Light pollution prolongs avian activity

Brent S. Pease†, Neil A. Gilbert†

† Shared first authorship

Data/code DOI:

Please contact the authors for questions about the code or data: Brent Pease (bpease1@siu.edu), Neil Gilbert (neil.gilbert@okstate.edu)

---

Abstract

Light pollution disrupts light–dark cues that organisms use as timetables for life. While studies, typically focusing on individual species, have documented earlier morning onset of bird vocalization in light-polluted landscapes, a synthesis of light pollution effects across species, space, and seasons is lacking. We used a global acoustic dataset of more than 60 million detections, representing 583 diurnal bird species, to synthesize effects of light pollution on avian vocalization. On average, light pollution prolonged vocal activity by 50 minutes. Light pollution responses were strongest for species with large eyes, open nests, migratory habits, and large ranges, and during the breeding season. Prolonged activity may confer negative, neutral, or positive fitness effects; documenting these fitness effects and curbing light pollution are challenges for 21st-century conservation.

$~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~$

Repository Directory

Scripts

• 101_data-prep_calculate_vocal_activity.R. Script to calculate morning onset and evening cessation from raw BirdWeather data downloads. NOTE: raw BirdWeather data files were too large to include in this directory, but are available for download at: BirdWeather Data Explorer.
• 102_data-prep_extract_viirs.R. After running 101_data-prep_calculate_vocal_activity.R, this script will annotate BirdWeather stations with VIIRs data. We also assigned grid cells to BirdWeather stations in this script for use in 201_analysis_fit_all_models_tmb.R. Monthly cloud-free VIIRS Day Night Band data publicly available for download from the Earth Observation Group. VIIRS data is not included in repository due to size. We downloaded every tile available from March 2023 - March 2024 from the Earth Observation Group. Example path to files: Home > nighttime_light > monthly > v10 > 2023 > 202301 > vcmslcfg
• 103_data-prep_resolve_names.R. Script reads in Elton traits database and joins with VIIRS annotated BirdWeather vocal acitivity. Deals with differences in taxonomy. Also preps for range map filtering. Output from this script is stored at birdweather_elton_botw_name_key.csv.
• 104_data-prep_range_map_filter.R. Script reads in range maps for all focal species. Range maps come from BirdLife International. Spatial data files are too large to upload in this repository but can be requested for download from BirdLife International. The script buffers range maps by 100km and removes detections of a species if outside of the buffered range. Range maps for a small number of species had invalid geometries, which prevented the automated spatial range map filtering. For these species, we plotted the range maps and species detections, saved as PDF in error_species_maps, and manually reviwed the maps to identify out-of-range records to remove.
• 105_data-prep_final_formatting.R. Final script for data prep prior to analysis. Resolves outstanding species name issues and omits potentially errorenous BirdNET detections from the BirdWeather output based on the previous range filtering step. Output from this script is stored in vocalization_activity and is read into the analysis script.
• 111_revisions_data-prep_extract_noisev2.R. Script to calculate distance to nearest road as a proxy for noise pollution for supplemental analysis.
• 112_revisions_calculate_spp_rich_tot_vocs.R. Calculate species richness and total number of vocalizations for each BirdWeather station-date.
• 113_revisions_calculate_moon_phase.R. Retrieve moon phase data for the supplemental analysis on nocturnal species.
• 114_revisions_nocturnal_vocal_activityV3.R. Calculate time of nocturnal detections relative to nadir for supplemental nocturnal analysis.
• 115_revisions_nocturnal_vocal_activity_tot_vocs.R. Calculate number of vocalizations per species per BirdWeather station-date for supplemental nocturnal analysis.
• 116_revisions_need_alan.R. Script to calculate light pollution data for additional sites for the supplemental nocturnal analysis (the "number of detections" analysis did not include as stringent of filters as the main text analysis, so there were some sites that did not appear in the diurnal analysis).
• 117_revisions_collate_road_distance_data.R. Road distance data were calculated by continent; this quick script joins the data up into one file.
• 118_revisions_collate_nocturnal_files.R. Similarly, nocturnal files are by continent; this script joins them into one.
• 119_revisions_collate_tot_vocs.R. Again, script to join up continent files.
• 201_analysis_fit_all_models_tmb.R. Script for running all analyses presented in the manuscript. Both vocalization onset and evening cessation analyzed within.
• 202_road_analysis.R Script to fit models with distance-to-road as a proxy for noise pollution (see supplement)
• 203_nocturnal_analysis.R Script to fit models for nocturnal species (see supplement)
• 301_figure_01b_inset.R. Script for creating Fig. 1b
• 302_figure_01d.R. Script for creating Fig. 1d
• 303_figure_02b-c.R. Script for creating Fig. 2b-c
• 304_figure_03a.R. Script for creating Fig 3a
• 305_figure_03b.R. Script for creating Fig. 3b
• 306_figure_04a.R. Script for creating Fig. 4a
• 307_figure_04b.R. Script for creating Fig. 4b
• 308_figure_04c.R. Script for creating Fig. 4c
• 309_figure_s01.R. Script for creating Fig. S1
• 310_model_summary_tables.R Script for creating Excel tables with parameters estimated by models
• 311_plotting_sp_parameters.R Script demonstrating how to join species-level parameters with spatial grid

