DOI: 10.5061/dryad.n2z34tn6s
title: Euphagus carolinus (Rusty Blackbird) from two different breeding populations in northeastern North America exhibit chain migration yet use the same region for stopover

description: Bird populations within the same species may follow different migratory
 strategies and phenology depending on their breeding location and
 latitude, and migratory strategies may be influenced by important stopover
 sites. Understanding these strategies and identifying important stopover
 sites is crucial for the conservation of species with regionally varying
 population trends. In this study, Euphagus carolinus (Rusty Blackbirds)
 from two populations in eastern North America were affixed with NanoTag
 (Lotek) transmitters and tracked using the Motus Wildlife Tracking System
 to determine migratory routes and connectivity, stopover locations, and
 wintering areas. During fall migration, birds tagged at Observatoire
 d’oiseaux de Tadoussac, Québec and breeding sites in New England
 maintained separate migratory routes north of 43° latitude, as indicated
 by positive Mantel statistics of migratory connectivity, before converging
 on stopover areas in the Chesapeake and Delaware Bays region of the
 mid-Atlantic U.S.. Migratory strategy differed between the two
 populations: birds from New England spent ~two months longer at breeding
 latitudes than birds from Québec, and Québec birds spent more time at fall
 stopover sites and wintering latitudes. Birds from both populations made
 &gt;one-week stopovers during spring and fall migrations and made
 long-distance (up to 645 km) nocturnal flights. The few winter detections
 suggested that Rusty Blackbirds from New England wintered at more southern
 latitudes than birds from Québec. Land cover data around stopover sites
 indicated that Rusty Blackbirds were positively associated with percent
 cover of wooded wetlands, croplands, and hay/pasture. Results from this
 study could help identify and protect regionally important stopover and
 wintering areas for Rusty Blackbirds, a species that has experienced
 dramatic long-term population declines linked to habitat loss in the
 nonbreeding range.
description: # Euphagus carolinus (Rusty Blackbird) from two different breeding
 populations in northeastern North America exhibit chain migration yet use
 the same region for stopover
 [https://doi.org/10.5061/dryad.n2z34tn6s](https://doi.org/10.5061/dryad.n2z34tn6s) ## Description of the data and file structure Rusty Blackbirds were affixed with NanoTag radio transmitters in Québec and New England and tracked with the Motus Wildlife Tracking System network of automated receivers to determine differences in their migratory strategies. Detection data were accessed through the Motus website ([https://motus.org/](https://motus.org/)), but are only available for download for members of each Motus project (Québec data are project #161 Migratory Connectivity of the Rusty Blackbird; New England data are project #252 New England Rusty Blackbird Project). The raw detection data were assessed graphically with a *shiny* application in R to remove false detections and identify migratory flights and stopovers. The clean detection, flight, and stopover data are available in this repository. ### Files and variables #### File: bandingdata\_161.csv **Description:** This file contains the data collected at Observatoire d’oiseaux de Tadoussac for each Rusty Blackbird captured. NA values are missing data that were not entered during banding activities so cannot be recovered. In 2020, birds were not scored for fat due to COVID-19 protocols. ##### Variables * BandA: Band number prefix * BandB: Band number suffix * Scientific: Common name in French * Age: AHY-after hatch year (adult); HY-hatch year (immature); U-unknown * Pneumatisation : score of skull ossification, 1-6. * Sex: F-female; M-male * Fat: 0-7, 0 is no fat, 7 is excessive fat * Wing: wing chord measurement in mm * Mass: mass in grams * Date: yyyy-mm-dd * CatchTime: hh:mm * ReleaseTIme: hh:mm * Filet : initials of scribe * Bander: initials of bander * mfgID: NanoTag id number (these are not unique as tag numbers range from 