DOI: 10.5061/dryad.83bk3jb65
title: Data and code from: Fitness consequences of parasitism in a changing world: A case study with bird blow flies and sagebrush songbirds

description: Host-parasite interactions increasingly are influenced by human-induced
 rapid environmental change (HIREC), and the fitness effects of parasitism
 may be compounded or exacerbated by host traits and/or exposure to
 additional extrinsic stressors associated with HIREC. Potential
 interactions between parasitism and different stressors associated with
 environmental change, however, remain poorly understood for most systems.
 We examined how parasitism by bird blow flies (Trypocalliphora braueri),
 ambient weather conditions, and habitat disturbance jointly affected
 offspring traits and juvenile mortality for two declining species of
 sagebrush songbirds (Brewer’s Sparrow, Spizella breweri; and Sage
 Thrasher, Oreoscoptes montanus) in Wyoming, USA. We evaluated two
 alternative hypotheses: that parasitism could act (i) in an independent
 and additive manner with temperature and habitat alteration (Multiple
 Stressors Hypothesis), or (ii) synergistically to exacerbate the effects
 of temperature and habitat alteration (Parasitism-HIREC Interaction
 Hypothesis) on offspring traits and juvenile mortality. We assessed
 morphometric traits of nestlings and survival of fledglings in relation to
 parasite loads, temperature, and habitat disturbance associated with
 natural gas development using liner mixed models and Cox
 proportional-hazard models. Higher parasite loads and colder temperatures
 were associated with different effects for nestlings of each host species,
 reducing tarsus and wing chord length for Brewer’s Sparrow and increasing
 mass for Sage Thrasher. Despite differences in the effect of parasitism on
 nestling traits, post-fledging mortality risk for both species increased
 with higher parasite loads. The effects of parasitism and temperature
 mainly were additive, with limited evidence that weather exacerbated the
 effects of parasitism. Habitat disturbance had a weak positive effect on
 nestling tarsus length and post-fledging survival probability for Brewer’s
 Sparrow. Although parasitism rarely results in direct mortality of hosts,
 parasites can nonetheless exert considerable fitness consequences,
 especially when combined with extrinsic stressors associated with
 human-induced environmental changes.
description: # Data and code from: Fitness consequences of parasitism in a changing
 world: A case study with bird blow flies and sagebrush songbirds Dataset
 DOI: [10.5061/dryad.83bk3jb65](https://doi.org/10.5061/dryad.83bk3jb65) ##
 Description of the data and file structure This dataset consists of the
 data and R code required to replicate analyses presented in Jones et al
 (in review), testing how bird blow fly parasitism, ambient temperature,
 and habitat disturbance affect nestling morphometric traits and
 post-fledging survival for two species of sagebrush songbirds. Data were
 collected from 2017-2023 in the Upper Green River Basin, WY, USA. Included
 here are proofed, raw data files with nestling measurements and parasite
 counts, and fledgling telemetry relocation events. Also included are data
 files with ambient temperature recorded at study plots, ambient
 temperature recorded at a nearby NWS weather station, and shapefiles
 hand-digitized from NAIP imagery used to calculate habitat disturbance.
 There is one set of R scripts containing code that reads in, cleans, and
 reformats all the raw data and covariates and writes out a finished
 datafile for analysis and visualization. There is a second set of R
 scripts that reads in this finished datafile, conducts analyses, and
 produces data visualizations. ### Files and variables #### README
 **Dataset Overview** This dataset consists of the data and R code required
 to replicate analyses presented in Jones et al (in press), testing how
 bird blow fly parasitism, ambient temperature, and habitat disturbance
 affect nestling morphometric traits and post-fledging survival for two
 species of sagebrush songbirds. Data were collected from 2017-2023 in the
 Upper Green River Basin, WY, USA. Included here are proofed, raw data
 files with nestling measurements, parasite counts, and fledgling telemetry
 relocation events. Also included are data files with ambient temperature
 recorded at study plots, ambient temperature recorded at a nearby NWS
 weather station, and shapefiles hand-digitized from NAIP imagery used to
 calculate habitat disturbance. There is one set of R scripts containing
 code that reads in, cleans, and reformats all the raw data and covariates
 and writes out a finished datafile for analysis and visualization. There
 is a second set of R scripts that reads in this finished datafile, runs
 models, and produces data visualizations presented in the manuscript.
