 concentration of Metschnikowia bicuspidata in all six lakes that were
 sampled, regardless of outbreak occurrence, June 2021 to November 2021.
 datetime = sampling dates. Lake = name of lakes sampled. Mean = mean spore
 concentration of Metschnikowia bicuspidata in spores per L. Outbreak = yes
 means that an outbreak of Metschnikowia bicuspidata occurred in the lake;
 no means that an outbreak of Metschnikowia bicuspidata did not occur in
 the lake. Pasteuria_Mean_Spores_and_Percent_Infected_Outbreak.csv: this
 data file contains the mean spore concentration of Pasteuria ramosa and
 percent infection of multiple zooplankton hosts. If fewer than 20
 individuals of a host species were observed in a field sample, percent
 infection was not recorded for that species and is either NA or blank.
 datetime = sampling dates. Lake = name of lake sampled. Mean = mean spore
 concentration of Pasteuria ramosa in spores per L. Dent_Per_Inf = percent
 infection of Daphnia dentifera by Pasteuria ramosa. Retro_Per_Inf =
 percent infection of Daphnia rectrocurva by Pasteuria ramosa.
 Cerio_Per_Inf = percent infection of Ceriodaphnia dubia by Pasteuria
 ramosa. Parv_Per_Inf = percent infection of Daphnia parvula by Pasteuria
 ramosa. Outbreak = yes means that an outbreak of Pasteuria ramosa occurred
 in the lake; no means that an outbreak of Pasteuria ramosa did not occur
 in the lake. Brood_Mean_Spores_and_Percent_Infected_OutbreakSize.csv: this
 data file contains the mean spore concentration of Blastulidium
 paedophthorum and percent infection of multiple zooplankton hosts. If
 fewer than 20 individuals of a host species were observed in a field
 sample, percent infection was not recorded for that species and is either
 NA or blank. datetime = sampling dates. Lake = name of lake sampled. Mean
 = mean spore concentration of Blastulidium paedophthorum in spores per L.
 Dent_Per_Inf = percent infection of Daphnia dentifera by Blastulidium
 paedophthorum. Cerio_Per_Inf = percent infection of Ceriodaphnia dubia by
 Blastulidium paedophthorum. Dubia_Per_Inf = percent infection of Daphnia
 dubia by Blastulidium paedophthorum. Retro_Per_Inf = percent infection of
 Daphnia rectrocurva by Blastulidium paedophthorum. Pulic_Per_Inf = percent
 infection of Daphnia pulicaria by Blastulidium paedophthorum. Parv_Per_Inf
 = percent infection of Daphnia parvula by Blastulidium paedophthorum.
 Outbreak = yes means that an outbreak of Blastulidium paedophthorum
 occurred in the lake; no means that an outbreak of Blastulidium
 paedophthorum did not occur in the lake. BroodOutbreakMeans.csv: this file
 contains the mean spore concentration of Blastulidium paedophthorum for
 all six lakes and documents the occurrence of an outbreak. Lake = name of
 lake sampled. Parasite = Blastulidium paedophthorum. LogMean = Log of the
 mean spore concentration plus 1. RawMean = the raw spore concentration
 data. SD = standard deviation of the spore concentration. Outbreak =
 "yes" means an outbreak occurred in the lake, "no"
 means there was not an outbreak in the lake. BroodOutbreakMeanStats.csv:
 this file contains the mean spore concentration of Blastulidium
 paedophthorum in lakes that had outbreaks and lakes that did not have
 outbreaks. Parasite = Blastulidium paedophthorum. NoOutbreakMean = mean
 spore concentration in lakes without outbreaks. OutbreakMean = mean spore
 concentration in lakes with outbreaks.
 MicG_Mean_Spores_and_Percent_Infected_OutbreakSize.csv: this data file
 contains the mean spore concentration of Ordospora pajunii and percent
 infection of multiple zooplankton hosts. If fewer than 20 individuals of a
 host species were observed in a field sample, percent infection was not
 recorded for that species and is either NA or blank. datetime = sampling
 dates. Lake = name of lake sampled. Mean = mean spore concentration of
 Ordospora pajunii in spores per L. Dent_Per_Inf = percent infection of
 Daphnia dentifera by Ordospora pajunii. Parv_Per_Inf = percent infection
 of Daphnia parvula by Ordospora pajunii. Ambig_Per_Inf = percent infection
 of Daphnia ambigua by Ordospora pajunii. Cerio_Per_Inf = percent infection
 of Ceriodaphnia dubia by Ordospora pajunii. OutbreakSize = relative size
 of Ordospora pajunii outbreaks (medium = 15-25% of host population
 infected; large = over 25% of host population infected). Outbreak = yes
 means that an outbreak of Ordospora pajunii occurred in the lake; no means
 that an outbreak of Ordospora pajunii did not occur in the lake.
 Spiro_Mean_Spores_and_Percent_Infected.csv: this data file contains the
 mean spore concentration of Spirobacillus cienkowskii and percent
 infection of multiple zooplankton hosts. If fewer than 20 individuals of a
 host species were observed in a field sample, percent infection was not
 recorded for that species and is either NA or blank. datetime = sampling
 dates. Lake = name of lake sampled. Mean = mean spore concentration of
 Spirobacillus cienkowskii in spores per L. dent.perinf = percent infection
 of Daphnia dentifera by Spirobacillus cienkowskii. dub.perinf = percent
 infection of Daphnia dubia by Spirobacillus cienkowskii. mend.perinf =
 percent infection of Daphnia mendotae by Spirobacillus cienkowskii.
 pulic.perinf = percent infection of Daphnia pulicaria by Spirobacillus
 cienkowskii. retro.perinf = percent infection of Daphnia retrocurva.
 cerio.perinf = percent infection of Ceriodaphnia dubia by Spirobacillus
 cienkowskii. ambig.perinf = percent infection of Daphnia ambigua by
 Spirobacillus cienkowskii. parv.perinf = percent infection of Daphnia
 parvula by Spirobacillus cienkowskii. LakeSporeMeans.csv: this data file
 contains the mean spore concentration over the entire sampling season for
 all six lakes. Lake = name of lake sampled. Parasite = parasite species.
