Long-term abundance time-series of the High Arctic terrestrial vertebrate community of Bylot Island, Nunavut
Data files
Nov 19, 2024 version files 16.06 KB
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DataS1.zip
7.31 KB
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README.md
8.75 KB
Jun 23, 2025 version files 12.90 MB
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Data_S1.zip
12.87 MB
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README.md
37.83 KB
Abstract
Arctic ecosystems present unique opportunities for community-wide monitoring, in part due to their relatively low species richness. However, conducting research in these remote environments poses significant logistical challenges, resulting in long-term monitoring being exceedingly rare. Here, we focus on the long-term, intensive ecological monitoring efforts conducted on the south plain of Bylot Island (~400 km2, Nunavut, Canada), which has generated a remarkable dataset spanning up to 30 years, a rarity in tundra ecosystems. Our goals are to i) provide long-term time series of annual species densities for the broadest possible range of species and years, measured across various spatial scales, to assess of interannual variability and trends in species density; and ii) upscale vertebrate abundance, annually when feasible, or otherwise as long-term averages, to the landscape scale (~400 km2) to allow food web modelling. We have standardized data obtained with different field methods to provide a readily usable data set for community ecologists. Monitoring data includes intensive capture-mark-recapture density estimates of lemmings on trapping grids, systematic or opportunistic nest monitoring conducted across the entire study area or within specific plots for all bird species, transects of vertebrate counts distributed throughout the study area, daily incidental observations of vertebrates and satellite tracking of fox movements. Long-term time series of species densities, measured at various spatial scales, span 3 to 27 years, with a median of 16.5 years across 22 species. Landscape-scale abundance estimates cover all 35 species of the community, with time series available for 15 of them (median duration: 17 years). For the remaining 20 species, only average abundance is provided. Furthermore, we provide body mass data for each species, based on empirical onsite measurements for 18 species and from literature sources for the remainder. Body mass is essential to convert species abundance into biomass for studies of trophic fluxes and ecosystem processes. Annual climatic data collected since 1992 from weather stations within the study area are publicly available and can be used to complement analyses of the dataset. The ecological data we present offer a rare opportunity for holistic empirical studies of community structure and dynamics. Considering that the study site is a pristine and protected area that has experienced minimal direct anthropogenic impact, it can also provide an ideal baseline for investigating the impacts of global changes on high-latitude terrestrial ecosystems.
Access data, metadata and code
Data - Data_S1/: https://doi.org/10.5061/dryad.44j0zpcnt
Methods and metadata - MetadataS1.pdf: https://doi.org/10.5281/zenodo.13993828
Code and R project - BYLOT_species_abundance_dataset.zip: https://doi.org/10.5281/zenodo.13993827
Objectives
With over a decade of additional community-wide monitoring compared to earlier studies, our goals are to i) provide long-term time series of annual vertebrate density measured at various spatial scales and for the broadest possible range of species and years, to allow the assessment of interannual variability and trends in species density; and ii) upscale annual vertebrate abundance or sometimes long-term averages to the landscape scale (400 km²) to allow food web modelling (Figure 2). We focus on the breeding season (May to August) here because it is the most appropriate period to conduct surveys for most species, especially migratory birds. Although we recognize that ecological dynamics during the non-breeding period, for both resident (Hutchison et al., 2020) and migratory species (Moisan et al., 2023), can influence the food web during the breeding season, it was not possible to cover this period in the present study. The abundance estimates include both breeding and non-breeding individuals that remain in the study area for a significant period of time (e.g., territorial breeding or non-breeding foxes), and excludes non-breeding individuals that stop only briefly during migration (e.g., shorebirds using Bylot Island for a short stopover) or leave the area shortly after arrival without attempting to breed in some years (e.g. long-tailed jaegers). We focus on adults, except for lemmings for which we have not distinguished between juveniles and adults. Additionally, we aim to provide the average body mass for each species in the community, enabling the conversion of abundances into biomasses.
Structure of the project
MetadataS1.pdf: Complete documentation describing the project’s context and objectives, the study site, the data collection process, the methods used to estimate species abundance, the resulting data set files with the associated metadata.
Data_S1/
BYLOT-species_taxonomy.csv: Species taxonomy.
- class: Taxonomic class for birds (Gill et al., 2024) and mammals species (Upham et al., 2024).
- order: Taxonomic order for birds (Gill et al., 2024) and mammals species (Upham et al., 2024).