 **Files and Variables** *Folder:* Code *Description:* Contains R scripts
 for reading in, reformatting, and analyzing data *File:* ‘Nestling Data
 Cleaning and Reformatting Script.R’ *Description:* Reads in raw, proofed
 data from a variety of sources and combines/compiles/extracts all
 necessary components and covariates into a single dataframe which is
 written out and subsequently used to run the nestling analysis and
 visualize results in another script. *File:* ‘Fledgling Data Cleaning and
 Reformatting Script.R’ *Description:* Reads in raw, proofed data from a
 variety of sources and combines/compiles/extracts all necessary components
 and covariates into a single dataframe which is used to run the fledgling
 analysis and visualize results in another script. *File:* ‘Nestling Data
 Analysis and Visualization Script.R’ *Description:* Reads in single
 dataframe containing reformatted, cleaned nestling data with covariates
 attached. Models the effects of parasitism, temperature, and habitat
 disturbance on nestling traits and generates model selection tables.
 Summarizes top models, generates model predictions, and creates figures
 and tables presented in manuscript. *File:* ‘Fledgling Data Analysis and
 Visualization Script.R’ *Description:* Reads in single dataframe
 containing reformatted, cleaned fledgling telemetry data with covariates
 attached. Models the effects of parasitism, temperature, and habitat
 disturbance on nestling traits and generates model selection tables.
 Summarizes top models, generates model predictions, and creates figures
 and tables presented in manuscript. \~~ *Folder:* Raw Proofed Data
 *Description:* Contains all raw datafiles that are read in, reformatted,
 and combined in ‘Nestling Data Cleaning and Reformatting Script.R’ and
 ‘Fledgling Data Cleaning and Reformatting Script.R’ *Subfolder:* Fledgling
 Telemetry Data *Description:* Contains raw proofed fledgling telemetry
 data *File:* ‘2023_Fledgling_Telemetry_Data_Raw_Proofed.xlsx’ *Variables:*
 -       NestId: Unique identifier for nest of origin for each tracked
 fledgling -       TagId: Unique alpha-numeric identifier for each radio
 telemetry tag -       BandCombo: Combination of color band and USGS
 aluminum band used to visually identify fledglings from the same nest
 -       BandNumber: Unique number embossed on USGS aluminum band for each
 fledgling -       Obs: Observer initials -       Date: Date of fledgling
 relocation event (M/D/Y) -       Time: Time of each fledgling relocation
 event (HH:MM). Blank cells represent missing data where time was not
 recorded. -       Found?: Indicates whether the fledgling was found and
 seen (Y/N) -       Flagged?: Indicates whether the fledgling location was
 marked with flagging (Y/N) -       Disposition: Indicates whether the
 fledgling was alive, dead, or unknown -       UTME: Universal Transverse
 Mercator easting for location (Zone 12T). This column left blank when
 fledglings were not found. -       UTMN: Universal Transverse Mercator
 northing for location (Zone 12T). This column left blank when fledglings
 were not found. *Subfolder:* Habitat Disturbance Data *Description:*
 Contains shapefiles of roads, well pads, and reclaimed areas
 hand-digitized from National Agricultural Imagery Program (NAIP) images
 *Subfolder:* 2017 Digitized Disturbance Layers *Description:* Contains
 layers from NAIP imagery collected in 2017. File ‘Pad2017_erase_diss.shp’
 is a layer consisting of all well pads; file ‘Rec2017_erase12_diss.shp’ is
 a layer consisting of all reclaimed areas; file ‘Road2017_diss.shp’ is a
 layer consisting of all roads. These layers are collectively used to
 calculate habitat disturbance for nests in 2017, 2018, and 2021.
