DOI: 10.5061/dryad.p2ngf1vnc
title: Data from: Current climate, but also long-term climate changes and human impacts, determine the geographic distribution of European mammal diversity

description: Aim. Historical climate variations, current climate and human impacts are
 known to influence current species richness, but their effects on
 phylogenetic and trait diversity have been seldom studied. We investigated
 the relationship of these three factors with the independent variations of
 species, phylogenetic and trait diversity of European mammals. Considering
 the position of the 0ºC isotherm in the Last Glacial Maximum as a tipping
 point, we tested the following hypotheses: northern European assemblages
 host less species than southern European ones; northern areas harbour
 trait and phylogenetically clustered assemblages, while the more stable
 southern areas host random or overdispersed assemblages; and, species
 richness increases with human influence, while phylogenetic and trait
 diversity show clustered patterns in areas with stronger human influence.
 Location. Western Palearctic. Time period. Current and Late-Pleistocene
 effects on present-day diversity. Major taxa studied. Terrestrial mammals.
 Methods. We used a novel analytical approach based on distance matrices to
 separate the independent variations of species, phylogenetic and trait
 diversity, and assessed their relationships with current climate, climate
 stability and human influence through structural equation models. Results.
 The species-poor assemblages from northern Europe show higher phylogenetic
 and trait clustering than the more stable richer southern areas. However,
 no assemblage presented trait nor phylogenetic overdispersion. Current
 climate is the primary driver of phylogenetic and trait diversity, while
 species richness is affected similarly by both current and past climates.
 Higher human influence correlates positively with species richness and
 trait diversity, both directly and by mediating indirect effects of
 present climate. Main conclusions. Current climate, climate stability and
 human influence affect the studied aspects of diversity, although the form
 and magnitude of their effects varies through space. Importantly, higher
 levels of human disturbances correlate with more speciose and trait
 diverse assemblages, an apparently counterintuitive result that deserves
 further study.
description: Data on the distribution of native terrestrial (both volant and
 non-volant) mammal species were obtained from IUCN (2016), using a 100 km
 equal-area grid (i.e. with 10,000 km<sup>2</sup> cells)
 encompassing the whole Western Palearctic, i.e. both Europe and the
 Mediterranean region (European grid, based on the ETRS89 Lambert Azimuthal
 Equal-Area projection; it also includes the Mediterranean Islands and
 Northern Africa). This region hosts 357 mammal species, which constitute
 the regional pool of species that can potentially colonise any grid cell,
 and therefore were used as the source pool for all community assembly
 analyses described below. The extent of the analyses was limited to
 mainland Europe (comprising Great Britain and Russia up to the Ural
 Mountains), the Anatolian Peninsula, Syria and Israel. In total, these
 territories host 354 mammal species. We excluded cells that had less than
 95% of land surface. <b>Species
 richness</b> (<b>S_R</b>) was calculated as the number
 of species recorded in each grid cell. We used a dated
 mammalian ‘supertree’ (Bininda-Emonds et al., 2007, updated by Fritz et
 al., 2009), modifying it according to the IUCN Red List taxonomic
 nomenclature (IUCN, 2016). For each assemblage (i.e. each grid cell), we
 calculated phylogenetic diversity (PD) using Faith’s (1992) index,
 corresponding to the total branch length of a phylogenetic tree that
 connects all species within an assemblage. Afterwards, we calculated
 <b>net phylogenetic diversity (nPD</b>; herein called
 phylogenetic diversity for simplicity), i.e. the PD that is independent of
 species richness. To do this, we first created 1000 random assemblages
 from the species pool with the same species richness of each real
 assemblage, by shuffling species labels across the tips of the phylogeny.
 Second, we calculated nPD as the difference between the observed PD and
 the mean PD of the randomisations, divided by the standard deviation of
 the randomised PD values; therefore, nPD corresponds to the standardised
 effect size of each assemblage (Gotelli & Rohde, 2002). Negative
 nPD values correspond to assemblages with species that are
 phylogenetically clustered (i.e. evolutionarily closer than expected by
 chance), whereas positive values indicate phylogenetically overdispersed
 assemblages (i.e. more distant than expected by chance).