- family: Taxonomic family for birds (Gill et al., 2024) and mammals species (Upham et al., 2024).
- genus: Taxonomic genus for birds (Gill et al., 2024) and mammals species (Upham et al., 2024).
- species_scientific: Taxonomic species for birds (Gill et al., 2024) and mammals species (Upham et al., 2024).
- species_en: Common names of species in English.
- species_fr: Common names of species in French.
- functional_group: Functional group for each species. The classification of species into functional groups is based on Moisan et al. (2023).
- migratory_status: Migratory status of each species. The classification of species migratory status is based on Gauthier et al., (2011) and Moisan et al. (2023).
BYLOT-species_density_monitoring.csv: Annual species density measured in the different zones of the study area (various spatial scales).
- species_en: Common names of species in English.
- year: Year in which species density was monitored in the corresponding zone.
- zone: Zone of the study area in which species density was measured.
- area_sampled_km2: Area (in square kilometers) sampled to measure species density.
- habitat: Habitat in which species density was measured.
- method: Method used to measure species density.
- monitoring: Type of monitoring conducted, distinguishing between systematic (planned, standardized data collection) and opportunistic (irregular or incidental).
- breeding_status: Reproductive status of the individuals.
- ind_density_km2: Density of individuals (number of individuals per square kilometer) measured in the corresponding year and zone.
BYLOT-species_abundance.csv: Long-term series or mean species abundance.
- species_en: Common names of species in English.
- year: Year corresponding to the estimate of annual abundance. If abundance has not been calculated for a given series of years, but rather as a general average, then NA has been assigned.
- breeding_status: Reproductive status of the individuals.
- abundance: Estimate of the number of individuals within the 389 km2 study area located on the southern part of Bylot Island during the breeding season (May to August). The estimates only consider adults, with the exception of lemmings, for which no distinction has been made between juveniles and adults.
- method_description: Brief overview of the method used to estimate the species abundance.
- method_quality: Qualitative measure of the method quality based on data available, method used for extrapolation (if necessary), and in some cases, from the fit of statistical models to estimate density.
- spatial_extrapolation: Indicates whether the abundance estimate was derived from monitoring across the entire study area (“no”) or was spatially extrapolated (“yes”).
BYLOT-community_composition.csv: Estimated annual or mean number of individuals for each species in the vertebrate community of Bylot Island between May and August. For all species, we estimated the abundance of adults, except for lemmings, for which juveniles and adults were not distinguished. When multiple independent methods were available to estimate the annual or mean abundance of a species, we retained the estimate from the method with the highest assigned quality. If methods had equal quality, we computed and presented the mean of their estimates.
- species_en: Common names of species in English.
- 1993 - 2023: Estimate of the annual number of individuals within the 389 km2 study area located on the southern part of Bylot Island during the breeding season (May to August) for the corresponding year. The estimates represent only breeding individuals, except for lemmings, for which the estimates include both breeding and non-breeding individuals. The estimates exclude non-breeding individuals that stop for only a few days during their migration. The estimates only consider adults, with the exception of lemmings, for which no distinction has been made between juveniles and adults. Note that 2020 does not appear since fieldwork was not possible due to Covid-19.
- mean: Estimate of the average annual number of individuals within the 389 km2 study area located on the southern part of Bylot Island during the breeding season (May to August). This includes both breeding and non-breeding individuals that stay in the study area for a significant period of time, and excludes non-breeding individuals that stop for only a few days during their migration. The estimates only consider adults. For species where abundance was estimated using multiple methods, we selected the method determined to be of the highest quality. In cases where multiple methods yielded equivalent quality, the mean value of their estimates was retained.
BYLOT-species_body_mass.csv: Mean individual body mass.
- species_en:Common names of species in English.
- site: Site where body mass measurements were taken.
- mean_body_mass_g: Mean individual body mass.
- sample_size: Number of individuals measured.
- reference: Reference from which estimate of mean body mass were derived.
raw/
avian_nest_monitoring/
nests.shp: Shapefile containing all nests found either systematically or opportunistically. See Table 2 of MetadataS1 for the monitoring years associated with each species.
- nest_id: Unique nest identifier within a given year. Combining the nest_id with the year produces a unique identifier across all years.
- species: Common species names in English, formatted in lowercase without dashes or apostrophes.
- year: Year in which the nest was found.
- utm_zone: UTM zone associated with the nest coordinates.
