DOI: 10.5061/dryad.pg4f4qs3m
title: Data from: Multi-decadal changes in co-occurrence of migrating landbirds are associated with species-specific changes in phenology and abundance

description: Human-induced changes to the climate and environment have precipitated
 dramatic declines in abundance and shifts in plant and animal phenologies.
 These changes have been especially pronounced for migratory species that
 rely on numerous geographic locations throughout the year. Migratory bird
 species are notable in the number of species that have experienced both
 declines in abundance and shifts in phenology over the past 50 years,
 although the magnitude and direction of changes vary considerably across
 species. The community-level impacts of species declines and phenological
 shifts have been explored in stationary communities, but we know little
 about the effects of these changes on species relationships during
 migration seasons when species may interact in ways that influence their
 route, timing, or success of the journey (e.g., through competition or
 access to information about resources). Therefore, we assessed the extent
 to which co-migrating bird communities have changed over time, and whether
 changes in species co-occurrence are associated with changes in abundance
 or shifts in migration timing. We used over 700,000 records of birds
 captured at five long-term migration monitoring stations in eastern North
 America and found that pairwise species co-occurrences have changed by as
 much as 40 % over the past 50 years. Changes in co-occurrence were
 consistently associated with species-specific changes in phenology and
 sometimes associated with changes in abundance. Overall, stopover
 communities at three sites have significantly changed over the past few
 decades. Numerous and dramatic changes in co-occurrence could be affecting
 the types and frequencies of interspecific interactions like competition
 and the exchange of social information, transforming the journeys of
 migratory birds in innumerable ways that could be altering their timing,
 energy, and safety.
description: We used long-term bird banding data collected during spring and
 fall migration at five stations across eastern North America: Powdermill
 Avian Research Center (“Powdermill;” lat long: 40.164, -79.268; spring
 seasons: 1970-2019; fall seasons: 1970–1972, 1974-2018), Braddock Bay Bird
 Observatory (“Braddock Bay;” 43.324, -77.717; spring seasons: 2009-2022;
 fall seasons: 2011-2022), Long Point Bird Observatory’s Old Cut Research
 Station (“Long Point;” 42.584, -80.398; spring seasons: 1984-2019,
 2021-2022; fall seasons: 1984-2022), Manomet Bird Observatory (“Manomet;”
 41.920, -70.543; spring seasons: 1987-1990, 1992-2019, 2021-2022; fall
 seasons: 1987-1988, 1992-2022) and Appledore Island Migration Station
 (“Appledore;” 42.989, -70.615; spring seasons: 1991-2019,
 2021-2023). Analyses from each site and season involve a few dozen species
 (Appledore spring N = 37; Braddock Bay spring N = 38; Braddock Bay fall N
 = 34; Long Point spring N = 44; Long Point fall N = 42; Manomet spring N =
 34; Manomet fall N = 36; Powdermill spring N = 42; Powdermill fall N = 41;
 Table S1), totaling 709,078 band records (Appledore spring N = 71,273;
 Braddock Bay spring N = 41,791; Braddock Bay fall N = 30,833; Long Point
 spring N = 109,958; Long Point fall N = 152,163; Manomet spring N =
 24,226; Manomet fall N = 25,824; Powdermill spring N = 59,956; Powdermill
 fall N = 193,054).
description: # Data from: Multi-decadal changes in co-occurrence of migrating landbirds
 are associated with species-specific changes in phenology and abundance
 Dataset DOI:
 [10.5061/dryad.pg4f4qs3m](https://doi.org/10.5061/dryad.pg4f4qs3m) ##
 Description of the data and file structure We used long-term bird banding
 data collected during spring and fall migration at five stations across
 eastern North America: Appledore Island Migration Station
 ("AIMS"), Braddock Bay Bird Observatory ("BBBO"), Long
 Point Bird Observatory's Old Cut Research Station ("CUT"),
 Manomet Bird Observatory ("MBO"), and Powdermill Avian Research
 Center ("PARC"). These stations set out mist nets during
 migration seasons, and capture, collect data on, and release all the birds
 that fly into these nets. Each station uses standardized protocols to
 collect data in the same way over decades. They keep track of daily net
 effort, which is calculated as the number of nets open on a given day,
 multiplied by the number of hours each net was open; we used seasonal net
 effort in our analyses, which is the sum of daily net effort across a
 migratory season. We use data from spring and fall for all sites except
 AIMS, for which we only have data from spring migration. We use
 four-letter species name abbreviations throughout our datasets, which
 refer to bird species common names as specified here: | 
 
