Data from: When do tropical birds breed? The case of Colombian species assemblages
Data files
Nov 21, 2025 version files 18.96 MB
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Breeding_database.csv
18.92 MB
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PrimaryCode_Moreno-Palacios(2025).R
12.27 KB
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README.md
12.13 KB
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Suppl_TimeSeries_.zip
2.12 KB
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SupplementaryCode_Moreno-Palacios(2025).R
16.31 KB
Abstract
Understanding when tropical birds breed is key to life-history theory and to predicting how species will respond to environmental change. While early views emphasized the potential for year-round breeding in the tropics, accumulating evidence suggests that reproductive activity in most tropical birds follows some degree of seasonality, often linked to rainfall and associated food pulses. However, large-scale evaluations across ecological gradients remain scarce. Here, we investigated the breeding seasonality of Colombian resident birds using over 80,000 records compiled from bird banding programs and the Global Biodiversity Information Facility (GBIF). These data included birds in breeding condition, active nests, nestlings, and adults displaying reproductive behavior. We asked four main questions: (a) Do Colombian birds exhibit seasonal breeding activity? (b) Does the degree of seasonality vary with latitude and elevation? (c) Are there geographic differences in breeding patterns across Colombia’s biogeographic regions? (d) How does breeding activity vary among feeding guilds? We used time-series analysis, circular statistics, and generalized additive models (GAMs) to evaluate breeding patterns at national and regional levels, incorporating geographic variables and trophic guild. We found a clear seasonal pattern in breeding activity, with a main peak in April and low but consistent activity throughout the year, especially in the Andes. Breeding was more synchronized at higher latitudes and more extended near the Equator. Elevation also shaped seasonality: lowland bird communities showed broader breeding seasons, while mid- and high-elevation assemblages had narrower windows, with peaks shifting toward mid-year. Regional and trophic variation was also marked. Breeding generally coincided with the onset of rains and avoided extreme dry or wet months. Our findings offer new insights into tropical bird reproduction, showing that breeding in Colombia follows clear seasonal patterns shaped by rainfall, elevation, and diet, and highlighting the complexity of tropical phenology.
Dataset DOI: 10.5061/dryad.44j0zpcs4
Description of the data and file structure
Dataset Description (Primary database)
This dataset comprises standardized records of breeding bird observations in Colombia, intended to support analyses of breeding seasonality, geographic patterns, and ecological traits. It consists of a single data table with 218,621 rows and 12 variables, covering the period from 1858 to 2021. A total of 9,568 records are identified as reproductive, based on the variable breedingCor = 1.
Variables Included
species(string) – Scientific name of the bird species observed.day(numeric) – Day of the month when the observation occurred; may be missing when only month and year are available.month(integer) – Month of observation (1–12).year(integer) – Year of observation (range: 1858–2021).region(string) – Geographic region or locality of the observation.latitude(numeric) – Latitude (in decimal degrees) of the observation site.status(string) – Reproductive status as reported in the original source (e.g., “breeding”, “nest with eggs”, “brooding”).breedingCor(integer: 0 or 1) – Standardized binary variable indicating confirmed reproductive condition (1 = reproductive, 0 = non-reproductive).database(string) – Source or program from which the record was obtained (e.g., bird banding program, GBIF).Elevation(numeric) – Elevation (in meters above sea level) of the observation site.family(string) – Taxonomic family to which the species belongs.guild(string) – Trophic guild or ecological foraging group (e.g., insectivore, frugivore).
Notes on Data Use
- The dataset includes both reproductive and non-reproductive observations; the variable
breedingCorprovides a harmonized reproductive classification across sources. - Missing values in the
dayfield indicate records with incomplete date information (month/year only). - No derived metrics (e.g., rates, seasonality indices) are included; such values were calculated separately for the analyses reported in the associated publication.
- This raw dataset is suitable for time-series analysis, ecological modeling, and macroecological assessments of bird breeding activity in the Neotropics.
Dataset Description (Supplementary Time Series file)*
*Databases needed to implement Time Series analysis throughout different methods.