- datum: Datum associated with the nest coordinates.
nests.csv: Coordinates of all nests found systematically or opportunistically on Bylot Island. See Table 2 of MetadataS1 for the monitoring years associated with each species.
- nest_id: Unique nest identifier within a given year. Combining the nest_id with the year produces a unique identifier across all years.
- species: Common species names in English, formatted in lowercase without dashes or apostrophes.
- year: Year in which the nest was found.
- lat: Latitude of the nest location, projected in NAD27 / UTM zone 17N coordinate system (EPSG: 26717).
- long: Longitude of the nest location, projected in NAD27 / UTM zone 17N coordinate system (EPSG: 26717).
- utm_zone: UTM zone associated with the nest coordinates.
- datum: Datum associated with the nest coordinates.
hawk_falcon_nests.csv: All nests of Rough-legged hawks and Peregrine falcons found on Bylot Island with the corresponding zone of the study area. See Table 2 of MetadataS1 for the monitoring years associated with each species.
- nest_id: Unique nest identifier within a given year. Combining the nest_id with the year produces a unique identifier across all years.
- species: Common species names in English, formatted in lowercase without dashes or apostrophes.
- year: Year in which the nest was found.
- zone: Zone of the study area where the nest was found. The spatial boundaries of the study area zones are provided in DataS1/study_area/study_area.shp.
snow_goose_nests_plots.csv: Systematic snow goose nest monitoring plots (see section b. Avian nest monitoring / Snow goose for more details).
- Year: Year in which the plot was sampled.
- Habitat: Dominant habitat in the plot (Mesic or Wetland).
- plot_number: Sequential plot number.
- R_plot_ID: Unique plot identifier within a given year.
- nb_nest: Total number of snow goose nests found in the plot.
- area_km2: Surface area (km2) of the plot that was sampled.
summary_nest_monitoring.csv: Summary of monitoring efforts for each species in the vertebrate community of Bylot Island. This file was used to generate Table 2 in the MetadataS1 document.
- species: Common species names in English, formatted in lowercase without dashes or apostrophes.
- zone: Zone of the study area where the species was monitored.
- year: Years in which the species was monitored. A dash indicates a continuous range (e.g., 2005–2010 means monitoring occurred each year from 2005 to 2010).
- number_years: Total number of years in which the species was monitored.
- monitoring: Type of monitoring conducted, distinguishing between systematic (planned, standardized data collection) and opportunistic (irregular or incidental).
summary_nest_monitoring_long_format.csv: Summary of monitoring efforts for each species in the vertebrate community of Bylot Island formatted in a long format.
- species: Species monitored. We use common species names in English, formatted in lowercase without dashes or apostrophes.
- zone: Zone of the study area where the species was monitored.
- year: Year during which the species was monitored.
- monitored: Indicates whether the species was monitored in the corresponding zone and year (“yes” if monitored, “no” if not).
- monitoring: Type of monitoring conducted, distinguishing between systematic (planned, standardized data collection) and opportunistic (irregular or incidental).
observation_of_individuals
vertebrate_count_transects_2010_2023.shp: Observations of individuals recorded along 500-meter vertebrate count transects between 2010 and 2023. See section c. Observation of Individuals / Vertebrate Count Transects in the MetadataS1 document for more details.
- transect: Unique transect identifier.
- year: Year in which the observation was made.
- status: Status of the individuals observed: “repro”” means the individuals were clearly showing breeding behavior, such as incubating eggs or defending nests. “non repro”” means the individuals were clearly not breeding, for example, seen in large groups without any breeding activity. “inconnu”” means it is uncertain or unknown whether the individuals were breeding or not.
- nb_ind: Total number of individuals observed along the transect.
- species: Observed species. We use common species names in English, formatted in lowercase without dashes or apostrophes.
- habitat: Type of habitat where the transect is located, classified as either “mesic” or “wetland”. If any part of the transect overlaps with wetland, the habitat is labeled “wetland” regardless of the proportion; otherwise, it is labeled “mesic”.
vertebrate_count_transects_2010-2023.csv: Same as the vertebrate_count_transects_2010_2023.shp formatted as .csv.
- transect: Unique transect identifier.
- year: Year in which the observation was made.
- status: Status of the individuals observed: “repro”” means the individuals were clearly showing breeding behavior, such as incubating eggs or defending nests. “non repro”” means the individuals were clearly not breeding, for example, seen in large groups without any breeding activity. “inconnu”” means it is uncertain or unknown whether the individuals were breeding or not.