 | 
 
 | | :--------------------------- | :----- | |  Acadian Flycatcher | ACFL
 | |  American Redstart | AMRE | |  American Tree Sparrow | ATSP | |
  Baltimore Oriole | BAOR | |  Barn Swallow | BARS | |  Black-and-White
 Warbler | BAWW | |  Bay-breasted Warbler | BBWA | | Blue-headed Vireo |
 BHVI | | Blue-gray Gnatcatcher | BGGN | | Blackburnian Warbler | BLBW | |
 Blackpoll Warbler | BLPW | | Brown Thrasher | BRTH | | Black-throated Blue
 Warbler | BTBW | | Black-throated Green Warbler | BTNW | | Blue-winged
 Warbler | BWWA | | Canada Warbler | CAWA | | Chipping Sparrow | CHSP | |
 Cape May Warbler | CMWA | | Common Yellowthroat | COYE | | Chestnut-sided
 Warbler | CSWA | | Dark-eyed Junco | DEJU | | Eastern Bluebird | EABL | |
 Eastern Phoebe | EAPH | | Eastern Towhee | EATO | | Eastern Wood Pewee |
 EAWP | | Fox Sparrow | FOSP | | Golden-crowned Kinglet | GCKI | | Great
 Crested Flycatcher | GCFL | | Gray-cheeked Thrush | GCTH | | Gray Catbird
 | GRCA | | Golden-winged Warbler | GWWA | | Hermit Thrush | HETH | |
 Hooded Warbler | HOWA | | House Wren | HOWR | | Indigo Bunting | INBU | |
 Kentucky Warbler | KEWA | | Least Flycatcher | LEFL | | Lincoln’s Sparrow
 | LISP | | Louisiana Waterthrush | LOWA | | Magnolia Warbler | MAWA | |
 Mourning Warbler | MOWA | | Myrtle Warbler | MYWA | | Nashville Warbler |
 NAWA | | Northern Parula | NOPA | | Northern Waterthrush | NOWA | |
 Orchard Oriole | OROR | | Ovenbird | OVEN | | Philadelphia Vireo | PHVI |
 | Prairie Warbler | PRAW | | Rose-breasted Grosbeak | RBGR | |
 Ruby-crowned Kinglet | RCKI | | Red-eyed Vireo | REVI | | Scarlet Tanager
 | SCTA | | Song Sparrow | SOSP | | Swamp Sparrow | SWSP | | Swainson’s
 Thrush | SWTH | | Tennessee Warbler | TEWA | | Tree Swallow | TRES | |
 Traill’s Flycatcher | TRFL | | Veery | VEER | | Warbling Vireo | WAVI | |
 White-crowned Sparrow | WCSP | | White-eyed Vireo | WEVI | | Wilson’s
 Warbler | WIWA | | Winter Wren | WIWR | | Wood Thrush | WOTH | | Western
 Palm Warbler | WPWA | | White-throated Sparrow | WTSP | | Yellow-bellied
 Flycatcher | YBFL | | Yellow Warbler | YEWA | ### Files and variables ####
 File: species_abundances.zip **Description:** We calculated species
 abundances for each species during each year at each site (AIMS, BBBO,
 CUT, MBO, and PARC) and season (spring and fall). Files in this compressed
 folder follow the naming convention
 "[SITE]_[season]_abundances.csv". Variables: * n: the number of
 individuals of each species captured in each year of data collection at
 the site during spring or fall migration * Species: the four-letter
 abbreviation of the species * Year: year of data collection 
 
