Data and code from: Coastal shorebirds delay maturity more than inland ones
Data files
Feb 03, 2026 version files 14.88 MB
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10000_trees.tre
14.84 MB
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dataset.csv
2.61 KB
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mcc_tree.tree
1.57 KB
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R_code_MCMCglmm_ECE.R
38.29 KB
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README.md
3.82 KB
Abstract
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.
Dataset DOI: 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:
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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.
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Marchant, S., & Higgins, P.J., Eds. (1993). Handbook of Australian, New Zealand and
Antarctic Birds. Volume 2: Raptors to Lapwings, Oxford University Press, Melbourne.
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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.
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.