GENERAL INFORMATION

1. Title of Dataset: Data from "Maternally-transferred thyroid hormones and life-history variation in birds"

2. Author information:
	Corresponding author: Bin-Yan Hsu, Department of Biology, University of Turku, Finland
						  email address: biyahs@utu.figures
	Co-authors:
		Veli-Matti Pakanen, Ecology and Genetics Research Unit, University of Oulu, Finland, and Department of Biological and Environmental Sciences, University of Gothenburg, Sweden
		Winnie Boner, Institute of Biodiversity, Animal Healthy and Comparative Medicine, University of Glasgow, Scotland, United Kingdom
		Blandine Doligez, Department of Biometry and Evolutionary Biology, CNRS UMR 5558, Université de Lyon 1, France
		Tapio Eeva, Department of Biology, University of Turku, Finland
		Ton G.G. Groothuis, Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, the Netherlands
		Erkki Korpimäki, Department of Biology, University of Turku, Finland
		Toni Laaksonen, Department of Biology, University of Turku, Finland
		Asmoro Lelono, Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, the Netherlands, and Biology Department, Natural Sciences and Mathematics Faculty, Jember University of Indonesia, Indonesia
		Pat Monaghan, Institute of Biodiversity, Animal Healthy and Comparative Medicine, University of Glasgow, Scotland, United Kingdom
		Tom Sarraude, Department of Biology, University of Turku, Finland, and Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, the Netherlands
		Robert L. Thomson, Fitzpatrick Institute of African Ornithology, DST-NRF Centre of Excellence, University of Cape Town, South Africa
		Barbara Tschirren, Centre for Ecology and Conservation, University of Exeter, United Kingdom
		Rodrigo A. Vásquez, Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
		Suvi Ruuskanen, Department of Biology, University of Turku, and Department of Biological and Environmental Sciences, University of Jyväskylä, Finland

3. Date of sample collection: 2011, 2014, 2016, 2017

4. Geographic location of sample collection:
	Thorn-tailed rayadito (Aphrastura spinicauda): Chile
	European greenfinch (Chloris chloris): Finland
	Little ringed plover (Charadrius dubius): Finland
	Common ringed plover (Charadrius hiaticula): Finland
	Rock pigeon (Columba livia livia): Groningen, the Netherlands
	Homing pigeon (Columba livia domesticus): Finland
	Jackdaw (Corvus monedula): Finland
	Japanese quail (Coturnix japonica): Finland
	Common cuckoo (Cuculus canorus): Finland
	Kestrel (Falco tinnunculus): Finland
	Collared flycatcher (Ficedula albicollis): Gotland, Sweden
	Pied flycatcher (Ficedula hypoleuca): Ruissalo, Turku, Finland
	Chaffinch (Fringilla coelebs): Finland
	Red junglefowl (Gallus gallus bankiva): Groningen, the Netherlands
	Chicken (Gallus gallus domesticus): Finland
	Eurasian jay (Garrulus glandarius): Finland
	Oystercatcher (Haematopus ostralegus): Finland
	Common gull (Larus canus): Finland
	Black-headed gull (Larus ridibundus): Finland
	Coal tit (Parus ater): Finland
	Blue tit (Cyanistes caeruleus): Ruissalo, Turku, Finland
	Great tit (Parus major): Ruissalo, Turku, Finland
	Tree sparrow (Passer montanus): Finland
	Grey partridge (Perdix perdix): Finland
	Pheasant (Phasianus colchicus): Finland
	Common redstart (Phoenicurus phoenicurus): Finland
	Common tern (Sterna hirundo): Finland
	Arctic tern (Sterna paradisaea): Finland
	European starling (Sturnus vulgaris): Finland
	Zebra finch (Taeniopygia guttata): Glasgow, Scotland
	Redshank (Tringa totanus): Finland
	Redwing (Turdus iliacus): Finland
	Blackbird (Turdus merula): Finland
	Song thrush (Turdus philomelos): Finland
	Fieldfare (Turdus pilaris): Finland
	Northern lapwing (Vanellus vanellus): Finland

5. Funding sources that supported the collection of the data: Academy of Finland

DATA & FILE OVERVIEW

1. Description of the data package:

The data package contains four parts:

Part I. datasets
Two datasets are included in this study:
egg_data.csv: Data set of yolk thyroid hormones measured in eggs of 34 bird species
life_histories.csv: life-history trait values used in the study, collected and compiled from the literature

The information of the variables included in each data set is described in two additional files:

info_eggdata.txt: variable information of egg_data.csv
info_lifehistories.txt: variable information of life_histories.csv

Part II. phylogeny

Phylogeny included time-calibrated supertrees for the phylogeny-informed statistical analyses we conducted for this paper.
According to data availability, we pruned the phylogeny accordingly and hence several folders are present, each representing each phylogeny subset.
Each phylogeny set contains tree topology and branche lengths from 100 possibles derived from two phylogenetic backbones: Ericson and Hackett.

List of phylogeny sets:

a. full_Ericon and full_Hackett:
	For the 34 species included in this study, 100 possible phylogenetic trees were obtained from two phylogenetic backbones via BirdTree.org.
b. subII_noJQ_Ericson and subII_noJQ_Hackett:
	This phylogeny excluded Coturnix japonica (Japanese quail) as it does not have the relevant data of clutch size and number of clutches per year.
c. subIII_noRJ_Ericon and subIII_noRJ_Hackett: 	
	This phylogeny excluded Gallus gallus (Rred junglefowl and chicken) as it does not have the relevant data of age at sexual maturity
d. BMR_Ericson and BMR_Hackett:
	This phylogeny subset only contains the species in which BMR data are available.
e. k_Ericson and k_Hatckett:
	This phylogeny subset only contains the species in which the data of growth constant k are available.

Part III. model results
Our statistical models were run across 100 possible trees from the two backbones. The final estimates were collected and stored in these files for each model.

Part IV. R codes
All R codes used to produce our results are provided.

List of R codes:
data_process_final.R: code to process data before model fitting
mls_size_corrected.R: code to run size correction on maximum lifespan
aafr_size_corrected.R: code to run size correction on age at sexual maturity
bmr_size_corrected.R: code to run size correction on mass-specific BMR
k_size_corrected.R: code to run size correction on the logistic growth rate constant k
models_final.R: code that runs the Bayesian phylogenetic mixed models
results_final: code that reads, checks and collects results from the Bayesian phylogenetic mixed models
phylogenetic_heritability.R: code that calculate phylogenetic heritability associated with our models and results
model_diagnostics_final.R: code to examine model performance
ggplot theme setting 2020.R: code that sets up the ggplot2 environment to produce the paper figures
summarySE: a small function to calculate means, SE, etc. for graphic purposes
phylogeny graph.R: code that produces Fig. 1A
graphs from raw data.R: code that produces Fig. 1B-E, 3, and 4B-E in the paper
graphs from model results.R: code that produces Fig. 2 and 4A in the paper