Data from: Phylogeny and biogeography of the American live oaks (Quercus subsection Virentes): a genomic and population genetics approach

Cavender-Bares J, González-Rodríguez A, Eaton DAR, Hipp AAL, Beulke A, Manos PS

Date Published: June 10, 2015

DOI: http://dx.doi.org/10.5061/dryad.855pg

 

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Title sub_c85d6m20p3
Downloaded 31 times
Description xml file used in BEAST analysis
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Title sub_c85d6m20p3b
Downloaded 8 times
Description xml file used in BEAST analysis.
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Title sub_c85d6m20p3c
Downloaded 9 times
Description xml file used in BEAST analysis
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Title Freezing vulnerability
Downloaded 8 times
Description Predicted vulnerability to freezing at -15oC are given as a percentage between 0 and 100 for individuals of each of seven Virentes species based on Bioclim 6 data (mean minimum temperature of the coldest month) for each geographic location. The equation for predicting vulnerability to freezing (FV) was based on empirical relationships from Koehler, Center and Cavender Bares 2012 using the electrolyte leakage method of freezing injury to stems at -15oC: FV =100-[81.202 - 1.4075*X], where X is the mean minimum temperature in the coldest month. Any negative values were assumed to indicate zero vulnerability to freezing at -15oC.
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Title Tree height (m) for Virentes species
Downloaded 14 times
Description Data show tree height data in meters for mature trees for seven Virentes species, including source locations and geographic coordinates.
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Title Leaf area and shape for Virentes species
Downloaded 15 times
Description Leaf laminar area (mm2) and shape variables based on the first six principal components from analysis of leaf shape for 5,818 scanned leaves from 695 individual trees of seven Virentes species. The approach is based on a quantitative evaluation of the contour shape of each leaf with elliptic Fourier descriptors using the Shape 1.2 imaging software (Iwata & Ukai 2002). The data file also includes source location information of each tree, geographic coordinates, and Bioclim variables associated with each location.
Download PCA_All_Virentes.csv (1.712 Mb)
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Title Concatenated alignment of RADseq data: sub_c85d6m20p3.phy
Downloaded 8 times
Description Concatenated alignments of RADseq data for seven Virentes taxa and eight outgroup taxa (25 samples total) used to infer phylogenetic trees. The sub_c85d6m20p3.phy alignment is 817673 bp in length. Filtered reads were clustered at an 85% threshold for within-sample clustering. The number of samples for which data needed to be recovered to include a RAD locus in the data set was 20.
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Title Concatenated alignment of RADseq data: virentes_ME_c85d6m20p3.phy
Downloaded 6 times
Description Concatenated alignments of RADseq data for seven Virentes taxa and eight outgroup taxa (35 samples total) used to infer phylogenetic trees. The c85d6m20p3.phy alignment is 1,703,783 bp in length. Filtered reads were clustered at an 85% threshold for within-sample clustering. The number of samples for which data needed to be recovered to include a RAD locus in the data set was 20.
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Title Concatenated alignment of RADseq data: virentes_ME_c85d6m4p3
Downloaded 7 times
Description Concatenated alignments of RADseq data for seven Virentes taxa and eight outgroup taxa (35 samples total) used to infer phylogenetic trees. The virentes_ME_c85d6m4p3.phy alignment is 6,252,421 bp in length. Filtered reads were clustered at an 85% threshold for within-sample clustering. The number of samples for which data needed to be recovered to include a RAD locus in the data set was 4.
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Title All Virentes SSRs in Structure format
Downloaded 21 times
Description Dinucleotide nuclear microsatellites (ZAG36, ZAG11, ZAG1/5, ZAG1/2, ZAG102, ZAG9, ZAG15, ZAG30, ZAG46, ZAG16, ZAG110) for seven Virentes species and 672 individuals, including source location information and geographic coordinates. This is the input file used for the Structure analysis.
Download All live oak microsats_Structure.csv (473.5 Kb)
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Title IMa input file
Downloaded 17 times
Description Input file (including chloroplast sequence data, NIA-i3 sequence data, and nuclear SSR data) and command line strings for IMa analyses
Download BR_FU_IMa_input.txt (129.4 Kb)
Download README.txt (890 bytes)
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Title Concatenated chloroplast sequence data: Virentes
Downloaded 23 times
Description Concatenated chloroplast DNA sequences from trnD-trnT and rpl32–trnL(UAG) regions or seven Virentes species, 215 individuals. Source information and geographic coordinates are in the ReadMe file.
Download CP.CONCAT.seq (314.1 Kb)
Download README.csv (21.87 Kb)
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Title Chloroplast trnD-trnT: all Virentes sequences
Downloaded 8 times
Description Chloroplast trnD-trnT region for 391 individuals from seven Virentes species. Sequence length is 615 bp.
Download trnD-trnT_all_sequences.seq (244.9 Kb)
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Title Chloroplast rp132 trnL region: all Virentes sequences
Downloaded 5 times
Description Chloroplast sequence data for rp132 trnL for seven Virentes species and 327 individuals. Sequence length is 835 bp.
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When using this data, please cite the original publication:

Cavender-Bares J, González-Rodríguez A, Eaton DAR, Hipp AAL, Beulke A, Manos PS (2015) Phylogeny and biogeography of the American live oaks (Quercus subsection Virentes): a genomic and population genetics approach. Molecular Ecology 24(14): 3668–3687. http://dx.doi.org/10.1111/mec.13269

Additionally, please cite the Dryad data package:

Cavender-Bares J, González-Rodríguez A, Eaton DAR, Hipp AAL, Beulke A, Manos PS (2015) Data from: Phylogeny and biogeography of the American live oaks (Quercus subsection Virentes): a genomic and population genetics approach. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.855pg
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