DOI: 10.5061/dryad.cfxpnvxhp
title: Data from: Unexpected migration patterns in a high-latitude breeding songbird: Evidence from multi-sensor geolocators and isotopes

description: Seasonal migration allows animals to use habitat where conditions are
 unfavorable for part of the year but may constrain breeding ranges due to
 the costs of longer migrations as ranges expand poleward. In species with
 large ranges, high-latitude breeding populations may employ different
 migration strategies allowing them to persist far from other core
 nonbreeding areas. The myrtle warbler (Setophaga coronata coronata) has
 two disjunct nonbreeding ranges in North and Central America—one along the
 Gulf Coast and the other on the Pacific. Previous work indirectly linked
 birds breeding in Alaska with the Pacific nonbreeding area, suggesting
 that high latitude populations evolved a shorter migration route. We
 directly tested this hypothesis using geolocators measuring both light and
 atmospheric pressure to track Alaskan myrtle warbler migration in fine
 detail and inferred nonbreeding areas using hydrogen isotopes for a larger
 sample of birds breeding in Alaska, British Columbia, and Alberta. We
 found, contrary to expectations, that all geolocator-tracked birds—and 95%
 of birds with stable isotope data—migrated to the southeastern United
 States, a much longer migration than expected for a species commonly
 considered a “short-distance” migrant. We additionally demonstrate the
 advantages of pressure geolocation for characterizing migratory behavior
 at a fine scale.
description: We deployed 30 multisensor geolocators (Migrate Tech
 BARP30Z11-DIP) on myrtle warblers (<em>Setophaga coronata
 coronata</em>) breeding in Far North Bicentennial Park, Anchorage,
 AK in June 2022 and recovered 6 of these geolocators in June 2023. The
 geolocators sampled light intensity every minute, recording the maximum
 intensity every 5 minutes, and recorded pressure and temperature every 20
 minutes. Light data (.lux) was adjusted for clock
 drift, and raw geolocator data files (.lux, .deg) were trimmed to remove
 data recorded after activation of the tag but before deployment on the
 bird, and after removal from the bird but before deactivation. 
 Light data was processed with the R packages
 <em>TwGeos</em> and <em>GeoLight</em>. Pressure
 data was processed both alone and in combination with light data using the
 R package <em>GeoPressureR</em>.  We
 inferred wintering areas for 167 myrtle warblers breeding in Anchorage,
 Alaska (<em>n</em> = 46), northern British Columbia
 (<em>n</em> = 54), and Alberta (<em>n</em> = 67)
 using stable hydrogen isotopes from greater covert feathers grown during
 the pre-alternate molt. We also assessed stable hydrogen isotopes in
 feathers grown during the pre-basic molt (i.e. on breeding grounds) for
 myrtle warblers breeding in Alaska (<em>n</em> = 12) and
 British Columbia (<em>n</em> = 12). Feather sample preparation
 and hydrogen pyrolysis were performed at the Cornell University Stable
 Isotope Laboratory. Stable isotope data was processed using the R package
 <em>assignR</em>. 