 #### File: phenology_by_species.zip **Description:** We quantified
 migration phenology for each species during each year at each site (AIMS,
 BBBO, CUT, MBO, and PARC) and season (spring and fall). We calculated the
 early, peak, and late passage dates for each species (the date by which 10
 %, 50 % or 90 % of a species' total captures were made,
 respectively). We did not calculate passage dates for a species in a year
 in which fewer than 5 individuals of that species were captured. Some
 individuals may be captured multiple times within a season: to determine
 migration phenology, we removed from our dataset any same-season
 recaptures. Files in this compressed folder follow the naming convention
 "[SITE]_[season]_phenology.csv". Variables: * Year: year of data
 collection * Species: four-letter abbreviation of species * net.hours: the
 seasonal net effort at the site * percentile: Values are 10, 50, or 90,
 referring to the day of the year by which 10 %, 50 % or 90 % of all
 individuals of a given species were captured. * dates: the day of the year
 by which 10 %, 50 %, or 90 % of all individuals of the species were
 captured. 
 
 #### File: abundance_slope_matrices.zip **Description:** These data files
 are matrices (row names are in the first column) for every site (AIMS,
 BBBO, CUT, MBO, and PARC) and season (spring and fall). Row and column
 names are four-digit bird species name abbreviations. Each cell contains
 the rate of change in relative abundance for each pair of species (with
 NAs along the diagonal). These values were calculated as follows: first,
 we calculated relative abundance for each pair of species as the sum of
 the number of captures of both species divided by the total number of
 captures of all species at the site during a given season and year.
 Second, we constructed a linear model for each pair of species, in which
 the response variable was their relative abundance and the predictor
 variables were year and net effort. We extracted the slope coefficients
 from each of these models for each species pair, which are the values
 contained in these matrices. The file names in this compressed folder
 follow the naming convention
 "[SITE]_[season]_abundance_slope.csv". 
 
 #### File: cooccurrence_slope_matrices.zip **Description:** These data
 files are matrices (row names are in the first column) for every site
 (AIMS, BBBO, CUT, MBO, and PARC) and season (spring and fall). Row and
 column names are four-digit bird species name abbreviations. Each cell
 contains the rate of change in co-occurrence for each pair of species
 (with NAs along the diagonal). These values were calculated as follows:
 first, we calculated co-occurrence as the proportion of individuals of
 both species that were captured on a day when both species were captured.
 Second, we constructed a linear model for each pair of species, in which
 the response variable was their co-occurrence and the predictor variables
 were year and net effort. We extracted the slope coefficients from each of
 these models for each species pair, which are the values contained in
 these matrices. The file names in this compressed folder follow the naming
 convention "[SITE]_[season]_assn_slope.csv". 
 
 #### File: phenology_slope_matrices.zip **Description:** These data files
 are matrices (row names are in the first column) for every site (AIMS,
 BBBO, CUT, MBO, and PARC) and season (spring and fall). Row and column
 names are four-digit bird species name abbreviations. Each cell contains
 the rate of change in phenological dissimilarity for each pair of species
 (with NAs along the diagonal). These values were calculated as follows:
 first, we calculated phenological dissimilarity as the difference (in
 number of days) between two species' peak migration passage dates.
 Second, we constructed a linear model for each pair of species, in which
 the response variable was their phenological dissimilarity and the
 predictor variables were year and net effort. We extracted the slope
 coefficients from each of these models for each species pair, which are
 the values contained in these matrices. The file names in this compressed
 folder follow the naming convention
 "[SITE]_[season]_phenology_slope.csv". 
 
