Data from: Temperature shapes opposing latitudinal gradients of plant taxonomic and phylogenetic β diversity

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.

Species 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.