description: # Myrtle warbler geolocation and stable isotope data and analysis code
 [https://doi.org/10.5061/dryad.cfxpnvxhp](https://doi.org/10.5061/dryad.cfxpnvxhp) ## Description of the data and file structure Full-year multisensor geolocator data (light, atmospheric pressure, temperature) collected for six myrtle warblers breeding in Anchorage, AK in June 2022-23. Stable hydrogen isotope data generated from greater covert feathers collected from 167 myrtle warblers breeding in Anchorage, AK, northern British Columbia, and Alberta. ### Files and variables #### Compressed archives (CG179.zip, CG181.zip, CG193.zip, CG194.zip, CG206.zip, CG207.zip) each contain data from one geolocator Archives are named for the geolocator ID (recorded in Geolocator_and_Control_Bird_Sampling.csv). All dates and times are GMT/UTC. Within each archive are the following directories and files: #### Directory: GeoID\_Raw Data – Contains raw data files produced by a geolocator ##### GeoID\_Date\_driftadj.lux * **Description:** Light level data adjusted for clock drift. Data has been trimmed to exclude the period after the geolocator was activated but before it was deployed on a bird, and after it was removed from the bird but before it was deactivated. - **Variables:** * DD/MM/YYYY: Date measurement was recorded * HH:MM:SS: Time measurement was recorded * light(lux): Measured light level in lux ##### GeoID\_Date.deg * **Description:** Atmospheric pressure and temperature data collected by a geolocator. Data has been trimmed to exclude the period after the geolocator was activated but before it was deployed on a bird, and after it was removed from the bird but before it was deactivated. * **Variables:** * DD/MM/YYYY: Date measurement was recorded * HH:MM:SS: Time measurement was recorded * T('C): Temperature in degrees Celsius * P(Pa): Atmospheric pressure in Pascals #### Directory: GeoID\_GeoLight – Contains output from analysis of light level data using the R packages TwGeos and GeoLight ##### GeoID\_geolight\_twilights.csv * **Description:** Twilight times estimated from geolocator light-level data using the R package TwGeos and formatted for GeoLight. Outliers were removed using the *twilightEdit* function in TwGeos and removal criteria of window = 4, outlier.mins = 25, and stationary.mins = 20. * **Variables:** * tFirst: Date and time of first twilight event * tSecond: Date and time of second twilight event * type: 1 = tFirst is sunrise, 2 = tFirst is sunset * sun_angle: Sun angle used for calibration * zero_angle: Zero angle used for calibration ##### GeoID\_geolight\_locations\_fullyear.csv * **Description:** Locations estimated in GeoLight for a geolocator over the full year from twilight table (GeoID_geolight_twilights.csv) * **Variables:** * tFirst: Date and time of first twilight event * lon: Longitude estimate in decimal degrees for a set of twilights * lat: Latitude estimate in decimal degrees for a set of twilights ##### GeoID\_geolight\_locations\_winter\_spring.csv * **Description:** Locations estimated in GeoLight for a geolocator over the wintering period and spring migration only. These points are plotted in Fig. S10, where fall migration coordinate estimates were omitted due to high latitudinal error around the fall equinox. * **Variables:** * tFirst: Date and time of first twilight event * lon: Longitude estimate in decimal degrees for a set of twilights * lat: Latitude estimate in decimal degrees for a set of twilights #### Directory: GeoID\_GeoPressureR – Contains output from analysis of atmospheric pressure and light level data using the R package GeoPressureR ##### GeoID-tag-labeled.csv * **Description:** Pressure data labeled in TRAINSET with flights, elevation changes, and outliers to discard. * **Variables:** * series: Data type (here, pressure) * timestamp: Date and time pressure was recorded * value: Atmospheric pressure measurement (hectopascals) * label: Blank if no label, discard=outlier to be discarded, flight=migratory flight, elev_#: label for bird changing elevation within a stationary period ##### GeoID-twilight-labeled.csv * **Description:** Twilight data labeled in TRAINSET with stationary periods and outliers to discard. * **Variables:** * series: Twilight type (Set = sunset, Rise = sunrise) * timestamp: Date and time pressure was recorded * value: Twilight time converted to numerical value for plotting * label: Numbers indicating stationary period #, "discard" for outliers to remove **Directory: GeoID_GeoPressureR_Output_PressureOnly – Contains HTML output from GeoPressureR analysis of pressure data alone** ##### GeoID\_altitude\_pressonly.html * Plot of altitude over time ##### GeoID\_margprob\_path\_pressonly.html * Marginal probability map for each stationary period ##### GeoID\_mostlikely\_path\_pressonly.html * Map of most likely migration path ##### GeoID\_mostlikely\_pressurepath\_pressonly.html * Plot of atmospheric pressure over time recorded by the geolocator (grey) vs. pressure recorded in the ERA5 weather reanalysis dataset for the most likely location of the stationary period (colored). Black dots are discarded data points and orange triangles are points considered outliers but retained in the dataset. ##### GeoID\_pressure\_likelihood\_pressonly.html * Likelihood map for each stationary period based on pressure data ##### Directory: GeoID\_GeoPressureR\_Output\_PressureAndLight – Contains HTML output from GeoPressureR analysis of pressure and light data combined Contains all files described above for the "Pressure Only" analysis, with the addition of: ##### GeoID\_light\_likelihood.html * Likelihood map for each stationary period based on light data #### File: Supporting\_Dataset\_1\_Geolocator\_and\_Control\_Bird\_Sampling.csv **Description:** Banding, location, and morphological data for each bird fitted with a geolocator or color banded as a control for assessing return rates. ##### Variables * record_number: Unique ID number for each bird banded * capture_date: Date bird was captured * capture_time: Time bird was captured (local time) * latitude: Latitude of banding location (decimal degrees) * longitude: Longitude of banding location (decimal degrees) * elevation_ft: Elevation of banding location (feet) * band_number: Band number * geo_or_control: Whether bird was fitted with a geolocator or only color banded (control) * geolocator_number: Unique ID number for geolocator, N = no geolocator * recapped_or_resighted: Y = bird was recaptured or resighted, N = bird was not resighted * age: Age of bird estimated from molt. SY = second year, ASY = after second year * sex: Sex of bird determined from presence of cloacal protuberance or brood patch. M = male, F = female * cp: Cloacal protuberance. 0 = no cloacal protuberance present, 1 = small, 2 = medium, 3 = large * bp: Brood patch. 0 = no brood patch, 2 = well developed brood patch * tarsus_mm: Tarsus length in millimeters * wing_mm: Wing length in millimeters * tail_mm: Tail length in millimeters * culmen_mm: Culmen length in millimeters * kipps_distance_mm: Kipp's distance (distance between longest primary and first secondary feather) in millimeters #### File: Supporting\_Dataset\_2\_Isotope\_Sampling.csv **Description:** Data (banding, location, morphological, isotope) for each feather sample that underwent stable hydrogen isotope analysis. ##### Variables * record_number: Unique ID number for each bird banded * state_prov: State or province where bird was banded * latitude: Latitude of banding location (decimal degrees) * longitude: Longitude of banding location (decimal degrees) * age: Age of bird estimated from molt. AHY = after hatch year, SY = second year, ASY = after second year * sex: Sex of bird determined from presence of cloacal protuberance or brood patch. M = male, F = female * wing_mm: Wing length in millimeters * tail_mm: Tail length in millimeters * feather: Type of feather analyzed. Basic = grown in pre-basic molt (i.e. on previous year's breeding ground). Alternate = grown in pre-alternate molt (i.e. on non-breeding ground). * delta2H: Hydrogen isotope ratio measured in feather sample ## Code/software **Light-level data** analyzed using the R packages **TwGeos** and **GeoLight** and the script: **GeoLight.R** **Atmospheric pressure data** analyzed independently and in combination with light-level data using the R package **GeoPressureR**, following **[A User Manual for GeoPressureR](https://raphaelnussbaumer.com/GeoPressureManual/)** and using the following scripts: 1. **GeoPressureR_TagLabelling.qmd** – Set up configuration file, create tag label file, label file using TRAINSET, and check labels 2. **GeoPressureR_TagTrajectory_PressureOnly.R** – Generate trajectories for each geolocator using pressure data alone 3. **GeoPressureR_TwilightLabelling.qmd** – Create twilight label file, label file using TRAINSET, and check labels 4. **GeoPressureR_TagTrajectory_PressureAndLight.R** – Generate trajectories for each geolocator using pressure and light data combined **Stable hydrogen isotope data** analyzed using the R package **assignR** and the script: **Isotopes.R** ## Access information Other publicly accessible locations of the data: * Geolocator data is also available on [Movebank](https://www.movebank.org/) (ID# 4549104814)