Data

• error_species_maps Folder containing output (PDFs with species range maps with BirdWeather detections overlaid) from 104_data-prep_range_map_filter.R for manual review.

• range_maps Folder used to hold range map files for focal species. We do not have share permission, so folder will not appear on repository. Range maps are available through BirdLife International, which can be accessed at the BirdLife Data Zone.

  • focal_spp_maps.dbf
  • focal_spp_maps.prj
  • focal_spp_maps.shp
  • focal_spp_maps.shx

• species_keys Folder containing several tables with name keys to join datasets

  • birdweather_elton_botw_name_key.csv Table containing key to connect BirdWeather, EltonTraits, and BirdLife International names

    Variable name	Meaning
    com_name	Common name
    sci_name_bw	Scientific name according to BirdWeather
    sci_name_elton	Scientific name according to EltonTraits database
    sci_name_botw	Scientific name according to BirdLife International
    nocturnal	Indicator variable for whether species is nocturnal (1) or not (0)
    cavity	Indicator variable for whether species nests in cavities (1) or not (0)

  • botw_scientific_names.csv List of scientific names used in BirdLife International range maps.

    Variable name	Meaning
    scientific	Scientific name according to BirdLife International

  • error_species.csv For manual review of species with range maps with invalid geometries

    Variable	Meaning
    sci_name_botw	Scientific name according to BirdLife
    good	Are the detection locations all good ("good") or are there out-of-range detections that need to be omitted ("no")
    notes	Instructions for manually reviewing/filtering bad records

  • review_sp_botw.csv Worksheet used to manually resolve some scientific names for BirdLife International range maps.

    Variable	Meaning
    com_name	Common name
    sci_name_bw	BirdWeather scientific name
    sci_name_elton	EltonTraits scientific name
    flag	variable used to identify taxa to manually resolve
    sci_name_botw	BirdLife scientific name (manually resolved
    nocturnal	Binary variable indicating whether species is nocturnal (1) or not (0)

  • review_species.csv Worksheet used to manually resolve some scientific names for EltonTraits

    Variable	Meaning
    com_name	Common name
    sci_name	BirdWeather scientific name
    sci_name_manual	Scientific name (for matching to EltonTraits), had to resolve these manually

  • taxize_scientific_synonyms.csv Table with BirdWeather scientific names and synonyms found using the taxize R package.

    Variable	Meaning
    sci_name	BirdWeather scientific name
    sci_name_syn	Synonym found using taxize R package

• traits Folder containing the trait tables

  • avonet.csv This table is from the AVONET database; see Tobias et al. 2022 for details. The relevant columns that we use in the analysis are Range.Size (area [sq. km] of the species' geographic range), Habitat.Density (1 = dense habitats, 2 = semi-open habitats, 3 = open habitats), and Migration (1 = sedentary, 2 = partial migrant, 3 = migrant).
  • cavity.csv

    Variable	Meaning
    com_name	Common name (BirdWeather)
    sci_name_bw	Scientific name (BirdWeather)
    cavity	Binary variable indicating whether species nests in cavities (1) or not (0)

  • elton.txt This table comes from EltonTraits 1.0. It contains many columns; the relevant ones used in our analyses are taxonomic family BLFamilyLatin and whether or not species is nocturnal Nocturnal.
  • ritland_clean.csv Eye size data from Stanley Ritland's dissertation; see this Dryad repository for full details. The relevant column for eye size is cd1, or minimum corneal diameter.

