DOI: 10.5061/dryad.r7sqv9sps
title: Data and code from: Coastal shorebirds delay maturity more than inland ones

description: On the basis of data from summer and winter counts of shorebirds,
 recaptures, and long-term banding studies from non-breeding grounds in
 Australia, we assess the age of first return migration (as a measure of
 maturity) and provide a comparative analysis of its association with
 habitat use (contrasting coastal and inland wetland habitats). Age
 structure: We used data from long-term banding studies of migratory
 shorebirds to describe the age structure of shorebird populations
 in south-eastern and north-western Australia during the breeding
 period. We analysed data collected between 1980 and 2005. Austral summer
 and winter comparisons:  We obtained data on winter-summer ratios
 from two sources. Shorebirds at key Australian sites are counted
 annually (Birdlife Australia 2020) during the austral
 summer (usually in January) and austral winter (June or early
 July). We analysed data collected between 1980 and 2005, when
 counts were carried out for the Population Monitoring Project of
 the Australasian Wader Studies Group. Ecological and life‐history traits:
 We assembled species-specific data on ecological and life‐history traits
 that may associate with age at maturity: non-breeding habitat, migration
 distance, breeding latitude and body size. Each species was classified
 into one of three categories of non-breeding habitat in Australia:
 ‘inland’ for species typically occurring in freshwater or other inland
 habitats; ‘coastal’ for species typically restricted to coastal habitats;
 and ‘mixed’ for species that use both habitats. This dataset is used for
 the statistical analyses shown in the article and the R code provided
 here.
description: We infer estimates of the age of first return migration from
 non-breeding grounds in Australia using (1) long-term banding datasets in
 which retraps and morphologically aged birds provide information on the
 age structure of birds that skip return migration; (2) comparisons of
 Australian summer and winter counts. We then compiled species-specific
 summaries of ecological traits (non-breeding habitat use, migration
 distance, breeding latitude, body size) and tested these as predictors of
 the age of first return migration using phylogenetic generalized linear
 mixed models in a Bayesian framework. Both estimates of the age of first
 return migration and statistical analysess re described in the Methods
 section in the article.
description: # Data and code from: Coastal shorebirds delay maturity more than inland
 ones Dataset DOI: [10.5061/dryad.r7sqv9sps](10.5061/dryad.r7sqv9sps) ##
 Description of the data and file structure ### Files and variables ####
 File: R_code_MCMCglmm_ECE.R **Description:** R code to make the analyses
 (MCMCglmm) and figures reproducible.   #### File: 10000_trees.tre
 **Description:** 10,000 phylogenetic trees from the Hackett backbone of
 the complete phylogeny of birds, downloaded from the ‘BirdTree project’
 (Jetz et al. 2012; birdtree.org). These trees include the 37 species used
 in the study. For any additional use of the BirdTree web tool, please see
 “birdtree.org” #### File: mcc_tree.tree **Description:** Maximum clade
 credibility tree based on the downloaded 10,000 phylogenetic trees (see
 above). #### File: dataset.csv **Description:** Dataset used for fitting
 Bayesian phylogenetic mixed models. ##### Variables * Species: common
 species names * Scientific: Latin species names * Age_migration1: Age of
 first return migration. Seven out of 37 species could not be unambiguously
 assigned to a single each of these species was assigned the alternative
 age category most consistent with the reduced dataset (i.e., a subset of
 the present dataset).  * Age_migration2: Alternative age of first return
 migration for sensitivity analyses (see R code). * Clutch_size: Modal
 clutch size (not used in the analyses as it is capped at four eggs in all
 species). * Nonbreeding_habitat: Each species was classified into one of
 three categories of non-breeding habitat in Australia: ‘inland’ for
 species typically occurring in freshwater or other inland habitats;
 ‘coastal’ for species typically restricted to coastal habitats; and
 ‘mixed’ for species that use both habitats. * Breeding_latitude: Breeding
 latitude (in degrees). * Migration_distance: expressed as the logarithm of
 the great circle distance from the breeding grounds to a point mid-way
 between the north-western and south-eastern Australia, except for those
 species which only occur regularly in south-eastern Australia (for which
 we treated Port Phillip Bay as the centre of the non-breeding range) or
 north-western Australia (for which we treated Roebuck Bay as the centre of
 the non-breeding range). * Wing_length:  median of average male and
 average female wing lengths (mm). * Nonbreeding_mass: Nonbreeding mass (g)
 ## Code/software The R code to reproduce analyses and figures has been
 uploaded. Version details are: platform x86_64-apple-darwin17.0 arch
 x86_64 os darwin17.0 system x86_64, darwin17.0 status major 4 minor 2.1
 year 2022 month 06 day 23 svn rev 82513 language R version.string R
 version 4.2.1 (2022-06-23) nickname Funny-Looking Kid Loaded packages:
 tidyverse; ape; geiger; MCMCglmm; coda; phytools; phangorn; geiger; car;
 cowplot The script includes code to read in the data and phylogenetic
 trees, as well as to perform the MCMCglmm models presented in the
 manuscript.  ## Access information Other publicly accessible locations of
 the data: * The code and data supporting this article were uploaded as
 Supplementary material. Data was derived from the following sources: *
 Jetz, W., Thomas, G.H.H., Joy, J.B.B., Hartmann, K. & Mooers, A.O.O.
 (2012). The global diversity of birds in space and time. Nature, 491,
 444–448. * Marchant, S., & Higgins, P.J., Eds. (1993). Handbook of
 Australian, New Zealand and Antarctic Birds. Volume 2: Raptors to
 Lapwings, Oxford University Press, Melbourne. * Higgins, P.J., &
 Davies, S.J.J.F., Eds. (1996). Handbook of Australian, New Zealand and
 Antarctic Birds. Volume 3, Snipe to Pigeons. Oxford University Press,
 Melbourne.