0-999). * motusTagID: unique Motus tag id number #### File: df.tagDeps252.csv **Description:** This file contains tag deployment information for each Motus NanoTag deployed in New England. Downloaded from Motus website. For more details on variables consult the Motus website ([https://motus.org/](https://motus.org/)). NA values were present in the data when downloaded from Motus, some reflect data that was not entered into the metadata (e.g. elevation) or metadata that was not linked to the file downloaded (e.g. bandNumber, id, and bi). ##### Variables * tagID: unique Motus tag id number * deployID: unique Motus tag deployment id number, as recovered tags can be redeployed on different birds. * projectID: Motus project number * tsStart: POSIX timestamp for beginning of tag deployment * tsEnd: POSIX timestamp for end of tag deployment * deferSec: not used * speciesID: numerical species code * markerType: not used * markerNumber: not used * sex: M-male, F-female, U-unknown * age: ad-adult, imm-immature, juv-juvenile * latitude: decimal degrees of capture location * longitude: decimal degrees of capture location * elevation: m above sea level of capture location * comments: notes * test: 0 for active tags, 1 if a test deployment * attachment: method of tag attachment * tsStartCode: not used * tsEndCode: not used * bandNumber: NA, not used * id: NA, not used * bi: NA, not used * fullID: not used * status: not used * timeStart: deployment start datetime yyyy-mm-dd-hh-mm UTC * timeEnd: deployment end datetime yyyy-mm-dd-hh-mm UTC #### File: df.tagDeps161.csv **Description:** This file contains tag deployment information for each Motus NanoTag deployed in Quebec. Downloaded from Motus website. For more details on variables consult the Motus website ([https://motus.org/](https://motus.org/)). NA values were present in the data when downloaded from Motus, some reflect data that was not entered into the metadata (e.g. elevation) or metadata that was not linked to the file downloaded (e.g. bandNumber, id, and bi). ##### Variables * tagID: unique Motus tag id number * deployID: unique Motus tag deployment id number, as recovered tags can be redeployed on different birds. * projectID: Motus project number * tsStart: POSIX timestamp for beginning of tag deployment * tsEnd: POSIX timestamp for end of tag deployment * deferSec: not used * speciesID: numerical species code * markerType: not used * markerNumber: not used * sex: M-male, F-female, U-unknown * age: ad-adult, imm-immature, juv-juvenile * latitude: decimal degrees of capture location * longitude: decimal degrees of capture location * elevation: m above sea level of capture location * comments: notes * test: 0 for active tags, 1 if a test deployment * attachment: method of tag attachment * tsStartCode: not used * tsEndCode: not used * bandNumber: not used * id: not used * bi: not used * fullID: not used * status: not used * timeStart: deployment start datetime yyyy-mm-dd-hh-mm UTC * timeEnd: deployment end datetime yyyy-mm-dd-hh-mm UTC #### File: active\_receivers2017\_2023.csv **Description:** This was downloaded from the Motus website and filtered to only include Motus receivers that were active during the time frame of our project (Sep 2017-Dec 2023). For more details on variables consult the Motus website ([https://motus.org/](https://motus.org/)). NA values were present in the data when downloaded from Motus, and could change in future downloads if Motus metadata are updated. ##### Variables * deployID: Receiver deployment ID number. The same receiver location may have multiple deployments for different date ranges of activity. * projectID: Project ID number denoting who deployed the receiver. * serno: serial number of receiver * receiverType: type of receiver * deviceID: device ID number * status: status at time of data download. Active or terminated. * name: receiver name * siteName: site name * stationName: station name * fixtureType: type of mount for antennas. * latitude: decimal degrees of receiver location * longitude: decimal degrees of receiver location * elevation: m above sea level of receiver location * isMobile: 0 for stationary receiver, 1 for mobile receiver * tsStart: POSIX timestamp for beginning of receiver deployment * tsEnd: POSIX timestamp for end of receiver deployment. NA values indicate that the receiver was still active at the time of download. * utcOffset: not used * stationID: not used * macAddress: not used * timeStart: datetime for beginning of receiver deployment yyyy-mm-dd hh:mm:ss UTC * timeEnd: datetime for beginning of receiver deployment yyyy-mm-dd hh:mm:ss UTC * active: flag for whether receiver was active during time frame. Should be True for all. #### File: flights.csv **Description:** This file was created using the *shiny* application while looking at the all.runs.clean.csv data graphically. Flights were series of detections of an individual in a migratory direction within a ~24 hour period. ##### Variables * motusTagID: Motus tag ID number indicating an individual bird. * region: OOT-Quebec, NH-New England * flightDepart: datetime yyyy-mm-dd hh:mm UTC. Recorded if there was an obvious departure from the capture site or a stopover site. NA values indicate that there was no obvious departure. * flightStart: datetime yyyy-mm-dd hh:mm UTC for first detection of a flight * flightEnd: datetime yyyy-mm-dd hh:mm UTC for last detection of a flight * season: Fall or Spring * comments: notes. NA values indicate that no notes were recorded. #### File: GPSstopovers.csv **Description:** This file was created using detection data from the NH_GPS_tag.csv file to identify beginning and end times, and locations of stopovers and wintering location. These data come from a pinpoint GPS tag that was affixed to a New England Rusty Blackbird and later recovered. ##### Variables * StopStart: yyyy-mm-dd hh:mm UTC of first detection during stopover/winter * StopEnd: yyyy-mm-dd hh:mm UTC of last detection during stopover/winter * LatStart: Latitude in decimal degrees of first detection during stopover/winter * LonStart: Longitude in decimal degrees of first detection during stopover/winter * LatEnd: Latitude in decimal degrees of last detection during stopover/winter * LonEnd: Longitude in decimal degrees of last detection during stopover/winter * season: Fall, Spring, or Winter #### File: NH\_GPS\_tag.csv **Description:** These data come from a pinpoint GPS tag that was affixed to a New England Rusty Blackbird and later recovered. ##### Variables * Date: yyyy-mm-dd * Latitude: decimal degrees of detection location * Longitude: decimal degrees of detection location * Sitename: Name of nearest locality * State: Two letter state code of detection location #### File: tagmodels.csv **Description:** This file contains specifications for each NanoTag deployed and was downloaded from the Motus website. For more details on variables consult the Motus website ([https://motus.org/](https://motus.org/)). ##### Variables * tagID: unique Motus tag identification number * projectID: Motus project number, 161(Quebec) or 252 (New England) for this study * mfgID: NanoTag ID number. Not unique as numbers range from 0-999. * type: tag type * codeSet: Lotek code set * manufacturer: tag manufacturer * model: NanoTag model number * lifeSpan: estimated battery lifespan in days * nomFreq: frequency Hz of transmitter * offsetFreq: offset frequency Hz * bi: burst interval in sec * pulseLen: pulse length * region: OOT is Quebec, NH is New England #### File: stopovers.csv **Description:** This file was created using the *shiny* application while looking at the all.runs.clean.csv data graphically. Stopovers were series of Motus detections of an individual over multiple days at approximately the same location (within 100 km). ##### Variables * motusTagID: Motus tag ID number indicating an individual bird. * region: Tadoussac is Quebec, NH is New England * stopoverStart: datetime yyyy-mm-dd hh:mm UTC of first stopover detection * stopoverEnd: datetime yyyy-mm-dd hh:mm UTC of last stopover detection * season: Fall, Spring, or Winter #### File: TadoussacDepartures.csv **Description:** This file was created using the *shiny* application while looking at the all.runs.clean.csv data graphically and determining when individuals left the capture area based on patterns in signal strength at local receivers