- nb_ind: Total number of individuals observed along the transect.
- species: Observed species. We use common species names in English, formatted in lowercase without dashes or apostrophes.
- begin_long: Longitude of the location at the beginning of the transect, projected in NAD27 / UTM zone 17N coordinate system (EPSG: 26717).
- begin_lat: Latitude of the location at the beginning of the transect, projected in NAD27 / UTM zone 17N coordinate system (EPSG: 26717).
- end_long: Longitude of the location at the end of the transect, projected in NAD27 / UTM zone 17N coordinate system (EPSG: 26717).
- end_lat: Latitude of the location at the end of the transect, projected in NAD27 / UTM zone 17N coordinate system (EPSG: 26717).
snow_goose_point_counts_2010_2023.shp: Observations of breeding pairs of snow geese in 125 m radius point counts performed between 2010 and 2023. See section c. Observation of Individuals / Snow goose point count in the MetadataS1 document for more details.
- year: Year in which the observation was made.
- point: Unique point count identifier.
- n_oie_125: Total number of breeding snow geese pairs observed within a 125 m radius around the observer.
- habitat: Type of habitat where the point count is located, classified as either “mesic” or “wetland”. If any part of the point count overlaps with wetland, the habitat is labeled “wetland” regardless of the proportion; otherwise, it is labeled “mesic”.
incidental_observations_2007_2019.csv: Incidental daily observations of vertebrates recorded between 2007 and 2019 on Bylot Island. See section c. Observation of Individuals / Incidental observations in the MetadataS1 document for more details.
- obs_id: Unique identifier assigned to each observation session.
- species: Observed species. We use common species names in English, formatted in lowercase without dashes or apostrophes.
- zone: Zone of the study area where the observation was made.
- year: Year in which the observation was made.
- nb_ind: Total number of individuals observed during the observation session.
- nb_hours: Number of hours spent on the field by the observer(s).
- nb_observers: Number of observers in the group.
incidental_obs_relative_abundance_upland.csv: Index of species abundance—measured as the number of individuals observed per hour of fieldwork—in upland and lowland habitats, based on incidental observations. Observations made during hawk nest visits were used as a proxy for upland habitat observations. All other observations were considered as lowland.
- species: Species observed. We use common species names in English, formatted in lowercase without dashes or apostrophes.
- nb_ind_hour_upland: Number of individuals observed per hour when performing fieldwork in upland habitat.
- nb_ind_hour_lowland: Number of individuals observed per hour when performing fieldwork in lowland habitat.
- ratio_difference: Ratio between nb_ind_hour_upland and nb_ind_hour_lowland.
relative_abundance_Gauthier_et_al_2024.csv: Index of species abundance, calculated as the number of individuals observed per 100 hours of fieldwork, based on incidental observations and reported in Gauthier et al. 2024b. The presented indices were used to compare the relative abundance of species with those for which absolute abundance was estimated (i.e., reference species).
- species: Common species names in English, formatted in lowercase without dashes or apostrophes.
- index_sp: Number of individuals of the corresponding “species” observed per 100 hours of fieldwork.
- ref_species: Reference species (i.e. a species for which absolute abundance has been estimated).
- index_ref_sp: Number of individuals of the corresponding “ref_species” observed per 100 hours of fieldwork.
american_golden_plover_distance.csv: Perpendicular distance (in meters) measured between the transect and American golden-plover individuals detected during vertebrate count transects.
- distance: Perpendicular distance (in meters) from the transect to the detected individuals.
ermine_index.csv: Annual index of American ermine abundance on Bylot Island, based on local testimonials reported in Bolduc et al. (2023; https://doi.org/10.1016/j.baae.2022.11.005).
- Year: Year in which the American ermine abundance index was estimated.
- Ermine: Index of American ermine abundance based on local testimonials. For details on data collection and usage, refer to Bolduc et al. (2023).
capture_of_individuals/
lemming_density_1993-2019.csv: Estimates of individual density (individuals/ha) for Nearctic brown and collared lemmings based on snap-trapping conducted in mesic and wetland grids of the Qarlikturvik Valley in late July from 1993 to 2019. See Section d. Capture of Individuals / Lemming Trapping for more details.
- Year: Year in which the density was estimated.
- Brown Wet habitat: Estimated density of Nearctic brown lemmings (individuals per hectare) within the trapping grid located in wetland habitat.
