DOI: 10.5061/dryad.n42g840
title: Data from: Temperature shapes opposing latitudinal gradients of plant taxonomic and phylogenetic β diversity

description: Latitudinal and elevational richness gradients have received much
 attention from ecologists but there is little consensus on underlying
 causes. One possible proximate cause is increased levels of species
 turnover, or β diversity, in the tropics compared to temperate regions.
 Here, we leverage a large botanical dataset to map taxonomic and
 phylogenetic β diversity, as mean turnover between neighboring 100 × 100
 km cells, across the Americas and determine key climatic drivers. We find
 taxonomic and tip‐weighted phylogenetic β diversity is higher in the
 tropics, but that basal‐weighted phylogenetic β diversity is highest in
 temperate regions. Supporting Janzen's ‘mountain passes’ hypothesis,
 tropical mountainous regions had higher β diversity than temperate regions
 for taxonomic and tip‐weighted metrics. The strongest climatic predictors
 of turnover were average temperature and temperature seasonality. Taken
 together, these results suggest β diversity is coupled to latitudinal
 richness gradients and that temperature is a major driver of plant
 community composition and change.
description: BIEN2 grafted phylogeny
 (rep. 1)Phylogeny of 81,274
 terrestrial vascular plants found in the BIEN2 database (Enquist et al.
 2016). To assemble this phylogeny a species-level multi-gene tree for
 ~65,000 species was made from the atpB-rbcL, ndhF, psbA, psbA-psbH, rbcL,
 and trnT-trnL-trnF regions via the software program PHLAWD (Smith et al.
 2009), which automatically queries GenBank sequence records. The tree was
 estimated using RAxML 7.3.0 (Stamatakis 2006) with the unconstrained
 maximum likelihood search method and treePL[2] (Smith & O’meara 2012)
 was used to estimate divergence times. Remaining taxa from the 88,824 in
 the BIEN2 database without genetic data were randomly placed within their
 genus or removed if generic affinities were not known. REFERENCES Enquist,
 B.J., Condit, R., Peet, R.K., Schildhauer, M. & Thiers, B.M. (2016).
 Cyberinfrastructure for an integrated botanical information network to
 investigate the ecological impacts of global climate change on plant
 biodiversity. PeerJ Preprints, e2615v1. Smith, S.A., Beaulieu, J.M. &
 Donoghue, M.J. (2009). Mega-phylogeny approach for comparative biology: an
 alternative to supertree and supermatrix approaches. BMC Evolutionary
 Biology, 9, 37. Smith, S.A. & O’meara, B.C. (2012). treePL: divergence
 time estimation using penalized likelihood for large phylogenies.
 Bioinformatics, 28, 2689-2690. Stamatakis, A. (2006). RAxML-VI-HPC:
 maximum likelihood-based phylogenetic analyses with thousands of taxa and
 mixed models. Bioinformatics, 22, 2688-2690.bien_grafted_phy_rep_1.treSpecies by site matrix for the BIEN2 databaseSpecies by site matrix for taxa in the BIEN2 database. Cells (rows in the matrix) are 100x100km in size and species lists for each cell contain all taxa with ranges that fall within the cell. See Goldsmith et al. (2016) and McFadden et al. (2019) for details on range size estimation. This dataset with additional information can also be found at https://knb.ecoinformatics.org/view/doi:10.5063/F16W9800. REFERENCES Goldsmith, G.R., Morueta-Holme, N., Sandel, B., Fitz, E.D., Fitz, S.D., Boyle, B. et al. (2016). Plant-O-Matic: a dynamic and mobile guide to all plants of the Americas. Methods Ecol. Evol., 7, 960–965. McFadden, I.R., Sandel, B., Tsirogiannis, C., Morueta-Holme, N., Svenning, J.-C., Enquist, B. and Kraft, N.J.B. Temperature shapes opposing latitudinal gradients of plant taxonomic and phylogenetic β diversity. Ecology Letters, in press.BIEN2_community_matrix_only_occupied_cells.Rdata