DOI: 10.5061/dryad.5hqbzkhf5
title: Data from: The city and forest bird flock together in a common garden: Genetic and environmental effects drive urban phenotypic divergence

description: Urban phenotypic divergences are documented across diverse taxa, but the
 underlying genetic and environmental drivers behind these phenotypic
 changes are unknown in most wild urban systems. We conduct a common garden
 experiment using great tit (Parus major) eggs collected along an
 urbanization gradient to: 1) determine whether documented morphological,
 physiological, and behavioural shifts in wild urban great tits are
 maintained in birds from urban and forest origins reared in a common
 garden (N = 73) and 2) evaluate how different sources of genetic, early
 maternal investment, and later environmental variation contributed to
 trait variation in the experiment. In line with the phenotypic divergence
 in the wild, common garden birds from urban origins had faster breath
 rates (i.e., higher stress response) and were smaller than birds from
 forest origins, while wild differences in aggression and exploration were
 not maintained in the experiment. Differences between individuals (genetic
 and environmentally induced) explained the most trait variation, while
 variation among foster nests and captive social groups was limited. Our
 results provide trait-specific evidence of evolution in an urban species
 where genetic change likely underlies urban differences in morphology and
 stress physiology, but that urban behavioural divergences are more
 strongly driven by plasticity.
description: Dataset collected from common garden experiment, and complemented
 by data collected as a part of long-term monitoring program of great tits
 in and around Montpellier, France. 
description: # Data from: The city and forest bird flock together in a common garden:
 Genetic and environmental effects drive urban phenotypic divergence
 Evolution 2025:
 [https://doi.org/10.1093/evolut/qpaf028](https://doi.org/10.1093/evolut/qpaf028) By Thompson, M.J., Réale, D., Chenet, B., Delaitre, S., Fargevieille, A., Romans, M., Caro, S.P., & Charmantier, A. ## Overview of the data and file structure Data list 1."ThompsonEA_CGdata.csv" 2."CG_GRM.csv" 3."ThompsonEA_CGegg.csv" 4."ThompsonEA_WILDdata(1).csv" 5."ThompsonEA_WILDdata(2).csv" Model objects (3 per trait in common garden and 1 per trait in wild context) 6\. "modeltars_nogrm_pub.rds" 7\. "modeltars_isa_nogrm_pub.rds" 8\. "modeltars_grm_pub.rds" 9\. "modelmass_nogrm_pub.rds" 10\. "modelmass_isa_nogrm_pub.rds" 11\. "modelmass_grm_pub.rds" 12\. "modelBRI_nogrm_pub.rds" 13\. "modelBRI_isa_nogrm_pub.rds" 14\. "modelBRI_grm_pub.rds" 15\. "modelagg_nogrm_pub.rds" 16\. "modelagg_isa_nogrm_pub.rds" 17\. "modelagg_grm_pub.rds" 18\. "modelexpl_nogrm_pub.rds" 19\. "modelexpl_isa_nogrm_pub.rds" 21\. "modelexpl_grm_pub.rds" 22\. "wildtars_pub.rds" 23\. "wildmass_pub.rds" 24\. "wildBRI_pub.rds" 25\. "wildagg_pub.rds" 26\. "wildexpl_pub.rds" R Scripts: 27\. "ThompsonEA_CGscripts.R" 28\. "ThompsonEA_Wildscripts.R" ## Description of the data and files 1."Thompson_CGdata.csv": Data collected from common garden experiment where great tit eggs from urban and forest origins were reared under common conditions. Missing values in the data are coded as "NA" and were not recorded during data collection. Column: Description $ ID : Individual ID (ID code 1-73) $ habitat : Urban or Forest habitat origin $ propurb100_NB: proportion of urbanization (ISA = impervious surface area, range = 0 - 1) within 100m-radius circular buffer around nest box of origin $ sex_mol : Sex determined by molecular sexing as F = female and M = male $ origin : Origin nest box ID (letters = site code, numbers = nest box number) $ foster : Foster nest box ID (letters = site code, numbers = nest box number) $ aviary : Captive housing aviary ID (social group during experiment 1-8) $ jdate : Date measured in Julian date format (days since Jan 1) $ Hcap_num : Time of capture in numerical format (h.mm/60) $ pheno_session: Phenotype measurement session where 1: June 2022, 2: July, 3: Oct 2022, 4: Jan 2023 $ AH : Aggression in hand score (range = 0 - 3) $ obs.AH : Code of observer who took aggression in hand measurement $ BRI : Breath rate index (amount of time to take 30 breaths, average of two consecutive measurements) $ obs.BRI : Code of observer who took breath rate measurement $ HBRI_num : Time of breath rate measurement in numerical format (h.mm/60) $ Hops : Exploration score (number of hops or flights while exploring a novel environment assay) $ Hof_num : Time of exploration assay in numerical format (h.mm/60) $ Tarsus : Length of right tarsus in millimeters (using Svensson's alternative method) $ Mass : Body mass in grams $ obs.m : Code of observer who took morphological (tarsus & body mass) measurements 2."CG_GRM.csv": Genetic relatedness matrix containing degree of relatedness between great tits reared in common garden experiment. Column: Description: Columns and rows are Individual IDs in common garden experiment and cells represent relatedness 3."ThompsonEA_CGegg.csv": Egg weight data on collected urban and forest eggs for common garden experiment. Column: Description $ date.taken : Date egg was collected from origin nest in dd-mm-yyyy format $ origin.habitat : Habitat of origin (URBAN or FOREST) $ origin.nest : Origin nest box ID (letters = site code, numbers = nest