- Brown Mesic habitat: Estimated density of Nearctic brown lemmings (individuals per hectare) within the trapping grid located in mesic habitat.
- Coll Wet habitat: Estimated density of Nearctic collared lemmings (individuals per hectare) within the trapping grid located in wetland habitat.
- Coll Mesic habitat: Estimated density of Nearctic collared lemmings (individuals per hectare) within the trapping grid located in mesic habitat.
- Both Wet habitat: Estimated density of both Nearctic brown and collared lemmings combined (individuals per hectare) within the trapping grid located in wetland habitat.
- Both Mesic habitat: Estimated density of both Nearctic brown and collared lemmings combined (individuals per hectare) within the trapping grid located in mesic habitat.
lemming_density_2004-2022.csv: Estimates of individual density (individuals/ha) for Nearctic brown and collared lemmings derived from live-trapping conducted between 2004 and 2022. See Section d. Capture of Individuals / Lemming Trapping for more details.
- site: Zone of the study area where trapping was conducted. Note that Goose camp here refer here to the trapping grids located in the Qarlikturvik valley.
- species: Lemming species, either “brown” or “collared” for Nearctic brown and Nearctic collared lemming respectively.
- grid: Unique identifier assigned of each trapping grid.
- habitat: Type of habitat where the trapping grid was located.
- year: Year during which trapping was conducted.
- period: Period during which trapping was conducted (“P1”= mid-June; “P2”= mid-July and “P3”= mid-August).
- density: Estimated density of individuals (individuals per hectare).
- se: Standard error associated with the estimate.
data_HomeRange.csv: Predicted Arctic fox home range sizes inside and outside the goose colony during years of low and high lemming density. The dataset is available at https://doi.org/10.5061/dryad.f1vhhmh30. For details and data usage, see Dulude-de Broin et al. (2023; https://doi.org/10.1111/1365-2656.14017) and section a. Field/laboratory / Arctic fox.
body_mass/
body_mass_measurements_bylot.csv: Body mass (in grams) of individuals measured on Bylot Island. The dataset also includes the average body mass of Cackling Geese captured on Baffin Island. For details on Cackling Goose measurements, see Neufeld (2021; http://hdl.handle.net/1993/35933).
- species: Common species names in English, formatted in lowercase without dashes or apostrophes.
- age: Age class of the individuals. “adult” indicates breeding individuals, while “NA” is used when the distinction between adults and juveniles was not available.
- site: Location where the measurement was taken. “bylot” refers to the study area on the southern plain of Bylot Island, while “baffin” refers to data for Cackling Goose from Baffin Island (see Neufeld, 2021).
- year: Year in which the measurement was taken.
- body_mass_g: Body mass of the individual, measured in grams.
- reference: Source or reference associated with the measurement.
metadata/
summary_methods.csv: Metadata used to generate Table 4 in the MetadataS1 document.
study_area/
study_area.shp: Spatial boundaries of the different zones of the study area on the southern plain of Bylot Island, Nunavut, Canada.
- zone: Zone of the study area.
- year: Year in which the snow goose colony area was delineated. “NA” for all zones except the “goose colony.”
- area_km2: Surface area of the zone, in square kilometers.
- prop_wet: Proportion of wetland habitat within the zone.
- prop_mesic: Proportion of mesic habitat within the zone.
- prop_up: Proportion of upland habitat within the zone.
lakes.shp: Spatial boundaries of lakes and ponds within the study area on the southern plain of Bylot Island, Nunavut, Canada (see Corbeil-Robitaille et al., 2024).
rivers.shp: Spatial boundaries of lakes and ponds within the study area on the southern plain of Bylot Island, Nunavut, Canada.
wetlands.shp: Spatial boundaries of wetlands within the study area on the southern plain of Bylot Island, Nunavut, Canada (Louis-Pierre Ouellet, unpublished data).
proportion_goose_colony_zone.csv: Annual proportion of each zone of the study area overlapping with the delineated snow goose colony.
- zone: Zone of the study area.
- year: Year in which the snow goose colony area was delineated.
- prop_overlap_colony: Proportion of the zone that overlaps with the goose colony boundary.
snow_goose_systematic_wetland_plot.shp: Spatial delineation of the primary wetland plot used for systematic monitoring of snow goose nests. All nests located within this plot are monitored annually.
script/
1_data_cleaning/
1.1_clean_year_monitoring_metadata.R: R script used to convert the compact summary table of species monitoring efforts into a long-format suitable for manipulation in R.
