DOI: 10.5061/dryad.44j0zpcs4
title: Data from: When do tropical birds breed? The case of Colombian species assemblages

description: 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.
description: # Data from: When do tropical birds breed? The case of Colombian species
 assemblages Dataset DOI:
 [10.5061/dryad.44j0zpcs4](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** 1. **`species`**
 *(string)* – Scientific name of the bird species observed. 2. **`day`**
 *(numeric)* – Day of the month when the observation occurred; may be
 missing when only month and year are available. 3. **`month`** *(integer)*
 – Month of observation (1–12). 4. **`year`** *(integer)* – Year of
 observation (range: 1858–2021). 5. **`region`** *(string)* – Geographic
 region or locality of the observation. 6. **`latitude`** *(numeric)* –
 Latitude (in decimal degrees) of the observation site. 7. **`status`**
 *(string)* – Reproductive status as reported in the original source (e.g.,
 “breeding”, “nest with eggs”, “brooding”). 8. **`breedingCor`** *(integer:
 0 or 1)* – Standardized binary variable indicating confirmed reproductive
 condition (1 = reproductive, 0 = non-reproductive). 9. **`database`**
 *(string)* – Source or program from which the record was obtained (e.g.,
 bird banding program, GBIF). 10. **`Elevation`** *(numeric)* – Elevation
 (in meters above sea level) of the observation site. 11. **`family`**
 *(string)* – Taxonomic family to which the species belongs. 12.
 **`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 `breedingCor`
 provides a harmonized reproductive classification across sources. *
 Missing values in the `day` field 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 reporteMonth**onth:** Month of the
 observation (1–12). - **year:** Year of the observation (1858–2021). -
 **region:** Name of the region where the record was
 obtaiL**atitudeitude:** 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
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