Data from: Birds that breed exclusively on islands have smaller clutches
Data files
Jan 16, 2025 version files 1.46 MB
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analysis_dataset.csv
897.04 KB
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Clutch_analysis_code.R
43.25 KB
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clutch_data_code.R
3.08 KB
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clutch_dataset.csv
479.22 KB
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dev_sp.csv
5.48 KB
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README.md
5.23 KB
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seabirds.csv
28.96 KB
Abstract
The ‘island syndrome’ refers to similarity in the biology of island organisms, but its generality is questionable, as the scope of species and traits examined are often limited. Here, I show that birds breeding exclusively on islands (breeding island endemics) evolved smaller clutches, using a dataset of 4,530 bird species. Using an inclusive definition of a breeding island endemic, which also encompasses migratory species and seabirds, I examine the evolution of clutch sizes in island breeding species using phylogenetic generalized linear models. Across disparate phylogenetic hypotheses, and after accounting for biological and geographical co-variables, I show that breeding island endemic landbirds (470 species) evolved smaller clutch sizes than continental breeding species (3,818 species). I show that the evolution of clutch size follows the expectations of the island syndrome, as among breeding island endemic landbirds there is a positive relationship between clutch size and breeding range area. Finally, I reinforce the view that the island syndrome is a general pattern in birds, spanning diverse phylogenetic and ecological groups, by showing that in a seabird-only dataset (242 species), breeding island endemic seabirds show evolution of smaller clutch sizes. In a model of the full dataset of both landbirds and seabirds (4,530 species) there was no evidence of an interaction of being a seabird with breeding island endemicity, showing that seabirds and landbirds respond in the same way. This study, using more than 40% of all bird species, provides the first evidence of a general evolutionary response in a life history trait, clearly showing the island syndrome as a general evolutionary tendency associated with island environments.
README: Data from: Birds that breed exclusively on islands have smaller clutches
Related article published in Ornithology in 2024 by M. T. Jezierski.
Data and code versioned 16th January 2024. README versioned 16th January 2025.
jezierski.m.t@gmail.com
https://github.com/jezierskim/clutch
Repository contents:
README file (this).
- clutch_data_code.R (R script for data preparation; uses files: clutch_dataset.csv and dev_sp.csv)
- clutch_dataset.csv (raw data for the above R script)
- dev_sp.csv (family level data on precociality)
- analysis_dataset.csv (final output of clutchdatacode.R; to be used with clutch_analysis_code.R)
- clutch_analysis_code.R (R script for data analysis; uses the file seabirds.csv)
- seabirds.csv (list of species identified as seabirds (see Methods))
In addition to files provided in the repository, clutch_data_code.R requires two extra files that cannot be provided due to copyrights. These are:
- BirdLife International data ranges; freely available at https://datazone.birdlife.org/species/requestdis upon request. NB: the code in uses version 2020.1. NB: file needs to be named 'BOTW.gpkg' in the code. Natively, it is downloaded as BOTW.gdb (and can be used if the extension is supplanted in the code.)
- Natural Earth data land file at 50 million resolution; freely available at https://www.naturalearthdata.com/downloads/50m-physical-vectors/. NB: file needs to ba named and located in directory: 'ne_50m_land/ne_50m_land.shp'. This is the native name.
In addition to files provided in the repository, clutch_analysis_code.R needs an extra file that cannot be provided due to copyrights. These are:
- 100 phylogenetic trees based on genetic data with Hackett backbone. These can be obtained in birdtree.org. The file should be named: 100_trees_Hackett_genetic.tre.
Dataset contents and metadata.
Below are the contents and metadata of original files provided in this repository. Metadata of external files (listed above) is provided by the providers.
clutch_dataset.csv
Main dataset file containing the data needed for analysis. Columns and descriptions are:
- order - taxonomic order according to Clements taxonomy 2019.
- family - taxonomic family according to Clements taxonomy 2019.
- ebird_name - binomial name according to Clements taxonomy 2019.
- treelabels - binomial names as used in the phylogenetic trees from birdtree.org.
- binomial - binomial names according to IUCN taxonomy 2020.
- clumin - minimum clutch size, units: 1 egg.
- clumax - maximum clutch size, units: 1 egg.
- bodmin - minimum body mass, units: 1g.
- bodmax - maximum body mass, units: 1g.
- is - binomial term indicating island endemic; Y - yes; N - no.
dev_sp.csv
Dataset on development mode in bird families. Columns and descriptions are:
- family - taxonomic family according to Clements taxonomy 2019; synonymous with family in clutch_dataset.csv.
- mode - binomial term indicating developmental mode; two states: altricial OR precocial.
analysis_dataset.csv
Analysis ready dataset produced by code file clutch_data_code.R. Columns and descriptions are:
- binomial - binomial names according to IUCN taxonomy 2020.
- latitude - latitude centroid obtained in clutch_data_code.R from IUCN species ranges, units: degrees.
- area - breeding range area obtained in clutch_data_code.R from IUCN species ranges, units: meters squared.
- order - taxonomic order according to Clements taxonomy 2019.
- family - taxonomic family according to Clements taxonomy 2019.
- ebird_name - binomial name according to Clements taxonomy 2019.
- treelabels - binomial names as used in the phylogenetic trees from birdtree.org.
- binomial - binomial names according to IUCN taxonomy 2020.
- clumin - minimum clutch size, units: 1 egg.
- clumax - maximum clutch size, units: 1 egg.
- bodmin - minimum body mass, units: grams.
- bodmax - maximum body mass, units: grams.
- is - binomial term indicating island endemic; Y - yes; N - no.
- migratory - binomial term indicating whether the species is migratory or not; migratory - yes, NA - no.
- mode - binomial term indicating developmental mode from dev_sp; two states: altricial OR precocial.
- clu_geom - geometric mean clutch size calculated in clutch_data_code.R.
- mass_geom - geometric mean body mass calculated in clutch_data_code.R.
seabirds.csv
Dataset containing data on marine habitat use of birds identified as seabirds (see Methods). Columns and descriptions are:
- order - taxonomic order according to Clements taxonomy 2019.
- family - taxonomic family according to Clements taxonomy 2019.
- name - common name according to Clements taxonomy 2019.
- genus - taxonomic genus according to Clements taxonomy 2019.
- species - taxonomic specific epithet according to Clements taxonomy 2019.
- sea - mode of marine habitat sea use; three states: coastal - uses water 'near' the coast; offshore - further away from the coast but along the continental shelf; pelagic - uses seas beyond the continental shelf.