• vocalization_activity Vocalization data. Contains output from 101_data-prep_calculate_vocal_activity.R, 104_data-prep_range_map_filter.R, and 105_data-prep_final_formatting.R.

  • cessation_data_conf_0.75_det_100_grid_10.RData. Final data formatted for modeling (evening cessation). The RData object contains one table, "final_cess", with the following columns.

    Variable	Meaning
    lat	Latitude (EPSG code: 4326) of sensor location
    lon	Longitude (EPSG code: 4326) of sensor location
    grid_ID_cell_5	Spatial grid cell ID (5°) for the sensor location
    grid_ID_cell_10	Spatial grid cell ID (10°) for the sensor location (we did not use this in analyses)
    grid_ID_cell_15	Spatial grid cell ID (15°) for the sensor location (we did not use this in analyses)
    week	Week of the year
    sci_name	BirdWeather scientific name
    value	Observed cessation of vocal activity in evening (minutes relative to local sunset); negative values represent final detection for the date occuring before sunset, while positive values represent final detection for the date occuring after sunset
    avg_rad	Measure of light pollution; radiance from VIIRS data product from sensor coordinates
    group	Grouping by species, spatial grid cell, and week (we re-created groupings for analysis the modeling script

  • nocturnal_nadir_v01.RData. Data for supplemental nocturnal species analysis for time relative to nadir. This RData object contains one table, "nadir", which has the following column meanings:

    Variable	Meaning
    sci_name	Scientific name according to BirdWeather
    com_name	Common name according to BirdWeather
    min_time_nadir	The minimum time (min) between a detection and nadir time for the day of, previous day, or next day of detection. This gives a measure of how close a detection is to the middle of the night.
    date	Date
    week	Week of the year
    lat	Latitude of BirdWeather sensor
    lon	Longitude of BirdWeather sensor
    det	Detection filter (not relevant)

  • nocturnal_species_tot_vocs.csv. Table with total number of detections per night for nocturnal species

    Variable	Meaning
    com_name	Common name according to BirdWeather
    station_date	ID for station-date combo
    sci_name	Scientific name according to BirdWeather
    lat	Latitude of BirdWeather sensor
    lon	Longitude of BirdWeather sensor
    N_dets	Number of detections for a species-site-date combination

  • onset_data_conf_0.75_det_100_grid_10.RData. Final data formatted for modeling (morning onset). The RData object contains one table, "final", which has the same column meanings as the cessation data (see table above). The one difference is that the value variable is the time of the first vocalization relative to local sunrise, with negative values representing onset prior to sunrise and positive values representing onset after sunrise.

  • species_site_combinations_final.csv. Table with valid (based on species range maps) species-site combinations; output of 104_data-prep_range_map_filter.R. The table has the following column meanings:

    Variable	Meaning
    site	Sensor ID
    lat	Latitude (EPSG code: 4326) of sensor location
    lon	Longitude (EPSG code: 4326) of sensor location
    com_name	BirdWeather common name
    sci_name_bw	BirdWeather scientific name
    sci_name_botw	BirdLife scientific name

  • tot_voc.RData Data on bird diversity at BirdWeather sensor-date combinations. RData object containing one table, "tot.voc", with the following columns:

    Variable	Meaning
    lat	Latitude of BirdWeather sensor
    lon	Longitude of BirdWeather sensor
    tot	Total number of vocalizations across all species
    sr	Number of species detected at station-date combination
    shan	Shannon diversity of species detections at station-date

  • vocal_activity_annotated_conf_0_det10.csv. Observed vocalization timing response variables with least conservative filtering (confidence >=0 with >=10 detections for a species per station-date). NOTE: this file is too large to share on GitHub (~2GB, 12.9 million rows). It can be downloaded with this GoogleDrive link. Download this file and put it in the data/vocalization_activity folder to run data preparation scripts 103_data-prep_resolve_names.R and 104_data-prep_range_map_filter.R.