 *Subfolder:* 2022 Digitized Disturbance Layers *Description:* Contains
 hand-digitized shapefiles from NAIP imagery collected in 2022. File
 ‘Pad2022.shp’ is a layer consisting of all well pads; file ‘Rec2022.shp’
 is a layer consisting of all reclaimed areas; file ‘Road2022_diss.shp’ is
 a layer consisting of all roads. These layers are collectively used to
 calculate habitat disturbance data for nests in 2022 and 2023 and for
 fledgling relocations in 2023. *Subfolder:* Nest Data *Description:*
 Contains separate tables with data on monitored nests for each year of the
 study (2017, 2018, 2021, 2022, and 2023) *Files:* ‘tbl_Nests_17.xlsx’,
 ‘tbl_Nests_18.xlsx’, ‘tbl_Nests_21.xlsx’, ‘tbl_Nests_22.xlsx’,
 ‘tbl_Nests_23.xlsx’ *Variables:* -       NestID: Unique identifier for
 each nest -       Plot: Study plot -       Year: Study year -      
 Species: 4-letter alpha code for bird species (BRSP=Brewer’s Sparrow,
 SATH=Sage Thrasher) -       HatchDate: Date on which the first nestling in
 each nest hatched (M/D/Y). This column left blank for nests that did not
 hatch. -       HatchDate_cert: Indicates whether or not the hatch date was
 known with certainty (Certain/Probable). This column left blank for nests
 that did not hatch. -       FledgeDate: Date on which the first nestling
 in each nest fledged (M/D/Y). This column left blank for nests that did
 not fledge. -       FledgeDate_cert: Indicates whether or not the fledge
 date was known with certainty (Certain/Probable). This column left blank
 for nests that did not fledge. -       UTME: Universal Transverse Mercator
 easting for nest location (Zone 12T) -       UTMN: Universal Transverse
 Mercator northing for nest location (Zone 12T) -       Male: If known,
 indicates unique color band combination for adult male bird associated
 with nest. This column left blank for nests where the male was not banded
 or the band combination was not known. -       Female: If known, indicates
 unique color band combination for adult female bird associated with nest.
 This column left blank for nests where the female was not banded or the
 band combination was not known. -       Notes: Additional notes recorded
 about nest, including signs of predation or abandonment in case of nest
 failure. This column left blank when no notes were recorded. -       Fate:
 Indicates whether one or more nestlings successfully fledged from nest
 (Success/Fail/Unknown) *Subfolder:* Nestling Banding Data *Description:*
 Contains raw proofed nestling banding, measurement, and parasite count
 data. Cells infilled with "null" represent missing data. *File:*
 ‘Nestling_Measurements_Complete.xlsx’ *Variables:* -       NestID: Unique
 identifier for each nest from which nestlings were banded and measured
 -       BandNumber: Unique identifier for each nestling which was banded
 and measured -       Age: Age of nestling in days when measured -      
 BroodSize: Number of nestlings in nest -       Date: Date measurements
 taken (M/D/Y) -       Mass: Nestling mass (g) -       Wing: Length of
 unflattened nestling wing chord (mm) -       Tarsus: Length of nestling
 tarsus (mm) -       Number_Blowflies: Number of *Trypocalliphora braueri*
 larvae observed feeding on each nestling at age of typical feather
 pinbreak (day 5 for Brewer’s Sparrow, day 7 for Sage Thrasher) -      
 Plot: Study plot -       Species: 4-letter alpha code for nestling species
 (BRSP=Brewer’s Sparrow, SATH=Sage Thrasher) -       HatchDate: Date on
 which the first nestling in each nest hatched (M/D/Y) -      
 HatchDate_cert: Indicates whether or not the hatch date was known with
 certainty (Certain/Probable) -       Year: Study year *File:*
 ‘Parasite_Loads_2023.xlsx’ *Variables:* -       BandNumber: Unique
 identifier for each nestling banded, measured, and checked for parasites
 in 2023 -       Blowflies: Number of *Trypocalliphora braueri* larvae
 observed feeding on each nestling at age of typical feather pinbreak (day
 5 for Brewer’s Sparrow, day 7 for Sage Thrasher) -       Species: 4-letter
 alpha code for nestling species (BRSP=Brewer’s Sparrow, SATH=Sage
 Thrasher) *Subfolder:* Weather Data *Description:* Contains ambient
 weather data from plot-level HOBO sensors and from the regional NWS
 weather station in Boulder, WY *Subfolder:* 2023 Plot Level Weather
 Sensors *Description:* Contains separate files with hourly ambient weather
 measurements recorded at each of the six plots in which fledglings were
 tagged and tracked in 2023 *Files:* ‘J0.csv’, ‘J11.csv’, ‘J17.csv’,
 ‘P0.csv’, ‘P8.csv’, ‘P34.csv’ *Variables:* -       DateTime: Date and time
 of weather measurement (M/D/Y HH:MM) -       Temp: Temperature (degrees F)
 -       RH: Relative humidity (%) *Subfolder:* Boulder Regional Weather
 Station *Description:* Contains a single file with daily weather data from
