DOI: 10.5061/dryad.2qk88
title: Data from: Sympatric parallel diversification of major oak clades in the Americas and the origins of Mexican species diversity

description: Oaks (Quercus, Fagaceae) are the dominant tree genus of North America in
 species number and biomass, and Mexico is a global center of oak
 diversity. Understanding the origins of oak diversity is key to
 understanding biodiversity of northern temperate forests. A phylogenetic
 study of biogeography, niche evolution and diversification patterns in
 Quercus was performed using 300 samples, 146 species. Next-generation
 sequencing data were generated using the restriction-site associated DNA
 (RAD-seq) method. A time-calibrated maximum likelihood phylogeny was
 inferred and analyzed with bioclimatic, soils, and leaf habit data to
 reconstruct the biogeographic and evolutionary history of the American
 oaks. Our highly resolved phylogeny demonstrates sympatric parallel
 diversification in climatic niche, leaf habit, and diversification rates.
 The two major American oak clades arose in what is now the boreal zone and
 radiated, in parallel, from eastern North America into Mexico and Central
 America. Oaks adapted rapidly to niche transitions. The Mexican oaks are
 particularly numerous, not because Mexico is a center of origin, but
 because of high rates of lineage diversification associated with high
 rates of evolution along moisture gradients and between the evergreen and
 deciduous leaf habits. Sympatric parallel diversification in the oaks has
 shaped the diversity of North American forests.
description: Loci file from pyRAD:
 c85d6m20p3.full.lociLoci file exported from
 clustering analysis performed in PyRAD. All molecular datasets referenced
 in study were exported by first importing this file into R using the
 RADami package
 (https://cran.r-project.org/web/packages/RADami/index.html), then
 subsetting individuals and loci and exporting as a phylip
 file.c85d6m20p3.full.loci.gzFull-taxa Phylip file: allTaxa.c85d6m20p3.2016.12.08.phyThe full phylogenetic analysis conducted on all individuals was conducted on this file, exported from RADami after importing the loci file (also in this repository) and removing individuals indicated in the paper.allTaxa.c85d6m20p3.2016.12.08.phy.gzRAxML original tree: bipart.oakTree.2017Tree from RAxML, unrooted, 300 tips, based on analysis of Phylip file in this repository, with RELL bootstrap support.bipart.oakTree.2017.treRooted, relabelled RAxML tree: bipart.oakTree.2017.tre.allTipsRAxML tree with all tips, relabelled to indicate taxon, geographic region, and extraction code.bipart.oakTree.2017.tre.allTips.treFossil-calibrated penalized likelihood tree, 4 calibrations: trs.calib.jackknife.4.annotatedTree calibrated using the discrete clock model, penalized likelihood, as implemented in the chronos function of ape (https://cran.r-project.org/web/packages/ape/index.html), 4 calibration points. File generated using Treeannotator (https://www.beast2.org/treeannotator/); uncertainty at nodes estimated by calibrating trees 500x, drawing dates from distributions as described in paper, on delete-half jackknife trees (as described in paper).trs.calib.jackknife.4.annotated.treTable S01: samples included in study.Metadata for all samples sequenced, including samples excluded from study as described in paper.TableS01.samples.csvTableS02.specimenRecordsSpecimens utilized in estimating soils and climatic niche, including information on which records were excluded from analysis and why.Soils and bioclim variables: all.eco.data.exportedFromR.2016-02-03Soil and bioclim variables utilized in niche diversification analyses.all.eco.data.exportedFromR.2016-02-03.csvTab-delimited soils.metadata.2016-02-03Description of soils variables and indication of which were used in niche diversification analyses.soils.metadata.2016-02-03.tsv