    Variable	Meaning
    lat_lon	Latitude-longitude grouping (unique location ID)
    value	Observed time of vocalization (minutes) relative to local sunrise (morning response variables) or sunset (cessation response variable)
    category	Which response variable: morning onset ("first_onset"), evening cessation ("ev_ces"), or morning median vocalization time ("median_dawn"); this latter variable was not used or included in analyses
    com_name	Species common name according to BirdWeather
    sci_name	Species scientific name according to BirdWeather
    date_time	date-time stamp of detection
    date	date of detection
    week	Week of the year
    lat	Latitude of station (EPSG code: 4326)
    lon	Longitude of station (EPSG code: 4326)
    conf_filter	Detection confidence filter used to calculate response variables. In this table, all values will be equal to 0.
    det_filter	How many species detections have to occur per station-date to be included. In this table, all values will be equal to 10.
    avg_rad	Average radiance for coordinates for the month of the detection
    rad_cat	Radiance category for coordinates (low, medium, high)
    grid_ID_cell_5	Spatial grid cell ID (5°) for the sensor location
    grid_ID_cell_10	Spatial grid cell ID (10°) for the sensor location (we did not use this in analyses)
    grid_ID_cell_15	Spatial grid cell ID (15°) for the sensor location (we did not use this in analyses)
    month	Month of the year
    day	Day of the year
    year	Year

  • vocal_activity_annotated_conf_0.75_det100.csv. Observed vocalization timing response variables with conservative filtering (confidence >=0.75 with >=100 detections for a species per station-date). NOTE: this file is too large to share on GitHub (7.5 million rows). It can be downloaded with this GoogleDrive link. Download this file and put it in the data/vocalization_activity folder to run data preparation script 105_data-prep_final_formatting.R. This file has the same column meanings as the table above.

• moon_data.csv Moonlight data for nocturnal analysis

  Variable	Meaning
  lat	Latitude of BirdWeather sensor
  lon	Longitufde of BirdWeather sensor
  date	Date
  ill	Illumination (brightness)
  phase	Percent of moon face illuminated

• noct_locs_id.csv Coordinate/date information for extracting light values for updated nocturnal analysis

  Variable	Meaning
  id	ID for latitude, longitude, date combination
  lat	Latitude of BirdWeather sensor
  lon	Longitude of BirdWeather sensor
  date	Date

• nocturnal_species.csv List of nocturnal species

  Variable	Meaning
  sci_name	Scientific name according to BirdWeather
  nocturnal	indicator column (1) flagging species as nocturnal (from EltonTraits)

• rd_dist.csv Distance-to-road data (proxy for noise pollution)

  Variable	Meaning
  lat	Latitude of BirdWeather sensor
  lon	Longitufde of BirdWeather sensor
  rd	Distance (m) between BirdWeather sensor and nearest road

• vocal_activity_annotated_revisions_noct_locs_id.csv Updated light data for nocturnal species analysis. We needed light data for more locations, since the total number of vocalizations analysis had more sites (b/c of the omission of the detection filter)

  Variable	Meaning
  id	ID for latitutde, longitude, date combination
  lat	Latitude of BirdWeather sensor
  lon	Longitude of BirdWeather sensor
  date	Date
  year	Year
  month	Month of the year
  avg_rad	Radiance (light pollution) extracted from VIIRS data product for coordinates and month

