Data from: Sympatric parallel diversification of major oak clades in the Americas and the origins of Mexican species diversity

Hipp AL, Manos PS, Gonzalez-Rodriguez A, Hahn M, Kaproth M, McVay JD, Valencia Avalos S, Cavender-Bares J

Date Published: September 28, 2017

DOI: https://doi.org/10.5061/dryad.2qk88

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Title Loci file from pyRAD: c85d6m20p3.full.loci
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Description Loci 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.
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Title Full-taxa Phylip file: allTaxa.c85d6m20p3.2016.12.08.phy
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Description The 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.
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Title RAxML original tree: bipart.oakTree.2017
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Description Tree from RAxML, unrooted, 300 tips, based on analysis of Phylip file in this repository, with RELL bootstrap support.
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Title Rooted, relabelled RAxML tree: bipart.oakTree.2017.tre.allTips
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Description RAxML tree with all tips, relabelled to indicate taxon, geographic region, and extraction code.
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Title Fossil-calibrated penalized likelihood tree, 4 calibrations: trs.calib.jackknife.4.annotated
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Description Tree 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).
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Title Table S01: samples included in study.
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Description Metadata for all samples sequenced, including samples excluded from study as described in paper.
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Title TableS02.specimenRecords
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Description Specimens utilized in estimating soils and climatic niche, including information on which records were excluded from analysis and why.
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Title Soils and bioclim variables: all.eco.data.exportedFromR.2016-02-03
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Description Soil and bioclim variables utilized in niche diversification analyses.
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Title Tab-delimited soils.metadata.2016-02-03
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Description Description of soils variables and indication of which were used in niche diversification analyses.
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When using this data, please cite the original publication:

Hipp AL, Manos PS, Gonzalez-Rodriguez A, Hahn M, Kaproth M, McVay JD, Valencia Avalos S, Cavender-Bares J (2017) Sympatric parallel diversification of major oak clades in the Americas and the origins of Mexican species diversity. New Phytologist, online in advance of print. https://doi.org/10.1111/nph.14773

Additionally, please cite the Dryad data package:

Hipp AL, Manos PS, Gonzalez-Rodriguez A, Hahn M, Kaproth M, McVay JD, Valencia Avalos S, Cavender-Bares J (2017) Data from: Sympatric parallel diversification of major oak clades in the Americas and the origins of Mexican species diversity. Dryad Digital Repository. https://doi.org/10.5061/dryad.2qk88
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