- Database contains 2 columns. Each row represents one month starting from January.
breeding(integer) - Active breeding records (1)nonbreeding(integer) - Non-breeding records (0)
This dataset was compiled to investigate the temporal patterns of breeding activity in resident bird species across Colombia. Data were gathered through long-term bird banding programs and curated citizen science records, with a focus on documenting reproductive condition (e.g., active nests, brood patches, fledglings) across diverse biogeographic regions. The main goal was to evaluate breeding seasonality at national and regional scales and assess its relationship with environmental gradients such as latitude, elevation, and trophic guild.
Files and variables
File: Suppl_TimeSeries_.zip
Description: Compressed file containing a univariate time series used for imputation exercises presented in the manuscript. Some rows include missing values (NA) by design, representing temporal gaps in the original data. These gaps are retained to demonstrate imputation methods and should not be removed.
File: Breeding_database.csv
Description: Main dataset containing standardized records of reproductive activity in Colombian birds from 1858 to 2021. The data include taxonomic, temporal, spatial, and ecological attributes compiled from bird banding programs, museum records, and citizen science sources. Each row corresponds to a species observation with associated reproductive information.
Variables
- species: Scientific name of the observed bird species.
- day: Day of the month when the observation was made (can be missing if not reporteMonthonth: Month of the observation (1–12).
- year: Year of the observation (1858–2021).
- region: Name of the region where the record was obtaiLatitudeitude: Latitude in decimal degrees for the observation.
- status: Description of status of residence (e.g., “Native”, “Migrant”).
- breedingCor: Standardized binary variable indicating confirmed reproductive condition (
1 = breeding,0 = non-breeding). - Database: Source from which the record was compiled (e.g., banding program, GBIF).
- Elevation: Elevation of the site in meters above sea level (can include decimal values).
- Family: Taxonomic family of the species.
- Guild: Ecological or trophic guild (e.g., insectivore, frugivore).
File: PrimaryCode_Moreno-Palacios(2025).R
Description: R script containing all primary data processing steps and analyses used in the main figures and models of the manuscript, including data cleaning, and seasonal modeling with GAMs and Circular statistics
File: SupplementaryCode_Moreno-Palacios(2025).R
Description: R script with additional analyses and exploratory figures not included in the main text. This includes visualizations, diagnostic checks, and extended seasonal modeling for supplementary material.
Code/software
All the data are analyzed in R.
PrimaryCode_Moreno-Palacios(2025): This R script contains the core analytical workflow used in the main manuscript by Moreno-Palacios et al. (2025), focused on evaluating breeding seasonality in Colombian birds. It includes data preparation steps, transformation of temporal variables, and statistical modeling. The primary analyses rely on Generalized Additive Models (GAMs) to assess the influence of day-of-year, elevation, latitude, region, and ecological guilds on the probability of observing reproductive activity. Additionally, the script implements circular statistics to explore phenological patterns in breeding dates using angular transformations. It concludes with the generation of all main figures included in the manuscript, including model-derived smooths, elevation and latitude effects, data-source comparisons, and circular visualizations of breeding activity. This script is designed to be reproducible and depends on the accompanying data. taset Breeding_database.csv.
SupplementaryCode_Moreno-Palacios(2025): This R script contains supplementary analyses used to explore the temporal dynamics of avian breeding activity in Colombia, with a focus on time series decomposition and seasonal modeling. The script begins with the imputation of missing values in monthly time series using multiple methods (Kalman smoothing, seasonal decomposition, structural models, interpolation), allowing comparisons of different imputation strategies. It proceeds with data transformation and rate standardization, followed by classical time-series analyses including autocorrelation, Ljung–Box tests, periodograms, and seasonal decompositions. The final sections implement parametric models of seasonality using both stationary and non-stationary cosinor models (via the season package), capturing annual and sub-annual cyclic patterns. This script complements the main analytical pipeline and provides in-depth methods for readers interested in modeling phenological data with periodic structure. This script is designed to be reproducible and depends on the accompanying datasets COL_Banding_TS.csv and COL_GBIF_TS.csv, contained in Suppl_TimeSeries.
