DOI: 10.6078/d1709v
title: Data from: Spatial phylogenetics of the North American flora

description: North America is a large continent with extensive climatic, geological,
 soil, and biological diversity. That biota is under threat from habitat
 destruction and climate change, making a quantitative assessment of
 biodiversity of critical importance. Rapid digitization of plant specimen
 records and accumulation of DNA sequence data enable a much-needed broad
 synthesis of species occurrences with phylogenetic data. Here we attempted
 the first such synthesis of a flora from such a large and diverse part of
 the world: all seed plants for the North American continent (here defined
 to include Canada, United States, and Mexico) with a focus on examining
 phylogenetic diversity and endemism. We collected digitized plant specimen
 records and chose a coarse grain for analysis, recognizing that this grain
 is currently necessary for reasonable completeness per sampling unit. We
 found that raw richness and endemism patterns largely support previous
 hypotheses of biodiversity hotspots. Application of phylogenetic metrics
 and a randomization test revealed novel results, including significant
 phylogenetic clustering across the continent, a striking east-west
 geographic difference in the distribution of branch lengths, and the
 discovery of centers of neo- and paleo-endemism in Mexico, the
 southwestern USA, and the southeastern USA. Finally, our examination of
 phylogenetic beta-diversity provides a new approach to comparing centers
 of endemism. We discuss the empirical challenges of working at the
 continental scale, and the need for more sampling across large parts of
 the continent, for both DNA data for terminal taxa and spatial data for
 poorly understood regions, to confirm and extend these results.
description: There are two datasets archived here: One is
 the full spatial dataset presented by Mishler et al. (2020), for seed
 plants of North America, defined as Canada, the United States, and
 Mexico (using a biogeographic barrier in Yucatan as the southern boundary
 of our study area).   We downloaded occurrence data from GBIF and iDigBio
 and carefully cleaned the data for taxonomic name matching (using the
 OpenTree Taxonomy and The Plant List) and georeference problems as
 described in the paper.  Following cleaning steps, the data set
 contains 11,067,080 records for 44,171 species of seed plants.  Note that
 only 19,649 of these species were actually included in the phylogenetic
 analysis presented in the paper, because those were the only ones that
 were represented in the phyogeny (deposited as a tree file in an
 accompanying data set). The other is a NEXUS file
 containing the phylogenetic tree that was used in a study on spatial
 phylogenetics of the North American flora (Mishler et al. 2020).  This
 tree was pruned from a dated phylogeny for seed plants originally
 consisting of 79,881 species described by Smith & Brown (2018).  
 The full unpruned tree is available from
 https://github.com/FePhyFoFum/big_seed_plant_trees/releases/tag/v0.1 with
 alignments linked therein.  This tree was pruned to include only the
 19,649 species that had spatial data from North America (the full spatial
 dataset is deposited in accompanying file). Literature
 cited:  Mishler, B.D., Guralnick, R., Soltis, P.S.,
 Smith, S.A., Soltis, D.E., Barve, N., Allen, J.M. and Laffan, S.W. 
 2020.  Spatial phylogenetics of the North American flora. J. Syst. Evol. 
 https://doi.org/10.1111/jse.12590 Smith S.A. and Brown J.W.. 2018. Constructing a broadly inclusive seed plant phylogeny. American Journal of Botany 105: 302–314.  https://doi.org/10.1002/ajb2.1019