DOI: 10.5061/dryad.5770gm7
title: Data from: Trait evolution, resource specialization and vulnerability to plant extinctions among Antillean hummingbirds

description: Species traits are thought to predict feeding specialisation and the
 vulnerability of a species to extinctions of interaction partners, but the
 context in which a species evolved and currently inhabits may also matter.
 Notably, the predictive power of traits may require that traits evolved to
 fit interaction partners. Furthermore, local abiotic and biotic conditions
 may be important. On islands, for instance, specialised and vulnerable
 species are predicted to be found mainly in mountains, whereas species in
 lowlands should be generalized and less vulnerable. We evaluated these
 predictions for hummingbirds and their nectar-food plants on Antillean
 islands. Our results suggest that the rates of hummingbird trait
 divergence were higher among ancestral mainland forms before the
 colonization of the Antilles. In correspondence with the limited trait
 evolution that occurred within the Antilles, local abiotic and biotic
 conditions – not species traits – correlate with hummingbird resource
 specialisation and the vulnerability of hummingbirds to extinctions of
 their floral resources. Specifically, hummingbirds were more specialised
 and vulnerable in conditions with high topographical complexity, high
 rainfall, low temperatures, and high floral resource richness, which
 characterize the Antillean Mountains. These findings show that resource
 specialisation and species vulnerability to extinctions of interaction
 partners are highly context dependent.
description: Data_and_codeTo run the extinction models, first download the Stochastic Coextinction Model code from the Supplementary Information of Vieira and Almeida-Neto (2015) (see references). The script netcascade (April 2014).R is required for the analyses in this paper. The supplementary information contains three scripts: 1. Main.R – This script runs simulations on the 8 networks to calculate PE, SE and VE for each species in each network. 2. IterativeNodeDeletion.R – A wrapper around netcascade (April 2014).R that calls netcascade() repeatedly to iteratively remove species from the network. 3. IterNodeDelMultiSim.R – A wrapper around IterativeNodeDeletion.R that runs IterativeNodeDeletion() multiple times to account for the stochasticity in the netcascade() algorithm. And four datasets: 1. data/rvalues.csv – The expert-assigned dependency categories for each plant species in each network used to determine R values 2. data/webs – Folder containing the 8 interaction matrices 3. data/phylogeny - contains (1) a set of 1000 phylogenies for the 13 Caribbean hummingbird species that were analysed (Caribbean_Phylogenies_.nex), (2) the maximum clade credibility (MCC) phylogeny (Caribbean_MCC_Phylogeny.nex) 4. data/traits - species-level data for body mass and bill length If you use the extinction modelling code please cite the following two papers: 1. Dalsgaard et al. (in press) Trait evolution, resource specialisation and vulnerability to plant extinctions among Antillean hummingbirds. Proceedings of the Royal Society B. 2. Vieira, M.C. and Almeida‐Neto, M., 2015. A simple stochastic model for complex coextinctions in mutualistic networks: robustness decreases with connectance. Ecology Letters, 18(2), pp.144-152. doi: 10.1111/ele.12394 If you use the data please cite: Dalsgaard et al. (in press) Trait evolution, resource specialisation and vulnerability to plant extinctions among Antillean hummingbirds. Proceedings of the Royal Society B. References: Vieira, M.C. and Almeida‐Neto, M., 2015. A simple stochastic model for complex coextinctions in mutualistic networks: robustness decreases with connectance. Ecology Letters, 18(2), pp.144-152. doi: 10.1111/ele.12394