DOI: 10.5061/dryad.w9ghx3g0x
title: Multidimensional plasticity of phenology: Assessing the effects of population density on plastic responses of breeding time to temperature

description: Phenotypic plasticity is the key adaptive mechanism behind annual
 adjustment of breeding time in response to temperature. In nature,
 organisms are not only subjected to variation in temperature but encounter
 multiple fluctuating environmental factors that affect phenotypic
 expression, including conspecific density, which affects individual
 performances through resource competition. We examined the interactive
 effects of temperature and conspecific density at two spatial scales
 (territory and patch level) on breeding time and success utilizing data
 obtained from long-term monitoring of a wild great tit (Parus major)
 population in a fragmented woodland. As expected, we detected earlier
 breeding in response to warmer spring temperatures. We report earlier
 laying at low territory level density (i.e. a larger available area per
 breeding pair), but no evidence of density effects at patch level
 (breeding pairs per hectare). Birds experiencing low territory level
 density throughout their life bred on average earlier, and this response
 was also seen at the within-individual level (earlier laying in years when
 individuals experienced a lower density than average). We found no
 context-dependence of plastic responses to warmer springs as we detected
 no interactive effects between density and temperature. In terms of
 breeding success, earlier laying decreased the risk of brood failure and
 increased the number of fledglings. The number of fledglings was higher at
 low territory level density, while higher patch level density increased
 the probability of brood failure. Altogether, these results indicate that
 density-related responses were likely mediated by food competition rather
 than by increased numbers of low-quality birds or increased occupation of
 poorer territories at higher densities. This study highlights the
 importance of examining parameters at different spatial scales, along with
 the study of individual responses to multivariate cues for a comprehensive
 understanding of the variations in phenological plasticity.
description: This study uses data from a long-term great and blue tit
 monitoring program in Belgium from 1994-2016. The “Boshoek” field site
 (51°08 N – 4°31 E) encompasses 12 patches of fragmented woodlands (1 to 15
 ha) in an approximately 10 km<sup>2</sup> area near Antwerp.
 For the purpose of this study, data from the four largest oak patches— ZZ,
 (11.1 ha with 96 boxes); KB, (10.1 ha with 90 boxes); LO, (6.2 ha with 62
 boxes) and HN (2.8 ha with 23 boxes)—were used due to their comparable
 habitat characteristics (Matthysen 2002). In all sites approximately 9
 boxes were available per hectare, whereby two thirds of boxes had a 32mm
 opening (allowing both blue and great tits) and one third had a 26mm
 opening (allowing blue tits only). These patches were characterised
 predominantly by mature stands of common oak<em>(Quercus
 robur)</em> , undergrowth of hazel <em>(Coryllus
 avellana)</em> and black cherry <em>(Prunus
 serotina)</em> , and had distinct boundaries well-defined by the
 sharp transition from closed-canopy forest to open areas such as fields or
 meadows, residential areas or small farms (Matthysen 2002). 
 Nestboxes were visited approximately weekly starting before egg
 laying. 80–90% of all parents were captured on the nest when they were
 feeding 8-day-old nestlings. Nestlings were ringed and their body mass
 measured to the nearest 0.1g. All nestboxes were checked at least twice
 each winter for roosting birds. In some years, additional captures were
 done with mistnests in autumn and/or winter. All chicks were ringed at day
 14 or 15 after hatching. Each year nearly all (&gt; 85%) of the
 parents were trapped when feeding young of ca. 8 days old.
 <strong>Phenological
 parameters</strong> First-egg dates were
 estimated from the first observation of a partially laid clutch, assuming
 one egg being laid per day. All laying dates are expressed as days since
 March 1.