box number) $ foster.nest : Foster nest box ID (letters = site code, numbers = nest box number) $ n.eggs : Number of eggs collected from origin nest box $ egg.weight.origin: Weight of egg collected in grams 4."ThompsonEA_WILDdata(1).csv": Long-term monitoring of wild urban and forest great tit populations in/around Montpellier France. WILDdata(1) includes tarsus length, body mass, and aggression in hand phenotypes. Missing values in the data are coded as "NA" and were not recorded during data collection. Column: Description $ habitat : Habitat type (URBAN or FOREST) $ site : Study site code (cef = Cefe, fac = Faculte des sciences, font = Fonte colombe, mas = Mas Nouguier, rou = La Rouviere) $ year : year in yyyy format $ NBID : Nestbox ID code where letters indicate site and numbers indicate nestbox number $ propurb100_NB: proportion of urbanization (ISA = impervious surface area, range = 0 - 1) within 100m-radius circular buffer around nest box $ ID : Individual ID (ID code 1-842) $ sex : Sex as F = female and M = male $ age_cat : Age category as Adult = &gt;1 year old or Juvenile = 1 year old or yearling $ jdate : Date measured in Julian date format (days since Jan 1) $ time_num : Time of capture in numerical format (h.mm/60) $ Tarsus : Tarsus length in millimeters $ Mass : Body mass in grams $ AH : Aggression in hand (score between 0-3) $ obs : Measuring observer code for tarsus length and body mass $ obs_agr : Measuring observer code for aggression in hand 5."ThompsonEA_WILDdata(2).csv": Long-term monitoring of wild urban and forest great tit populations in/around Montpellier France. WILDdata(2) includes breath rate index and exploration phenotypes. Missing values in the data are coded as "NA" and were not recorded during data collection. Column: Description $ habitat : Habitat type (urb = URBAN or rur = FOREST) $ site : Study site code (cef = Cefe, fac = Faculte des sciences, font = Fonte colombe, mas = Mas Nouguier, rou = La Rouviere) $ year : year in yyyy format $ NBID : Nestbox ID code where letters indicate site and numbers indicate nestbox number $ propurb100_NB: proportion of urbanization (ISA = impervious surface area, range = 0 - 1) within 100m-radius circular buffer around nest box $ ID : Individual ID (ID code 1-604) $ sex : Sex as F = female and M = male $ age : Age category as ad = Adult (&gt;1 year old) or juv = Juvenile (1 year old or yearling) $ capdate_julian: Date measured in Julian date format (days since Jan 1) $ time_num : Time of capture in numerical format (h.mm/60) $ temperature : Air temperature in degrees Celsius when measuring breath rate index $ RR : Breath rate index, average amount of time it take for individual to take 30 breaths $ hops : Exploration score or number of hops/flights during open field exploration assay $ protocole_RR : Protocol type for breath rate index measure as new = nouveau or old = vieux $ obs_RR : Measuring observer code for breath rate index $ protocole_of : Protocol type for exploration score as new = nouveau or old = vieux 6-21. Model objects for traits measured in the common garden Model objects are outputs from fitted models using R package MCMCglmm where there are three models for each trait (tars = tarsus length, mass = body mass, BRI = breath rate index, agg = agression in hand, expl = exploration in novel environment) Model format: Description modeltrait_nogrm_pub: models of this format examine trait difference between categorical urban vs forest without genetic relatedness matrix (non-animal model) modeltrait_isa_nogrm_pub: models of this format examine trait difference across continuous urbanization without genetic relatedness matrix (non-animal model) modeltrait_grm_pub: models of this format examine trait difference between categorical urban vs forest with genetic relatedness matrix (animal model) 22-26. Model objects for traits measured in the wild Model objects are outputs from fitted models using R package MCMCglmm where there is one model for each trait (tars = tarsus length, mass = body mass, BRI = breath rate index, agg = agression in hand, expl = exploration in novel environment) Model format: Description wildtrait_pub: models of this format examine trait difference between categorical urban vs forest in wild populations 27."ThompsonEA_CGscripts.R": R script relies on common garden datasets (1-3) and model objects (6-21). Work flow includes i) loading packages and functions, ii) loading and preparing data, iii) defining priors, and for iv) each trait: a) model fitting, b) loading model objects, c) diagnostics, d) model summary and computed estimates. 28."ThompsonEA_Wildscripts.R": R script relies on wild datasets (4-5) and model objects (22-26). Work flow includes i) loading packages and functions, ii) loading and preparing data, iii) defining priors, and for iv) each trait: a) model fitting, b) loading model objects, c) diagnostics, d) model summary and computed estimates. ## Code/Software Data compiled and analyzed using R scripts: "ThompsonEA_CGscripts.R" and "ThompsonEA_Wildscripts.R" with free open software R v4.3.3 ([https://www.r-project.org/](https://www.r-project.org/)). Note that saved model objects (.rds files 6-26) for each trait used in the scripts can be downloaded here in the file list. Model scripts use R packages: "MCMCglmm"" (v2.36), "QGglmm" (v0.7.4), "purrr" (v1.0.2), "bayestestR" (v0.13.2), "ASRgenomics" (v1.1.4), and "MCMCqpcr" v(1.2.4).