Data from: Extinction selectivity obscures patterns of trait-dependent endangerment in Columbiformes
Data files
May 03, 2024 version files 15.60 MB
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MartinezRubio_2023.zip
15.60 MB
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README.md
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Abstract
Understanding how extinction has occurred in the recent past is crucial to unravel its main drivers as well as to implement effective conservation practices to minimize global biodiversity loss. It has long been hypothesized that extinction risk is not randomly distributed among traits of species. However, the actual traits making species more prone to extinction may have been overlooked because already extinct species are often not considered in comparative analyses of extinction risk. We characterized the drivers of extinction in a cosmopolitan bird clade, including Holocene and contemporary extinctions potentially related to human impacts, and provided evidence of an ‘extinction selectivity’ in species traits. We constructed a new phylogenetic hypothesis of the Columbiformes, a cosmopolitan bird clade consisting of 33 recently extinct and 351 extant species. Then, we integrated data on geography, behaviour, and morphology to reveal the drivers of extinction risk. We used phylogenetic generalized least square models to test the effect of geography, behaviour, and morphology on the risk of extinction and identified differences in the drivers of extinction when including vs. excluding recently extinct species. Our analysis revealed that Columbiformes endemic from islands with ground-foraging habits, weak flying abilities, migratory behaviour, and larger body sizes are more vulnerable to extinction. Our results also show that excluding recently extinct species identifies extinction drivers differently from those when including recently extinct species. Only by accurately identifying the traits that increase extinction risk can we develop targeted conservation measures that promote the long-term persistence of threatened species. Extinction selectivity has important implications for the conservation of biological communities and ultimately ecosystem functioning, considering the critical role Columbiformes often play as seed dispersers.
README: Data from: Extinction selectivity obscures patterns of trait-dependent endangerment in Columbiformes
https://doi.org/10.5061/dryad.rv15dv4b8
This repository contains a folder with datasets, phylogenies, and R scripts to perform all the analyses displayed in this manuscript.
Description of the data and file structure
This repository comprises four main folders: Data, Outputs, and Scripts.
1) Data: Contains the datasets utilized for the analysis conducted in this study.
- DB_Master.xlsx: List of behavioural, geographical, and morphological variables for 384 extant and already extinct Columbiformes. This file contains Metadata with information for every variable and a reference list for every species.
- DB_ColumbaTaxonomy.xlsx: List of the names of species from Jetz, from Gene Bank and from Handbook of Birds of the World.
- DB_ColumbiformesPhylogenetics.xlsx: Includes a list of the 143 species of Columbiformes which need to be added to the phylogenetic hypothesis. This file consists of 8 columns: "speciesAdd" (list of the species names to add), "Taxonomic_affinities" (List of the taxonomic affinities of each species), "BirdTree_position" (Place to add each species in the phylogenetic hypothesis), "Sister_genus" (List of the sister genus of each species), "Sister_species" (List of the sister species for each species), "Sister_species_group" (List of the sister species group for each species), "Source" (reference list), and "comments taxonomy" (information of taxonomic affinities extracted from literature).
2) Outputs: Contains a multiphylo file featuring the 100 phylogenetic topologies created for the Columbiformes clade, alongside the maximum clade credibility tree and the selected models in R file format for PGLS analysis.
3) Scripts: This folder contains four Quarto documents, arranged by priority, each facilitating the execution of specific analyses outlined in the manuscript.
- 1_PhylogeneticTrees_Representations.qmd: In this R script you can find attached how to update taxonomically the most recent phylogeny for the Columbiformes clade. Then, you will find attached how to construct a new phylogenetic hypothesis for 384 species of the Columbiformes clade, encompassing 33 already extinct species. Also, you have instructions to calculate the Robinson-Foulds distance and for creating a layered plotTree.wBars style fan-tree visualization.
- 2_pPCA_CorrelationPlots.qmd: In this R script you can find attached how to calculate the phylogenetic principal component analysis for each morphological trait and how to perform correlation analysis and plots.
- 3_PGLS models.qmd: In this R script you can find how to run the models of extinction risk as a function of species traits, using PGLS models. Specifically, you will find instructions on how to run 100 PGLS models for all extinct and extant species of Columbiformes (n=384 sp.), for extant species of the Columbiformes clade (n=351 sp.), or extant and extinct species of the Columbiformes clade without behavioural inferences (n=359 sp.), for extant and extinct species of the Columbiformes clade with behavioural inferences done randomly (n=384 sp), and for extant and extinct species of the Columbiformes clade without morphological inferences (n=354 sp.). Moreover, you will find how to calculate effect size measures and how to plot them.
- 4_PhylogeneticSignal.qmd: In this R script you can find attached how to calculate the phylogenetic signals for sp. with genetic data, for all sp. and for sp. without behavioural imputations. Moreover, above you can find attached how to represent graphically the density of phylogenetic signal for each trait.
Sharing/Access information
Some data used to conduct this analysis come from previously published studies and as such cannot be included in this repository. However, for the reader's convenience, we include links to the original repositories where these datasets are stored.
Tobias et al.'s (2021) avian morphological database AVONET is available in the Figshare digital repository at https://figshare.com/s/b990722d72a26b5bfead
Lapiedra et al.'s (2021) phylogenetic hypothesis with genetic information is available via the publication's supporting information at https://datadryad.org/stash/dataset/doi:10.5061/dryad.rjdfn2zbc
Methods
Here, we present a database for the Columbiformes clade encompassing a list of 384 species (including 351 extant and 33 extinct species) with information about the threat status (based on the IUCN Red List), and behavioural, geographical, and morphological trait information. Specifically, for behavioural traits, we gathered information on flight ability, habitat, migratory behaviour, and ground foraging from published sources. For morphological traits, we focused on measurements of beak length from culmen, beak width, tarsus length, wing length, Kipp’s distance, tail length (all in mm), and body mass (in grams). Finally, for geographical traits we recorded its geographical distribution and whether the species was an island endemic.
To achieve complete coverage of species traits, we employed an inference approach to estimate missing data for behavioural and morphological traits. Specifically, for behavioural traits, we inferred habitat (n=17; 4.4%) and ground-foraging (n=21;5.4%) using a probabilistic approach based on the taxonomic relationships between species (the genus). For morphological traits (n=31; 8.07%), we employed the Bayesian Hierarchical Probabilistic Matrix Factorization (BHPFM) method (Schrodt et al., 2015), a statistical model that fills gaps by incorporating a hierarchy of probability distributions to capture uncertainty and dependencies in the data.