1.2_extract_species_body_mass.R: R script to extract the mean individual body mass (in grams) for each species in the vertebrate community of Bylot Island.
1.3_detection function_american_golden_plover.R: R script used to identify the parameter combination that yields the lowest AIC values in the distance sampling model for American golden-plover.
2_extract_species_density_abundance/
2.1_extract_species_density_monitoring.R: Extract annual density of individuals measured in the different zones of the study area (see BYLOT-species_density_monitoring.csv).
2.2_extract_species_abundance.R: Estimate the annual or mean abundance of all vertebrate species in the community at the scale of the study area (389 km2; see BYLOT-species_abundance.csv).
2.3_extract_community_composition.R: Extract the annual or mean abundance of all vertebrate species in the Bylot Island community using the method with the highest quality rating, when applicable (see BYLOT-community_composition.csv).
species/
american_ermine.R: Script used to estimate American ermine abundance across the entire study area.
american_golden_plover.R: Script used to estimate American golden-plover abundance across the entire study area.
arctic_fox.R: Script used to estimate Arctic fox abundance across the entire study area.
arctic_hare.R: Script used to estimate Arctic hare abundance across the entire study area.
bairds_sandpiper.R: Script used to estimate Baird’s sandpiper abundance across the entire study area.
black_bellied_plover.R: Script used to estimate Black-bellied plover abundance across the entire study area.
cackling_goose.R: Script used to estimate Cackling goose abundance across the entire study area.
common_raven.R: Script used to estimate Common raven abundance across the entire study area.
common_ringed_plover.R: Script used to estimate Common-ringed plover abundance across the entire study area.
ducks.R: Script used to estimate the abundance of King eider and Long-tailed duck across the entire study area.
glaucous_gull.R: Script used to estimate Glaucous gull abundance across the entire study area.
lapland_longspur.R: Script used to estimate Lapland longspur abundance across the entire study area.
lemmings.R: Script used to estimate the abundance of Nearctic brown lemming and Nearctic collared lemming across the entire study area.
long_tailed_jaeger.R: Script used to estimate Long-tailed jaeger abundance across the entire study area.
loons.R: Script used to estimate the abundance of Pacific loon and Red-throated loon across the entire study area.
other_passerine.R: Script used to estimate the abundance of Horned lark, American pipit and Snow bunting across the entire study area.
other_sandpiper.R: Script used to estimate the abundance of Ruddy turnstone, Red knot, Pectoral sandpiper, White-rumped sandpiper, Buff-breasted sandpiper and Red phalarope across the entire study area.
parasitic_jaeger.R: Script used to estimate Parasitic jaeger abundance across the entire study area.
peregrine_falcon.R: Script used to estimate Peregrine falcon abundance across the entire study area.
rock_ptarmigan.R: Script used to estimate Rock ptarmigan abundance across the entire study area.
rough_legged_hawk.R: Script used to estimate Rough-legged hawk abundance across the entire study area.
sandhill_crane.R: Script used to estimate Sandhill crane abundance across the entire study area.
snow_goose.R: Script used to estimate Snow goose abundance across the entire study area.
snowy_owl.R: Script used to estimate Snowy owl abundance across the entire study area.
tundra_swan.R: Script used to estimate Tundra swan abundance across the entire study area.
3_tables_figures/
3.1_table_species_name_strategy.R: Code to generate Table 1 in the MetadataS1 document.
3.2_table_species_year_monitoring.R: Code to generate Table 2 in the MetadataS1 document.
3.3_table_species_relative_abundance_upland.R: Code to generate Table 3 in the MetadataS1 document.
3.4_table_summary_methods_and_abundance.R: Code to generate Table 4 in the MetadataS1 document.
3.5_figures_species_temporal_series.R: Code to generate Figure 11 in the MetadataS1 document.
3.6_maps.R: Code to generate Figure 3, 4, 5, 6 in the MetadataS1 document.
3.7_table_variables_definition.R: Code to generate Table 6 in the MetadataS1 document.
3.8_table_variables_format.R: Code to generate Table 7 in the MetadataS1 document.
3.9_table_expert_based_uncertainty.R: Code to generate Table 5 in the MetadataS1 document.