or detections of migratory flights leaving the area. ##### Variables * motusTagID: Motus tag ID number indicating an individual bird. * region: Tadoussac, Quebec * capturedate: yyyy-dd-mm * departdate: yyyy-dd-mm. NA indicates that no departure was recorded in the Motus detection data. * departStartTime: yyyy-dd-mm hh:mm UTC of departure. NA indicates that no departure was recorded in the Motus detection data. * departEndTime: yyyy-dd-mm hh:mm UTC of last detection of departure flight. NA indicates that no departure was recorded in the Motus detection data. * Comments: notes. NA indicated no notes were made. #### File: all.runs.clean.csv **Description:** This is the cleaned Motus detection dataset after false detections were removed using the *shiny* application. This data is derived from the "allruns" table from the Motus project download. For more details on variables consult the Motus website ([https://motus.org/](https://motus.org/)). Some NA values were present in the data from the Motus download. ##### Variables * runID: Motus identification number for each run, a series of detections on a receiver antenna. * motusTagID: Motus tag ID number indicating an individual bird. * runLen: the number of detections in the run * tsBegin: POSIX timestamp of first detection in a run * tsEnd: POSIX timestamp of last detection in a run * tsBeginCorrected: POSIX timestamp of first detection in a run corrected for time offset * tsEndCorrected: POSIX timestamp of last detection in a run corrected for time offset * mfgID: NanoTag ID number. Not unique as numbers range from 0-999 and are recycled. * tagModel: NanoTag model * tagBI: Burst interval in seconds * tagDeployID: tag deployment ID number * markerNumber: NA, not used * tagDeployStart: POSIX timestamp for tag deployment start * tagDeployLat: Latitude in decimal degrees of capture location * tagDeployLon: Longitude in decimal degrees of capture location * tagDepComments: notes. NA indicates no notes were made. * deviceID: device ID number * recvDeployID: receiver deployment ID number * recvDeployLat: Receiver latitude in decimal degrees * recvDeployLon: Receiver longitude in decimal degrees * recv: Receiver ID number * recvDeployName: Receiver name * recvSiteName: Receiver Site name. NA indicates no site name was entered other than the recvDeployName. * isRecvMobile: 0 for stationary, 1 for mobile * recvProjID: Motus project number indicating who deployed the receiver * antType: type of antenna. NA indicates that the antenna type was not recorded in the Motus metadata. * antBearing: direction in degrees of antenna orientation. In the case of omnidirectional antennas, the bearing is NA because the antenna points straight up. Otherwise, NA values indicate the bearing was not recorded in the Motus metadata. * speciesEN: Common name of species tagged * timeBegin: yyyy-mm-dd hh:mm:ss UTC of first detection of run * timeEnd: yyyy-mm-dd hh:mm:ss UTC of last detection of run * deployDate: yyyy-mm-dd hh:mm:ss UTC for date the NanoTag was deployed * region: OOT is Quebec, NH is New England * depyear: Year the NanoTag was deployed * year: integer Year of detection * month: integer month of detection * date: yyyy-mm-dd of detection * season: Spring, Summer, Fall, Winter ## Code/software The analyses were conducted in R version 4.3.3. The RUBL_motus.R script provided shows how to download and prepare Motus data for analysis, and uses the files cleaned Motus data files provided to analyze the data and produce the figures and tables from the manuscript. The landcover data must be downloaded separately from this website: [https://www.mrlc.gov/data?f%5B0%5D=category%3ALand%20Cover](https://www.mrlc.gov/data?f%5B0%5D=category%3ALand%20Cover). Instructions are included in that section of the script. To use the map backgrounds from this study, the user must acquire an free API key. Instructions are included in the R script. R packages used in the script are: tidyverse 2.0.0 motus 6.1.0 DBI 1.2.2 RSQLite 2.3.6 rnatururalearth 1.0.1 ggmap 4.0.0 suncalc 0.5.1 MuMin 1.47.5 cowplot 1.1.3 mgcv 1.9-1 AICcmodavg 2.3-3 vegan 2.6-4 ecodist 2.1.3 geosphere 1.5-18 terra 1.7-71 sf 1.0-16 elevatr 0.99.0