 Trait (functional) diversity was calculated using Petchey
 & Gaston’s (2002) FD (herein named FD). Trait data were obtained
 from PanTheria database (Jones et al., 2009) and updated using additional
 sources (as in Hidasi-Neto et al., 2015; Safi et al., 2011). The selected
 traits include: (i) body mass (in grams), (ii) diet (i.e. vertebrates,
 invertebrates, foliage, stems and bark, grass, fruits, seeds, flowers,
 nectar and pollen, roots and tuber); (iii) habitat (aquatic, fossorial,
 ground-dwelling, aboveground dwelling, aerial) and activity period
 (cathemeral, crepuscular, diurnal, nocturnal). When trait data were
 missing for a given species, median values for the genus were used. To
 calculate FD we started by producing a distance matrix from a trait matrix
 (using a modified version of Gower’s distance; Pavoine et al., 2009),
 converting it into a dendrogram (using UPGMA), and calculating the sum of
 branch lengths across it. In this case, the dendrogram was built using
 trait information of all mammal species present in the species pool. We
 also calculated net trait diversity (nFD), i.e. the FD that is independent
 of species richness, in the same way as nPD. Finally, we calculated
 phylogenetically-independent trait diversity from the residuals of the
 regression between the trait and phylogenetic distance matrices (using
 absolute distance values). These residuals were then used to construct a
 new dendrogram, which in turn was used to calculate the net
 <b>phylogenetically-independent trait diversity (npiFD</b>),
 following the same steps as for nPD and nFD. As in the case of nPD,
 negative values of npiFD indicate assemblages with species that are
 functionally clustered (i.e. species with trait values more similar than
 expected by chance), whereas positive values indicate trait overdispersed
 assemblages (i.e. more different than expected by chance)
 Current and historical climate data were gathered from the ECHAM3
 paleoclimatic model (Braconnot et al., 2007; processed as in Calatayud et
 al., 2016; Hortal et al., 2011), and included <b>current temperature
 (TEMP_0K) and precipitation (PCIP_0K)</b>, and <b>temperature
 and precipitation stability since the LGM (TSTAB_0-21k;
 PSTAB_0-21k</b>, respectively<b>)</b>. Comparability
 between these variables was attained by extracting all information from
 the same Atmosphere-Ocean General circulation model, i.e. using a
 downscaled version of the ECHAM3 paleoclimatic model (Braconnot et al.,
 2007). The impact of human activities (i.e. anthropogenic effects) was
 measured with the <b>Human Influence Index (HII</b>; Sanderson
 et al., 2002). References: Bininda-Emonds, O. R. P., Cardillo, M., Jones, K. E., MacPhee, R. D. E., Beck, R. M. D., Grenyer, R., … Purvis, A. (2007). The delayed rise of present-day mammals. Nature, 446, 507-512. Corrigendum (2008) Nature, 456, 274. Braconnot, P., Otto-Bliesner, B., Harrison, S., Joussaume, S., Peterchmitt, J. Y., Abe-Ouchi, A., ... Zaho, Y. (2007). Results of PMIP2 coupled simulations of the Mid-Holocene and Last Glacial Maximum -  Part 1: experiments and large-scale features. Climate of the Past, 3, 261-277. Calatayud, J., Hortal, J., Medina, N. G., Turin, H., Bernard, R., Casale, A. … Rodríguez, M. A. (2016). Glaciations, deciduous forests, water availability and current geographical patterns in the diversity of European Carabus species. Journal of Biogeography, 43, 2343-2353. Faith, D. P. (1992). Systematics and conservation: on predicting the feature diversity of subsets of taxa. Cladistics, 8, 361-373. Fritz, S. A., Bininda-Emonds, O. R. P., & Purvis, A. (2009). Geographical variation in predictors of mammalian extinction risk: big is bad, but only in the tropics. Ecology Letters, 12, 538–549. Gotelli, N. J., & Rohde, K. (2002). Co-occurrence of ectoparasites of marine fishes: a null model analysis. Ecology Letters, 5, 86-94. Hidasi-Neto, J., Loyola, R., & Cianciaruso, M. V. (2015). Global and local evolutionary and ecological distinctiveness of terrestrial mammals: identifying priorities across scales. Diversity & Distributions, 21, 548-559. Hortal, J., Diniz-Filho, J. A. F., Bini, L. M., Rodríguez, M. Á., Baselga, A., Nogués-Bravo, D., ... Lobo, J. M. (2011). Ice age climate, evolutionary constraints and diversity patterns of European dung beetles. Ecology Letters, 14, 741-748. IUCN (2016). The IUCN Red List of Threatened Species. Version 2016-3. &lt;www.iucnredlist.org&gt;. Jones, K. E., Bielby, J., Cardillo, M., Fritz, S. A., O'Dell, J., Orme, C. D. L., … Michener, W. K. (2009). PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals. Ecology, 90, 2648-2648. Pavoine, S., Vallet, J., Dufour, A.-B., Gachet, S., & Daniel, H. (2009). On the challenge of treating various types of variables: application for improving the measurement of functional diversity. Oikos, 118, 391-402. Petchey, O. L., & Gaston, K. J. (2002). Functional diversity (FD), species richness and community composition. Ecology Letters, 5, 402-411. Safi, K., Cianciaruso, M. V., Loyola, R. D., Brito, D., Armour-Marshall, K., & Diniz-Filho, J. A. F. (2011). Understanding global patterns of mammalian functional and phylogenetic diversity. Philosophical Transactions of the Royal Society B, 366, 2536-2544. Sanderson, E. W., Jaiteh, M., Levy, M. A., Redford, K. H., Wannebo, A. V., & Woolmer, G. (2002). The human footprint and the last of the wild. Bioscience, 52, 891-904.
description: Table Headers: ET_ID: Grid Cell
 Identifier X: Longitude of the centroid in UTM
 coordinates Y: Latitude of the centroid in UTM
 coordinates S_R: Species Richness
 PD: Phylogenetic Diversity (<i>sensu</i> Faith,
 1992) nPD: Net Phylogenetic Diversity
 FD: Functional Diversity (<i>sensu</i> Petchey
 & Gaston, 2002) nFD: Net Functional
 Diversity npiFD: Net phylogenetically-independent
 functional diversity TEMP_0K: Current
 temperature PCIP_0K: Current precipitation
 TSTAB_0-21k: Temperature stability since the Last Glacial
 Maximum PSTAB_0-21k: Precipitation stability since the
 Last Glacial Maximum HII: Human Influence
 Index N_S: Cell placed North or South of the 0ºC
 isotherm of the Last Glacial Maximum (categorical)