 #### File: Mantel_results.zip **Description:** We tested whether stopover
 communities have changed significantly during the time frame of the study.
 For this analysis, we used repeated Mantel tests to conduct pairwise
 comparisons of the average co-occurrence network of the first five years
 of the dataset with each subsequent year. We extracted the correlation
 coefficient of each Mantel test, which represents the similarity of each
 pair of networks. Files in this compressed folder follow the naming
 convention "[SITE]_[season]_MantelR.csv". Variables: * Year: the
 year of data collection * mantel.r: the Mantel's R coefficient from a
 comparison of that year's co-occurrence matrix with a matrix of the
 average of the co-occurrence matrices from the first five years of data
 collection. * net.hours: the net effort that year, during the given season
 * hrs.diff: the difference in net effort between that year of data
 collection and the average net effort of the first five years of data
 collection 
 
 #### File: node_strength.zip **Description:** We assessed how a
 species' abundance and relative phenological shifts relate to
 it's co-occurrence with all other species at the site. We calculated
 "node strength," which is the sum of a species'
 co-occurrences with all other species. The files in this compressed folder
 follow the naming convention
 "[SITE]_[season]_node_strength.csv". Variables: * Year: the year
 of data collection * Species: the four-letter abbreviation of the species
 name * node.strength: the sum of a species' co-occurrences with all
 other species that year * n.individuals: the number of individuals of a
 species captured that year * net.hours: the net effort of that year's
 migration season * median.passage: the date by which 50 % of the
 individuals of a species were captured * baseline.passage.date: the
 average of a specie's peak passage dates in the first five years of
 the dataset. ("Peak" passage date is the date by which 50 % of
 the individuals of a species were captured). * species.shift: the
 difference (in days) between the species median.passage and
 baseline.passage.date * overall.median.shift: the median species.shift
 across all species in a given year * shift.difference: the difference
 between a species' phenological shift (species.shift) and the
 community's overall phenological shift (overall.median.shift). 
 
 #### File: proportion_foliage_gleaners.csv **Description:** We tested
 whether the relative proportions of foraging guilds (birds using different
 foraging tactics) have changed over time. We only used the longest-term
 dataset for this question (from PARC). We selected three weeks of data
 from each season and year: a week of early migration, centered on the date
 by which 10 % of the season's birds were captured, a week of peak
 migration, centered on the date by which 50 % of the season's birds
 were captured, and a week of late migration, centered on the date by which
 90 % of the season's birds were captured. Foraging categories (aerial
 forager, flycatching, foliage gleaner, and ground forager) are from
 Cornell Lab of Ornithology's "All About Birds." #####
 Variables * Year: year of data collection * Aerial_Forager: the number of
 captured individuals that were aerial foragers * Flycatching: the number
 of captured individuals that were flycatchers * Foliage_Gleaner: the
 number of captured individuals that were foliage gleaners *
 Ground_Forager: the number of captured individuals that were ground
 foragers * total: the total number of individuals captured *
 Proportion_Foliage: the proportion of total individuals that were foliage
 gleaners * Season: the season of data collection (Spring or Fall) * Week:
 the week of data collection (early, median, or late) 
 
 #### Co-occurrence arrays: At each site, during both seasons, we
 calculated co-occurrence for each species pair. Co-occurrence was
 calculated as the proportion of individuals of both species that were
 captured on a day when both species were captured. For each year of data
 collection, we constructed a co-occurrence network: these are matrices in
 which every row and column refers to a species, and every cell contains
 that species pair's co-occurrence that year. These matrices are saved
 in a compressed folder, with one matrix for every year of data collection,
 following the naming convention:
 "association_matrix_[SITE]*[season]*[year].csv". The first
 column in each dataset are the row names for the matrix, and the row and
 column names of each matrix are the four-letter species abbreviations. The
 diagonals are "NA." These matrices are stored in the following
 compressed files, following the naming convention
 "[SITE]_[season]_cooccurrence_array.zip" #### File:
 AIMS_spring_cooccurrence_array.zip #### File:
 BBBO_spring_cooccurrence_array.zip #### File:
 BBBO_fall_cooccurrence_array.zip #### File:
 CUT_spring_cooccurrence_array.zip #### File:
 CUT_fall_cooccurrence_array.zip #### File:
 MBO_spring_cooccurrence_array.zip #### File:
 MBO_fall_cooccurrence_array.zip #### File:
 PARC_spring_cooccurrence_array.zip #### File:
 PARC_fall_cooccurrence_array.zip #### ## Code/software All analyses were
 conducted in R (version 4.5.0) and RStudio (version 2024.12.1+563).