DOI: 10.6084/m9.figshare.5616424.v1
title: Global trade-offs of functional redundancy and functional dispersion for birds and mammals

description: Code and data to accompany: Cooke <i>et al</i>., 2019 - Global trade-offs of functional redundancy and functional dispersion for birds and mammals. Global Ecology and Biogeography https://onlinelibrary.wiley.com/doi/pdf/10.1111/geb.12869<br>Six traits are here made available for all 15,485 terrestrial extant bird and mammal species: body mass, litter/clutch size, diel activity, diet, volancy and habitat breadth<br><b>The trait data were compiled from four main sources: PanTHERIA (Jones <i>et al</i>., 2009), </b><b>Pacifici database (Pacifici <i>et al</i>., 2013)</b><b>, EltonTraits database (Wilman <i>et al</i>., 2014) and </b><b>Amniote database (Myhrvold <i>et al</i>., 2015)</b><b>, which should be cited, along with this paper, when using this trait data.</b><br>Where computing power allows, analyses should be performed across the 25 imputed datasets (trait_25_mi_data.csv) or imputation can be performed by the user of the data for the compiled trait data (trait_data.csv).<br><b>Fileset:</b><i>functional-tradeoffs.R - </i>Code for the analysis<br><i>species_site.csv - </i>Ecoregion scale species-by-site matrix <br><i>trait_data.csv - </i>Compiled trait data (includes missing-data species, i.e., excludes imputed data); see below for details on the data compilation process)<br><i>trait_25_mi_data.csv - </i>Compiled and imputed trait data (25 imputed trait datasets for the 4 imputed traits [litter_clutch_size, activity, hab_breadth, diet_5cat], body_mass_median and volant were complete for all species - see trait_data.csv; see Supporting Information of paper for multiple imputation process)<br><i>trait_mi_selected_data.csv - </i>Single, randomly selected, compiled and imputed trait data (single imputed dataset used in the analyses; see Supporting Information of paper for multiple imputation process)<br><i>functional_tradeoffs_results_combined.csv - </i>Outputs from the analyses for birds and mammals combined (empirical and null values for functional dispersion and functional redundancy per ecoregion)<br><i>functional_tradeoffs_results_birds.csv - </i>Outputs from the analyses for birds (empirical and null values for functional dispersion and functional redundancy per ecoregion for birds)<i><br></i><br><i>functional_tradeoffs_results_mammals.csv - </i>Outputs from the analyses for mammals (empirical and null values for functional dispersion and functional redundancy per ecoregion for mammals)<i><br></i><b><br></b><b>Metadata:</b>'eco' - ecoregion code (see https://www.lib.ncsu.edu/gis/esridm/2004/help/world/wwf_terr.sdc.htm)'binomial' - species scientific names'class' - species Class (Aves or Mammalia)'body_mass_median' - median adult body mass (g) across databases (see Trait data compilation)'litter_clutch_size' - litter size for mammals and clutch size for birds'activity' - diel activity (1 = diurnal, 2 = nocturnal)'hab_breadth' - habitat breadth, number of IUCN habitats occupied by species (See Trait data compilation)'volant' - flight capability (1 = non-volant, 2 = volant)'diet_5cat' - 5 diet categories, (1 = plant/seed, 2 = fruit/nectar, 3 = vertebrates, including carrion, 4 = invertebrates and 5 = omnivore, score of ≤ 50 in the four other diet categories) (see Wilman <i>et al</i>., 2014 and Trait data compilation)'spp' - species richness'fred_emp' - empirical values for functional redundancy'fred_null' - mean functional redundancy across 999 null model runs (global species pool)'fred_sd' - standard deviation of functional redundancy across null model runs'fred_ses' - standardized effect size for functional redundancy across null model runs'fred_p_g' - p-value for one-tailed permutation test (greater)'fred_p_l' - p-value for one-tailed permutation test (less)'fdisp_emp' - empirical values for functional dispersion'fdisp_null' - mean functional dispersion across 999 null model runs (global species pool)'fdisp_sd' - standard deviation of functional dispersion across null model runs'fdisp_ses' - standardized effect size for functional dispersion across null model runs'fdisp_p_g' - p-value for one-tailed permutation test (greater)'fdisp_p_l' - p-value for one-tailed permutation test (less)'tradeoff' - trade-off between functional redundancy and functional dispersion (fdisp_ses - fred_ses)<br><b>Trait data compilation:</b>Specifically, body mass data were sourced from three databases for mammals: Pacifici, EltonTraits