 Mean = log of the mean spore concentration + 1 for the entire sampling
 period. SD = standard deviation of the mean spore concentration. Outbreak
 = "yes" means an outbreak occurred in the lake, "no"
 means there was not an outbreak in the lake.
 Clean_Data_2021_Lakes_All_Host_Densities.csv: this file contains host
 density, total number of hosts, and infection prevalence. If fewer than 20
 individuals of a host species were observed in a field sample, infection
 prevalence was not recorded for that species and is either NA or blank.
 Date, Julian.Day, Julian = sampling dates. Lake = name of lake sampled.
 Host.Species = name of the host species (ambigua = Daphnia ambigua;
 ceriodaphnia = Ceriodaphnia dubia; dentifera = Daphnia dentifera; dubia =
 Daphnia dubia; mendotae = Daphnia mendotae; pulicaria = Daphnia pulicaria;
 parvula = Daphnia parvula). Total = total number of individuals.
 Uninfected.Adult, Uninfected.Juv, Uninfected.Males = number of uninfected
 adults, juveniles, and males respectively. All columns ending in .inf =
 number of individuals infected by each parasite species (pasteuria =
 Pasteuria ramosa; metsch = Metschnikowia bicuspidata, spiro =
 Spirobacillus cienkowskii; brood = Blastulidium paedophthorum; larssonia,
 spider, gurleya, caullerya, and coke were not included in our spore
 sampling study). All columns ending in .prev = infection prevalence of
 each parasite species. All columns ending in .inf.density = infected host
 density organized by each parasite species. All columns ending in .density
 = host density organized by each host species.
 Brood_Density_PercentInfection.csv: this file contains host density for
 host species that experienced an outbreak of B. paedophthorum. The file
 also includes percent infection and environmental mean B. paedophthorum
 spore concentration data. If fewer than 20 individuals of a host species
 were observed in a field sample, infection prevalence was not recorded for
 that species and is either NA or blank. All columns ending in .PerInf =
 percent infection for B. paedophthorum organized by host species. All
 columns ending in .density = host density organized by each host species.
 datetime = sampling dates. Lake = name of lake sampled. MeanSpore = mean
 B. paedophthorum spore concentration. MicG_Density_PercentInfection.csv:
 this file contains host density for host species that experienced an
 outbreak of Ordospora pajunii. The file also includes percent infection
 and environmental mean O. pajunii spore concentration data. If fewer than
 20 individuals of a host species were observed in a field sample,
 infection prevalence was not recorded for that species and is either NA or
 blank. All columns ending in .PerInf = percent infection for O. pajunii
 organized by host species. All columns ending in .density = host density
 organized by each host species. datetime = sampling dates. Lake = name of
 lake sampled. MeanSpore = mean O. pajunii spore concentration.
 Pasteuria_density_percentinfection.csv: this file contains host density
 for host species that experienced an outbreak of Pasteuria ramosa. The
 file also includes percent infection and environmental mean P. ramosa
 spore concentration data. If fewer than 20 individuals of a host species
 were observed in a field sample, infection prevalence was not recorded for
 that species and is either NA or blank. All columns ending in .PerInf =
 percent infection for P. ramosa organized by host species. All columns
 ending in .density = host density organized by each host species. datetime
 = sampling dates. Lake = name of lake sampled. MeanSpore = mean P. ramosa
 spore concentration. Walsh_Metsch_DentiferaDensity.csv: this file contains
 host density for Daphnia dentifera that experienced an outbreak of
 Metschnikowia bicuspidata in Walsh Lake. The file also includes percent
 infection and environmental mean M. bicuspidata spore concentration data.
 datetime = sampling dates. Lake = Walsh Lake. Mean = mean M. bicuspidata
 spore concentration. PercentInfected = percent of the D. dentifera
 population infected with M. bicuspidata. Dent.density = total density of
 D. dentifera. SporeConcentrationBeginningVersusEnd.csv: this data file
 contains spore concentrations at the beginning of disease outbreaks and at
 the end of disease outbreaks. Lake = name of lake sampled. HostSpecies =
 host species experiencing an outbreak. Parasite = parasite species.
 Date_outbreak_reached_1% = the date that at least one percent of the host
 population was infected. SporeConcentration_OutbreakStart = the mean spore
 concentration on the sampling date that the outbreak began.
 Date_Outbreak_Ends = the date that no infections were observed or the end
 of the sampling season. SporeConcentration_OutbreakEnds = mean spore
 concentration on the sampling date when the outbreak ended.
 Change_in_Spore_Concentration = change in mean spore concentration from
 the beginning of the outbreak to the end of the outbreak.
 SporeConcentrationBeginningVersusEndFigure.csv: this data file contains
 spore concentrations at the beginning of disease outbreaks and at the end
 of disease outbreaks. Lake = name of lake sampled. HostSpecies = host
 species experiencing an outbreak. Parasite = parasite species. Date =
 sampling date when the outbreak either started or ended.
 SporeConcentration = mean spore concentration. LogSporeConcentrationPlus1
 = log of the mean spore concentration plus one. OutbreakStatus = the
 outbreak is either starting or ending. OutbreakID = numbering the
 outbreaks to group the starting and ending spore concentrations together.
 ---