Data and code from: Fitness consequences of parasitism in a changing world: A case study with bird blow flies and sagebrush songbirds
Data files
Dec 03, 2025 version files 1.68 MB
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Code_and_Data.zip
1.66 MB
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README.md
16.66 KB
Abstract
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.
Dataset DOI: 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.
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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)
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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 1k2 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 1k2 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 (1km2) of fledgling location disturbed by natural gas development