3.10_figure_time_line.R: Code to generate Table 5 in the MetadataS1 document.
functions/
FUNS.R: Code loading all local functions found in the “standalone_functions” and “nested_functions”.
standalone_functions/
get_nest_density.R: R function to extract the density of nests and individuals for a given list of zones and years.
get_nest_density_missing_coordinates.R: R function to calculate the density of nests and individuals for a given list of zones and years when exact coordinates of nests are missing.
number_ind_transects.R: R function to calculate the mean number of individual observed per transect for a given list of zones and years.
extract_density_distance_sampling.R: R function to estimate the abundance of individuals for a given list of zones and years based on distance sampling.
nested_functions/
extend_temporal_series_from_single_zone_nest.R: R function used to extend a temporal abundance series by scaling nest density measured in a single zone to the entire study area, using the relationship between densities at the two spatial scales.
extend_temporal_series_from_single_zone_missing_coordinates.R: R function used to extend a temporal abundance series by scaling nest density measured in a single zone to the entire study area, using the relationship between densities at the two spatial scales; when exact nests coordinates are missing (Rough-legged hawks and Peregrine falcons).
spatial_extrapolation_species_density.R: R function used to extrapolate local nest density to the entire study area based on observations collected along transects across different zones.
estimate_density_from_reference_species.R: R function used to estimate the absolute abundance of a given species by applying the ratio of its relative abundance to that of a reference species with known absolute abundance.
Sharing/access information
The data set will also be available as supplementary information by the journal upon publication of the related manuscript.
Version history (Changelog)
Version 1 (19-11-2024)
- The data set (
Data_S1/) includes originally only the following files:
BYLOT-species_taxonomy.csv,
BYLOT-species_abundance.csv,
BYLOT-species_body_mass.csvand
BYLOT-interannual_variation_nest_density.csv.
Version 2 (18-06-2025)
- The folders
raw/,study_area/, andmetadata/and the fileMetadataS1.pdfwere added toData_S1/. These folders and files were previously archived on Zenodo. - The following objective was added:*
“i) provide long-term time series of annual species densities for the broadest possible range of species and years, measured across various spatial scales, to assess of interannual variability and trends in species density” BYLOT-interannual_variation_nest_density.csvwas replaced byBYLOT-species_density_monitoring.csv, which now provides raw measurements of species density (instead of only mean and standard deviation).BYLOT-community_composition.csvwas added, presenting full tabular estimates of annual or mean species abundance at the landscape scale (389 km²).- A new column
spatial_extrapolation, indicating whether estimates of abundance were spatially extrapolated, was added toBYLOT-species_abundance.csv. - The method used to estimate cackling goose abundance at the landscape scale between 2004 and 2016 was updated; corresponding values were modified in
BYLOT-species_abundance.csv. - The average body mass of cackling goose measured on Baffin Island was added to
BYLOT-species_body_mass.csv. - Timelines representing the time series of each species in the dataset (Figure 2), and a map showing the distribution of habitat types across the study area (Figure 3), were added to
MetadataS1.pdf. - Minor clarifications and edits were made throughout
MetadataS1.pdf.
Citation
Please use the following citation when referencing this data set until publication:
Moisan, L., Bideault, A., Gauthier, G., Duchesne, É., Fauteux, D., Berteaux, D., Legagneux, P., Cadieux, M.-C. and Bêty, J. (2025). Long-term abundance time-series of the High Arctic terrestrial vertebrate community of Bylot Island, Nunavut. Dryad. https://doi.org/10.5061/dryad.44j0zpcnt
*The manuscript is currently under review in Ecology
Code/Software
Operating system: Data preparation was performed on x86_64-pc-linux-gnu (64-bit) with Ubuntu 22.04.3 LTS.
Program: R version 4.4.1 (2024-06-14)
Packages:
dplyr 1.1.4 (Wickham et al., 2023a)
tidyr 1.3.1 (Wickham et al., 2024)
sf 1.0-20 (Pebesma et al., 2018)
stringr 1.5.1 (Wickham, 2023)
xtable 1.8-4 (Dahl et al., 2019)
Distance 1.0.9 (Miller et al., 2019)
ggplot2 3.5.1 (Wickham, 2016)
lme4 1.1-35.3 (Bates et al., 2015)
AICcmodavg 2.3-3 (Mazerolle, 2023)
scales 1.3.0 (Wickham et al., 2023b)
ggmap 4.0.1 (Kahle and Wickham, 2013)
ggspatial 1.1.9 (Dunnington, 2023)
Contact persons
Overall project: Joël Bêty (joel_bety@uqar.ca)
Data set and code: Louis Moisan (louis.moisan.bio@gmail.com)
References
D. Bates, M. Mächler, B. Bolker, and S. Walker. Fitting linear mixed-effects models using lme4. Journal of Statistical Software, 67(1):1–48, 2015.