Access information
Data was derived from the following sources:
| Department | Locality | Captures | Nests | Author/owner of the dataset |
|---|---|---|---|---|
| Antioquia | Remedios | 607 | 335 | Londoño, G. |
| Chocó | Darién | 924 | SELVA | |
| Cundinamarca | Bojacá | 1646 | Echeverry-Galvis, M.A. | |
| Cundinamarca | La Fragua | 196 | González, A.M. | |
| Cundinamarca | Los Vientos | 434 | González, A.M. | |
| Guajira | RN Refugio Guajiro | 531 | SELVA | |
| Magdalena | Sierra Nevada de Santa Marta | 11573 | SELVA | |
| Risaralda | Tatamá | 3938 | 235 | Londoño, G. |
| Tolima | 18 municipalities | 5081 | Losada-Prado, S. (GIZ-UT) | |
| Tolima | Ibagué | 2215 | Moreno-Palacios, M. | |
| Valle del Cauca | Anchicayá | 3659 | 279 | Londoño, G. |
| Valle del Cauca | Chicoral | 1278 | 23 | Londoño, G. |
| Valle del Cauca | Farallones | 2478 | Londoño, G. |
Datasets references (datasets accessed from the GBIF platform)
Morales Rozo A, Pachón Y, Valderrama M, Cruz Mora H J, Rodríguez L (2020). Monitoreo participativo de aves en la laguna de Fúquene. Fundación Humedales. Occurrence dataset https://doi.org/10.15472/3tzxfy accessed via GBIF.org on 2021-03-06.
Jiménez Neira A, Santa Méndez A L, García Vargas W V, Vela Sanabria J, Arroyo S, Zuluaga V, Palacios S, Zabala D R, Ramírez Martínez N M (2020). Aves de los Parques Ecológicos Distritales Humedales Bogotá, D.C. Versión 1.7. Secretaría Distrital de Ambiente. Sampling event dataset https://doi.org/10.15472/2200ee accessed via GBIF.org on 2021-03-06.
Trombone T (2013). AMNH Bird Collection. American Museum of Natural History. Occurrence dataset https://doi.org/10.15468/xvzdcm accessed via GBIF.org on 2021-03-06.
Orrell T, Informatics Office (2021). NMNH Extant Specimen Records. Version 1.41. National Museum of Natural History, Smithsonian Institution. Occurrence dataset https://doi.org/10.15468/hnhrg3 accessed via GBIF.org on 2021-03-06.
Ueda K (2021). iNaturalist Research-grade Observations. iNaturalist.org. Occurrence dataset https://doi.org/10.15468/ab3s5x accessed via GBIF.org on 2021-03-06.
Vellinga W (2021). Xeno-canto - Bird sounds from around the world. Xeno-canto Foundation for Nature Sounds. Occurrence dataset https://doi.org/10.15468/qv0ksn accessed via GBIF.org on 2021-03-06.
Cardona-Salazar, L. J., Y. A. Benavides-Ossa, A. M. Vargas-Daza, J. F. Betancurt-Grisales, M. Bohada-Murillo, E. T. Martínez-Sánchez, M. Cardona-Romero, A. Busi, W. D. Tobón-Escobar, M. Ortiz-Giraldo, D. Gómez Castillo, J. Álvarez-Londoño, D. A. Molina-Marín, J. C. Rodas-Rúa, L. D. Grisales-Muñoz, V. Velásquez-Trujillo, L. F. Salazar-Ramírez, D. M. Pineda-Gómez, A. Hoyos-Jaramillo, R. R. Santisteban-Arenas, J. G. Salazar-Ramírez, G. Patricia Orozco-Montoya, S. A. Ramos-Valencia, G. Gómez-Londoño, F. Ospina-Bautista, J. V. Estévez-Varón, P. A. Ossa-López, F. A. Rivera-Páez, J. E., Pérez Cárdenas, F. E., Fonturbel, and G. J. Castaño-Villa. 2020. A morphological, reproductive, and molt phenology database for 379 bird species from the Colombian Tropical Andes. Ecology 101(6):e03016.10.1002/ecy.3016