 NWS weather station located in Boulder, WY covering all years of the
 study. *File:* ‘Boulder_Daily_Weather_102016_122023.csv’ *Variables:*
 -       Date: Date of weather measurement (Y-M-D) -       MaxTemperature:
 Maximum daily temperature -       MinTemperature: Minimum daily
 temperature -       AvgTemperature: Average daily temperature -      
 Precipitation: Total daily precipitation (in) -       Snowfall: Total
 daily snowfall (in) -       SnowDepth: Total snow depth on ground (in)  ~~
 *Folder:* Cleaned and Reformatted Data for Analysis *Description:*
 Contains cleaned, reformatted final datafiles ready for analysis and
 visualization in ‘Nestling Data Analysis and Visualization Script.R’ and
 ‘Fledgling Data Analysis and Visualization Script.R’. Cells infilled with
 "#N/A" represent missing data. *File:*
 ‘BRSP_Day8_Nestling_Measurements_Cleaned_And_Reformatted_For_Analysis.xlsx’ *Variables:* -       BandNumber: Unique identifier for each nestling -       Species: 4-letter alpha code for nestling species (BRSP=Brewer’s Sparrow) -       Age: Age of nestling in age when measured -       Date: Date of nestling measurement (M/D/Y) -       Year: Study year -       NestID: Unique identifier for each nest from which nestlings were measured -       BroodSize: Number of nestlings in brood -       Plot: Study plot -       Number_Blowflies: Number of *Trypocalliphora braueri* larvae observed feeding on each nestling at age of typical feather pinbreak (day 5 for Brewer’s Sparrow) -       prop_disturbed: Proportion of surrounding 1k^2^ around each nest consisting of habitat disturbed by roads, well pads, and reclaimed areas -       avgdailytemp: Average daily temperature between hatching and fledging date for each nest (degrees C) -       Mass: Nestling mass (g) -       Wing: Nestling unflattened wing chord length (mm) -       Tarsus: Nestling tarsus length (mm) *File:* ‘Proportion_Fledglings_Surviving_By_Age.xlsx’ *Variables:* -       Species: 4-letter alpha code for nestling species (BRSP=Brewer’s Sparrow, SATH=Sage Thrasher) -       Parasite_Status: Classification for severity of prior parasite load (Unparasitized=0 larvae, Lightly Parasitized=1-3 larvae, Heavily Parasitized=4+larvae) -       Age: Days since fledging -       Number_Starting: Total starting number of tracked fledglings of species with parasite status -       Number_Surviving: Number of tracked fledglings of species with parasite status still surviving -       Prop_Surviving: Proportion of tracked fledglings of species with parasite status still surviving *File:* ‘SATH_Day10_Nestling_Measurements_Cleaned_And_Reformatted_For_Analysis.xlsx’ *Variables:* -       BandNumber: Unique identifier for each nestling -       Species: 4-letter alpha code for nestling species (SATH=Sage Thrasher) -       Age: Age of nestling in age when measured -       Date: Date of nestling measurement (M/D/Y) -       Year: Study year -       NestID: Unique identifier for each nest from which nestlings were measured -       BroodSize: Number of nestlings in brood -       Plot: Study plot -       Number_Blowflies: Number of *Trypocalliphora braueri* larvae observed feeding on each nestling at age of typical feather pinbreak (day 8 for Sage Thrasher) -       prop_disturbed: Proportion of surrounding 1k^2^ around each nest consisting of habitat disturbed by roads, well pads, and reclaimed areas -       avgdailytemp: Average daily temperature between hatching and fledging date for each nest (degrees C) -       Mass: Nestling mass (g) -       Wing: Nestling unflattened wing chord length (mm) -       Tarsus: Nestling tarsus length (mm) *File:* ‘Telemetry_Data_2023_Cleaned_And_Reformatted_For_Analysis.xlsx’ *Variables:* -       BandNumber: Unique identifier for each fledgling -       Species: 4-letter alpha code for fledgling species (BRSP=Brewer’s Sparrow, SATH=Sage Thrasher) -       NestID: Unique identifier for nest of origin for each tracked fledgling -       Plot: Study plot -       FledgeDate: Date on which each fledgling fledged (M/D/Y) -       Date: Date of fledgling relocation event (M/D/Y) -       Time1: Fledgling age in days when previously relocated -       Time2: Fledgling age in days at time of relocation -       event: Indicates whether a relocated fledging had survived or experienced a mortality event (0=survived, 1=mortality) -       Blowflies: Number of *Trypocalliphora braueri* larvae observed feeding on each fledgling while in the nest, prior to fledging, at age of typical feather pinbreak (day 5 for Brewer’s Sparrow, day 8 for Sage Thrasher) -       avgtemp: Average hourly temperature recorded on the plot where a fledging was being tracked between current and previous relocations -       prop_disturbed: proportion of habitat within 564m (1km^2^) of fledgling location disturbed by natural gas development ## Access information