Results

• BirdWeather Contains raw output from 101_data-prep_calculate_vocal_activity.R
  • birdweather_row_counter.csv Information on number of detections used to create barplot in Fig. 1.
• Figures Manuscript figures.
  • figure_01.png. Figure 1.
  • figure_01.pptx. Figure 1, PowerPoint file for assembling panels.
  • figure_01b.png. Figure 1B; map created in QGIS.
  • figure_01b_inset.png. Histogram of light pollution values from sensor locations; inset for Fig. 1B.
  • figure_01d.png. Figure 1D
  • figure_02.png Figure 2
  • figure_02.pptx Figure 2, PowerPoint file for assembling panels
  • figure_02b.png Figure 2B
  • figure_02c.png Figure 2C
  • figure_03.png Figure 3
  • figure_03.pptx Figure 3, PowerPoint file for assembling panels
  • figure_03a.png Figure 3A
  • figure_03b.png Figure 3B
  • figure_04.png Figure 4
  • figure_04.pptx Figure 4, PowerPoint file for assembling panels
  • figure_04a.png Figure 4A
  • figure_04b.png Figure 4B
  • figure_04c.png Figure 4C
  • figure_s01.png Figure S1
  • figure_s02.png Figure S2
  • figure_s02.pptx Figure S2, PowerPoint file for annotation
  • figure_s03.png Figure S3
• Tables Contains several supplemental tables summarizing model output
  • family_level_parameters.csv Family-level parameters (intercepts and slopes) from base onset and cessation models

    Variable	Meaning
    family	Taxonomic family
    onset_intercept	Estimated average onset; 0 = sunrise, negative = before sunrise, positive = after sunrise
    onset_slope	Estimated effect of light pollution; negative = earlier onset with light pollution, positive = later onset with light pollution
    cessation_intercept	Estimated average cessation; 0 = sunset, negative = before sunset, positive = after sunset
    cessation_slope	Estimated effect of light pollution; negative = earlier cessation with light pollution, positve = later cessation with light pollution

  • formatted_model_summaries.csv Summary of higher-level model parameters

    Variable	Meaning
    response	Response variable (onset or cessation)
    predictors	Predictor variables in model
    term	Term within the model. These include fixed effects, standard deviation for random terms (SD), correlations between random terms (Cor), and several model fit statitics( R2 Cond, AIC, RMSE). In this column, light is light pollution, cavity is nest type (cavity: 1; open: 0), eye size is corneal diameter, semi-open habitat is the 2nd-level of the habitat density variable, open habitat is the 3rd-level of the habitat density variable (intercept for this model representes closed habitats), latitude is latitude, partial migrant is the 2nd-level of the migration variable, migrant is the 3rd-level of the migration variable (intercept for this model represents sedentary species), species richness is the number of species present at a BirdWeather station, and range_size is geographic range size
    estimate	Value of the point estimate
    std_error	Standard error of the estimate
    gof	Value of the goodness of fit stats

  • model_summaries.csv Same information as above, but in a less intuitive and friendly format.
  • species_level_parameters.csv Species-grid cell-week level parameters. Refer to 311_plotting_sp_parameters.R for information on joining these species-level parameters to the spatial grid cells to which estimates correspond for mapping, etc.

    Variable	Meaning
    family	Taxonomic family
    sci_name	Scientific name according to BirdWeather
    grid_ID_cell_5	Identity of 5-degree grid cell
    week	Week of the year
    onset_intercept	Estimated average onset; 0 = sunrise, negative = before sunrise, positive = after sunrise
    onset_slope	Estimated effect of light pollution; negative = earlier onset with light pollution, positive = later onset with light pollution
    cessation_intercept	Estimated average cessation; 0 = sunset, negative = before sunset, positive = after sunset
    cessation_slope	Estimated effect of light pollution; negative = earlier cessation with light pollution, positve = later cessation with light pollution

• onset.RData. Model outputs for the onset models. NOTE: this file is too large to share on GitHub. It can be downloaded with this GoogleDrive link. Download the file and put it in the Results directory to reproduce figures.
• cessation.RData. Model outputs for cessation models. NOTE: this file is too large to share on GitHub. It can be downloaded with this GoogleDrive link. Download the file and put it in the Results directory to reproduce figures.
• distance_to_road_models.RData. Model outputs for distance-to-road models. NOTE: this file is too large to share on GitHub. It can be downloaded with this GoogleDrive link. Download the file and put it in the Results directory to reproduce figures.