and Amniote. The Pacifici database builds on PanTHERIA, but for species that lacked body mass data (1,047 species) they calculated the average body mass of congeneric or confamilial species, we extended this for the 11 species from our global list that were missing data. We took the median across these databases, with 84% of species having values from all three datasets and all species having at least one value (this was required so that all species overlapped in at least one trait dimension). For birds, we calculated the median across two databases: Amniote and EltonTraits. We sourced estimates of body mass values for 573 birds that were missing data, using the average from congeners, as we recognized body mass as a key trait that is strongly related to many aspects of a species’ ecology and therefore their contribution to various functions (see Supporting Information of paper). Therefore all species had at least one estimate of body mass and 72% received the average from two estimates. Diel activity was obtained from the EltonTraits database for both mammals and birds. Diet information was available as both semi-quantitative records (percentage use of different dietary categories) or as an aggregated score (assignment to the dominant diet category based on the summed scores of constituent individual diets). We chose to use the more coarse representation, as the semi-quantitative diet data have been shown to differ between databases (Olalla-Tárraga <i>et al</i>., 2016). Thus species were classified into five groups according to their primary diet (Wilman <i>et al</i>., 2014): plant/seed, fruit/nectar, invertebrates, vertebrates (including carrion), and omnivore (score of ≤ 50 in the four other diet categories). Habitat breadth was coded using the IUCN Habitats Classification Scheme (http://www.iucnredlist.org/technical-documents/classification-schemes/habitats-classification-scheme-ver3) and was quantified as the number of habitats listed for each species. These habitat affinities were extracted via the IUCN Red List Application Programming Interface (API) using the <i>rl_habitats</i> function (<i>rredlist</i> package (Chamberlain 2016)). Litter size was calculated as the median across the Amniote and PanTHERIA databases (46% had values from both databases), whereas clutch size was only sourced from the Amniote database. Data on volancy (flight capability) were compiled from the literature, where it is established that bats (Chiroptera) are the only true flying mammals and that most extant birds - apart from ratites, penguins and some flightless rails and waterfowl - are volant (Findley, 1993; Healy <i>et al</i>., 2014). The volancy of birds was validated using two main sources (del Hoyo <i>et al</i>., 2013; BirdLife International, 2017).<br><br>BirdLife International. (2017) IUCN Red List for birds.Chamberlain, S. (2016) rredlist: ‘IUCN’ Red List Client. <i>R Package. version 0.1.0</i>.Findley, J. S. <i>Bats: A community perspective. Cambridge Studies in Ecology</i> (Cambridge University Press, 1993). doi:10.2307/1382335<br>Healy, K. <i>et al.</i> Ecology and mode-of-life explain lifespan variation in birds and mammals. <i>Proc. Biol. Sci. </i><b>281</b>, 20140298 (2014).del Hoyo, J., Elliott, A., Sargatal, J., Christie, D. A. & de Juana, E. eds. (2013) <i>Handbook of the Birds of the World Alive, </i>Lynx Edicions, Barcelona, Spain.<br>Jones, K. E. <i>et al</i>. (2009). PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals. <i>Ecology,</i> <b>90</b>, 2648–2648. Data available at: http://esapubs.org/archive/ecol/e090/184/Myhrvold, N. P., Baldridge, E., Chan, B., Freeman, D. L. & Ernest, S. K. M. (2015) An amniote life-history database to perform comparative analyses with birds, mammals, and reptiles. <i>Ecology,</i> <b>96</b>, 3109. Data available at: http://www.esapubs.org/archive/ecol/E096/269/default.php<br>Olalla-Tárraga, M. Á., González-Suárez, M., Bernardo-Madrid, R., Revilla, E. & Villalobos, F. (2016) Contrasting evidence of phylogenetic trophic niche conservatism in mammals worldwide. <i>Journal of Biogeography </i><b>44</b>, 99–110.<br>Pacifici, M. <i>et al. </i>(2013) Generation length for mammals. <i>Nature Conservation,</i> <b>5</b>, 87–94. Data available at: http://datadryad.org/resource/doi:10.5061/dryad.gd0m3<br>Wilman, H. <i>et al.</i> (2014) EltonTraits 1.0: Species-level foraging attributes of the world’s birds and mammals. <i>Ecology, </i><b>95</b>, 2027. Data available at: https://figshare.com/articles/Data_Paper_Data_Paper/3559887<br>