DOI: 10.5061/dryad.05qfttf8t
title: Data from: Global variation in the relationship between avian phylogenetic diversity and functional distance is driven by environmental context and constraints

description: Aim: If evolutionary distance is akin to evolutionary chance,
 then it follows that species assemblages that are distantly related will
 also be more disparate in terms of their traits, features and the niches
 they occupy. Yet, studies have found that the total phylogenetic distance
 of an assemblages, known as phylogenetic diversity, is an unreliable
 surrogate for functional diversity. We investigate global variation in the
 relationship between Faith’s Phylogenetic Diversity (PD) and Mean Pairwise
 Functional Distance (MPFD) across latitude and the influence of migratory
 species on both these aspects of diversity. Location: Global.
 Time period: Present day. Major taxa studied: Birds.
 Methods: We measure PD and MPFD for over 9,000 species of bird
 across more than 17,000 globally distributed assemblages. We obtain
 standardised effect sizes for both indices by simulating assemblage
 composition under an ecologically informed null model. We employ path
 analysis to characterise variation in the relationship between PD’s and
 MPFD across latitude, elevation and with proportion of migratory species.
 Results: Globally, assemblages that were phylogenetically diverse
 tended to be less functionally dispersed than expected; however this
 relationship showed considerable variation across latitude decreasing with
 distance from the equator. The proportion of migratory species in an
 assemblage was found to be an important predictor of functional diversity,
 with migrant rich assemblages generally showing less functional diversity
 than expected. We identify the Andes and Hengduan Mountains as regions of
 exceptional bird functional diversity. Main conclusions: The
 relationship between phylogenetic diversity and function diversity is
 context specific, varying across environmental gradients such as latitude,
 and influenced by ecological phenomena such a migration. Thus, care should
 be taken using phylogenetic diversity as a proxy for functional diversity,
 particularly in clades with sparse functional data. Instead we recommend
 that studies consider how phylogenetic diversity’s surrogacy for
 functional diversity may be impacted by environmental context and evaluate
 empirical observations against biogeographically constrained and
 ecological informed null models.
description: # Global variation in the relationship between avian phylogenetic
 diversity and functional distance is driven by environmental context and
 constraints
 [https://doi.org/10.5061/dryad.05qfttf8t](https://doi.org/10.5061/dryad.05qfttf8t) This repository contains the R code necessary to replicate the analyses presented in the associated publication. We have also included summary statistics of each analysis. The original data used in this paper is all publicly available and can be accessed via the Sharing/Access information section below. ## Description of the data and file structure We include two datasets which summarise the outputs of the analyses conducted for this study: * functional\_div\_in.csv includes the functional dispersion and principle coordinates of each site analysed, as well as their phylogenetic diversity, mean pairwise phylogenetic distance and the latitude and longitude coordinates of the centroid. * standerdised\_effect\_sizes.csv – includes for each site the mean phylogenetic diversity (PDn), mean pairwise distance (MPDn), mean pairwise functional distance (MPFD) and standard deviation (sd) for the simulated assemblages at each site. It also includes the empirical score for each of those indices (e) and the standardised effect sizes of each (ses), as well as the species richness, latitude and longitude of each site. * bins.Rdata – spatial lag distance bins produced as part of script 4. This is included as a convenience for anyone seeking to replicate the analysis, because deriving the spatial bins is a computationally intensive process. * covariances\_migration\_ses.Rdata – covariance matrix used for spatially explicated structural equation modelling in script 4. Again, this matrix is included for the convenience of anyone trying to replicate the analysis as the construction of the covariance matrix is extremely computationally intensive. * distance\_matrix.Rdata – pairwise great circle distances between assemblages, used for spatially explicated structural equation modelling in script 4. * sp\_faxes\_coord\_by\_bodysize.Rdata – results of principle coordinate analysis of AVONET traits, produced by script 1. Includes principle coordinates for every species of bird in the AVONET database based on six morphological traits. ## Sharing/Access information The original 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](https://figshare.com/s/b990722d72a26b5bfead) * Dufour et al.'s (2019) list of migratory bird species is available via the publication's supporting information at [https://doi.org/10.1111/jbi.13700](https://doi.org/10.1111/jbi.13700) * Weeks et al.'s (2021) presence-absence matrix of global bird assemblages and associated bioclimatic data and their majority rules consensus bird phylogeny are available in the Zenodo digital repository at https://zenodo.org/record/5139951 * Dinnerstein et al.'s (2017) map of global ecoregions is available via the publication's supporting information at [https://doi.org/10.1093/biosci/bix014](https://doi.org/10.1093/biosci/bix014) ## Code/Software We include the following sets of scripts for anyone looking to reproduce the analysis: * ECO\_REGION\_NULL.R script for generating synthetic presence-absence matrix based on the biomes and realms of Dinnerstein et al. (2017) * SES\_Eco\_null.R script for comparing diversity indices of empirical and synthetic bird assemblages and calculating standardised effect sizes. * SES\_w\_migration.R script for reproducing the figures in the manuscript, implementing path analysis of standardised effect sizes with lavaan and undertaking spatially explicit structural equation modelling