description: # Multidimensional plasticity of phenology: Assessing the effects of
 population density on plastic responses of breeding time to temperature
 Vaishnavi Purushotham, Paul Cuchot, Celine Teplitsky, and Erik Matthysen
 [https://doi.org/10.5061/dryad.w9ghx3g0x](https://doi.org/10.5061/dryad.w9ghx3g0x) ## Description of the data and file structure ### Files and variables #### File: Density\_data\_gtbtfinal.xlsx Note: The data set has certain missing values in columns columns K, Q, S, T. These data are missing from the long term data set. The script when run on R treats these blanks as "NA's", and does not interfere with the results.   **Description:** Basic phenological data of great tits and blue tits collected by conducting weekly nest box checks before egg laying. First-egg dates were estimated from the first observation of a partially laid clutch, as one egg is usually laid per day (average clutch size = 8.7). Parents were captured at the nest when the chicks were eight days old, ringed and aged (first-years vs adults [≥ 2 years]) based on plumage characteristics. Chicks were counted and ringed on day 15 post hatching and the number of fledged young was recorded after checking for dead nestlings after the nest fledged. We have used data from first clutches only in all our models. ##### Variables | Column name  | Key | | :--------------- | :----------------------------------------------------------------------------------------------------------------------------------- | | Patch ID | Plot within Boshoek field site (character) | | NNestbox | Nestbox number (Numeric) | | NN\_Patch | Nestbox number coupled with patch ID (character) | | coorx | East west coordinate (in km) (Numeric) | | coory | North south coordinate (in km) (Numeric) | | Brood | Breeding attempt in a breeding season; 1= first brood (character) | | RingN | Female ring number, unknown= unringed individual (character) | | NestID | Unique nest ID (numeric) | | Year | Year of breeding (numeric) | | Temperature | Average yearly temperature calculated from sliding window (in degree Celsius; Numeric) | | Age | Female age; 1st year= First breeding attempt ; older= second breeding attempt and above (character) | | ID | Unique individual ID's with dummies for "unknown" RingN (numeric) | | Laying date | Laying date (first egg laying date) (dd/mm/yyyy) (Numeric) | | Julian days | First egg laying date in julian days (1st January=1; Numeric) | | Patch density | Patch level density calculated as the number of occupied nest boxes per hectare, in each of the four patches per year (Numeric) | | Area | Tessellated area around the nest box (in square meters; numeric) | | Fledglings | Number of fledged young (Numeric) | | Species | Specie of the individual; BT= Blue tit, GT= Great tit (Character) | | neighgt1 | Distance (in m) to nearest nestbox occupied by a great tit (with eggs laid; Numeric) | | neigh1 | Distance (in m) to nearest occupied nestbox irrespective of bird specie (with eggs laid; Numeric) | | Area AM | Among-individual component of tessellated area (mean Area per individual ID; Numeric) | | Area WI | Within-individual component of  tessellated area (difference between the Area AM and Area per individual ID; Numeric) | | Patch density AM | Among-individual component of patch density (mean patch density per individual ID; Numeric) | | Patch density WI | Within-individual component of patch density (difference between the Patch density AM and Patch density per individual ID; Numeric) | | Among nest area | Among- nestbox variation of tessellated area (mean Area per NN\_Patch; Numeric) | | Within nest area | Within- nestbox variation of tessellated area (difference between the Among nest area and Area per NN\_Patch; Numeric) | ## Access information Other publicly accessible locations of the data: * [Boshoek | Netherlands Institute of Ecology (NIOO-KNAW)](https://nioo.knaw.nl/en/projects/spi-birds/study/boshoek) ## Supplementary information Description: The supplementary information provides additional details and analyses supporting the study on how population density affects the plasticity of breeding time responses to temperature. It includes data descriptions and distributions (Appendix 1), along with results examining the effects of nearest-neighbor distance on great tits, the combined effects of density on laying dates for blue and great tits, and the influence of density and timing on breeding success (Appendix 2). Generalized Additive Model (GAM) analyses are presented to assess how patch-level and territory-level densities impact laying dates. The document also includes tessellation code used for spatial analyses. ## Software file Filename: Density chapter manuscript figures.Rmd Description: This R Markdown file contains annotated R code to generate all the figures presented in the manuscript. It loads the necessary libraries and creates all figures using ggplot2 and other relevant R packages. Each figure corresponds to the same figure number and labels as mentioned in the manuscript and can be saved in a designated output directory in high-resolution formats (e.g., PNG, PDF, or SVG).