D. Bolduc, D. Fauteux, C. A. Gagnon, G. Gauthier, J. Bêty, and P. Legagneux. Testimonials to reconstruct past abundances of wildlife populations. Basic and Applied Ecology, 68:23–34, 2023.
M.-Z. Corbeil-Robitaille, É. Duchesne, D. Fortier, C. Kinnard, and J. Bêty. Linking geomorphological processes and wildlife microhabitat selection: nesting birds select refuges generated by permafrost degradation in the arctic. Biogeosciences, 21(14):1101 3401–3423, 2024.
D. B. Dahl, D. Scott, C. Roosen, A. Magnusson, and J. Swinton. xtable: Export Tables to LaTeX or HTML, 2019. URL https://CRAN.R project.org/package=xtable. R package version 1.8-4.
F. Dulude-de Broin, J. Clermont, A. Beardsell, L.-P. Ouellet, P. Legagneux, J. Bêty, and D. Berteaux. Predator home range size mediates indirect interactions between prey species in an arctic vertebrate community. Journal of Animal Ecology, 92(12): 2373–2385, 2023.
D. Dunnington. ggspatial: Spatial Data Framework for ggplot2, 2023. URL https://CRAN.R-project.org/package=ggspatial. R package version 1.1.9.
G. Gauthier, D. Berteaux, J. Bêty, A. Tarroux, J.-F. Therrien, L. McKinnon, P. Legagneux, and M.-C. Cadieux. The tundra food web of bylot island in a changing climate and the role of exchanges between ecosystems. Ecoscience, 18(3):223–235, 2011.
G. Gauthier, M.-C. Cadieux, D. Berteaux, J. Bêty, D. Fauteux, P. Legagneux, E. Lévesque, and C.-A. Gagnon. Long-term study of the tundra food web at a hotspot of arctic biodiversity, the bylot island field station. Arctic Science, 10(1):108–124, 2024b.
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M. J. Mazerolle. AICcmodavg: Model selection and multimodel inference based on (Q)AIC(c), 2023. URL https://cran.r-project.org/package=AICcmodavg. R package version 2.3.3.
D. L. Miller, E. Rexstad, L. Thomas, L. Marshall, and J. L. Laake. Distance sampling in r. Journal of Statistical Software, 89(1):1–28, 2019.
L. Moisan, D. Gravel, P. Legagneux, G. Gauthier, D.-J. Léandri-Breton, M. Somveille, J.-F. Therrien, J.-F. Lamarre, and J. Bêty. Scaling migrations to communities: An empirical case of migration network in the arctic. Frontiers in Ecology and Evolution, 10:1077260, 2023.
L. Neufeld. Comparing migration ecology among geographically distinct populations of
Canada Geese (Branta canadensis) and Cackling Geese (Branta hutchinsii). Master’s
thesis, University of Manitoba, 2021.
E. J. Pebesma et al. Simple features for r: standardized support for spatial vector data. The R Journal, 10(1):439–446, 2018.
N. Upham, C. Burgin, J. Widness, S. Liphardt, C. Parker, M. Becker, I. Rochon, D. Huckaby, and J. Zijlstra. Mammal diversity database, 2024.
H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016. ISBN 978-3-319-24277-4. URL https://ggplot2.tidyverse.org.
H. Wickham, R. François, L. Henry, K. Müller, and D. Vaughan. dplyr: A Grammar of Data Manipulation, 2023a. URL https://CRAN.R-project.org/package=dplyr. R package version 1.1.4.
H. Wickham, T. L. Pedersen, and D. Seidel. scales: Scale Functions for Visualization, 2023b. URL https://CRAN.R-project.org/package=scales. R package version 1.3.0.
H. Wickham. stringr: Simple, Consistent Wrappers for Common String Operations, 2023. URL https://CRAN.R-project.org/package=stringr. R package version 1.5.1.
H. Wickham, D. Vaughan, and M. Girlich. tidyr: Tidy Messy Data, 2024. URL https://CRAN.R-project.org/package=tidyr. R package version 1.3.1.
Complete documentation describing the project’s context and objectives, the study site, the data collection process, the methods used to estimate species abundance, the resulting data set files with the associated metadata can be found in MetadataS1.pdf at: https://doi.org/10.5281/zenodo.13993828.